張鵬霞，周秀文，梁雪，郭營，趙巖，李斯深，孔凡美

小麥苗期生物量及氮效率相關(guān)性狀的全基因組關(guān)聯(lián)分析

張鵬霞1，周秀文1，梁雪2，郭營1，趙巖1，李斯深1，孔凡美1

1山東農(nóng)業(yè)大學(xué)/作物生物學(xué)國家重點實驗室/土肥資源高效利用國家工程實驗室，山東泰安 271018；2山東省曹縣土壤肥料工作站，山東曹縣 274400

【】探究不同氮素供應(yīng)環(huán)境下與小麥苗期生物量及氮效率相關(guān)性狀顯著關(guān)聯(lián)的SNP位點，預(yù)測相關(guān)候選基因，為小麥氮效率的基因克隆及其在育種中的應(yīng)用提供參考。以134個小麥品種（系）組成的群體為供試群體，設(shè)置低氮、正常氮和高氮3個處理，各處理重復(fù)4次，并在2年（2013和2014年）進(jìn)行了2次完全重復(fù)的營養(yǎng)液培養(yǎng)試驗。試驗對小麥苗期生物量及氮效率相關(guān)的14個性狀進(jìn)行了表型鑒定，采用MLM+K+Q混合線性模型，利用90K SNP芯片對小麥生物量及氮效率相關(guān)性狀進(jìn)行全基因組關(guān)聯(lián)分析（genome-wide association study，GWAS），獲得顯著關(guān)聯(lián)的SNP位點。與正常氮處理相比，低氮處理條件下，根系、地上部及植株氮含量和氮積累量均顯著下降，而根生物量和根、植株氮效率均顯著增加，高氮處理下，幾乎所有鑒定性狀均顯著增加；14個性狀的廣義遺傳力均在40%以上，其中，植株總干重的遺傳力最高（95.73%）。利用9 329個SNP標(biāo)記進(jìn)行關(guān)聯(lián)分析，共檢測到838個SNP標(biāo)記位點與供試材料的14個性狀存在顯著關(guān)聯(lián)（≤0.001），分布在21條染色體上。有435個（51.91%）SNP標(biāo)記位點僅在一個關(guān)聯(lián)分析環(huán)境中被檢測到；有403個位點至少在2個處理環(huán)境（包含均值環(huán)境）中被檢測到與同一性狀顯著關(guān)聯(lián)（穩(wěn)定關(guān)聯(lián)標(biāo)記）。其中8個SNP標(biāo)記位點至少在3個環(huán)境中被檢測到。在4個環(huán)境下（包括均值環(huán)境）均檢測到的穩(wěn)定關(guān)聯(lián)位點有2個：Kukri_c65481_121和tplb0025f09_1052，分別與植株總氮利用效率（total nitrogen use efficiency of plant，TNUE）和根系總氮利用效率（root nitrogen use efficiency，RNUE）顯著關(guān)聯(lián)；同時與至少6個性狀（生物量及養(yǎng)分效率相關(guān)性狀）顯著關(guān)聯(lián)的SNP標(biāo)記位點共5個，分別位于1A、1B（3）和2A染色體上；根據(jù)小麥基因組注釋及LD衰減水平，在同時定位了6個性狀的5個SNP位點和2個多環(huán)境（4個環(huán)境）穩(wěn)定關(guān)聯(lián)的SNP位點的214 kb的基因組區(qū)域中共篩選候選基因84個，根據(jù)已知克隆氮效率基因的編碼蛋白類型、候選基因功能注釋信息及利用植物比較基因組學(xué)資源庫蛋白序列同源比對分析，篩選到3個候選基因與生物量及氮效率相關(guān)。不同氮素處理顯著影響小麥苗期生物量、氮效率相關(guān)性狀及其相關(guān)QTL的表達(dá)，大多數(shù)SNP位點僅在1個氮素檢測環(huán)境中被檢測到，但也存在環(huán)境穩(wěn)定性較強(qiáng)的位點。生物量及氮效率相關(guān)性狀之間存在顯著相關(guān)關(guān)系，并在一定程度上受到相同的QTL/基因控制。

小麥；全基因組關(guān)聯(lián)分析；生物量；氮效率

0 引言

【研究意義】小麥?zhǔn)侵袊钪匾募Z食作物之一，人類消耗熱量的五分之一來自于小麥。氮元素是植物生長發(fā)育過程中最重要的礦質(zhì)營養(yǎng)元素，目前，全球肥料使用量的62%來自于氮肥（FAO，2011），自2000年以來，氮肥消耗量以每年10%的速度急劇增長[1]。隨著氮肥施用量的增多，小麥表現(xiàn)出耐肥的特性，使得氮肥利用率持續(xù)降低[2-4]，中國氮肥利用率僅有21.2%—35.9%，氮肥的過量使用不僅導(dǎo)致了一系列環(huán)境污染問題[5-7]，而且還增加了生產(chǎn)成本[8]，因此，提高氮肥利用率以選育氮高效的小麥新品種是當(dāng)前農(nóng)業(yè)生產(chǎn)上面臨的緊迫且重要的課題之一?！厩叭搜芯窟M(jìn)展】國內(nèi)外大量研究表明，不同基因型的小麥對礦質(zhì)元素的吸收和利用存在顯著差異[9-11]，并且認(rèn)為可以通過遺傳改良來實現(xiàn)小麥氮素的高效利用。因此，對小麥氮效率的相關(guān)性狀進(jìn)行遺傳學(xué)研究，充分挖掘其氮高效利用潛力，是提高小麥氮素利用效率、選育氮高效的小麥新品種和促進(jìn)農(nóng)業(yè)可持續(xù)發(fā)展的有效途徑[12-14]。隨著分子生物學(xué)技術(shù)及基因組測序技術(shù)的快速發(fā)展，全基因組關(guān)聯(lián)分析成為一種獲取候選基因的有效方法，由于該方法能夠快速構(gòu)建作圖群體并繪制高分辨率的遺傳圖譜，通過多年多點處理快速鎖定并分離出顯著關(guān)聯(lián)位點的候選基因，顯著提高候選基因的準(zhǔn)確度，逐漸在各類作物氮效率研究中得到應(yīng)用[15-17]。迄今為止，基于SNP標(biāo)記的全基因組關(guān)聯(lián)分析（genome-wide association study，GWAS）在小麥加工品質(zhì)[18-19]、生理[20-21]和抗病性[19, 22-23]等相關(guān)性狀基因的研究中均有廣泛報道?！颈狙芯壳腥朦c】目前，小麥氮素相關(guān)性狀的遺傳學(xué)研究相對較少，盡管不同作物中氮素利用效率相關(guān)性狀的QTL定位已有較多研究，然而據(jù)此克隆到的氮效率相關(guān)基因卻鮮見報道。其主要原因在于，氮效率相關(guān)性狀受環(huán)境影響大，表型鑒定相對繁瑣；同時，受遺傳圖譜密度、供試群體大小及其特性的影響，鑒定的QTL覆蓋基因組區(qū)間比較大，環(huán)境穩(wěn)定性差，精確度有限，因此很難據(jù)此預(yù)測和分離相關(guān)候選基因。隨著小麥基因組測序結(jié)果的公開，利用GWAS分析進(jìn)行候選基因挖掘的可靠度不斷增加，獲得穩(wěn)定可靠的顯著關(guān)聯(lián)SNP位點成為候選基因篩選和預(yù)測的關(guān)鍵，而群體表型性狀精確鑒定和高精度SNP圖譜是獲得可靠SNP關(guān)聯(lián)位點的前提。苗期是小麥生長的關(guān)鍵時期，苗期對氮素環(huán)境的適應(yīng)能力在一定程度上能夠反映其對養(yǎng)分環(huán)境的適應(yīng)潛力。此外，營養(yǎng)液培養(yǎng)的試驗條件可以實現(xiàn)精確控制，獲得的表型性狀精確度大幅度提高，從而為獲得可靠的SNP關(guān)聯(lián)位點提供關(guān)鍵數(shù)據(jù)基礎(chǔ)。【擬解決的關(guān)鍵問題】本研究以134份小麥品種（系）組成的自然群體為供試群體，采用營養(yǎng)液培養(yǎng)的方法，連續(xù)2年分別設(shè)置低氮、正常氮和高氮處理，測定小麥苗期生物量及氮效率相關(guān)性狀，并進(jìn)行全基因組關(guān)聯(lián)分析，期望定位到小麥苗期生物量及氮效率相關(guān)性狀的重要QTL，挖掘、預(yù)測氮素高效利用的相關(guān)基因，為進(jìn)一步開展小麥氮效率基因的克隆及其遺傳改良提供依據(jù)。

1 材料與方法

1.1 試驗材料

以134份小麥品種（系）組成的自然群體為試驗材料，包括國內(nèi)山東省品種66個、河北省品種24個、河南省品種16個、陜西省品種14個、山西省品種8個、江蘇省品種2個和四川省品種2個，以及國外澳大利亞品種1個和加拿大品種1個（電子附表1）。

1.2 試驗設(shè)計

1.2.1 試驗處理 在山東農(nóng)業(yè)大學(xué)本部玻璃溫室進(jìn)行營養(yǎng)液培養(yǎng)，參考Hoagland營養(yǎng)液配方配制試驗所用營養(yǎng)液，并根據(jù)小麥的營養(yǎng)特性進(jìn)行適當(dāng)修改（正常營養(yǎng)液配方見表1），設(shè)置低氮（0.4 mmol·L-1，T1）、正常氮（4 mmol·L-1，T2）和高氮（8 mmol·L-1，T3）3個處理，各處理重復(fù)4次，隨機(jī)區(qū)組設(shè)計。

表1 小麥苗期試驗正常營養(yǎng)液組分

1.2.2 試驗方案 選擇大小基本一致的134份供試小麥品種（系）種子，用10%的H2O2消毒滅菌5 min后用蒸餾水沖洗，擺放在發(fā)芽網(wǎng)上進(jìn)行發(fā)芽。幼苗長至1葉1心時（約7 d），每個材料選擇長勢一致的3株幼苗，去掉幼苗胚乳后移至育苗盤中，每個品種（系）的3株幼苗放置在同一穴中。134個材料統(tǒng)一放置在同一個育苗盤中并置于盛有Hoagland營養(yǎng)液的黑色塑料水產(chǎn)盒中（容積25 L），添加營養(yǎng)液20 L。前3 d采用1/2濃度的營養(yǎng)液進(jìn)行緩苗，之后用完全培養(yǎng)液（加處理）進(jìn)行培養(yǎng)，每隔3 d更換1次營養(yǎng)液，用稀NaOH和0.1 mmol·L-1HCl調(diào)節(jié)pH至6.0—6.2，24 h不間斷通氣，培養(yǎng)28 d收獲。

第一次試驗時間（E1）為2013年11月25日—2014年1月17日，溫度為5.8—28.6℃，濕度為8.6%—85.9%，光照強(qiáng)度為0—57.8 klx；第二次試驗時間（E2）為2014年3月2日—2014年4月22日，溫度為7.5—33.9℃，濕度為10.1%—91.3%，光照強(qiáng)度為0—69.0 klx。

1.2.3 測定指標(biāo)、方法及計算方法 用烘箱105℃將樣品烘干，然后用千分之一電子天平稱量地上部生物量（shoot dry weight，SDW）與根系生物量（root dry weight，RDW），計算植株總生物量（total dry weight of plant，TDW）=SDW+RDW。采用H2SO4-H2O2消煮法和凱氏定氮儀測定地上部氮含量（shoot nitrogen concentration，SNC）與根系氮含量（root nitrogen concentration，RNC），計算植株總氮含量（total nitrogen concentration of plant，TNC）=（SNC×SDW+RNC× RDW）/TDW、地上部氮累積量（shoot nitrogen accumulation，SNA）=SDW×SNC、根系氮累積量（root nitrogen accumulation，RNA）=RDW×RNC、植株氮累積量（total nitrogen accumulation of plant，TNA）=TDW×TNC、氮累積量根冠比（root/shoot ratio of nitrogen accumulation，RSNA）=RNA/SNA、地上部氮利用效率（shoot nitrogen use efficiency，SNUE）=SDW/SNC、根系氮利用效率（root nitrogen use efficiency，RNUE）=RDW/RNC和植株氮利用效率（total nitrogen use efficiency of plant，TNUE）=TDW/ TNC[24]。

1.3 數(shù)據(jù)統(tǒng)計方法

1.3.1 遺傳多樣性分析和群體結(jié)構(gòu)分析 利用SPSS 19.0軟件和R語言進(jìn)行數(shù)據(jù)統(tǒng)計分析和結(jié)果可視化，計算性狀廣義遺傳力：2=2/（2+2）[25]，其中，2表示環(huán)境方差，2表示遺傳方差。用Structure 2.3.1軟件對供試群體進(jìn)行群體遺傳結(jié)構(gòu)分析，并計算其相應(yīng)的Q值。依據(jù)似然值最大的原則選取合適的K值作為群體數(shù)目。利用Powermarker V3.25軟件對SNP的多態(tài)性信息含量、基因多樣性和遺傳距離進(jìn)行分析，結(jié)合軟件NJ phylogenetic tree繪制聚類圖，利用TASSEL V5.0進(jìn)行供試群體主成分分析，最終結(jié)合以上3種方法確定供試群體的群體結(jié)構(gòu)和亞群數(shù)目。

1.3.2 遺傳圖譜和全基因組關(guān)聯(lián)分析 利用小麥90K（含81 587個SNP）基因芯片對134份小麥品種（系）組成的自然群體進(jìn)行掃描，在得到的SNP標(biāo)記位點中，刪除缺失率大于15%，最小等位基因頻率（minimum allele frequency，MAF）小于5%的SNP標(biāo)記位點，最終剩余9 329個SNP位點，大約85.24%（7952/9329）SNP有遺傳位置信息，分布在21條染色體上[26]。試驗分別對2次試驗環(huán)境（E1和E2）下的3個氮處理（T1E1、T2E1、T3E1、T1E2、T2E2和T3E2）以及2個環(huán)境下相同處理的平均值（T1AV、T2AV和T3AV）的14個性狀（共126個性狀-環(huán)境）進(jìn)行關(guān)聯(lián)分析。利用TASSEL V5.0軟件中Analysis模塊下的Link.Diseq和Kinship計算親緣關(guān)系K矩陣，采用TASSEL V5.0軟件中的MLM+Q+K混合線性模型進(jìn)行全基因組關(guān)聯(lián)分析，≤0.001時認(rèn)為存在顯著關(guān)聯(lián)。曼哈頓圖和Q-Q圖可視化在R環(huán)境中通過CMplot程序包完成。

2 結(jié)果

2.1 小麥苗期氮效率相關(guān)性狀表型數(shù)據(jù)分析

通過對小麥苗期氮效率相關(guān)性狀表型進(jìn)行分析（表2），與正常氮處理相比，低氮和高氮處理下苗期生物量及氮效率相關(guān)性狀均差異顯著。低氮處理條件下，根系、地上部及植株氮含量和氮積累量均顯著下降，而根生物量及根、植株氮效率均顯著增加，高氮處理下，幾乎所有指標(biāo)均顯著增加。各供試性狀在2次試驗間均表現(xiàn)出顯著差異，如，2014年（E2）的植株生物量、植株氮累積量及植株氮利用效率均顯著高于2013年（E1），這可能與試驗中的其他因素（如溫度、濕度以及光照的差異等）有關(guān)。

此外，供試群體生物量及氮效率相關(guān)性狀也表現(xiàn)出顯著的基因型差異（表2）。供試群體變異系數(shù)范圍為3.41%（地上部氮含量）—37.13%（氮累積量根冠比），生物量及氮效率相關(guān)性狀均表現(xiàn)出連續(xù)變異，為典型的數(shù)量性狀，遺傳率為41.34%（植株總氮利用效率）—95.37%（植株總干重）。對2個環(huán)境下的均值進(jìn)行相關(guān)性分析（圖1），結(jié)果表明，除了根系干重與地上部累積量，植株總干重與植株總氮利用效率，植株總氮累積量與根系氮利用效率不相關(guān)，苗期生物量與氮效率相關(guān)性狀間均呈顯著正相關(guān)或負(fù)相關(guān)。

2.2 群體結(jié)構(gòu)分析

用Structure 22.3.4軟件進(jìn)行群體結(jié)構(gòu)分析（圖2-a和圖2-c），結(jié)果表明，K=2時，ΔK達(dá)到峰值。利用Power Marker V3.25分析SNP的多態(tài)性信息含量和基因多樣性，計算自然群體兩兩間的遺傳距離，構(gòu)建NJ聚類圖（圖2-b）。利用TASSEL V5.0軟件進(jìn)行供試群體主成分分析，結(jié)果顯示，前2個主成分可解釋14.85%的群體信息。綜合以上3種方法來研究供試群體結(jié)構(gòu)，最終將供試群體確定為2個亞群，分別為13個小麥品種/系（亞群1）和121個小麥品種/系（亞群2）[26]。

2.3 小麥苗期氮效率相關(guān)性狀的穩(wěn)定位點

共調(diào)查了14個生物量及氮效率相關(guān)性狀，分別對2次試驗（E1和E2）的3個氮處理（T1E1、T2E1、T3E1、T1E2、T2E2和T3E2）以及2次試驗相同處理的平均值（T1AV、T2AV和T3AV）共9個關(guān)聯(lián)分析環(huán)境的126個環(huán)境-性狀進(jìn)行關(guān)聯(lián)分析，共定位到838個顯著（≤0.001）關(guān)聯(lián)的SNP標(biāo)記，分布在小麥21條染色體上（電子附表2和電子附圖1）。在定位到的838個顯著關(guān)聯(lián)的SNP標(biāo)記位點中，僅在一個關(guān)聯(lián)分析環(huán)境中被檢測到SNP標(biāo)記位點有435個（51.91%），至少在2個關(guān)聯(lián)分析環(huán)境中被檢測到SNP標(biāo)記位點有403個，其中有8個SNP標(biāo)記位點（RAC875_c29540_391、BobWhite_c9881_1312、GENE-0427_442、wsnp_RFL_Contig3060_2967139、Kukri_c65481_121、tplb0025f09_1052、wsnp_Ku_c1765_ 3452586、BS00022498_51）至少在3個關(guān)聯(lián)分析環(huán)境中被檢測到，分別與根系氮利用效率、根系干重、地上部累積量、植株總干重、植株總氮累積量、植株總氮利用效率、地上部干重和生物量根冠比顯著關(guān)聯(lián)。其中，Kukri_c65481_121和tplb0025f09_1052分別與植株總氮利用效率（TNUE）和根系總氮利用效率（RNUE）顯著關(guān)聯(lián)并在4個環(huán)境下（包括均值環(huán)境）被檢測到，tplb0025f09_1052對根系氮利用效率的貢獻(xiàn)率達(dá)到36.09%（表3）。

表2 小麥苗期生物量和氮效率相關(guān)性狀的統(tǒng)計參數(shù)和遺傳力

SDW：地上部干重；TDW：植株總干重；RSDW：生物量根冠比；SNC：地上部氮含量；RNC：根系氮含量；TNC：植株總氮含量；SNA：地上部氮累積量；RNA：根系氮累積量；TNA：植株總氮累積量；RSNC：氮累積量根冠比；SNUE：地上部氮利用效率；RNUE：根系氮利用效率；TNUE：植株總氮利用效率。E1和E2代表2個試驗?zāi)攴?；T1、T2、T3代表低氮、正常氮和高氮處理。同列數(shù)據(jù)后的不同小寫字母表示同一年份2個處理之間差異顯著（＜0.05）。下同

SDW: Shoot dry weight; TDW: Total dry weight of plant; RSDW: Root/shoot ratio of biomass; SNC: Shoot nitrogen concentration; RNC: Root nitrogen concentration; TNC: Total nitrogen concentration of plant; SNA: Shoot nitrogen accumulation; RNA: Root nitrogen accumulation; TNA: Total nitrogen accumulation of plant; RSNC: Root/shoot ratio of nitrogen accumulation; SNUE: Shoot nitrogen use efficiency; RNUE: Root nitrogen use efficiency; TNUE: Total nitrogen use efficiency of plant. E1 and E2 represent the two experimental years; T1, T2 and T3 represent low nitrogen, normal nitrogen and high nitrogen treatments. Values followed by different lowercase letters indicate significant between two treatments in the same year at the 0.05 level. The same as below

SDW：地上部干重；TDW：植株總干重；RSDW：生物量根冠比；SNC：地上部氮含量；RNC：根系氮含量；TNC：植株總氮含量；SNA：地上部氮累積量；RNA：根系氮累積量；TNA：植株總氮累積量；RSNC：氮累積量根冠比；SNUE：地上部氮利用效率；RNUE：根系氮利用效率；TNUE：植株總氮利用效率。下同

2.4 小麥苗期氮效率相關(guān)性狀共同關(guān)聯(lián)位點和單倍型分析

試驗篩選出211個同時與至少3個性狀顯著關(guān)聯(lián)的SNP標(biāo)記，其中同時與至少6個性狀顯著關(guān)聯(lián)的SNP標(biāo)記有5個（表4），1A染色體的BS00077492_51與SDW、TDW、SNC、TNC、SNUE和TNUE均顯著關(guān)聯(lián)，1B染色體的BS00065737_51、IACX16577和GENE-0427_442與SDW、TDW、SNC、TNC、SNUE和TNUE均顯著關(guān)聯(lián)，2A染色體的wsnp_RFL_ Contig3060_2967139與SDW、TDW、SNC、TNC、SNUE和TNUE均顯著關(guān)聯(lián)，這些位點相對更為可靠，可用于分子標(biāo)記輔助育種和QTL精細(xì)定位。對共定位的5個位點進(jìn)行單倍型分析（圖3），結(jié)果表明，在SNP位點BS00065737_51、IACX16577和GENE-0427_442存在3個單倍型（1B-Hap1、1B-Hap2和1B-Hap3），單倍型為1B-Hap3材料的地上部干重和地上部氮含量均顯著高于1B-Hap2的，在SNP位點wsnp_RFL_Contig3060_2967139存在3個單倍型（2A-Hap1、2A-Hap2和2A-Hap3），單倍型為2A-Hap3材料的地上部干重均顯著高于2A-Hap2的地上部干重，單倍型為2A-Hap2材料的植株總干重、地上部氮含量、植株總氮含量、地上部氮利用效率和植株總氮利用效率均顯著高于2A-Hap1和2A-Hap3。

a：供試材料的K值與ΔK的關(guān)系；b：基于遺傳距離的NJ聚類圖；c：群體結(jié)構(gòu)；2個亞群用不同顏色表示

表3 與苗期生物量及氮效率相關(guān)性狀顯著關(guān)聯(lián)（P≤0.001）的環(huán)境穩(wěn)定SNP標(biāo)記

粗體為多環(huán)境（4個環(huán)境）穩(wěn)定關(guān)聯(lián)位點的SNP

SNPs associated with stable sites in multiple environments (4 environments) in bold

2.5 候選基因預(yù)測

根據(jù)小麥基因組注釋及LD衰減水平，對與6個性狀共同定位的5個SNP位點和2個多環(huán)境（4個環(huán)境）關(guān)聯(lián)的SNP位點進(jìn)行了候選基因的篩選。據(jù)目標(biāo)SNP附近214 kb的基因組區(qū)域中共鑒定出候選基因84個，根據(jù)已知克隆氮效率基因的編碼蛋白類型、候選基因功能注釋信息及利用植物比較基因組學(xué)資源庫蛋白序列同源比對分析，篩選到3個候選基因與氮效率相關(guān)（表5和圖3），其中，編碼的Agamous MADS-box transcription factor已經(jīng)有研究報道參與小麥氮效率調(diào)控，該基因主要在根部表達(dá)；編碼Membrane-associated 30 kD protein；編碼R3h domain containing protein。

表4 小麥苗期同時與6個性狀顯著關(guān)聯(lián)的SNP位點

a：SNP位點BS00065737_51、IACX16577和GENE-0427_442的單倍型分析；b：SNP位點snp_RFL_Contig3060_2967139的單倍型分析。*、**、***分別表示在0.05、0.01、0.001水平差異顯著

表5 候選基因預(yù)測

根據(jù)3個目標(biāo)候選基因的不同時期表達(dá)模式和氮響應(yīng)情況的分析（電子附圖4），表明和在根系中具有較高的表達(dá)量，而在葉中具有較高的表達(dá)量。在氮缺乏處理下表達(dá)，而和在氮缺乏處理下表達(dá)量相對較低。

3 討論

氮素是植物葉綠素、蛋白質(zhì)、核酸、酶類、生物堿、植物激素以及維生素類等物質(zhì)的重要組成成分，是決定作物產(chǎn)量的首要因素，選育氮高效品種是維持我國小麥生產(chǎn)安全和可持續(xù)發(fā)展的重要途徑。長期以來，由于育種群體大，選擇頻率高，氮素測定消耗大，導(dǎo)致氮素利用效率評價困難，育種家主要依據(jù)地上部表型性狀來判斷品種氮素利用效率[27-28]。近年來，小麥基因芯片的大量開發(fā)和應(yīng)用，促進(jìn)了數(shù)量性狀遺傳研究的進(jìn)程，為育種過程中氮素效率的評價提供了新的思路[19,29]。GWAS分析是解析數(shù)量性狀遺傳特性的重要工具，一方面，與雙親群體相比，自然群體積累了廣泛的重組事件，可以提供更多有效重組信息，可以更加精細(xì)定位QTL，且可短時間內(nèi)發(fā)現(xiàn)更多關(guān)聯(lián)位點。此外，GWAS分析具有更高的分辨率，有利于了解目標(biāo)基因的位置、遺傳效應(yīng)和基因網(wǎng)絡(luò)等信息以及遺傳位點的精細(xì)定位和圖位克隆。本研究利用小麥90K SNP芯片，在不同的氮素水平下，通過GWAS分析對小麥苗期的生物量及氮效率相關(guān)性狀進(jìn)行相關(guān)研究，以期發(fā)掘與氮素利用效率相關(guān)的SNP標(biāo)記和遺傳位點，預(yù)測相關(guān)性狀的候選基因，為小麥氮效率相關(guān)性狀的基因克隆及其在育種中的應(yīng)用提供參考。

目前，在小麥不同氮處理試驗中已經(jīng)有大量的QTL和QTL簇被檢測到[30-34]，其中大部分QTL只能在單一的環(huán)境中被檢測到。本研究對14個生物量及氮效率相關(guān)性狀進(jìn)行全基因組關(guān)聯(lián)分析，共檢測到838個顯著關(guān)聯(lián)的SNP位點，分布在21條染色體上。其中，435個SNP位點僅在一個關(guān)聯(lián)分析環(huán)境中被檢測到，占總數(shù)的51.91%。這些SNP位點的相關(guān)基因極有可能與不同氮素環(huán)境下的特異調(diào)控有關(guān)，但是由于數(shù)量眾多、貢獻(xiàn)率小和穩(wěn)定性差，難以進(jìn)行這些SNP位點相關(guān)基因的下一步研究。但與此同時，有8個SNP位點（RAC875_c29540_391、BobWhite_c9881_1312、GENE-0427_442、wsnp_RFL_Contig3060_2967139、Kukri_c65481_121、tplb0025f09_1052、wsnp_Ku_ c1765_3452586、BS00022498_51）至少在3個關(guān)聯(lián)分析環(huán)境中被檢測到，這些SNP位點存在氮素利用效率相關(guān)基因的可能性較大，但迄今尚未有進(jìn)一步的研究，無法探討其遺傳機(jī)制。盡管前人針對小麥氮素利用效率遺傳機(jī)制開展過多項研究，也在小麥2A、2B、4A、5A、7A和7B染色體上發(fā)現(xiàn)一批控制小麥氮素利用效率相關(guān)遺傳位點[15, 35-37]，但是由于試驗群體、標(biāo)記類型和標(biāo)記來源的差異較大，無法進(jìn)行可靠的對比，無法確定是否與本研究發(fā)現(xiàn)位點一致。

另外，本研究篩選出5個多性狀共定位的SNP位點（BS00077492_51、BS00065737_51、GENE-0427_ 442、IACX16577和wsnp_RFL_Contig3060_2967139），分布于1A、1B（2）和2A（2）染色體上，共同定位的性狀主要有地上部干重（SDW）、植株總干重（TDW）、地上部氮累積量（SNC）、植株總氮累積量（TNC）、地上部氮利用效率（SNUE）和植株總氮利用效率（TNUE）。相關(guān)性分析結(jié)果表明，這6個性狀均在＜0.01水平呈極顯著相關(guān)，表明同一SNP位點可同時與多個性狀顯著關(guān)聯(lián)，同時也表明這些性狀（生物量和氮效率）之間存在著密切關(guān)系，可能受相同的SNP/基因調(diào)控。大量QTL分析結(jié)果也表明，在染色體上存在著熱點QTL區(qū)域[32, 38]。張國華[39]研究結(jié)果表明多個性狀之間存在相互關(guān)聯(lián)現(xiàn)象，這種現(xiàn)象可能與QTL相互連鎖或一因多效有關(guān)。在5個共定位SNP位點中，4個SNP位點在低氮或高氮條件下表達(dá)，而在正常施氮條件下不表達(dá)，表明這些SNP位點與小麥對不同氮素環(huán)境的適應(yīng)性密切相關(guān)。這些與小麥氮效率相關(guān)的高頻表達(dá)SNP位點和多性狀共定位SNP位點可能對小麥氮效率利用有重要的調(diào)控作用，在進(jìn)行小麥氮效率遺傳分子機(jī)制的研究中值得進(jìn)一步探討。通過對5個位點的單倍型分析，發(fā)現(xiàn)SNP位點wsnp_RFL_Contig3060_2967139的單倍型2A-Hap2為地上部氮利用效率和植株總氮利用效率的優(yōu)異單倍型，在所有試驗材料中，濟(jì)麥20、魯麥14、洛旱6號、新麥26、衡0628、冀5265、金麥1號、石麥18號、石新618、陜農(nóng)534、西農(nóng)85、西農(nóng)213、淮麥16和澳大利亞紅麥等品種具有較高的氮素利用效率，含有優(yōu)異等位基因，可作為氮高效品種推廣或作為氮高效育種的優(yōu)異種質(zhì)材料應(yīng)用。

根據(jù)小麥基因組注釋及連鎖不平衡（linkage disequilibrium，LD）衰減水平，在5個與6個性狀共同定位的SNP位點和2個多環(huán)境（4個環(huán)境）關(guān)聯(lián)的SNP位點214 kb的基因組區(qū)域中共鑒定出候選基因84個，初步篩選得到3個候選基因與氮效率相關(guān)。其中，在1B染色體上檢測到一個編碼Agamous MADS-boxtranscription factor的候選基因（）。MADS-box基因家族在植物生長發(fā)育和信號傳導(dǎo)過程中起著不可替代的作用[40]，它的功能主要是參與調(diào)控植物生殖生長階段，如控制開花時間、決定分生組織特性、花器官形態(tài)建成和果實成熟等，同時調(diào)節(jié)著植物根、葉、花和果實的發(fā)育，尤其在生殖發(fā)育中控制花分生組織和花器官中的基因表達(dá)，此外，也有研究表明MADS-box基因的表達(dá)也參與胚形態(tài)建成[41]、抗逆境[42]、以及決定開花時間[43]等過程的調(diào)控。最新的研究表明[44-45]，MADS-box基因家族參與調(diào)控小麥氮效率，在根部硝酸鹽供應(yīng)中起重要作用，這為進(jìn)一步發(fā)掘該基因的功能提供了新線索。以上研究結(jié)果也為本試驗鑒定得到的氮效率相關(guān)候選基因提供了可靠依據(jù)。此外。在4B染色體上檢測到一個編碼R3h domain containing protein的候選基因（）,在含有優(yōu)異單倍型的SNP位點wsnp_RFL_Contig3060_ 2967139檢測到一個編碼Membrane-associated 30 kDa protein的候選基因（），尚未有關(guān)小麥氮效率的研究，值得深入探討。

隨著小麥基因組序列的釋放，基因功能驗證與發(fā)掘成為小麥后基因組時代的重要課題。生物體中普遍存在的一因多效現(xiàn)象也讓基因功能的確定成為一大難題，仍需要扎實的基因功能驗證工作。目前基于可靠的關(guān)聯(lián)標(biāo)記的生物信息分析是發(fā)掘復(fù)雜農(nóng)藝性狀相關(guān)候選基因的有效方法，然而，由于小麥氮效率涉及到多個復(fù)雜的生理、生化過程，要確定特定基因的功能還需要后續(xù)進(jìn)一步的功能驗證工作。

4 結(jié)論

不同氮素處理顯著影響小麥苗期生物量、氮效率相關(guān)性狀及其相關(guān)QTL的表達(dá)，大多數(shù)SNP位點僅在1個氮素檢測環(huán)境中被檢測到，但也存在環(huán)境穩(wěn)定性較強(qiáng)的位點。生物量及氮效率相關(guān)性狀之間存在顯著相關(guān)關(guān)系，并在一定程度上受到相同的QTL/基因控制，相關(guān)候選基因的功能有待進(jìn)一步驗證。

[1] GUTTIERI M J, FRELS K, REGASSA T, WATERS B M, BAENZIGER P S. Variation for nitrogen use efficiency traits in current and historical great plains hard winter wheat. Euphytica, 2017, 213(4): 87.

[2] GU B, JU X, CHANG S X, GE Y, CHANG J. Nitrogen use efficiencies in Chinese agricultural systems and implications for food security and environmental protection. Regional Environmental Change, 2017, 17(4): 1217-1227.

[3] LIANG S, LI Y, ZHANG X, SUN Z, SUN N, DUAN Y, XU M, WU L. Response of crop yield and nitrogen use efficiency for wheat-maize cropping system to future climate change in northern China. Agricultural and Forest Meteorology, 2018, 262: 310-321.

[4] SCHACHTMAN D P, SHIN R. Nutrient sensing and signaling: NPKS. Annual Review Plant Biology, 2007, 58: 47/69.

[5] DAVIDSON E.A. The contribution of manure and fertilizer nitrogen to atmospheric nitrous oxide since 1860. Nature Geoscience, 2009, 2(9): 659-662.

[6] PALME K, LI X, TEALE W D. Towards second green revolution: engineering nitrogen use efficiency. Genet Genomics, 2014, 41(6): 315-326.

[7] YIN L, DAI X, HE M. Delayed sowing improves nitrogen utilization efficiency in winter wheat without impacting yield. Field Crops Research, 2018, 221: 90/97.

[8] CEOTTO E. The issues of energy and carbon cycle: new perspectives for assessing the environmental impact of animal waste utilization. Bioresour Technology, 2005, 96(2): 191-196.

[9] HITZ K, CLARK A J, VAN SANFORD D A. Identifying nitrogen-use efficient soft red winter wheat lines in high and low nitrogen environments. Field Crops Research, 2017, 200: 1-9.

[10] MAHJOURIMAJD S, KUCHEL H, LANGRIDGE P, OKAMOTO M. Evaluation of Australian wheat genotypes for response to variable nitrogen application. Plant and Soil, 2015, 399(1/2): 247-255.

[11] WANG Y Y, SUN X Y, ZHAO Y, KONG F M, GUO Y, ZHANG G Z, PU Y Y, WU K, LI S S. Enrichment of a common wheat genetic map and QTL mapping for fatty acid content in grain. Plant Science, 2011, 181(1): 65-75.

[12] FRELS K, GUTTIERI M, JOYCE B, LEAVITT B, BAENZIGER P S. Evaluating canopy spectral reflectance vegetation indices to estimate nitrogen use traits in hard winter wheat. Field Crops Research, 2018, 217: 82-92.

[13] JIN D, GAO J, JIANG P, LV X, WANG Y, ZHANG W. Nitrogen use efficiency and rice yield of different locations in Northeast China. National Academy Science Letters, 2017, 40(4): 227-232.

[14] RENGEL Z, MARSCHNER P. Nutrient availability and management in the rhizosphere: Exploiting genotypic differences. New Phytology, 2005, 168(2): 305-312.

[15] QUARRIE S A, STEED A, CALESTANI C, SEMIKHODSKII A, LEBRETON C, CHINOY C, STEELE N, PLJEVLJAKUSIC D, WATERMAN E, WEYEN J, SCHONDELMAIER J, HABASH D Z, FARMER P, SAKER L, CLARKSON D T, ABUGALIEVA A, YESSIMBEKOVA M, TURUSPEKOV Y, ABUGALIEVA S, TUBEROSA R, SANGUINETI M C, HOLLINGTON P A, ARAGUES R, ROYO A, DODIG D. A high-density genetic map of hexaploid wheat (L.) from the cross Chinese Spring× SQ1 and its use to compare QTLs for grain yield across a range of environments. Theoretical and Applied Genetics, 2005, 110(5): 865-880.

[16] LéTIZIA C K, JEAN-BAPTISTE V, DELPHINE M, VALéRIE C, MARIE F, STéPHANIE B, PIERRE D, BRIGITTE G, DOMENICA M, ALAIN C. Maize adaptation to temperate climate: relationship between population structure and polymorphism in thegene. Genetics, 172(4): 2449-2463.

[17] THORNSBERRY J M, GOODMAN M M, DOEBLEY J, KRESOVICH S, NIELSEN D, BUCKLER E S. Dwarf8 polymorphisms associate with variation in flowering time. Nature Genetics, 2001, 28(3): 286-289

[18] DONG Y, LIU J, ZHANG Y, GENG H, HE Z J P O. Genome-wide association of stem water soluble carbohydrates in bread wheat. PLoS ONE, 2016, 11(11): e0164293.

[19] LIU J, HE Z, RASHEED A, WEN W, YAN J, ZHANG P, WAN Y, ZHANG Y, XIE C, XIA X J B P B. Genome-wide association mapping of black point reaction in common wheat (L.). BMC Plant Biology, 2017, 17(1): 220.

[20] GUO J, SHI W, ZHANG Z, CHENG J, SUN D, YU J, LI X, GUO P, HAO C J B P B. Association of yield-related traits in founder genotypes and derivatives of common wheat (L.). BMC Plant Biology, 2018, 18(1): 38.

[21] RASHEED A, XIA X, OGBONNAYA F, MAHMOOD T, ZHANG Z, MUJEEB-KAZI A, HE Z J B P B. Genome-wide association for grain morphology in synthetic hexaploid wheats using digital imaging analysis.BMC Plant Biology, 2014, 14(1): 128.

[22] BULL P, ZHANG J, CHAO S, CHEN X, PUMPHREY M. Genetic architecture of resistance to stripe rust in a global winter wheat germplasm collection. Genetics, 2016, 6(8): 2237-2253.

[23] MACCAFERRI M, RICCI A, SALVI S, MILNER S G, JOURNAL R T J P B. A high-density, SNP-based consensus map of tetraploid wheat as a bridge to integrate durum and bread wheat genomics and breeding. Biotechnology, 2015, 13(5): 648-663.

[24] SIDDIQI M Y, GLASS A D M. Utilization index: A modified approach to the estimation and comparison of nutrient utilization efficiency in plants. Journal of Plant Nutrition, 1981, 4(3): 289-302.

[25] KNAPP S J, STROUP W W, ROSS W M. Exact confidence intervals for heritability on a progeny mean basis. Theoretical and Applied Genetics, 1985, 25(1): 192-204.

[26] 屈春艷. 水旱條件下小麥產(chǎn)量性狀和抗旱性的全基因組關(guān)聯(lián)分析[D]. 泰安: 山東農(nóng)業(yè)大學(xué), 2018.

QU C Y. Genome-wide association study on yield traits and drought tolerance under irrigation and drought conditions in wheat [D]. Taian: Shandong Agricultural University, 2018. (in Chinese)

[27] MARCO M, WALID E F, GHASEMALI N, SILVIO S, ANGELA C M, CHIARA C M, SANDRA S, ROBERTO T. Prioritizing quantitative trait loci for root system architecture in tetraploid wheat. Journal of experimental botany, 2016, (4): 1161-1178

[28] BISHOPP A, LYNCH J P. The hidden half of crop yields. Nature Plants, 2015, 1(8): 15117.

[29] CHENYANG H, YUQUAN W, SHIAOMAN C, TIAN L, HONGXIA L, LANFEN W, XUEYONG Z. The iSelect 9 K SNP analysis revealed polyploidization induced revolutionary changes and intense human selection causing strong haplotype blocks in wheat. Scientific reports, 2017, 7: 41247.

[30] CUI F, ZHAO C, DING A, LI J, WANG L, LI X, BAO Y, LI J, WANG H. Construction of an integrative linkage map and QTL mapping of grain yield-related traits using three related wheat RIL populations. Theoretical and Applied Genetics, 2014, 127(3): 659-675.

[31] FONTAINE J X, RAVEL C, PAGEAU K, HEUMEZ E, DUBOIS F, HIREL B, LE GOUIS J. A quantitative genetic study for elucidating the contribution of glutamine synthetase, glutamate dehydrogenase and other nitrogen-related physiological traits to the agronomic performance of common wheat. Theoretical and Applied Genetics, 2009, 119(4): 645-662.

[32] GUO Y, KONG F M, XU Y F, ZHAO Y, LIANG X, WANG Y Y, AN D G, LI S S. QTL mapping for seedling traits in wheat grown under varying concentrations of N, P and K nutrients. Theoretical and Applied Genetics, 2012, 124(5): 851-865.

[33] HABASH D Z, BERNARD S, SCHONDELMAIER J, WEYEN J, QUARRIE S A. The genetics of nitrogen use in hexaploid wheat: N utilisation, development and yield. Theoretical and Applied Genetics, 2007, 114(3): 403-419.

[34] XU Y, WANG R, TONG Y, ZHAO H, XIE Q, LIU D, ZHANG A, LI B, XU H, AN D. Mapping QTLs for yield and nitrogen-related traits in wheat: influence of nitrogen and phosphorus fertilization on QTL expression. Theoretical and Applied Genetics, 2014, 127(1): 59-72.

[35] AN D, SU J, LIU Q, ZHU Y, TONG Y, LI J, JING R, LI B, LI Z. Mapping QTLs for nitrogen uptake in relation to the early growth of wheat (L.). Plant and Soil, 2006, 284(1/2): 73-84.

[36] CUI F, FAN X, ZHAO C, ZHANG W, CHEN M, JI J, LI J. A novel genetic map of wheat: utility for mapping QTL for yield under different nitrogen treatments. BMC genetics, 2014, 15(1): 57.

[37] FONTAINE J X, RAVEL C, PAGEAU K, HEUMEZ E, DUBOIS F, HIREL B, GOUIS J. A quantitative genetic study for elucidating the contribution of glutamine synthetase, glutamate dehydrogenase and other nitrogen-related physiological traits to the agronomic performance of common wheat. Theoretical and Applied Genetics, 2009, 119(4): 645-662.

[38] KONG F M, GUO Y, LIANG X, WU C H, WANG Y Y, ZHAO Y, LI S S. Potassium (K) effects and QTL mapping for K efficiency traits at seedling and adult stages in wheat.Plant and Soil, 2013, 373(1/2): 877-892.

[39] 張國華. 黃淮麥區(qū)小麥品種(系)產(chǎn)量性狀與分子標(biāo)記的關(guān)聯(lián)分析[D]. 泰安: 山東農(nóng)業(yè)大學(xué), 2013.

ZHANG G H. Association analysis of yield traits and molecular markers of wheat varieties (lines) in Huanghuai wheat region [D]. Tai'an: Shandong Agricultural University, 2013. (in Chinese)

[40] MESSENGUY F, DUBOIS E J G. Role of MADS box proteins and their cofactors in combinatorial control of gene expression and cell development. Gene, 2003, 316(1): 1-21.

[41] HECK G O. AGL15, a MADS domain protein expressed in developing embryos. The Plant Cell, 1995, 7(8): 1271-1282.

[42] KUO M H, NADEAU E T, GRAYHACK E J J M, BIOLOGY C. Multiple phosphorylated forms of the Saccharomyces cerevisiae Mcm1 protein include an isoform induced in response to high salt concentrations. Molecular and celluar biology, 1997, 17(2): 819-832.

[43] LOZANO, PHYSIOLOGY R J P. Tomato flower abnormalities induced by low temperatures are associated with changes of expression of MADS-box genes. Plant Physiology, 1998, 117(1): 91-100.

[44] LEI L, LI G, ZHANG H, POWERS C, FANG T, CHEN Y, WANG S, ZHU X and YAN L. Nitrogen use efficiency is regulated by interacting proteins relevant to development in wheat. Plant Biotechnology Journal, 2018, 16(6): 1214-1226.

[45] WANG M, ZHANG P, LIU Q, LI G, SHI W. TaANR1-TaBG1 and TaWabi5-TaNRT2s/NARs link ABA metabolism and nitrate acquisition in wheat roots. Plant Physiology, 2020, 182: 1440-1453.

附表1 苗期生物量及氮效率相關(guān)性狀關(guān)聯(lián)分析Supplement table 1 Association analysisbetween traits related to biomassand nitrogen efficiency atm seedling

?

RSDW LNE1 IAAV5406 1A 7836333 1.43E-06 0.224637322 RSDW LNE1 wsnp_Ex_c34344_42676379 1A 7836333 1.42E-06 0.224756726 RSDW LNE1 wsnp_Ex_rep_c66628_64934660 1A 7836333 1.55E-05 0.181482278 RSDW LNE1 BobWhite_c12568_900 1A 7918917 9.83E-05 0.149015768 RSDW LNE1 Ra_c105707_788 1A 8054288 9.66E-05 0.14931625 RSDW LNE1 IAAV5535 1A 8079549 5.64E-04 0.11917587 RSDW LNE1 IACX3047 1A 8079549 5.64E-04 0.11917587 RSDW LNE1 RAC875_c29540_391 1A 8290703 1.08E-04 0.147382874 RSDW LNE1 BS00065324_51 1A 8370371 2.58E-04 0.132433662 RSDW LNE1 wsnp_Ra_c9209_15425473 1A 8370371 7.13E-05 0.15457565 RSDW LNE1 RFL_Contig22_387 1A 8432552 4.15E-17 0.767034838 RSDW LNE1 Kukri_c31891_1355 1A 8442267 3.11E-04 0.129250222 RSDW LNE1 wsnp_Ex_c20489_29564938 1A 8442267 3.97E-04 0.125077313 RSDW LNE1 Kukri_c54678_88 1A 8660222 2.11E-05 0.176002547 RSDW LNE1 wsnp_Ku_c33917_43336069 1A 10119192 8.40E-04 0.112474058 RSDW LNE1 BS00110130_51 1A 10291807 9.82E-04 0.10985468 RSDW LNE1 IAAV8446 1A 15122437 3.20E-05 0.168614787 RSDW HNE1 GENE-1118_58 1A 2533846 7.33E-04 0.114752184 RSNC LNAV BS00022677_51 1A 1373147 2.48E-04 0.134166126 RSNC LNAV Excalibur_c35316_154 1A 1667208 4.45E-04 0.124154223 RSNC LNAV RAC875_c37934_225 1A 4593891 4.50E-04 0.123969161 RSNC LNAV wsnp_RFL_Contig373_3974834 1A 7010178 7.76E-04 0.114701791 RSNC LNE1 BS00022677_51 1A 1373147 2.00E-07 0.272980189 RSNC LNE1 Excalibur_c35316_154 1A 1667208 1.98E-07 0.273165403 RSNC LNE1 BS00067961_51 1A 3811132 6.04E-04 0.122858368 RSNC LNE1 RAC875_c37934_225 1A 4593891 6.43E-04 0.121752833 RSNC LNE1 Excalibur_c55677_217 1A 4844879 5.99E-04 0.123000787 RSNC LNE1 wsnp_Ex_c10783_17555091 1A 5109469 2.05E-04 0.141977457 RSNC LNE1 wsnp_Ex_c17684_26426672 1A 7010178 2.24E-04 0.140420511 RSNC LNE1 BS00102492_51 1A 7078511 3.46E-04 0.132716312 RSNC LNE1 BobWhite_c12977_65 1A 9361046 5.62E-04 0.124119682 RSNC LNE1 BS00022848_51 1A 10481586 1.91E-04 0.143323687 SDW LNE1 BS00077492_51 1A 3811132 3.69E-04 0.126336186 SNC LNE1 BS00077492_51 1A 3811132 8.29E-04 0.117346827 SNUE LNE1 BS00077492_51 1A 3811132 5.62E-04 0.124172375 TDW LNE1 BS00077492_51 1A 3811132 8.11E-04 0.113057686 TNC LNE1 BS00077492_51 1A 3811132 8.18E-04 0.117587163 TNCe HNE1 RFL_Contig5001_1099 1A 7109601 4.66E-13 0.560500588 TNUE LNE1 BS00077492_51 1A 3811132 7.97E-04 0.118031244 RDW CKE1 BobWhite_c9881_1312 1B 10256166 3.58E-04 0.100946416 RDW CKE1 RAC875_rep_c114694_99 1B 10739616 1.30E-04 0.144195997 RDW CKE1 BobWhite_c20621_541 1B 10841412 2.25E-05 0.174796965 RDW CKE2 Tdurum_contig8580_586 1B 12034561 8.37E-04 0.112522446 RDW LNAV Kukri_c39223_871 1B 11046918 6.81E-04 0.091037929 RDW LNAV wsnp_Ex_c27176_36392758 1B 11408469 4.67E-04 0.09684339 RDW LNAV Ex_c25733_348 1B 11518562 4.81E-04 0.096374584 RDW LNE1 wsnp_Ex_c27176_36392758 1B 11408469 3.71E-04 0.100415415 RDW HNAV BobWhite_c9881_1312 1B 10256166 3.49E-04 0.101344418 RDW HNAV BS00039135_51 1B 11015646 4.78E-04 0.121949968 RDW HNAV BobWhite_c2844_569 1B 11015646 4.78E-04 0.121949968 RDW HNE2 Ku_c13532_1753 1B 6062434 9.78E-04 0.109918869

RDW HNE2 BobWhite_c9881_1312 1B 10256166 3.57E-04 0.100981411 RDW HNE2 BS00039135_51 1B 11015646 4.52E-04 0.122904304 RDW HNE2 BobWhite_c2844_569 1B 11015646 4.52E-04 0.122904304 RNC CKE1 BobWhite_c9881_1312 1B 10256166 3.59E-04 0.100926696 RNC LNAV IACX7107 1B 6062434 9.64E-04 0.110166337 RNC LNAV Tdurum_contig62993_316 1B 6062434 6.98E-04 0.115565718 RNC LNAV wsnp_Ex_c27176_36392758 1B 11408469 6.77E-04 0.091130452 RNC LNAV JD_c954_2440 1B 11412936 6.13E-04 0.117764036 RNC LNE1 wsnp_Ex_c27176_36392758 1B 11408469 4.33E-04 0.097988927 RNCe LNE1 RAC875_c2040_564 1B 4366369 5.44E-04 0.119784614 RNCe HNAV Excalibur_c5562_380 1B 967857 5.63E-04 0.093958724 RNCe HNE1 Excalibur_c10528_347 1B 6062434 9.11E-04 0.088691035 RNUE CKAV BobWhite_c9881_1312 1B 10256166 7.45E-04 0.090359892 RNUE CKAV RAC875_rep_c114694_99 1B 10739616 9.71E-04 0.110920663 RNUE CKE1 BobWhite_c9881_1312 1B 10256166 3.75E-05 0.13692562 RNUE CKE1 RAC875_rep_c114694_99 1B 10739616 3.77E-04 0.125986984 RNUE LNAV BS00034925_51 1B 7078158 2.90E-04 0.130405542 RNUE LNAV BobWhite_rep_c66032_270 1B 7078158 4.62E-04 0.122546539 RNUE LNAV BS00023142_51 1B 7085179 7.10E-04 0.115288217 RNUE LNAV CAP7_c3456_113 1B 7085179 7.10E-04 0.115288217 RNUE LNAV GENE-0142_178 1B 7085179 7.10E-04 0.115288217 RNUE LNAV RAC875_c87890_234 1B 7184741 4.28E-04 0.12382041 RNUE LNAV Tdurum_contig44255_814 1B 7184741 7.10E-04 0.115288217 RNUE LNAV CAP8_c818_370 1B 7977408 6.88E-04 0.115817199 RNUE LNAV Kukri_c39223_871 1B 11046918 8.25E-04 0.088098734 RNUE LNAV wsnp_Ex_c27176_36392758 1B 11408469 1.43E-04 0.115372094 RNUE LNAV JD_c954_2440 1B 11412936 5.87E-04 0.118486881 RNUE LNAV Ex_c25733_348 1B 11518562 2.93E-04 0.104070283 RNUE LNE1 wsnp_Ex_c27176_36392758 1B 11408469 7.07E-04 0.090464843 RNUE LNE2 RAC875_c87890_234 1B 7184741 7.45E-04 0.114470234 RNUE HNAV BS00039135_51 1B 11015646 2.30E-04 0.135452008 RNUE HNAV BobWhite_c2844_569 1B 11015646 2.30E-04 0.135452008 RNUE HNAV BS00070285_51 1B 11781188 4.44E-04 0.124186507 RNUE HNE1 BobWhite_c9881_1312 1B 10256166 8.93E-05 0.126942891 RNUE HNE2 Excalibur_c46114_572 1B 4121294 8.17E-04 0.11293718 RNUE HNE2 BS00021902_51 1B 4385835 9.99E-04 0.109570637 RNUE HNE2 IAAV268 1B 4385835 9.99E-04 0.109570637 RNUE HNE2 IAAV4559 1B 4385835 9.99E-04 0.109570637 RNUE HNE2 Kukri_c25654_382 1B 4385835 9.99E-04 0.109570637 RNUE HNE2 RAC875_c10050_620 1B 4385835 9.69E-04 0.110083485 RNUE HNE2 RAC875_rep_c109118_164 1B 4385835 9.99E-04 0.109570637 RNUE HNE2 GENE-0189_45 1B 6062434 9.99E-04 0.109570637 RNUE HNE2 RAC875_c1276_717 1B 6062434 9.99E-04 0.109570637 RNUE HNE2 tplb0026b15_350 1B 6062434 9.99E-04 0.109570637 RNUE HNE2 BS00030667_51 1B 6258048 9.99E-04 0.109570637 RNUE HNE2 BS00091317_51 1B 6258048 9.99E-04 0.109570637 RNUE HNE2 GENE-0403_110 1B 6258048 9.69E-04 0.110083485 RNUE HNE2 IACX3431 1B 6258048 9.99E-04 0.109570637 RNUE HNE2 IACX6800 1B 6258048 9.99E-04 0.109570637 RNUE HNE2 Kukri_c7886_195 1B 6258048 9.99E-04 0.109570637 RNUE HNE2 Excalibur_c19291_571 1B 6379948 9.99E-04 0.109570637

RNUE HNE2 Kukri_rep_c104321_201 1B 6379948 9.99E-04 0.109570637 RNUE HNE2 Tdurum_contig29228_114 1B 6803725 6.09E-04 0.117858743 RNUE HNE2 BS00039135_51 1B 11015646 7.40E-05 0.153933342 RNUE HNE2 BobWhite_c2844_569 1B 11015646 7.40E-05 0.153933342 RSNC LNAV Kukri_c38845_821 1B 3103974 6.93E-04 0.116629074 RSNC LNAV BobWhite_c28295_256 1B 4093531 6.93E-04 0.116629074 RSNC LNAV BobWhite_c14258_434 1B 4366369 5.69E-04 0.119968243 RSNC LNAV BS00005004_51 1B 4385835 3.28E-04 0.129350446 RSNC LNAV BS00066398_51 1B 4385835 4.50E-04 0.123969161 RSNC LNAV BS00067709_51 1B 4385835 3.28E-04 0.129350446 RSNC LNAV BS00073199_51 1B 4385835 4.50E-04 0.123969161 RSNC LNAV BS00084722_51 1B 4385835 4.50E-04 0.123969161 RSNC LNAV BS00088256_51 1B 4385835 3.28E-04 0.129350446 RSNC LNAV BobWhite_c3068_393 1B 4385835 4.50E-04 0.123969161 RSNC LNAV Excalibur_c31375_558 1B 4385835 4.50E-04 0.123969161 RSNC LNAV IAAV8714 1B 4385835 3.28E-04 0.129350446 RSNC LNAV Kukri_c5221_506 1B 4385835 5.69E-04 0.119968243 RSNC LNAV RAC875_c82649_146 1B 4385835 4.50E-04 0.123969161 RSNC LNAV Tdurum_contig27840_760 1B 4385835 4.50E-04 0.123969161 RSNC LNAV Excalibur_c34148_481 1B 5310294 4.98E-04 0.122239758 RSNC LNAV BS00065314_51 1B 6062434 4.50E-04 0.123969161 RSNC LNAV BS00098306_51 1B 6062434 4.50E-04 0.123969161 RSNC LNAV BS00109971_51 1B 6062434 5.69E-04 0.119968243 RSNC LNAV Ex_c3312_446 1B 6062434 4.50E-04 0.123969161 RSNC LNAV Excalibur_rep_c112996_167 1B 6062434 3.28E-04 0.129350446 RSNC LNAV GENE-0456_190 1B 6062434 4.50E-04 0.123969161 RSNC LNAV GENE-3075_364 1B 6062434 3.28E-04 0.129350446 RSNC LNAV IAAV7602 1B 6062434 4.50E-04 0.123969161 RSNC LNAV IAAV7845 1B 6062434 4.50E-04 0.123969161 RSNC LNAV Kukri_c11707_160 1B 6062434 3.28E-04 0.129350446 RSNC LNAV Kukri_c26168_423 1B 6062434 4.50E-04 0.123969161 RSNC LNAV Kukri_rep_c102887_300 1B 6062434 3.28E-04 0.129350446 RSNC LNAV RAC875_c11123_186 1B 6062434 3.28E-04 0.129350446 RSNC LNAV Tdurum_contig12173_284 1B 6062434 4.50E-04 0.123969161 RSNC LNAV tplb0053b16_1030 1B 6062434 4.50E-04 0.123969161 RSNC LNAV Excalibur_c20610_251 1B 6253900 5.00E-04 0.122150454 RSNC LNAV BS00004981_51 1B 6258048 4.50E-04 0.123969161 RSNC LNAV BS00110120_51 1B 6258048 3.28E-04 0.129350446 RSNC LNAV BobWhite_c11817_376 1B 6258048 4.50E-04 0.123969161 RSNC LNAV Excalibur_c5881_398 1B 6258048 5.69E-04 0.119968243 RSNC LNAV GENE-0121_495 1B 6258048 4.50E-04 0.123969161 RSNC LNAV RAC875_c24429_132 1B 6258048 7.15E-04 0.116081795 RSNC LNAV RAC875_c68119_594 1B 6258048 5.69E-04 0.119968243 RSNC LNAV Tdurum_contig25732_112 1B 6258048 4.50E-04 0.123969161 RSNC LNAV GENE-0158_358 1B 6385692 5.69E-04 0.119968243 RSNC LNAV JG_c8473_141 1B 6385692 5.69E-04 0.119968243 RSNC LNAV BS00066135_51 1B 6391117 5.69E-04 0.119968243 RSNC LNAV BS00068096_51 1B 6391117 5.69E-04 0.119968243 RSNC LNAV BobWhite_c14258_383 1B 6391117 5.69E-04 0.119968243 RSNC LNAV Excalibur_c64533_980 1B 6409944 1.41E-04 0.143961087 RSNC LNAV GENE-0400_297 1B 6409944 5.69E-04 0.119968243

RSNC LNE1 Excalibur_rep_c112996_167 1B 6062434 1.82E-07 0.274863897 RSNC LNE1 GENE-0456_190 1B 6062434 6.43E-04 0.121752833 RSNC LNE1 GENE-3075_364 1B 6062434 1.82E-07 0.274863897 RSNC LNE1 IAAV7602 1B 6062434 6.43E-04 0.121752833 RSNC LNE1 IAAV7845 1B 6062434 6.43E-04 0.121752833 RSNC LNE1 Kukri_c11707_160 1B 6062434 1.82E-07 0.274863897 RSNC LNE1 Kukri_c26168_423 1B 6062434 6.43E-04 0.121752833 RSNC LNE1 Kukri_rep_c102887_300 1B 6062434 1.82E-07 0.274863897 RSNC LNE1 RAC875_c11123_186 1B 6062434 1.82E-07 0.274863897 RSNC LNE1 Tdurum_contig12173_284 1B 6062434 6.43E-04 0.121752833 RSNC LNE1 tplb0053b16_1030 1B 6062434 6.43E-04 0.121752833 RSNC LNE1 Excalibur_c20610_251 1B 6253900 2.32E-07 0.270028048 RSNC LNE1 BS00004981_51 1B 6258048 6.43E-04 0.121752833 RSNC LNE1 BS00110120_51 1B 6258048 1.82E-07 0.274863897 RSNC LNE1 BobWhite_c11817_376 1B 6258048 6.43E-04 0.121752833 RSNC LNE1 Excalibur_c5881_398 1B 6258048 2.21E-07 0.270990225 RSNC LNE1 GENE-0121_495 1B 6258048 6.43E-04 0.121752833 RSNC LNE1 RAC875_c24429_132 1B 6258048 2.12E-07 0.271876231 RSNC LNE1 RAC875_c68119_594 1B 6258048 2.21E-07 0.270990225 RSNC LNE1 Tdurum_contig25732_112 1B 6258048 6.43E-04 0.121752833 RSNC LNE1 GENE-0158_358 1B 6385692 2.21E-07 0.270990225 RSNC LNE1 JG_c8473_141 1B 6385692 2.21E-07 0.270990225 RSNC LNE1 BS00066135_51 1B 6391117 2.21E-07 0.270990225 RSNC LNE1 BS00068096_51 1B 6391117 2.21E-07 0.270990225 RSNC LNE1 BobWhite_c14258_383 1B 6391117 2.21E-07 0.270990225 RSNC LNE1 Excalibur_c64533_980 1B 6409944 8.29E-04 0.117307029 RSNC LNE1 GENE-0400_297 1B 6409944 2.21E-07 0.270990225 RSNC LNE1 IAAV587 1B 6409944 2.21E-07 0.270990225 RSNC LNE1 IAAV7445 1B 6409944 2.21E-07 0.270990225 RSNC LNE1 TA002664-0848 1B 6409944 2.21E-07 0.270990225 RSNC LNE1 wsnp_Ex_rep_c69266_68192766 1B 6409944 5.78E-04 0.12362368 RSNC LNE1 BS00094498_51 1B 6714055 6.46E-04 0.121678429 RSNC LNE1 Excalibur_c59016_839 1B 6803725 6.21E-04 0.122373092 RSNC LNE1 Kukri_c12151_467 1B 6803725 2.32E-07 0.270058449 RSNC LNE1 Kukri_c12151_769 1B 6803725 2.32E-07 0.270058449 RSNC LNE1 BS00034925_51 1B 7078158 1.12E-05 0.195143105 RSNC LNE1 BobWhite_rep_c66032_270 1B 7078158 8.90E-06 0.199512912 RSNC LNE1 BS00023142_51 1B 7085179 2.29E-04 0.139999724 RSNC LNE1 CAP7_c3456_113 1B 7085179 2.29E-04 0.139999724 RSNC LNE1 GENE-0142_178 1B 7085179 2.29E-04 0.139999724 RSNC LNE1 Ra_c3837_797 1B 7085179 6.50E-05 0.162724224 RSNC LNE1 wsnp_BE443332B_Ta_2_2 1B 7085179 3.22E-04 0.133982827 RSNC LNE1 Tdurum_contig44255_814 1B 7184741 2.29E-04 0.139999724 RSNC LNE1 Excalibur_c30955_479 1B 7844978 2.20E-07 0.271083157 RSNC LNE1 Tdurum_contig83770_218 1B 7844978 4.37E-04 0.128566645 RSNC LNE1 BobWhite_c5812_440 1B 8443307 2.29E-07 0.270323402 RSNC LNE1 wsnp_Ex_c21198_30326388 1B 8443307 2.29E-07 0.270323402 RSNC LNE1 Tdurum_contig27843_142 1B 9457436 2.02E-07 0.272802956 RSNC LNE1 RAC875_c52957_154 1B 9541681 1.94E-07 0.273604221 RSNC LNE1 RFL_Contig2176_1111 1B 9541681 1.94E-07 0.273604221 RSNC LNE1 BS00022577_51 1B 9640924 2.33E-07 0.269977834

RSNC LNE1 BS00077498_51 1B 12170821 6.90E-04 0.120522338 RSNC LNE1 Tdurum_contig10354_270 1B 14839849 9.50E-04 0.114936579 RSNC LNE1 RAC875_c9770_123 1B 15859084 1.82E-07 0.27493116 RSNC LNE1 BS00063302_51 1B 16024382 7.04E-04 0.120180002 SDW CKE1 Kukri_c39223_871 1B 11046918 8.45E-04 0.087745017 SDW LNE1 BS00065737_51 1B 5688119 1.59E-04 0.113709021 SDW LNE1 GENE-0427_442 1B 5688119 2.19E-04 0.108632468 SDW LNE1 IACX16577 1B 5688119 1.19E-04 0.118284937 SDW HNE2 BS00065737_51 1B 5688119 7.62E-04 0.089315923 SDW HNE2 GENE-0427_442 1B 5688119 1.33E-04 0.116537321 SDW HNE2 IACX16577 1B 5688119 5.28E-04 0.094945879 SNC CKE1 Kukri_c39223_871 1B 11046918 3.12E-04 0.103931206 SNC CKE2 Tdurum_contig8580_586 1B 12034561 9.44E-04 0.11228858 SNC LNE1 BS00065737_51 1B 5688119 5.57E-04 0.097995862 SNC LNE1 GENE-0427_442 1B 5688119 4.40E-04 0.101792752 SNC LNE1 IACX16577 1B 5688119 5.03E-04 0.0996104 SNC LNE2 IACX9290 1B 13420771 3.57E-04 0.127916739 SNC HNAV GENE-0427_442 1B 5688119 5.79E-04 0.093531061 SNC HNE1 CAP12_c2858_94 1B 8556910 8.32E-04 0.089372128 SNC HNE1 RAC875_c97479_160 1B 8556910 8.32E-04 0.089372128 SNC HNE1 RFL_Contig2686_571 1B 8556910 8.32E-04 0.089372128 SNC HNE2 GENE-0427_442 1B 5688119 8.62E-05 0.12345049 SNC HNE2 IACX16577 1B 5688119 7.66E-04 0.089229535 SNUE CKE1 Excalibur_rep_c107218_71 1B 7977408 7.33E-04 0.115670676 SNUE LNE1 BS00065737_51 1B 5688119 3.10E-04 0.107485791 SNUE LNE1 IACX16577 1B 5688119 2.62E-04 0.110176661 SNUE HNE2 BS00065737_51 1B 5688119 3.54E-04 0.101147173 SNUE HNE2 GENE-0427_442 1B 5688119 2.88E-04 0.104375077 SNUE HNE2 IACX16577 1B 5688119 2.25E-04 0.108199847 TDW CKE1 Tdurum_contig17609_117 1B 5777151 8.82E-04 0.111646573 TDW LNE1 BS00065737_51 1B 5688119 9.45E-04 0.086039579 TDW LNE1 GENE-0427_442 1B 5688119 6.54E-04 0.091662033 TDW LNE1 IACX16577 1B 5688119 8.20E-04 0.088199723 TDW HNAV GENE-0427_442 1B 5688119 5.76E-04 0.093599081 TDW HNE1 RAC875_rep_c114694_99 1B 10739616 7.12E-04 0.11524626 TDW HNE2 GENE-0427_442 1B 5688119 1.88E-04 0.111062351 TDW HNE2 IACX16577 1B 5688119 7.44E-04 0.089677421 TNC CKE1 Kukri_c39223_871 1B 11046918 2.14E-04 0.109895497 TNC LNE1 BS00065737_51 1B 5688119 9.97E-04 0.088711996 TNC LNE1 GENE-0427_442 1B 5688119 3.90E-04 0.103740597 TNC LNE1 IACX16577 1B 5688119 7.63E-04 0.092951272 TNC LNE2 IACX9290 1B 13420771 2.59E-04 0.133412002 TNC HNAV GENE-0427_442 1B 5688119 6.25E-04 0.092339143 TNC HNE1 CAP12_c2858_94 1B 8556910 8.67E-04 0.091664339 TNC HNE1 RAC875_c97479_160 1B 8556910 8.67E-04 0.091664339 TNC HNE1 RFL_Contig2686_571 1B 8556910 8.67E-04 0.091664339 TNC HNE2 GENE-0427_442 1B 5688119 1.08E-04 0.119820927 TNC HNE2 IACX16577 1B 5688119 8.78E-04 0.087152144 TNUE CKE1 Tdurum_contig17609_117 1B 5777151 8.76E-04 0.112664972 TNUE LNE1 IACX16577 1B 5688119 8.17E-04 0.091872807 TNUE HNAV GENE-0427_442 1B 5688119 5.02E-04 0.096475148

TNUE HNE2 BS00065737_51 1B 5688119 7.25E-04 0.090075371 TNUE HNE2 GENE-0427_442 1B 5688119 1.63E-04 0.113337497 TNUE HNE2 IACX16577 1B 5688119 4.32E-04 0.098052587 RNCe LNE1 Ex_c6145_833 1D 3947728 7.03E-04 0.11545343 RNCe LNE1 RAC875_c7752_1223 1D 3947728 7.03E-04 0.11545343 RNCe LNE1 RAC875_c7752_2913 1D 3947728 7.03E-04 0.11545343 RNCe LNE1 RAC875_c7752_549 1D 3947728 7.03E-04 0.11545343 RNCe LNE1 BS00023049_51 1D 13399386 6.74E-04 0.116160477 RNCe LNE1 BS00104199_51 1D 13399386 2.16E-04 0.135455951 RSDW LNE1 Tdurum_contig13681_628 1D 16193957 6.51E-04 0.091731832 RSNC LNAV BobWhite_c14526_271 1D 350176 4.50E-04 0.123969161 RSNC LNAV Excalibur_c12254_2003 1D 350176 3.97E-04 0.126080879 RSNC LNAV IACX6586 1D 350176 5.69E-04 0.119968243 RSNC LNAV D_F5XZDLF01A85DT_301 1D 6135865 6.48E-04 0.117765209 RSNC LNAV Ra_c4899_609 1D 7081901 8.98E-04 0.112230259 RSNC LNAV Excalibur_c23906_303 1D 11562047 7.73E-04 0.114768543 RSNC LNAV wsnp_Ra_c193_406396 1D 11562047 7.73E-04 0.114768543 RSNC LNAV RAC875_c40434_373 1D 16385528 6.81E-04 0.116925762 RSNC LNAV RAC875_rep_c118202_115 1D 16385528 1.74E-04 0.140275445 RSNC LNE1 Kukri_c26168_713 1D 340224 3.31E-04 0.133490311 RSNC LNE1 BobWhite_c14526_271 1D 350176 6.43E-04 0.121752833 RSNC LNE1 Excalibur_c12254_2003 1D 350176 2.32E-07 0.270007647 RSNC LNE1 IACX6586 1D 350176 2.21E-07 0.270990225 RSNC LNE1 D_F5XZDLF01A85DT_301 1D 6135865 2.30E-07 0.270241284 RSNC LNE1 BS00051826_51 1D 6771532 2.56E-05 0.179808237 RSNC LNE1 D_contig16934_681 1D 6771532 2.18E-05 0.182773222 RSNC LNE1 IAAV4760 1D 6771532 2.71E-05 0.17876761 RSNC LNE1 IAAV4794 1D 6771532 2.71E-05 0.17876761 RSNC LNE1 Kukri_c9864_1220 1D 6771532 2.18E-05 0.182773222 RSNC LNE1 RAC875_c17951_108 1D 6771532 2.56E-05 0.179808237 RSNC LNE1 RAC875_c35094_476 1D 6771532 2.18E-05 0.182773222 RSNC LNE1 Ra_c4899_609 1D 7081901 6.43E-04 0.121769723 RSNC LNE1 BS00024262_51 1D 7190126 2.30E-05 0.181800981 RSNC LNE1 BS00033405_51 1D 7190126 2.30E-05 0.181800981 RSNC LNE1 RAC875_c48997_1160 1D 7190126 2.30E-05 0.181800981 RSNC LNE1 wsnp_CAP8_c458_368125 1D 7190126 2.30E-05 0.181800981 RSNC LNE1 Excalibur_c23906_303 1D 11562047 2.27E-07 0.270472721 RSNC LNE1 wsnp_Ra_c193_406396 1D 11562047 2.27E-07 0.270472721 RSNC LNE1 RAC875_c40434_373 1D 16385528 8.10E-08 0.291174006 RSNC LNE1 RAC875_rep_c118202_115 1D 16385528 8.09E-08 0.29118685 RSNC LNE1 IACX7617 1D 16407919 2.49E-04 0.138575141 RSNC LNE1 Excalibur_c20532_785 1D 16501216 4.34E-04 0.12868807 RSNC LNE1 BobWhite_c14422_282 1D 16547865 2.49E-04 0.138575141 SNCe LNAV BS00004282_51 1D 8735755 4.84E-04 0.0970414 RDW CKE1 wsnp_Ex_c905_1748920 2A 15129243 5.99E-04 0.093001852 RDW LNAV Excalibur_c37649_125 2A 9843438 3.18E-04 0.12884285 RDW LNAV RAC875_c13116_116 2A 9928033 3.18E-04 0.12884285 RDW LNAV Tdurum_contig48302_532 2A 9928033 3.18E-04 0.12884285 RDW LNAV wsnp_Ex_c29940_38921491 2A 10197360 5.88E-04 0.118460301 RDW LNAV Excalibur_c16393_274 2A 10362065 4.43E-04 0.12322417 RDW LNE1 wsnp_Ex_c15822_24204224 2A 9346633 5.03E-04 0.121087422

RDW LNE1 Excalibur_c37649_125 2A 9843438 2.76E-11 0.442716893 RDW LNE1 BS00062843_51 2A 9928033 9.37E-06 0.190442944 RDW LNE1 RAC875_c13116_116 2A 9928033 2.76E-11 0.442716893 RDW LNE1 Tdurum_contig48302_532 2A 9928033 2.76E-11 0.442716893 RDW LNE1 BobWhite_c38716_323 2A 10197360 3.41E-04 0.127701176 RDW LNE1 Ex_c24398_831 2A 10197360 1.34E-06 0.225909027 RDW LNE1 Excalibur_rep_c66270_789 2A 10197360 1.45E-04 0.14227462 RDW LNE1 IAAV5270 2A 10197360 1.48E-06 0.224001603 RDW LNE1 IAAV531 2A 10197360 8.02E-06 0.193240397 RDW LNE1 IAAV9024 2A 10197360 3.55E-04 0.126977372 RDW LNE1 Ku_c2359_569 2A 10197360 3.03E-04 0.129707726 RDW LNE1 Ra_c29240_628 2A 10197360 3.45E-04 0.127477621 RDW LNE1 TA001220-1276 2A 10197360 3.55E-04 0.126977372 RDW LNE1 Tdurum_contig75565_1388 2A 10197360 1.45E-04 0.14227462 RDW LNE1 wsnp_Ex_c29940_38921491 2A 10197360 2.65E-11 0.443579998 RDW LNE1 Ex_c4639_2631 2A 10362065 3.03E-04 0.129707726 RDW LNE1 Excalibur_c16393_274 2A 10362065 2.71E-11 0.443127635 RDW LNE1 GENE-0922_327 2A 10362065 2.95E-04 0.130125307 RDW LNE1 RAC875_c3102_959 2A 10362065 1.36E-06 0.225538146 RDW LNE1 Ra_c15292_990 2A 10362065 3.03E-04 0.129707726 RDW LNE1 wsnp_Ex_rep_c66800_65171259 2A 10413180 1.48E-06 0.224001603 RDW LNE1 wsnp_Ex_rep_c75827_73041653 2A 10413180 1.40E-06 0.225026057 RDW LNE1 Excalibur_c84687_162 2A 10685795 9.38E-04 0.110617664 RDW LNE1 CAP7_c1527_136 2A 14321560 2.59E-04 0.132357905 RDW LNE1 IACX3245 2A 14321560 4.66E-07 0.245542002 RDW LNE1 BS00023075_51 2A 14384035 2.33E-06 0.215649462 RDW LNE1 BobWhite_c4517_120 2A 14384035 9.68E-06 0.189854022 RDW LNE1 Tdurum_contig47508_250 2A 14384035 2.33E-06 0.215649462 RDW LNE1 Tdurum_contig94203_610 2A 14520043 6.32E-04 0.117254933 RDW LNE1 wsnp_Ra_c6586_11477949 2A 14964836 8.42E-04 0.112420344 RDW HNE2 Excalibur_c92241_336 2A 6564883 1.36E-04 0.143363678 RNC LNAV Excalibur_c37649_125 2A 9843438 3.52E-04 0.127151873 RNC LNAV RAC875_c13116_116 2A 9928033 3.52E-04 0.127151873 RNC LNAV Tdurum_contig48302_532 2A 9928033 3.52E-04 0.127151873 RNC LNAV wsnp_Ex_c29940_38921491 2A 10197360 3.42E-04 0.127630191 RNC LNAV Excalibur_c16393_274 2A 10362065 2.91E-04 0.130400921 RNC LNAV IACX3245 2A 14321560 6.59E-05 0.155956643 RNC LNE1 wsnp_Ex_c15822_24204224 2A 9346633 5.68E-04 0.119043201 RNC LNE1 Excalibur_c37649_125 2A 9843438 1.28E-10 0.409685599 RNC LNE1 BS00062843_51 2A 9928033 1.80E-05 0.178760821 RNC LNE1 RAC875_c13116_116 2A 9928033 1.28E-10 0.409685599 RNC LNE1 Tdurum_contig48302_532 2A 9928033 1.28E-10 0.409685599 RNC LNE1 Ex_c24398_831 2A 10197360 7.13E-06 0.195354452 RNC LNE1 Excalibur_rep_c66270_789 2A 10197360 5.20E-04 0.120538047 RNC LNE1 IAAV5270 2A 10197360 8.40E-06 0.19240206 RNC LNE1 IAAV531 2A 10197360 1.47E-05 0.182400591 RNC LNE1 Ku_c2359_569 2A 10197360 7.34E-04 0.114739553 RNC LNE1 Tdurum_contig75565_1388 2A 10197360 5.20E-04 0.120538047 RNC LNE1 wsnp_Ex_c29940_38921491 2A 10197360 1.28E-10 0.40969888 RNC LNE1 Ex_c4639_2631 2A 10362065 7.34E-04 0.114739553 RNC LNE1 Excalibur_c16393_274 2A 10362065 1.36E-10 0.408382408

RNC LNE1 GENE-0922_327 2A 10362065 8.21E-04 0.112844331 RNC LNE1 RAC875_c3102_959 2A 10362065 6.53E-06 0.196934614 RNC LNE1 Ra_c15292_990 2A 10362065 7.34E-04 0.114739553 RNC LNE1 wsnp_Ex_rep_c66800_65171259 2A 10413180 8.40E-06 0.19240206 RNC LNE1 wsnp_Ex_rep_c75827_73041653 2A 10413180 8.28E-06 0.19266201 RNC LNE1 CAP7_c1527_136 2A 14321560 4.74E-04 0.122089874 RNC LNE1 IACX3245 2A 14321560 1.48E-07 0.267271684 RNC LNE1 BS00023075_51 2A 14384035 3.12E-06 0.210340937 RNC LNE1 BobWhite_c4517_120 2A 14384035 2.03E-05 0.176618098 RNC LNE1 Tdurum_contig47508_250 2A 14384035 3.12E-06 0.210340937 RNCe LNAV BS00024643_51 2A 15129840 2.56E-04 0.106219874 RNCe LNAV Tdurum_contig10048_207 2A 15475990 4.19E-05 0.135083924 RNCe LNAV Kukri_c53501_305 2A 16289351 4.88E-04 0.096162712 RNCe LNE1 RAC875_c38018_278 2A 11013113 8.36E-04 0.112547225 RNCe LNE2 BS00024643_51 2A 15129840 1.43E-04 0.115369245 RNCe LNE2 Tdurum_contig10048_207 2A 15475990 3.55E-04 0.1010782 RNCe LNE2 Kukri_c53501_305 2A 16289351 7.94E-04 0.088689519 RNUE LNAV Excalibur_c37649_125 2A 9843438 7.28E-05 0.154226208 RNUE LNAV RAC875_c13116_116 2A 9928033 7.28E-05 0.154226208 RNUE LNAV Tdurum_contig48302_532 2A 9928033 7.28E-05 0.154226208 RNUE LNAV wsnp_Ex_c29940_38921491 2A 10197360 1.22E-04 0.145330387 RNUE LNAV Excalibur_c16393_274 2A 10362065 9.92E-05 0.148859197 RNUE LNAV IACX3245 2A 14321560 7.36E-04 0.114688498 RNUE LNE1 wsnp_Ex_c15822_24204224 2A 9346633 1.79E-05 0.178873671 RNUE LNE1 Excalibur_c37649_125 2A 9843438 2.69E-13 0.547300468 RNUE LNE1 BS00062843_51 2A 9928033 1.77E-06 0.220704158 RNUE LNE1 RAC875_c13116_116 2A 9928033 2.69E-13 0.547300468 RNUE LNE1 Tdurum_contig48302_532 2A 9928033 2.69E-13 0.547300468 RNUE LNE1 BS00078923_51 2A 10197360 7.75E-04 0.11382505 RNUE LNE1 BobWhite_c38716_323 2A 10197360 1.52E-04 0.141505114 RNUE LNE1 Ex_c24398_831 2A 10197360 1.67E-07 0.264958108 RNUE LNE1 Excalibur_rep_c66270_789 2A 10197360 3.40E-06 0.208755568 RNUE LNE1 IAAV5270 2A 10197360 1.75E-07 0.264111598 RNUE LNE1 IAAV531 2A 10197360 1.77E-06 0.220708824 RNUE LNE1 IAAV9024 2A 10197360 1.52E-04 0.141505591 RNUE LNE1 Ku_c2359_569 2A 10197360 1.46E-04 0.142218504 RNUE LNE1 Ra_c29240_628 2A 10197360 1.50E-04 0.141679201 RNUE LNE1 TA001220-1276 2A 10197360 1.52E-04 0.141505591 RNUE LNE1 Tdurum_contig75565_1388 2A 10197360 3.40E-06 0.208755568 RNUE LNE1 wsnp_Ex_c29940_38921491 2A 10197360 2.76E-13 0.54673084 RNUE LNE1 wsnp_Ex_c33196_41722217 2A 10197360 1.14E-04 0.146446375 RNUE LNE1 Ex_c4639_2631 2A 10362065 1.46E-04 0.142218504 RNUE LNE1 Excalibur_c16393_274 2A 10362065 2.60E-13 0.548099559 RNUE LNE1 GENE-0922_327 2A 10362065 1.41E-04 0.142737604 RNUE LNE1 RAC875_c3102_959 2A 10362065 1.71E-07 0.264531536 RNUE LNE1 Ra_c15292_990 2A 10362065 1.46E-04 0.142218504 RNUE LNE1 IAAV3570 2A 10413180 7.77E-04 0.11376519 RNUE LNE1 Ra_c22880_760 2A 10413180 8.82E-05 0.150894979 RNUE LNE1 Ra_c37220_262 2A 10413180 3.55E-04 0.127012683 RNUE LNE1 wsnp_Ex_c23720_32957892 2A 10413180 7.77E-04 0.11376519 RNUE LNE1 wsnp_Ex_rep_c66800_65171259 2A 10413180 1.75E-07 0.264111598

RSDW LNE1 CAP12_c1437_261 2A 10362065 4.02E-04 0.124895444 RSDW LNE1 CAP7_rep_c6939_197 2A 10362065 7.36E-04 0.114682778 RSDW LNE1 Ex_c4639_2631 2A 10362065 8.75E-07 0.233759993 RSDW LNE1 Excalibur_c16393_274 2A 10362065 5.57E-17 0.759149505 RSDW LNE1 GENE-0922_327 2A 10362065 8.40E-07 0.234522109 RSDW LNE1 RAC875_c3102_959 2A 10362065 7.33E-10 0.372975093 RSDW LNE1 RAC875_c4346_111 2A 10362065 4.02E-04 0.124895444 RSDW LNE1 Ra_c15292_990 2A 10362065 8.75E-07 0.233759993 RSDW LNE1 wsnp_CD452951A_Ta_2_1 2A 10362065 1.81E-04 0.138532453 RSDW LNE1 wsnp_Ex_c11437_18454413 2A 10362065 4.02E-04 0.124895444 RSDW LNE1 BS00067792_51 2A 10413180 1.92E-04 0.137513782 RSDW LNE1 BS00077438_51 2A 10413180 1.59E-04 0.140697331 RSDW LNE1 BS00097263_51 2A 10413180 4.02E-04 0.124895444 RSDW LNE1 IAAV3570 2A 10413180 1.81E-04 0.138507254 RSDW LNE1 IAAV8481 2A 10413180 4.02E-04 0.124895444 RSDW LNE1 Kukri_c53546_104 2A 10413180 4.02E-04 0.124895444 RSDW LNE1 Kukri_rep_c70207_560 2A 10413180 7.95E-05 0.152698442 RSDW LNE1 RAC875_rep_c101788_71 2A 10413180 1.74E-04 0.139207288 RSDW LNE1 Ra_c22880_760 2A 10413180 2.36E-04 0.133978373 RSDW LNE1 Ra_c37220_262 2A 10413180 5.09E-05 0.160454054 RSDW LNE1 wsnp_BE517627A_Ta_2_1 2A 10413180 1.81E-04 0.138532453 RSDW LNE1 wsnp_Ex_c20649_29731279 2A 10413180 1.79E-04 0.138709927 RSDW LNE1 wsnp_Ex_c23720_32957892 2A 10413180 1.81E-04 0.138507254 RSDW LNE1 wsnp_Ex_rep_c66800_65171259 2A 10413180 8.31E-10 0.370395781 RSDW LNE1 wsnp_Ex_rep_c75827_73041653 2A 10413180 7.46E-10 0.372628114 RSDW LNE1 Excalibur_c84687_162 2A 10685795 2.51E-06 0.214354438 RSDW LNE1 wsnp_Ex_c22271_31463382 2A 12364531 1.27E-04 0.144524382 RSDW LNE1 CAP7_c1527_136 2A 14321560 3.15E-05 0.168857095 RSDW LNE1 IACX3245 2A 14321560 7.78E-08 0.279631298 RSDW LNE1 BS00023075_51 2A 14384035 4.72E-06 0.202826 RSDW LNE1 BobWhite_c4517_120 2A 14384035 3.44E-10 0.388751547 RSDW LNE1 Tdurum_contig47508_250 2A 14384035 4.72E-06 0.202826 RSDW LNE1 wsnp_Ra_c6586_11477949 2A 14964836 5.90E-05 0.157886935 RSNC LNAV IAAV691 2A 9751072 2.44E-04 0.13445891 RSNC LNAV IACX3245 2A 14321560 3.22E-05 0.169896764 RSNC LNE1 IAAV691 2A 9751072 5.54E-04 0.124378289 RSNC LNE1 Tdurum_contig60298_219 2A 13896496 3.87E-04 0.130703935 RSNC LNE1 IACX3245 2A 14321560 7.13E-08 0.293768096 RSNC LNE1 RAC875_c27530_860 2A 15103236 1.03E-04 0.154392009 SDW CKAV wsnp_RFL_Contig3060_2967139 2A 9928033 1.90E-04 0.13766475 SDW CKE1 wsnp_RFL_Contig3060_2967139 2A 9928033 2.36E-04 0.133946666 SNC CKAV wsnp_RFL_Contig3060_2967139 2A 9928033 2.57E-04 0.132493585 SNC CKE1 wsnp_RFL_Contig3060_2967139 2A 9928033 1.87E-04 0.139060193 SNC LNE2 BS00011101_51 2A 4721741 9.05E-04 0.087379164 SNC LNE2 BS00086364_51 2A 4721741 9.05E-04 0.087379164 SNC LNE2 wsnp_RFL_Contig3060_2967139 2A 9928033 8.05E-04 0.114080072 SNUE CKAV wsnp_RFL_Contig3060_2967139 2A 9928033 2.99E-04 0.129927089 SNUE CKE1 wsnp_RFL_Contig3060_2967139 2A 9928033 2.12E-04 0.136858258 TDW CKAV wsnp_RFL_Contig3060_2967139 2A 9928033 3.25E-04 0.128509185 TDW CKE1 wsnp_RFL_Contig3060_2967139 2A 9928033 2.14E-04 0.135652701 TNC CKAV wsnp_RFL_Contig3060_2967139 2A 9928033 2.95E-04 0.133301501

TNC CKE1 wsnp_RFL_Contig3060_2967139 2A 9928033 2.05E-04 0.137449421 TNC LNE2 wsnp_RFL_Contig3060_2967139 2A 9928033 4.07E-04 0.125686801 TNUE CKAV wsnp_RFL_Contig3060_2967139 2A 9928033 6.58E-04 0.120377181 TNUE CKE1 wsnp_RFL_Contig3060_2967139 2A 9928033 3.70E-04 0.127285825 RDW CKE1 wsnp_RFL_Contig3802_4108582 2B 9973081 8.09E-04 0.113098055 RDW CKE1 Excalibur_c31737_169 2B 10656310 9.14E-04 0.111056498 RDW LNAV Excalibur_c25921_230 2B 9698667 5.01E-04 0.121175693 RDW LNAV BS00075410_51 2B 9915703 2.41E-04 0.133567642 RDW LNAV BobWhite_c47357_535 2B 11432153 5.71E-04 0.118952187 RDW LNAV Tdurum_contig14707_251 2B 11500757 8.51E-04 0.11225649 RDW LNAV BS00102614_51 2B 11586199 5.86E-04 0.118526347 RDW LNE1 Excalibur_c25921_230 2B 9698667 2.66E-11 0.443504709 RDW LNE1 BS00111324_51 2B 9852713 1.08E-04 0.147432325 RDW LNE1 BS00075410_51 2B 9915703 1.13E-09 0.364097637 RDW LNE1 Excalibur_c20647_643 2B 9915703 7.74E-05 0.153165252 RDW LNE1 IACX7718 2B 10738946 9.42E-06 0.190352774 RDW LNE1 Ra_c31353_172 2B 10913573 4.97E-05 0.160887067 RDW LNE1 wsnp_Ra_c31353_40494768 2B 10952552 3.15E-04 0.12901988 RDW LNE1 IAAV2917 2B 11385066 1.39E-05 0.183388301 RDW LNE1 BobWhite_c47357_535 2B 11432153 2.77E-11 0.442610913 RDW LNE1 Tdurum_contig14707_251 2B 11500757 4.21E-08 0.291566636 RDW LNE1 Tdurum_contig72054_94 2B 11500757 2.61E-05 0.172181767 RDW LNE1 Excalibur_c2484_2113 2B 11572790 3.62E-06 0.207642493 RDW LNE1 BS00102614_51 2B 11586199 2.33E-11 0.446426325 RDW LNE1 CAP11_c1820_244 2B 15308252 1.79E-04 0.111812531 RNC LNAV Excalibur_c25921_230 2B 9698667 2.86E-04 0.130698503 RNC LNAV BS00075410_51 2B 9915703 2.52E-04 0.132845867 RNC LNAV BobWhite_c47357_535 2B 11432153 2.55E-04 0.132613154 RNC LNAV Tdurum_contig14707_251 2B 11500757 6.28E-04 0.117351107 RNC LNAV BS00102614_51 2B 11586199 3.10E-04 0.129277029 RNC LNE1 Excalibur_c25921_230 2B 9698667 1.36E-10 0.408416343 RNC LNE1 BS00075410_51 2B 9915703 4.80E-09 0.334572574 RNC LNE1 Excalibur_c20647_643 2B 9915703 4.87E-04 0.121633837 RNC LNE1 IACX7718 2B 10738946 4.76E-05 0.161624959 RNC LNE1 Ra_c31353_172 2B 10913573 4.37E-05 0.163145532 RNC LNE1 wsnp_Ra_c31353_40494768 2B 10952552 3.46E-04 0.127445157 RNC LNE1 IAAV2917 2B 11385066 2.94E-05 0.170121541 RNC LNE1 BobWhite_c47357_535 2B 11432153 1.31E-10 0.409135187 RNC LNE1 Tdurum_contig14707_251 2B 11500757 2.71E-07 0.255744335 RNC LNE1 Tdurum_contig72054_94 2B 11500757 3.53E-05 0.166881968 RNC LNE1 Excalibur_c2484_2113 2B 11572790 4.78E-05 0.161544025 RNC LNE1 BS00102614_51 2B 11586199 8.80E-11 0.417666315 RNC LNE1 CAP11_c1820_244 2B 15308252 9.75E-04 0.085562408 RNCe LNE1 Tdurum_contig54704_176 2B 7374878 1.62E-04 0.140412731 RNCe HNE2 BS00046164_51 2B 11385066 7.28E-04 0.114862719 RNCe HNE2 BS00046165_51 2B 11385066 2.44E-04 0.133374674 RNCe HNE2 wsnp_Ex_c5123_9088111 2B 11385690 3.96E-04 0.125147147 RNUE CKE1 Kukri_c26288_419 2B 7446912 6.46E-04 0.091832906 RNUE LNAV Excalibur_c25921_230 2B 9698667 1.50E-04 0.141740011 RNUE LNAV BS00075410_51 2B 9915703 4.03E-05 0.164554333 RNUE LNAV BobWhite_c47357_535 2B 11432153 6.40E-05 0.156457811

RNUE LNAV BS00102614_51 2B 11586199 1.51E-04 0.141567202 RNUE LNE1 Excalibur_c25921_230 2B 9698667 2.75E-13 0.546776107 RNUE LNE1 BS00111324_51 2B 9852713 1.83E-04 0.138271339 RNUE LNE1 BS00075410_51 2B 9915703 7.75E-11 0.420366465 RNUE LNE1 Excalibur_c20647_643 2B 9915703 3.24E-05 0.168409882 RNUE LNE1 IACX7718 2B 10738946 4.00E-06 0.205804309 RNUE LNE1 Ra_c31353_172 2B 10913573 4.68E-05 0.161943575 RNUE LNE1 wsnp_Ra_c31353_40494768 2B 10952552 4.84E-05 0.161339014 RNUE LNE1 BS00046164_51 2B 11385066 6.83E-04 0.115945477 RNUE LNE1 Excalibur_c36280_764 2B 11385066 3.12E-04 0.12921017 RNUE LNE1 IAAV2917 2B 11385066 2.73E-07 0.255640935 RNUE LNE1 RAC875_c103094_120 2B 11418744 6.71E-04 0.116242178 RNUE LNE1 BobWhite_c2521_117 2B 11432153 6.71E-04 0.116242178 RNUE LNE1 BobWhite_c47357_535 2B 11432153 2.70E-13 0.547188533 RNUE LNE1 BobWhite_c4831_490 2B 11432153 1.96E-04 0.137080707 RNUE LNE1 RAC875_c4465_549 2B 11436831 6.71E-04 0.116242178 RNUE LNE1 Ex_c16948_754 2B 11456788 1.96E-04 0.137080707 RNUE LNE1 Tdurum_contig14707_251 2B 11500757 1.61E-08 0.310409592 RNUE LNE1 Tdurum_contig72054_94 2B 11500757 8.21E-07 0.234956936 RNUE LNE1 Excalibur_c2484_2113 2B 11572790 1.40E-06 0.225028924 RNUE LNE1 BS00102614_51 2B 11586199 1.76E-13 0.55727624 RNUE LNE1 CAP11_c1820_244 2B 15308252 2.71E-05 0.142197266 RNUE HNAV Kukri_c16758_443 2B 2719817 8.54E-04 0.113087106 RNUE HNE2 wsnp_Ra_c4321_7860456 2B 4135856 3.81E-04 0.125786875 RSDW LNAV Excalibur_c25921_230 2B 9698667 2.44E-10 0.39598858 RSDW LNAV BS00111324_51 2B 9852713 7.05E-04 0.115402656 RSDW LNAV BS00075410_51 2B 9915703 2.01E-08 0.306092231 RSDW LNAV Excalibur_c20647_643 2B 9915703 8.19E-04 0.112890902 RSDW LNAV IACX7718 2B 10738946 1.72E-04 0.139332038 RSDW LNAV Ra_c31353_172 2B 10913573 3.43E-04 0.127582096 RSDW LNAV wsnp_Ra_c31353_40494768 2B 10952552 7.36E-05 0.154028133 RSDW LNAV BS00011825_51 2B 11082275 5.63E-04 0.119183844 RSDW LNAV BS00046164_51 2B 11385066 8.07E-04 0.113132247 RSDW LNAV IAAV2917 2B 11385066 6.71E-07 0.238728869 RSDW LNAV RAC875_c103094_120 2B 11418744 6.93E-04 0.115684521 RSDW LNAV BobWhite_c2521_117 2B 11432153 6.93E-04 0.115684521 RSDW LNAV BobWhite_c47357_535 2B 11432153 2.07E-10 0.399439099 RSDW LNAV BobWhite_c4831_490 2B 11432153 9.16E-05 0.15023838 RSDW LNAV RAC875_c4465_549 2B 11436831 6.93E-04 0.115684521 RSDW LNAV Ex_c16948_754 2B 11456788 9.16E-05 0.15023838 RSDW LNAV Tdurum_contig14707_251 2B 11500757 3.19E-07 0.252680156 RSDW LNAV Tdurum_contig72054_94 2B 11500757 2.43E-04 0.133444214 RSDW LNAV Excalibur_c2484_2113 2B 11572790 4.15E-06 0.205143866 RSDW LNAV BS00102614_51 2B 11586199 2.43E-10 0.396087417 RSDW LNE1 Excalibur_c25921_230 2B 9698667 5.42E-17 0.75986858 RSDW LNE1 BS00111324_51 2B 9852713 8.63E-05 0.151268926 RSDW LNE1 BS00075410_51 2B 9915703 2.83E-10 0.392899255 RSDW LNE1 Excalibur_c20647_643 2B 9915703 3.00E-04 0.129872272 RSDW LNE1 IACX7718 2B 10738946 6.43E-06 0.197220027 RSDW LNE1 Ra_c31353_172 2B 10913573 4.09E-06 0.205418016 RSDW LNE1 wsnp_Ex_c17845_26604587 2B 10913573 3.60E-04 0.126774396

RSDW LNE1 Tdurum_contig74826_330 2B 10952552 4.90E-05 0.161137836 RSDW LNE1 wsnp_Ra_c31353_40494768 2B 10952552 4.29E-07 0.247093609 RSDW LNE1 BS00011825_51 2B 11082275 1.45E-05 0.18266373 RSDW LNE1 BS00046164_51 2B 11385066 2.61E-06 0.213633003 RSDW LNE1 Excalibur_c36280_764 2B 11385066 4.53E-07 0.246062316 RSDW LNE1 IAAV2917 2B 11385066 3.48E-10 0.388533341 RSDW LNE1 RAC875_c103094_120 2B 11418744 2.43E-06 0.214911371 RSDW LNE1 BobWhite_c2521_117 2B 11432153 2.43E-06 0.214911371 RSDW LNE1 BobWhite_c47357_535 2B 11432153 5.47E-17 0.759614117 RSDW LNE1 BobWhite_c4831_490 2B 11432153 8.16E-08 0.278713928 RSDW LNE1 RAC875_c4465_549 2B 11436831 2.43E-06 0.214911371 RSDW LNE1 Ex_c16948_754 2B 11456788 8.16E-08 0.278713928 RSDW LNE1 Tdurum_contig14707_251 2B 11500757 8.12E-11 0.41938097 RSDW LNE1 Tdurum_contig72054_94 2B 11500757 5.21E-05 0.160040671 RSDW LNE1 Excalibur_c2484_2113 2B 11572790 8.96E-11 0.417268439 RSDW LNE1 BS00102614_51 2B 11586199 5.70E-17 0.758533692 RSDW LNE1 Tdurum_contig54784_485 2B 11586199 9.91E-06 0.189440978 RSDW LNE1 CAP11_c1820_244 2B 15308252 4.88E-04 0.096166869 RSDW LNE2 BS00094172_51 2B 15721433 7.38E-04 0.114650444 RSDW HNE1 BobWhite_c2988_2161 2B 5627048 3.57E-04 0.101009857 RSDW HNE1 RAC875_rep_c109207_706 2B 7899383 9.98E-06 0.189302279 RSDW HNE1 Excalibur_c31864_179 2B 13445978 5.46E-04 0.119705584 RSNC LNAV RAC875_c34516_316 2B 7670185 4.15E-04 0.125324606 RSNC LNAV BS00067337_51 2B 8195314 1.84E-04 0.139277052 RSNC LNAV IACX6223 2B 8212465 1.44E-04 0.14358026 RSNC LNAV Excalibur_c22315_894 2B 8718572 2.70E-04 0.132702635 RSNC LNAV wsnp_BE499478B_Ta_2_1 2B 9129258 7.99E-04 0.114217301 RSNC LNAV BS00075410_51 2B 9915703 5.13E-04 0.121736571 RSNC LNAV tplb0040e02_1293 2B 9915703 8.12E-04 0.113940877 RSNC LNAV Excalibur_c35074_257 2B 11843151 5.24E-04 0.121372181 RSNC LNAV Excalibur_c18966_1008 2B 13029056 7.19E-04 0.116005369 RSNC LNAV BS00009791_51 2B 13445978 4.24E-04 0.12497305 RSNC LNAV Excalibur_c48404_59 2B 16141473 8.07E-04 0.114053531 RSNC LNE1 BS00066184_51 2B 3216257 6.66E-04 0.121142174 RSNC LNE1 RAC875_c34516_316 2B 7670185 2.07E-07 0.272350288 RSNC LNE1 BS00067337_51 2B 8195314 8.80E-04 0.116266105 RSNC LNE1 IACX6223 2B 8212465 6.53E-04 0.121496662 RSNC LNE1 Excalibur_c22315_894 2B 8718572 2.05E-07 0.272517367 RSNC LNE1 Kukri_c4632_115 2B 9097139 6.68E-04 0.121089334 RSNC LNE1 wsnp_Ex_c7738_13195349 2B 9097139 6.68E-04 0.121089334 RSNC LNE1 Kukri_c106282_114 2B 9110236 1.46E-04 0.148158584 RSNC LNE1 wsnp_BE499478B_Ta_2_1 2B 9129258 2.31E-07 0.270161835 RSNC LNE1 BS00092275_51 2B 9346606 9.12E-04 0.115646149 RSNC LNE1 BS00075410_51 2B 9915703 2.23E-07 0.270800051 RSNC LNE1 tplb0040e02_1293 2B 9915703 2.23E-07 0.270800051 RSNC LNE1 TA001720-0874 2B 10739569 5.45E-04 0.124684736 RSNC LNE1 RAC875_rep_c108548_163 2B 10924487 6.72E-04 0.121002981 RSNC LNE1 Excalibur_c35074_257 2B 11843151 2.33E-07 0.26994981 RSNC LNE1 BS00022295_51 2B 11907077 3.50E-04 0.132500044 RSNC LNE1 Excalibur_c18966_1008 2B 13029056 1.64E-07 0.27699316 RSNC LNE1 BS00009791_51 2B 13445978 2.24E-07 0.270735714

RSNC LNE1 Ra_c23717_380 2B 15721433 9.61E-04 0.114727549 RSNC LNE1 Excalibur_c48404_59 2B 16141473 2.23E-07 0.27080467 RSNC LNE1 Kukri_c498_1817 2B 16141473 6.24E-04 0.12230566 RSNC HNE1 BobWhite_c2988_2161 2B 5627048 7.26E-04 0.094505286 RSNC HNE1 RAC875_rep_c109207_706 2B 7899383 8.11E-05 0.160091726 RSNC HNE1 Excalibur_c31864_179 2B 13445978 7.59E-04 0.11986685 SNCe CKE2 BS00076003_51 2B 13061799 1.45E-04 0.144594648 SNCe CKE2 BS00046601_51 2B 13445978 2.90E-04 0.132565063 SNCe CKE2 IAAV1535 2B 14512763 9.72E-05 0.151654757 SNCe LNAV Excalibur_c31737_169 2B 10656310 5.96E-04 0.11916779 SNCe LNE1 RAC875_rep_c109207_706 2B 7899383 1.79E-04 0.144422332 SNCe LNE2 BS00070120_51 2B 9097139 2.43E-04 0.134501659 SNCe LNE2 Excalibur_c31737_169 2B 10656310 6.18E-06 0.199564333 TNCe LNE1 Jagger_c6853_60 2B 10298324 4.67E-04 0.127374853 TNCe LNE2 Excalibur_c31737_169 2B 10656310 1.13E-04 0.147717847 RDW LNAV Kukri_c16477_157 2D 4004568 5.02E-05 0.160704991 RDW LNAV RAC875_rep_c72220_143 2D 4313642 4.90E-04 0.121540893 RDW LNAV BS00021940_51 2D 4429825 2.23E-04 0.134941412 RDW LNAV wsnp_BE444144D_Ta_1_1 2D 4429825 2.23E-04 0.134941412 RDW LNAV wsnp_Ex_c1944_3663988 2D 15283940 8.27E-04 0.112728876 RDW LNE1 wsnp_Ex_c29666_38670435 2D 3873118 2.70E-04 0.131649497 RDW LNE1 Kukri_c16477_157 2D 4004568 3.82E-07 0.249291897 RDW LNE1 BS00076261_51 2D 4120005 9.70E-04 0.110063492 RDW LNE1 IAAV1002 2D 4120005 4.22E-04 0.124044798 RDW LNE1 Kukri_c16557_855 2D 4120005 9.70E-04 0.110063492 RDW LNE1 Kukri_c59403_339 2D 4147561 3.93E-04 0.125279824 RDW LNE1 RAC875_rep_c72220_143 2D 4313642 2.76E-06 0.212549038 RDW LNE1 BS00021940_51 2D 4429825 7.46E-07 0.236741125 RDW LNE1 wsnp_BE444144D_Ta_1_1 2D 4429825 7.46E-07 0.236741125 RDW LNE1 wsnp_Ex_c1944_3663988 2D 15283940 6.06E-07 0.240608194 RDW HNE1 Kukri_c2561_179 2D 8034830 2.17E-04 0.135412918 RNC LNAV Kukri_c16477_157 2D 4004568 3.58E-05 0.166623502 RNC LNAV RAC875_rep_c72220_143 2D 4313642 6.07E-04 0.117917377 RNC LNAV BS00021940_51 2D 4429825 3.16E-04 0.128963097 RNC LNAV wsnp_BE444144D_Ta_1_1 2D 4429825 3.16E-04 0.128963097 RNC LNE1 wsnp_Ex_c29666_38670435 2D 3873118 5.00E-04 0.121188581 RNC LNE1 Kukri_c16477_157 2D 4004568 7.79E-07 0.235937009 RNC LNE1 BS00076261_51 2D 4120005 7.49E-04 0.114394587 RNC LNE1 Kukri_c16557_855 2D 4120005 7.49E-04 0.114394587 RNC LNE1 RAC875_rep_c72220_143 2D 4313642 1.26E-05 0.18510382 RNC LNE1 BS00021940_51 2D 4429825 2.87E-06 0.211845972 RNC LNE1 wsnp_BE444144D_Ta_1_1 2D 4429825 2.87E-06 0.211845972 RNC LNE1 wsnp_Ex_c1944_3663988 2D 15283940 3.11E-06 0.210403565 RNCe LNE1 GENE-0787_549 2D 4004568 2.91E-04 0.130378144 RNCe LNE1 IAAV1002 2D 4120005 9.53E-04 0.110355825 RNCe LNE1 RAC875_c31560_141 2D 4120005 7.26E-04 0.090055766 RNCe LNE1 RAC875_rep_c103893_601 2D 4120005 6.61E-04 0.116483169 RNUE LNAV Kukri_c16477_157 2D 4004568 7.47E-05 0.153774682 RNUE LNAV RAC875_rep_c72220_143 2D 4313642 3.35E-05 0.167813618 RNUE LNAV BS00021940_51 2D 4429825 6.11E-04 0.117822583 RNUE LNAV wsnp_BE444144D_Ta_1_1 2D 4429825 6.11E-04 0.117822583

RNUE LNAV wsnp_Ex_c1944_3663988 2D 15283940 2.17E-04 0.135368243 RNUE LNE1 wsnp_Ex_c29666_38670435 2D 3873118 5.28E-05 0.159818293 RNUE LNE1 Kukri_c16477_157 2D 4004568 1.14E-07 0.272337671 RNUE LNE1 BS00076261_51 2D 4120005 4.40E-04 0.123356338 RNUE LNE1 IAAV1002 2D 4120005 1.92E-04 0.137473978 RNUE LNE1 Kukri_c16557_855 2D 4120005 4.40E-04 0.123356338 RNUE LNE1 Kukri_c59403_339 2D 4147561 8.06E-05 0.152445533 RNUE LNE1 RAC875_rep_c72220_143 2D 4313642 7.61E-07 0.236362034 RNUE LNE1 BS00021940_51 2D 4429825 5.66E-07 0.241899651 RNUE LNE1 wsnp_BE444144D_Ta_1_1 2D 4429825 5.66E-07 0.241899651 RNUE LNE1 wsnp_Ex_c1944_3663988 2D 15283940 9.35E-09 0.321219059 RNUE HNE2 BS00067757_51 2D 4004568 8.06E-04 0.113155253 RNUE HNE2 Kukri_c1016_2269 2D 4004568 8.06E-04 0.113155253 RNUE HNE2 BS00032252_51 2D 4237305 9.72E-04 0.110026015 RSDW LNAV wsnp_Ex_c29666_38670435 2D 3873118 2.12E-05 0.175884141 RSDW LNAV Kukri_c16477_157 2D 4004568 2.27E-07 0.259104831 RSDW LNAV BS00076261_51 2D 4120005 1.22E-04 0.145232032 RSDW LNAV IAAV1002 2D 4120005 1.22E-04 0.145209553 RSDW LNAV Kukri_c16557_855 2D 4120005 1.22E-04 0.145232032 RSDW LNAV RAC875_rep_c103893_601 2D 4120005 5.25E-04 0.120370144 RSDW LNAV Kukri_c59403_339 2D 4147561 2.70E-05 0.171604679 RSDW LNAV RAC875_rep_c72220_143 2D 4313642 7.62E-06 0.194166557 RSDW LNAV BS00021940_51 2D 4429825 5.78E-06 0.199150647 RSDW LNAV wsnp_BE444144D_Ta_1_1 2D 4429825 5.78E-06 0.199150647 RSDW LNAV wsnp_Ex_c1944_3663988 2D 15283940 2.39E-06 0.215221599 RSDW LNE1 wsnp_Ex_c29666_38670435 2D 3873118 5.67E-06 0.199480072 RSDW LNE1 Kukri_c16477_157 2D 4004568 2.31E-08 0.30329413 RSDW LNE1 BS00076261_51 2D 4120005 1.61E-04 0.140529202 RSDW LNE1 IAAV1002 2D 4120005 1.04E-04 0.148059307 RSDW LNE1 Kukri_c16557_855 2D 4120005 1.61E-04 0.140529202 RSDW LNE1 RAC875_rep_c103893_601 2D 4120005 3.15E-05 0.168864319 RSDW LNE1 Kukri_c59403_339 2D 4147561 1.66E-04 0.139960351 RSDW LNE1 RAC875_rep_c72220_143 2D 4313642 8.54E-06 0.192111873 RSDW LNE1 BS00021940_51 2D 4429825 1.00E-06 0.231205553 RSDW LNE1 wsnp_BE444144D_Ta_1_1 2D 4429825 1.00E-06 0.231205553 RSDW LNE1 wsnp_Ex_c1944_3663988 2D 15283940 5.55E-10 0.378766613 RSNC LNAV BS00082604_51 2D 4237305 1.50E-04 0.142815531 RSNC LNAV RAC875_rep_c72220_143 2D 4313642 5.36E-04 0.120968365 RSNC LNAV BS00021940_51 2D 4429825 2.87E-04 0.13165737 RSNC LNAV wsnp_BE444144D_Ta_1_1 2D 4429825 2.87E-04 0.13165737 RSNC LNAV Excalibur_c12922_1888 2D 6842843 7.35E-04 0.115624174 RSNC LNAV RAC875_c21300_131 2D 7639363 3.30E-04 0.129280953 RSNC LNAV RFL_Contig1892_2214 2D 7639363 7.12E-04 0.116158531 RSNC LNAV wsnp_Ex_c10751_17505459 2D 7656865 3.39E-04 0.128794383 RSNC LNAV GENE-4595_130 2D 8034830 4.89E-04 0.122537428 RSNC LNAV Excalibur_c44325_92 2D 8040788 4.89E-04 0.122537428 RSNC LNAV Kukri_rep_c68088_633 2D 8040788 7.00E-04 0.116449066 RSNC LNAV RAC875_c19225_739 2D 8282090 8.11E-04 0.113963704 RSNC LNE1 BS00082604_51 2D 4237305 4.75E-04 0.127076601 RSNC LNE1 BS00021940_51 2D 4429825 6.61E-04 0.121288871 RSNC LNE1 wsnp_BE444144D_Ta_1_1 2D 4429825 6.61E-04 0.121288871

RSNC LNE1 Excalibur_c12922_1888 2D 6842843 2.14E-07 0.271673886 RSNC LNE1 Excalibur_c16438_318 2D 7639363 2.29E-07 0.270283782 RSNC LNE1 RAC875_c21300_131 2D 7639363 2.29E-07 0.270283782 RSNC LNE1 RFL_Contig1892_2214 2D 7639363 2.32E-07 0.270008304 RSNC LNE1 BobWhite_c18906_680 2D 7656865 2.22E-07 0.270883831 RSNC LNE1 wsnp_Ex_c10751_17505459 2D 7656865 1.61E-07 0.27730169 RSNC LNE1 RFL_Contig5204_503 2D 7955141 3.42E-04 0.132899167 RSNC LNE1 GENE-4595_130 2D 8034830 2.16E-07 0.27143846 RSNC LNE1 Excalibur_c44325_92 2D 8040788 2.16E-07 0.27143846 RSNC LNE1 Kukri_rep_c68088_633 2D 8040788 1.99E-07 0.273083777 RSNC LNE1 RAC875_c19225_739 2D 8282090 2.22E-07 0.270883831 SNC CKAV Excalibur_c44325_545 2D 8506635 2.95E-04 0.130164296 SNC CKE2 Excalibur_c44325_545 2D 8506635 4.33E-04 0.125613199 SNC LNE2 Kukri_c4790_893 2D 4237305 1.81E-05 0.180173767 SNCe CKE2 Excalibur_c54115_317 2D 8282090 2.80E-04 0.133146731 SNCe CKE2 Excalibur_c95161_72 2D 8282090 4.41E-04 0.125323948 SNCe CKE2 Excalibur_rep_c89066_287 2D 9713516 6.30E-04 0.119198054 SNCe CKE2 BS00015680_51 2D 10332783 1.82E-04 0.140687899 SNCe LNAV Kukri_c4790_893 2D 4237305 4.87E-08 0.29118715 SNCe LNE2 Kukri_c4790_893 2D 4237305 2.07E-14 0.614316948 TNC CKE2 Excalibur_c44325_545 2D 8506635 7.88E-04 0.115360958 TNCe LNAV Kukri_c4790_893 2D 4237305 4.84E-05 0.168085802 TNCe LNE2 Kukri_c4790_893 2D 4237305 2.80E-10 0.396578775 RDW LNAV BS00065468_51 3A 7751230 1.61E-04 0.140527759 RDW LNAV BS00094366_51 3A 7756567 1.24E-04 0.144927219 RDW LNAV RAC875_c2464_274 3A 7756567 1.61E-04 0.140527759 RDW LNAV Tdurum_contig86206_149 3A 7805856 1.61E-04 0.140527759 RDW LNE1 wsnp_Ex_c15674_24005648 3A 5900855 2.56E-07 0.256884844 RDW LNE1 wsnp_Ku_c4568_8243646 3A 5900855 5.23E-06 0.20096594 RDW LNE1 BS00065468_51 3A 7751230 1.07E-09 0.365155026 RDW LNE1 BS00021694_51 3A 7756567 5.48E-07 0.242498329 RDW LNE1 BS00094366_51 3A 7756567 1.02E-09 0.366059924 RDW LNE1 BobWhite_c11298_512 3A 7756567 5.48E-07 0.242498329 RDW LNE1 Excalibur_c24123_165 3A 7756567 5.80E-07 0.241450866 RDW LNE1 IAAV2646 3A 7756567 5.48E-07 0.242498329 RDW LNE1 RAC875_c2464_274 3A 7756567 1.07E-09 0.365155026 RDW LNE1 Tdurum_contig86206_149 3A 7805856 1.07E-09 0.365155026 RDW LNE1 RAC875_c10669_714 3A 8948291 4.63E-04 0.122488083 RDW LNE1 wsnp_Ku_c9316_15647115 3A 9031172 9.59E-06 0.190025439 RDW LNE1 Ku_c14313_1194 3A 9055031 7.28E-04 0.11487822 RDW HNAV BS00066230_51 3A 1610209 4.94E-04 0.121390677 RDW HNAV Kukri_c2123_1254 3A 1610209 7.78E-04 0.113748592 RDW HNAV Ku_c13307_1116 3A 8801680 2.69E-04 0.131692675 RDW HNAV wsnp_Ex_c8334_14049699 3A 9049381 3.24E-04 0.12853797 RDW HNAV RAC875_rep_c111698_383 3A 9055031 3.24E-04 0.12853797 RDW HNE2 BS00066230_51 3A 1610209 3.19E-04 0.128821562 RDW HNE2 BobWhite_c9468_453 3A 8801680 7.73E-04 0.113859581 RDW HNE2 BobWhite_c9468_478 3A 8801680 7.73E-04 0.113859581 RDW HNE2 Ku_c13307_1116 3A 8801680 7.94E-04 0.113412627 RDW HNE2 Excalibur_rep_c76510_255 3A 8935733 7.73E-04 0.113859581 RDW HNE2 wsnp_Ex_c8334_14049699 3A 9049381 8.26E-04 0.112754584

RDW HNE2 RAC875_rep_c111698_383 3A 9055031 8.26E-04 0.112754584 RDW HNE2 wsnp_Ex_c8517_14315660 3A 10994566 8.91E-04 0.111474651 RNC LNAV BS00065468_51 3A 7751230 2.18E-04 0.135312488 RNC LNAV BS00094366_51 3A 7756567 1.91E-04 0.137601746 RNC LNAV RAC875_c2464_274 3A 7756567 2.18E-04 0.135312488 RNC LNAV Tdurum_contig86206_149 3A 7805856 2.18E-04 0.135312488 RNC LNE1 wsnp_Ex_c15674_24005648 3A 5900855 5.74E-06 0.199270141 RNC LNE1 wsnp_Ku_c4568_8243646 3A 5900855 8.61E-05 0.151313612 RNC LNE1 BS00065468_51 3A 7751230 4.40E-09 0.33634717 RNC LNE1 BS00021694_51 3A 7756567 2.99E-06 0.211106944 RNC LNE1 BS00094366_51 3A 7756567 3.84E-09 0.339075952 RNC LNE1 BobWhite_c11298_512 3A 7756567 2.99E-06 0.211106944 RNC LNE1 Excalibur_c24123_165 3A 7756567 3.25E-06 0.209589309 RNC LNE1 IAAV2646 3A 7756567 2.99E-06 0.211106944 RNC LNE1 RAC875_c2464_274 3A 7756567 4.40E-09 0.33634717 RNC LNE1 Tdurum_contig86206_149 3A 7805856 4.40E-09 0.33634717 RNC LNE1 RAC875_c10669_714 3A 8948291 9.44E-04 0.110523444 RNC LNE1 wsnp_Ku_c9316_15647115 3A 9031172 2.10E-05 0.176088637 RNCe HNAV Kukri_c13830_601 3A 3366401 1.02E-09 0.366098909 RNCe HNE1 Excalibur_c63477_90 3A 1505038 1.46E-04 0.145681262 RNCe HNE1 Kukri_c13830_601 3A 3366401 2.58E-15 0.679617177 RNUE LNAV wsnp_Ex_c15674_24005648 3A 5900855 1.86E-04 0.137988228 RNUE LNAV wsnp_Ku_c4568_8243646 3A 5900855 2.55E-04 0.132627066 RNUE LNAV BS00065468_51 3A 7751230 2.46E-05 0.17324103 RNUE LNAV BS00094366_51 3A 7756567 2.17E-05 0.175479076 RNUE LNAV RAC875_c2464_274 3A 7756567 2.46E-05 0.17324103 RNUE LNAV Tdurum_contig86206_149 3A 7805856 2.46E-05 0.17324103 RNUE LNE1 wsnp_Ex_c15674_24005648 3A 5900855 1.78E-08 0.308431234 RNUE LNE1 wsnp_Ku_c4568_8243646 3A 5900855 6.62E-07 0.238970989 RNUE LNE1 GENE-1533_226 3A 6865599 3.44E-04 0.127521909 RNUE LNE1 Ku_c18096_552 3A 6865599 9.63E-04 0.110178892 RNUE LNE1 BS00065468_51 3A 7751230 6.36E-11 0.424615394 RNUE LNE1 BS00021694_51 3A 7756567 9.88E-08 0.275032086 RNUE LNE1 BS00094366_51 3A 7756567 5.90E-11 0.426251757 RNUE LNE1 BobWhite_c11298_512 3A 7756567 9.88E-08 0.275032086 RNUE LNE1 Excalibur_c24123_165 3A 7756567 1.04E-07 0.274021773 RNUE LNE1 IAAV2646 3A 7756567 9.88E-08 0.275032086 RNUE LNE1 RAC875_c2464_274 3A 7756567 6.36E-11 0.424615394 RNUE LNE1 Tdurum_contig86206_149 3A 7805856 6.36E-11 0.424615394 RNUE LNE1 RAC875_c10669_714 3A 8948291 3.87E-04 0.125546679 RNUE LNE1 wsnp_Ku_c9316_15647115 3A 9031172 1.85E-07 0.263068047 RNUE LNE1 wsnp_Ku_rep_c68484_67500021 3A 9049381 6.44E-04 0.116927524 RNUE LNE1 Ku_c14313_1194 3A 9055031 5.64E-04 0.119153287 RNUE HNAV BS00066230_51 3A 1610209 1.01E-05 0.19068363 RNUE HNAV Kukri_c2123_1254 3A 1610209 6.54E-04 0.117609246 RNUE HNAV Kukri_rep_c112061_617 3A 8538597 4.01E-04 0.125940202 RNUE HNAV wsnp_BE443995B_Ta_2_2 3A 8538597 4.01E-04 0.125940202 RNUE HNAV RFL_Contig1798_1606 3A 8666371 3.90E-04 0.126406074 RNUE HNAV BS00070511_51 3A 8801680 6.62E-04 0.117394082 RNUE HNAV BS00101401_51 3A 8801680 6.62E-04 0.117394082 RNUE HNAV BobWhite_c9468_453 3A 8801680 2.67E-04 0.132879288

RNUE HNAV BobWhite_c9468_478 3A 8801680 2.67E-04 0.132879288 RNUE HNAV Ex_c104581_457 3A 8801680 9.44E-04 0.111390762 RNUE HNAV IAAV1334 3A 8801680 6.62E-04 0.117394082 RNUE HNAV IAAV5030 3A 8801680 6.62E-04 0.117394082 RNUE HNAV Ku_c13307_1116 3A 8801680 2.38E-04 0.134912462 RNUE HNAV wsnp_Ex_c37208_45002588 3A 8801680 6.62E-04 0.117394082 RNUE HNAV wsnp_Ra_c35889_44345459 3A 8801680 6.62E-04 0.117394082 RNUE HNAV wsnp_Ra_c4858_8709000 3A 8801680 4.66E-04 0.123382551 RNUE HNAV Excalibur_rep_c76510_255 3A 8935733 2.67E-04 0.132879288 RNUE HNAV GENE-3343_183 3A 9049381 9.10E-04 0.112017424 RNUE HNAV wsnp_Ex_c8334_14049699 3A 9049381 3.27E-04 0.129407957 RNUE HNAV Kukri_rep_c105819_114 3A 9055031 2.43E-04 0.134547084 RNUE HNAV RAC875_rep_c111698_383 3A 9055031 3.27E-04 0.129407957 RNUE HNAV wsnp_Ex_c8517_14315660 3A 10994566 9.92E-04 0.110565641 RNUE HNE2 BS00066230_51 3A 1610209 2.26E-06 0.21626944 RNUE HNE2 Kukri_c2123_1254 3A 1610209 8.43E-04 0.112404815 RNUE HNE2 BS00070511_51 3A 8801680 4.27E-04 0.123874804 RNUE HNE2 BS00101401_51 3A 8801680 4.27E-04 0.123874804 RNUE HNE2 BobWhite_c9468_453 3A 8801680 7.86E-05 0.152887822 RNUE HNE2 BobWhite_c9468_478 3A 8801680 7.86E-05 0.152887822 RNUE HNE2 CAP7_c3367_68 3A 8801680 2.60E-04 0.132295362 RNUE HNE2 Ex_c104581_457 3A 8801680 8.18E-04 0.112917658 RNUE HNE2 IAAV1334 3A 8801680 4.27E-04 0.123874804 RNUE HNE2 IAAV5030 3A 8801680 4.27E-04 0.123874804 RNUE HNE2 Ku_c13307_1116 3A 8801680 1.40E-04 0.142890437 RNUE HNE2 Tdurum_contig59782_86 3A 8801680 2.60E-04 0.132295362 RNUE HNE2 wsnp_Ex_c37208_45002588 3A 8801680 4.27E-04 0.123874804 RNUE HNE2 wsnp_Ex_c9510_15761235 3A 8801680 2.70E-04 0.131666913 RNUE HNE2 wsnp_Ra_c35889_44345459 3A 8801680 4.27E-04 0.123874804 RNUE HNE2 BS00067190_51 3A 8904025 4.11E-04 0.124522103 RNUE HNE2 Excalibur_rep_c76510_255 3A 8935733 7.86E-05 0.152887822 RNUE HNE2 RAC875_c10669_714 3A 8948291 6.92E-04 0.115725176 RNUE HNE2 GENE-3343_183 3A 9049381 3.73E-04 0.126170274 RNUE HNE2 IAAV8768 3A 9049381 7.48E-04 0.114424482 RNUE HNE2 wsnp_Ex_c8334_14049699 3A 9049381 1.21E-04 0.145487216 RNUE HNE2 wsnp_Ku_c3286_6111360 3A 9049381 7.15E-04 0.115182973 RNUE HNE2 BS00071823_51 3A 9055031 6.44E-04 0.11693111 RNUE HNE2 Ku_c14313_1194 3A 9055031 1.75E-04 0.139047683 RNUE HNE2 RAC875_c67309_634 3A 9055031 8.09E-04 0.113103897 RNUE HNE2 RAC875_rep_c111698_383 3A 9055031 1.21E-04 0.145487216 RNUE HNE2 BS00080879_51 3A 10100459 3.35E-04 0.127985872 RNUE HNE2 wsnp_Ex_c8517_14315660 3A 10994566 4.01E-04 0.124936758 RNUE HNE2 wsnp_Ra_c19079_28210937 3A 11127991 2.96E-04 0.130093735 RNUE HNE2 BS00076751_51 3A 15174705 3.87E-04 0.099742665 RSDW LNAV wsnp_Ex_c15674_24005648 3A 5900855 9.45E-07 0.232347493 RSDW LNAV wsnp_Ku_c4568_8243646 3A 5900855 1.08E-05 0.187872689 RSDW LNAV GENE-1533_226 3A 6865599 2.36E-04 0.133951851 RSDW LNAV BS00065468_51 3A 7751230 1.31E-08 0.31447496 RSDW LNAV BS00021694_51 3A 7756567 1.74E-05 0.179359927 RSDW LNAV BS00094366_51 3A 7756567 1.30E-08 0.314594901 RSDW LNAV BobWhite_c11298_512 3A 7756567 1.74E-05 0.179359927

RSDW LNAV Excalibur_c24123_165 3A 7756567 1.59E-05 0.180969474 RSDW LNAV IAAV2646 3A 7756567 1.74E-05 0.179359927 RSDW LNAV RAC875_c2464_274 3A 7756567 1.31E-08 0.31447496 RSDW LNAV Tdurum_contig86206_149 3A 7805856 1.31E-08 0.31447496 RSDW LNAV RAC875_c10669_714 3A 8948291 2.58E-04 0.132421204 RSDW LNAV wsnp_Ku_c9316_15647115 3A 9031172 5.61E-07 0.242057488 RSDW LNAV wsnp_Ku_rep_c68484_67500021 3A 9049381 1.60E-04 0.140582867 RSDW LNE1 BS00025191_51 3A 5559286 7.11E-04 0.115275413 RSDW LNE1 wsnp_Ex_c15674_24005648 3A 5900855 7.40E-08 0.280595684 RSDW LNE1 wsnp_Ku_c4568_8243646 3A 5900855 1.32E-06 0.226126671 RSDW LNE1 GENE-1533_226 3A 6865599 3.58E-07 0.250533644 RSDW LNE1 Ku_c18096_552 3A 6865599 7.85E-05 0.152907561 RSDW LNE1 BS00065468_51 3A 7751230 3.16E-10 0.390565319 RSDW LNE1 BS00021694_51 3A 7756567 3.13E-07 0.253052885 RSDW LNE1 BS00094366_51 3A 7756567 3.10E-10 0.390977933 RSDW LNE1 BobWhite_c11298_512 3A 7756567 3.13E-07 0.253052885 RSDW LNE1 Excalibur_c24123_165 3A 7756567 3.15E-07 0.252926956 RSDW LNE1 IAAV2646 3A 7756567 3.13E-07 0.253052885 RSDW LNE1 RAC875_c2464_274 3A 7756567 3.16E-10 0.390565319 RSDW LNE1 Tdurum_contig86206_149 3A 7805856 3.16E-10 0.390565319 RSDW LNE1 wsnp_Ex_c9510_15761235 3A 8801680 1.66E-04 0.139970978 RSDW LNE1 RAC875_c10669_714 3A 8948291 2.21E-05 0.175112738 RSDW LNE1 wsnp_Ku_c9316_15647115 3A 9031172 3.26E-10 0.389915755 RSDW LNE1 wsnp_Ku_rep_c68484_67500021 3A 9049381 1.04E-06 0.230592573 RSDW LNE1 Ku_c14313_1194 3A 9055031 5.54E-05 0.158976138 RSDW LNE2 BS00023337_51 3A 12300565 8.64E-04 0.11199602 RSNC LNAV BS00065468_51 3A 7751230 4.23E-04 0.125005754 RSNC LNAV BS00032524_51 3A 7756567 6.23E-04 0.118432753 RSNC LNAV BS00094366_51 3A 7756567 4.91E-04 0.122478849 RSNC LNAV RAC875_c2464_274 3A 7756567 4.23E-04 0.125005754 RSNC LNAV Tdurum_contig86206_149 3A 7805856 4.23E-04 0.125005754 RSNC LNAV BS00023337_51 3A 12300565 3.06E-04 0.130552835 RSNC LNAV BS00059887_51 3A 12300565 6.20E-04 0.118518661 RSNC LNAV BS00011231_51 3A 12392236 5.33E-04 0.121064642 RSNC LNE1 wsnp_Ex_c15674_24005648 3A 5900855 6.77E-04 0.120874141 RSNC LNE1 BS00065468_51 3A 7751230 2.19E-07 0.271198781 RSNC LNE1 BS00032524_51 3A 7756567 2.25E-07 0.270640488 RSNC LNE1 BS00094366_51 3A 7756567 2.26E-07 0.270574044 RSNC LNE1 RAC875_c2464_274 3A 7756567 2.19E-07 0.271198781 RSNC LNE1 Tdurum_contig86206_149 3A 7805856 2.19E-07 0.271198781 RSNC LNE1 Tdurum_contig92540_1265 3A 9332556 1.55E-05 0.189133957 RSNC LNE1 BS00023337_51 3A 12300565 4.64E-04 0.1275173 RSNC LNE1 BS00059887_51 3A 12300565 2.33E-07 0.269947025 RSNC LNE1 BS00011231_51 3A 12392236 2.07E-07 0.272283952 RSNC LNE1 Tdurum_contig50577_620 3A 18032520 7.78E-05 0.159460325 RSNC LNE2 BS00066230_51 3A 1610209 8.47E-04 0.113225218 SDW LNE1 BS00076751_51 3A 15174705 7.23E-04 0.090120807 SNCe CKE2 BS00073062_51 3A 2601324 9.09E-04 0.112928885 SNCe CKE2 BS00022129_51 3A 8615826 4.22E-04 0.099982757 TNCe HNAV Kukri_c13830_601 3A 3366401 1.09E-07 0.273074811 TNCe HNE1 Kukri_c13830_601 3A 3366401 4.65E-13 0.560596168

RDW LNAV RAC875_c15667_1134 3B 13483435 7.33E-05 0.154091446 RDW LNE1 BS00071041_51 3B 12536549 2.90E-04 0.130405036 RDW LNE1 BS00071598_51 3B 12536549 3.04E-05 0.169485259 RDW LNE1 BS00074629_51 3B 12536549 3.04E-05 0.169485259 RDW LNE1 RAC875_c24401_277 3B 12536549 6.41E-07 0.239573912 RDW LNE1 RAC875_c15667_1134 3B 13483435 1.55E-11 0.455376486 RDW LNE1 Tdurum_contig63460_144 3B 13591451 4.82E-05 0.16140812 RDW HNAV Ra_c29672_532 3B 8099162 8.74E-04 0.111804267 RDW HNAV Kukri_c33386_112 3B 13635957 4.15E-04 0.1243427 RDW HNE2 Ra_c29672_532 3B 8099162 4.53E-04 0.122849237 RNC LNAV RAC875_c15667_1134 3B 13483435 5.27E-05 0.159840279 RNC LNE1 BS00071041_51 3B 12536549 1.52E-04 0.141516602 RNC LNE1 BS00071598_51 3B 12536549 5.58E-05 0.158840084 RNC LNE1 BS00074629_51 3B 12536549 5.58E-05 0.158840084 RNC LNE1 RAC875_c24401_277 3B 12536549 9.19E-07 0.23286371 RNC LNE1 RAC875_c15667_1134 3B 13483435 1.04E-10 0.413989819 RNC LNE1 Tdurum_contig63460_144 3B 13591451 1.57E-04 0.140889222 RNC HNAV Kukri_c33386_112 3B 13635957 7.62E-04 0.114103153 RNCe LNE1 RFL_Contig3008_1370 3B 864124 9.39E-04 0.110608631 RNCe LNE1 wsnp_JD_rep_c63654_40605158 3B 6972001 2.08E-04 0.136086885 RNCe LNE1 wsnp_Ex_c3722_6786328 3B 7724609 2.09E-04 0.136063869 RNCe HNE1 BS00071041_51 3B 12536549 6.82E-06 0.201121167 RNUE LNAV RAC875_c15667_1134 3B 13483435 4.24E-05 0.163671949 RNUE LNE1 BS00071041_51 3B 12536549 1.69E-05 0.17994551 RNUE LNE1 BS00071598_51 3B 12536549 5.98E-07 0.240879951 RNUE LNE1 BS00074629_51 3B 12536549 5.98E-07 0.240879951 RNUE LNE1 RAC875_c24401_277 3B 12536549 2.35E-08 0.302940528 RNUE LNE1 RAC875_c15667_1134 3B 13483435 2.11E-13 0.55298806 RNUE LNE1 Tdurum_contig63460_144 3B 13591451 1.22E-05 0.185764263 RNUE HNAV Kukri_c48601_98 3B 14474328 8.88E-04 0.112439049 RNUE HNE2 Kukri_c25794_863 3B 7194532 2.53E-04 0.132757662 RNUE HNE2 Tdurum_contig63110_433 3B 7335303 2.27E-04 0.134629878 RNUE HNE2 BS00022611_51 3B 7519079 8.76E-04 0.111758431 RNUE HNE2 BobWhite_c40087_93 3B 7519079 9.12E-04 0.111086171 RNUE HNE2 wsnp_Ex_c12220_19528388 3B 7519079 8.76E-04 0.111758431 RNUE HNE2 BobWhite_c22794_111 3B 8099162 7.48E-04 0.114417207 RNUE HNE2 Ra_c29672_532 3B 8099162 8.72E-04 0.111850564 RSDW LNAV BS00071041_51 3B 12536549 1.14E-05 0.186949291 RSDW LNAV BS00071598_51 3B 12536549 2.43E-04 0.133435448 RSDW LNAV BS00074629_51 3B 12536549 2.43E-04 0.133435448 RSDW LNAV RAC875_c24401_277 3B 12536549 4.17E-07 0.247646944 RSDW LNAV RAC875_c15667_1134 3B 13483435 1.57E-10 0.405359723 RSDW LNAV Tdurum_contig63460_144 3B 13591451 2.64E-04 0.132045262 RSDW LNE1 wsnp_Ra_c7158_12394405 3B 11990221 2.36E-04 0.133927986 RSDW LNE1 BS00071041_51 3B 12536549 8.14E-10 0.370825814 RSDW LNE1 BS00071598_51 3B 12536549 1.79E-07 0.263625301 RSDW LNE1 BS00074629_51 3B 12536549 1.79E-07 0.263625301 RSDW LNE1 RAC875_c24401_277 3B 12536549 1.73E-11 0.452971414 RSDW LNE1 RAC875_c15667_1134 3B 13483435 5.62E-17 0.758901875 RSDW LNE1 Tdurum_contig63460_144 3B 13591451 8.75E-07 0.233760105 RSDW HNE1 BS00068473_51 3B 10535512 8.59E-04 0.11210335

?

RNUE LNE1 wsnp_Ku_c2317_4448102 4A 6827629 1.89E-04 0.137740612 RNUE LNE1 RAC875_c25124_182 4A 7207084 2.73E-13 0.546908272 RNUE LNE1 BS00064269_51 4A 7818200 5.74E-08 0.285537455 RNUE HNAV wsnp_BE405275A_Ta_1_1 4A 2986288 1.52E-04 0.142620836 RNUE HNAV BS00066891_51 4A 11013138 4.31E-04 0.124717395 RNUE HNE2 wsnp_BE405275A_Ta_1_1 4A 2986288 2.91E-04 0.130370039 RNUE HNE2 IAAV5722 4A 10671782 3.37E-04 0.127889374 RNUE HNE2 BS00066891_51 4A 11013138 8.41E-04 0.112446823 RSDW CKAV IAAV2216 4A 860677 5.82E-04 0.11862684 RSDW CKE1 BobWhite_c7260_197 4A 4101896 6.17E-04 0.092549137 RSDW CKE2 IAAV2216 4A 860677 5.82E-04 0.118621057 RSDW LNAV BS00037357_51 4A 6792087 1.83E-04 0.138292456 RSDW LNAV RAC875_c17918_321 4A 6827629 6.26E-05 0.156853306 RSDW LNAV wsnp_Ku_c2317_4448102 4A 6827629 7.07E-05 0.154733071 RSDW LNAV RAC875_c25124_182 4A 7207084 1.44E-10 0.407136174 RSDW LNAV BS00064269_51 4A 7818200 1.58E-06 0.222826839 RSDW LNE1 BS00037357_51 4A 6792087 1.71E-06 0.221340006 RSDW LNE1 RAC875_c17918_321 4A 6827629 2.41E-07 0.258028003 RSDW LNE1 wsnp_Ku_c2317_4448102 4A 6827629 4.75E-06 0.202681655 RSDW LNE1 Ra_c23848_305 4A 6918401 1.54E-04 0.141208607 RSDW LNE1 RAC875_c25124_182 4A 7207084 5.72E-17 0.758455938 RSDW LNE1 BS00064269_51 4A 7818200 1.14E-10 0.412124048 RSNC CKAV IAAV2216 4A 860677 8.95E-04 0.111403201 RSNC CKE2 IAAV2216 4A 860677 6.22E-04 0.120398249 RSNC LNE1 Kukri_c25832_687 4A 8737432 2.98E-04 0.135364812 RSNC LNE1 Ku_c1125_814 4A 10038420 1.55E-04 0.147063774 RSNC LNE1 RAC875_c83401_115 4A 11013138 7.07E-04 0.12009793 RSNC LNE1 BobWhite_c20306_111 4A 13727876 2.79E-05 0.178266367 RSNC LNE1 BobWhite_c20322_559 4A 13790778 5.60E-04 0.12420531 TDW HNE1 wsnp_Ex_c539_1072859 4A 6038547 9.37E-04 0.110647113 RDW LNAV tplb0025f09_1052 4B 1591267 3.12E-05 0.169072033 RDW LNAV tplb0025f09_973 4B 1591267 2.00E-04 0.136770969 RDW LNAV TA002925-3757 4B 6039137 5.90E-04 0.118417319 RDW LNAV BS00022090_51 4B 6183767 5.39E-04 0.119917001 RDW LNAV Tdurum_contig31250_273 4B 6256424 5.00E-04 0.121205258 RDW LNAV wsnp_Ex_c3119_5763762 4B 6632392 5.96E-04 0.118243921 RDW LNAV wsnp_Ex_c5769_10136243 4B 7090614 2.28E-04 0.134567012 RDW LNAV RAC875_c39226_131 4B 7213652 3.43E-04 0.12758908 RDW LNE1 tplb0025f09_1052 4B 1591267 2.64E-08 0.300681599 RDW LNE1 tplb0025f09_973 4B 1591267 2.05E-11 0.449158183 RDW LNE1 Kukri_c66885_230 4B 3533826 6.08E-04 0.117896717 RDW LNE1 Kukri_rep_c74376_188 4B 4165466 1.80E-04 0.138561535 RDW LNE1 wsnp_Ex_c30695_39579408 4B 4457467 2.37E-07 0.25831468 RDW LNE1 Ku_c63300_1309 4B 4546575 5.31E-04 0.120180911 RDW LNE1 Kukri_rep_c69273_148 4B 4571936 6.43E-07 0.239523987 RDW LNE1 BS00022534_51 4B 4686063 2.29E-07 0.258928103 RDW LNE1 wsnp_Ex_c7362_12622736 4B 4686063 2.29E-07 0.258928103 RDW LNE1 Tdurum_contig41902_1524 4B 5005482 7.76E-04 0.11378688 RDW LNE1 RAC875_c15835_454 4B 5994241 3.32E-07 0.251949276 RDW LNE1 TA002925-3757 4B 6039137 2.72E-11 0.443024972 RDW LNE1 BS00022090_51 4B 6183767 2.71E-11 0.443141335

RDW LNE1 BS00040159_51 4B 6183767 2.55E-04 0.132653909 RDW LNE1 BS00062691_51 4B 6183767 1.80E-04 0.138594023 RDW LNE1 BS00067428_51 4B 6183767 3.32E-05 0.167953262 RDW LNE1 BS00075631_51 4B 6183767 3.17E-05 0.168784823 RDW LNE1 BS00075746_51 4B 6183767 3.58E-04 0.126833047 RDW LNE1 BS00105308_51 4B 6183767 8.68E-07 0.233912588 RDW LNE1 Excalibur_c100336_106 4B 6183767 3.34E-05 0.167827862 RDW LNE1 BS00018707_51 4B 6256424 9.68E-04 0.110097967 RDW LNE1 Tdurum_contig31250_273 4B 6256424 1.99E-11 0.449798015 RDW LNE1 IAAV4595 4B 6559049 1.27E-05 0.185063708 RDW LNE1 BS00022194_51 4B 6632392 1.33E-05 0.184185461 RDW LNE1 IAAV1630 4B 6632392 3.75E-07 0.249635119 RDW LNE1 wsnp_Ex_c3119_5763762 4B 6632392 1.62E-11 0.454318933 RDW LNE1 Excalibur_c65023_62 4B 7065938 1.94E-06 0.219074594 RDW LNE1 wsnp_Ex_c5769_10136243 4B 7090614 8.98E-07 0.233277117 RDW LNE1 Kukri_c89906_197 4B 7113234 8.20E-05 0.152156297 RDW LNE1 RAC875_c39226_372 4B 7128999 6.83E-05 0.155334452 RDW LNE1 IAAV3421 4B 7136539 9.20E-04 0.11094824 RDW LNE1 IAAV4665 4B 7136539 2.07E-04 0.13617987 RDW LNE1 RAC875_c5087_310 4B 7136539 4.04E-06 0.205654375 RDW LNE1 Tdurum_contig55374_309 4B 7136539 4.04E-06 0.205654375 RDW LNE1 BS00072206_51 4B 7146136 7.50E-04 0.114377933 RDW LNE1 CAP8_c3273_136 4B 7146136 7.92E-04 0.113453692 RDW LNE1 Excalibur_c18660_1719 4B 7146136 7.51E-06 0.194416609 RDW LNE1 Kukri_c5502_2513 4B 7146136 7.50E-04 0.114377933 RDW LNE1 wsnp_CAP12_rep_c4278_1949802 4B 7146136 7.92E-04 0.113453692 RDW LNE1 wsnp_Ku_c5502_9765942 4B 7146136 4.82E-05 0.161405431 RDW LNE1 wsnp_Ku_rep_c68318_67259259 4B 7146136 2.33E-04 0.13416981 RDW LNE1 BS00031652_51 4B 7191375 6.71E-05 0.155643094 RDW LNE1 Excalibur_rep_c70127_360 4B 7191375 1.68E-04 0.139759288 RDW LNE1 Ku_c24961_1176 4B 7191375 6.28E-06 0.197633066 RDW LNE1 RAC875_c39226_131 4B 7213652 3.32E-07 0.251953114 RDW LNE1 wsnp_CAP12_rep_c4278_1949864 4B 7213652 3.47E-06 0.208409779 RDW LNE1 BS00022364_51 4B 7416545 2.34E-05 0.174103872 RDW LNE1 Tdurum_contig60114_525 4B 7416545 2.34E-05 0.174103872 RDW LNE1 BS00074787_51 4B 7564601 7.50E-04 0.114377933 RDW LNE1 BS00077411_51 4B 7564601 4.04E-06 0.205654375 RDW LNE1 BobWhite_c17457_89 4B 7564601 6.28E-06 0.197633066 RDW LNE1 Excalibur_c56741_119 4B 7564601 6.28E-06 0.197633066 RDW LNE1 IACX9010 4B 7564601 7.50E-04 0.114377933 RNC LNAV tplb0025f09_1052 4B 1591267 4.99E-05 0.160799783 RNC LNAV tplb0025f09_973 4B 1591267 2.11E-04 0.135885333 RNC LNAV TA002925-3757 4B 6039137 3.40E-04 0.127728971 RNC LNAV BS00022090_51 4B 6183767 2.75E-04 0.13133161 RNC LNAV Tdurum_contig31250_273 4B 6256424 2.52E-04 0.132795044 RNC LNAV wsnp_Ex_c3119_5763762 4B 6632392 3.44E-04 0.127527353 RNC LNAV wsnp_Ex_c5769_10136243 4B 7090614 4.43E-04 0.12324119 RNC LNAV RAC875_c39226_131 4B 7213652 9.16E-04 0.111012104 RNC LNE1 tplb0025f09_1052 4B 1591267 5.58E-08 0.28606292 RNC LNE1 tplb0025f09_973 4B 1591267 1.29E-10 0.409488156 RNC LNE1 Kukri_rep_c74376_188 4B 4165466 8.70E-04 0.111876749

RNC LNE1 wsnp_Ex_c30695_39579408 4B 4457467 7.28E-06 0.194968011 RNC LNE1 Kukri_rep_c69273_148 4B 4571936 1.92E-05 0.177661177 RNC LNE1 BS00022534_51 4B 4686063 4.13E-06 0.205235504 RNC LNE1 wsnp_Ex_c7362_12622736 4B 4686063 4.13E-06 0.205235504 RNC LNE1 BobWhite_c38340_243 4B 5994241 6.33E-04 0.117207439 RNC LNE1 RAC875_c15835_454 4B 5994241 3.82E-06 0.206638 RNC LNE1 TA002925-3757 4B 6039137 1.33E-10 0.408779328 RNC LNE1 BS00022090_51 4B 6183767 9.87E-11 0.415204515 RNC LNE1 BS00040159_51 4B 6183767 1.71E-04 0.139456246 RNC LNE1 BS00062691_51 4B 6183767 8.48E-05 0.1515665 RNC LNE1 BS00067428_51 4B 6183767 8.30E-06 0.192622227 RNC LNE1 BS00075631_51 4B 6183767 7.57E-06 0.194273857 RNC LNE1 BS00075746_51 4B 6183767 2.32E-04 0.134258814 RNC LNE1 BS00105308_51 4B 6183767 6.03E-07 0.24072814 RNC LNE1 Excalibur_c100336_106 4B 6183767 3.33E-04 0.128103546 RNC LNE1 BS00018707_51 4B 6256424 3.64E-04 0.126557222 RNC LNE1 Tdurum_contig31250_273 4B 6256424 5.86E-11 0.426403341 RNC LNE1 IAAV2880 4B 6403796 6.87E-04 0.115843696 RNC LNE1 IAAV4595 4B 6559049 2.93E-05 0.170157988 RNC LNE1 BS00022194_51 4B 6632392 2.90E-05 0.17035286 RNC LNE1 IAAV1630 4B 6632392 2.88E-07 0.254611737 RNC LNE1 wsnp_Ex_c3119_5763762 4B 6632392 9.17E-11 0.416762126 RNC LNE1 Excalibur_c65023_62 4B 7065938 1.74E-05 0.179383614 RNC LNE1 wsnp_Ex_c5769_10136243 4B 7090614 5.24E-06 0.200932737 RNC LNE1 Kukri_c89906_197 4B 7113234 4.78E-04 0.121959773 RNC LNE1 RAC875_c39226_372 4B 7128999 8.96E-04 0.111394087 RNC LNE1 RAC875_c5087_310 4B 7136539 1.01E-05 0.189142414 RNC LNE1 Tdurum_contig55374_309 4B 7136539 1.01E-05 0.189142414 RNC LNE1 Excalibur_c18660_1719 4B 7146136 4.83E-05 0.161383591 RNC LNE1 wsnp_Ku_c5502_9765942 4B 7146136 1.37E-04 0.143319944 RNC LNE1 wsnp_Ku_rep_c68318_67259259 4B 7146136 6.61E-04 0.116487347 RNC LNE1 BS00031652_51 4B 7191375 3.23E-04 0.128584314 RNC LNE1 Excalibur_rep_c70127_360 4B 7191375 9.07E-04 0.111175496 RNC LNE1 Ku_c24961_1176 4B 7191375 2.02E-05 0.176755913 RNC LNE1 RAC875_c39226_131 4B 7213652 1.22E-06 0.227597576 RNC LNE1 wsnp_CAP12_rep_c4278_1949864 4B 7213652 7.86E-06 0.193589203 RNC LNE1 BS00022364_51 4B 7416545 1.73E-04 0.139219739 RNC LNE1 Tdurum_contig60114_525 4B 7416545 1.73E-04 0.139219739 RNC LNE1 BS00077411_51 4B 7564601 1.01E-05 0.189142414 RNC LNE1 BobWhite_c17457_89 4B 7564601 2.02E-05 0.176755913 RNC LNE1 Excalibur_c56741_119 4B 7564601 2.02E-05 0.176755913 RNCe HNE2 BS00060041_51 4B 2335320 8.21E-04 0.112861646 RNUE LNAV tplb0025f09_1052 4B 1591267 1.77E-05 0.179104181 RNUE LNAV tplb0025f09_973 4B 1591267 7.09E-05 0.154671336 RNUE LNAV wsnp_Ex_c30695_39579408 4B 4457467 6.41E-04 0.116996041 RNUE LNAV BS00022534_51 4B 4686063 1.27E-04 0.144610301 RNUE LNAV wsnp_Ex_c7362_12622736 4B 4686063 1.27E-04 0.144610301 RNUE LNAV TA002925-3757 4B 6039137 1.59E-04 0.140725656 RNUE LNAV BS00022090_51 4B 6183767 1.17E-04 0.146064779 RNUE LNAV Tdurum_contig31250_273 4B 6256424 1.12E-04 0.14669051 RNUE LNAV wsnp_Ex_c3119_5763762 4B 6632392 1.52E-04 0.141488312

RNUE LNAV wsnp_Ex_c5769_10136243 4B 7090614 5.99E-04 0.118136358 RNUE LNAV RAC875_c5087_310 4B 7136539 8.64E-04 0.112000767 RNUE LNAV Tdurum_contig55374_309 4B 7136539 8.64E-04 0.112000767 RNUE LNAV RAC875_c39226_131 4B 7213652 1.09E-04 0.147193933 RNUE LNAV BS00077411_51 4B 7564601 8.64E-04 0.112000767 RNUE LNE1 tplb0025f09_1052 4B 1591267 1.32E-09 0.360882259 RNUE LNE1 tplb0025f09_973 4B 1591267 2.64E-13 0.547743552 RNUE LNE1 Kukri_c66885_230 4B 3533826 3.34E-04 0.12802255 RNUE LNE1 Kukri_rep_c74376_188 4B 4165466 8.62E-06 0.191941721 RNUE LNE1 wsnp_Ex_c30695_39579408 4B 4457467 9.42E-09 0.321057698 RNUE LNE1 Ku_c63300_1309 4B 4546575 1.46E-04 0.142226886 RNUE LNE1 Kukri_rep_c69273_148 4B 4571936 2.02E-08 0.305942599 RNUE LNE1 BS00022534_51 4B 4686063 1.81E-08 0.30809718 RNUE LNE1 wsnp_Ex_c7362_12622736 4B 4686063 1.81E-08 0.30809718 RNUE LNE1 Tdurum_contig41902_1524 4B 5005482 9.85E-05 0.148970278 RNUE LNE1 BobWhite_c38340_243 4B 5994241 5.77E-05 0.158280228 RNUE LNE1 RAC875_c15835_454 4B 5994241 1.96E-08 0.306520863 RNUE LNE1 BS00084904_51 4B 6039137 5.62E-05 0.158728162 RNUE LNE1 GENE-2462_1056 4B 6039137 1.50E-04 0.141723496 RNUE LNE1 Kukri_c42458_499 4B 6039137 5.62E-05 0.158728162 RNUE LNE1 TA002925-3757 4B 6039137 2.46E-13 0.549429323 RNUE LNE1 Tdurum_contig50123_97 4B 6039137 5.62E-05 0.158728162 RNUE LNE1 Tdurum_contig76677_1142 4B 6039137 5.62E-05 0.158728162 RNUE LNE1 wsnp_BE422566B_Ta_1_2 4B 6039137 5.62E-05 0.158728162 RNUE LNE1 BS00022090_51 4B 6183767 2.49E-13 0.549070996 RNUE LNE1 BS00040159_51 4B 6183767 7.83E-06 0.193665657 RNUE LNE1 BS00062691_51 4B 6183767 1.83E-05 0.1785328 RNUE LNE1 BS00067428_51 4B 6183767 1.65E-06 0.221999948 RNUE LNE1 BS00075631_51 4B 6183767 1.59E-06 0.222686996 RNUE LNE1 BS00075746_51 4B 6183767 4.63E-05 0.162127216 RNUE LNE1 BS00102182_51 4B 6183767 1.50E-04 0.141723496 RNUE LNE1 BS00105308_51 4B 6183767 3.02E-08 0.298048464 RNUE LNE1 Excalibur_c100336_106 4B 6183767 3.66E-05 0.166228821 RNUE LNE1 BS00018707_51 4B 6256424 1.04E-04 0.14805367 RNUE LNE1 Tdurum_contig31250_273 4B 6256424 1.73E-13 0.557615357 RNUE LNE1 Tdurum_contig93168_52 4B 6256424 3.22E-04 0.128668717 RNUE LNE1 IAAV2880 4B 6403796 6.20E-05 0.157009774 RNUE LNE1 IAAV4595 4B 6559049 2.75E-07 0.255526168 RNUE LNE1 BS00022194_51 4B 6632392 2.57E-07 0.256771279 RNUE LNE1 IAAV1630 4B 6632392 1.36E-08 0.313782247 RNUE LNE1 wsnp_Ex_c3119_5763762 4B 6632392 1.61E-13 0.5594143 RNUE LNE1 Excalibur_c65023_62 4B 7065938 3.46E-07 0.251156761 RNUE LNE1 wsnp_Ex_c5769_10136243 4B 7090614 5.58E-07 0.242159118 RNUE LNE1 wsnp_Ex_c5769_10136788 4B 7090614 3.69E-04 0.126358272 RNUE LNE1 Kukri_c89906_197 4B 7113234 8.37E-06 0.192460101 RNUE LNE1 RAC875_c39226_372 4B 7128999 2.80E-05 0.170963718 RNUE LNE1 IAAV3421 4B 7136539 2.01E-04 0.136683762 RNUE LNE1 IAAV4665 4B 7136539 1.00E-04 0.148654966 RNUE LNE1 RAC875_c5087_310 4B 7136539 1.72E-07 0.264398676 RNUE LNE1 Tdurum_contig55374_309 4B 7136539 1.72E-07 0.264398676 RNUE LNE1 BS00022184_51 4B 7146136 6.84E-04 0.115924388

RNUE LNE1 BS00072206_51 4B 7146136 1.63E-04 0.140243969 RNUE LNE1 BS00091035_51 4B 7146136 7.79E-04 0.113731428 RNUE LNE1 CAP8_c3273_136 4B 7146136 1.77E-04 0.138824467 RNUE LNE1 Excalibur_c18660_1719 4B 7146136 1.33E-06 0.226070203 RNUE LNE1 Kukri_c5502_2513 4B 7146136 1.63E-04 0.140243969 RNUE LNE1 wsnp_CAP12_rep_c4278_1949802 4B 7146136 1.77E-04 0.138824467 RNUE LNE1 wsnp_Ku_c31283_41033384 4B 7146136 7.79E-04 0.113731428 RNUE LNE1 wsnp_Ku_c5502_9765942 4B 7146136 4.28E-06 0.204598299 RNUE LNE1 wsnp_Ku_rep_c68318_67259259 4B 7146136 1.11E-05 0.187363416 RNUE LNE1 BS00031652_51 4B 7191375 6.81E-06 0.196174983 RNUE LNE1 Excalibur_rep_c70127_360 4B 7191375 8.21E-05 0.152137739 RNUE LNE1 Ku_c24961_1176 4B 7191375 1.43E-06 0.22471646 RNUE LNE1 RAC875_c39226_131 4B 7213652 4.66E-08 0.289571376 RNUE LNE1 wsnp_CAP12_rep_c4278_1949864 4B 7213652 1.52E-07 0.266735744 RNUE LNE1 BS00022364_51 4B 7416545 2.44E-05 0.173392598 RNUE LNE1 Tdurum_contig60114_525 4B 7416545 2.44E-05 0.173392598 RNUE LNE1 BS00074787_51 4B 7564601 1.63E-04 0.140243969 RNUE LNE1 BS00077411_51 4B 7564601 1.72E-07 0.264398676 RNUE LNE1 BobWhite_c17457_89 4B 7564601 1.43E-06 0.22471646 RNUE LNE1 Excalibur_c56741_119 4B 7564601 1.43E-06 0.22471646 RNUE LNE1 IACX9010 4B 7564601 1.63E-04 0.140243969 RNUE HNAV tplb0025f09_1052 4B 1591267 5.55E-04 0.120387895 RNUE HNE2 tplb0025f09_1052 4B 1591267 7.25E-04 0.114935575 RNUE HNE2 Ku_c63300_1309 4B 4546575 9.25E-04 0.110847578 RSDW LNAV tplb0025f09_1052 4B 1591267 3.54E-08 0.294950688 RSDW LNAV tplb0025f09_973 4B 1591267 1.82E-10 0.40216741 RSDW LNAV Kukri_rep_c74376_188 4B 4165466 1.99E-05 0.176979435 RSDW LNAV wsnp_Ex_c30695_39579408 4B 4457467 9.08E-07 0.233082103 RSDW LNAV Kukri_rep_c69273_148 4B 4571936 1.17E-06 0.228396881 RSDW LNAV BS00022534_51 4B 4686063 8.47E-07 0.234382308 RSDW LNAV wsnp_Ex_c7362_12622736 4B 4686063 8.47E-07 0.234382308 RSDW LNAV Tdurum_contig41902_1524 4B 5005482 6.31E-04 0.117279223 RSDW LNAV BobWhite_c38340_243 4B 5994241 3.70E-05 0.166051834 RSDW LNAV RAC875_c15835_454 4B 5994241 7.00E-06 0.195696455 RSDW LNAV BS00084904_51 4B 6039137 6.38E-05 0.156516213 RSDW LNAV GENE-2462_1056 4B 6039137 5.89E-04 0.118432915 RSDW LNAV Kukri_c42458_499 4B 6039137 6.38E-05 0.156516213 RSDW LNAV TA002925-3757 4B 6039137 2.47E-10 0.395730183 RSDW LNAV Tdurum_contig50123_97 4B 6039137 6.38E-05 0.156516213 RSDW LNAV Tdurum_contig76677_1142 4B 6039137 6.38E-05 0.156516213 RSDW LNAV wsnp_BE422566B_Ta_1_2 4B 6039137 6.38E-05 0.156516213 RSDW LNAV BS00022090_51 4B 6183767 1.22E-10 0.410756843 RSDW LNAV BS00040159_51 4B 6183767 1.10E-05 0.187547563 RSDW LNAV BS00062691_51 4B 6183767 1.43E-04 0.142487361 RSDW LNAV BS00067428_51 4B 6183767 1.17E-05 0.186510717 RSDW LNAV BS00075631_51 4B 6183767 1.03E-05 0.188805103 RSDW LNAV BS00075746_51 4B 6183767 8.99E-04 0.111323848 RSDW LNAV BS00102182_51 4B 6183767 5.89E-04 0.118432915 RSDW LNAV BS00105308_51 4B 6183767 1.74E-07 0.264196434 RSDW LNAV Excalibur_c100336_106 4B 6183767 5.46E-05 0.159225174 RSDW LNAV Tdurum_contig31250_273 4B 6256424 1.58E-10 0.40523755

RSDW LNE1 wsnp_BE422566B_Ta_1_2 4B 6039137 3.97E-07 0.248552793 RSDW LNE1 BS00022090_51 4B 6183767 4.39E-17 0.76550302 RSDW LNE1 BS00040159_51 4B 6183767 1.39E-07 0.268451713 RSDW LNE1 BS00062691_51 4B 6183767 3.15E-07 0.252951667 RSDW LNE1 BS00067428_51 4B 6183767 1.15E-08 0.317132907 RSDW LNE1 BS00075631_51 4B 6183767 1.07E-08 0.318505367 RSDW LNE1 BS00075746_51 4B 6183767 2.45E-05 0.173286183 RSDW LNE1 BS00102182_51 4B 6183767 7.77E-06 0.19381157 RSDW LNE1 BS00105308_51 4B 6183767 1.24E-11 0.460250272 RSDW LNE1 Excalibur_c100336_106 4B 6183767 2.80E-08 0.299534832 RSDW LNE1 BS00018707_51 4B 6256424 4.99E-06 0.201796645 RSDW LNE1 Tdurum_contig31250_273 4B 6256424 4.04E-17 0.767712628 RSDW LNE1 Tdurum_contig93168_52 4B 6256424 7.67E-06 0.194044013 RSDW LNE1 IAAV2880 4B 6403796 6.99E-07 0.237966833 RSDW LNE1 IAAV4595 4B 6559049 3.47E-10 0.388580697 RSDW LNE1 BS00022194_51 4B 6632392 3.40E-10 0.388983838 RSDW LNE1 IAAV1630 4B 6632392 3.21E-10 0.39021337 RSDW LNE1 wsnp_Ex_c3119_5763762 4B 6632392 5.72E-17 0.758460029 RSDW LNE1 Excalibur_c65023_62 4B 7065938 2.54E-05 0.172659834 RSDW LNE1 wsnp_Ex_c5769_10136243 4B 7090614 1.06E-06 0.23016948 RSDW LNE1 Kukri_c89906_197 4B 7113234 1.55E-04 0.141184893 RSDW LNE1 RAC875_c39226_372 4B 7128999 1.04E-04 0.148034457 RSDW LNE1 IAAV3421 4B 7136539 3.70E-04 0.126297262 RSDW LNE1 IAAV4665 4B 7136539 1.17E-05 0.186517851 RSDW LNE1 RAC875_c5087_310 4B 7136539 1.73E-07 0.264344202 RSDW LNE1 Tdurum_contig55374_309 4B 7136539 1.73E-07 0.264344202 RSDW LNE1 BS00072206_51 4B 7146136 3.68E-04 0.1263889 RSDW LNE1 BS00091035_51 4B 7146136 3.34E-04 0.128029134 RSDW LNE1 CAP8_c3273_136 4B 7146136 3.56E-04 0.126950806 RSDW LNE1 Excalibur_c18660_1719 4B 7146136 1.33E-10 0.408845795 RSDW LNE1 Kukri_c5502_2513 4B 7146136 3.68E-04 0.1263889 RSDW LNE1 wsnp_CAP12_rep_c4278_1949802 4B 7146136 3.56E-04 0.126950806 RSDW LNE1 wsnp_Ku_c31283_41033384 4B 7146136 3.34E-04 0.128029134 RSDW LNE1 wsnp_Ku_c5502_9765942 4B 7146136 2.71E-06 0.212903078 RSDW LNE1 wsnp_Ku_rep_c68318_67259259 4B 7146136 2.67E-05 0.171829336 RSDW LNE1 BS00031652_51 4B 7191375 1.55E-04 0.141197311 RSDW LNE1 Excalibur_rep_c70127_360 4B 7191375 1.15E-05 0.18678194 RSDW LNE1 Ku_c24961_1176 4B 7191375 1.98E-06 0.218706362 RSDW LNE1 RAC875_c39226_131 4B 7213652 8.09E-08 0.278898577 RSDW LNE1 wsnp_CAP12_rep_c4278_1949864 4B 7213652 1.65E-07 0.265230477 RSDW LNE1 BS00022364_51 4B 7416545 2.46E-08 0.302059345 RSDW LNE1 Tdurum_contig60114_525 4B 7416545 2.46E-08 0.302059345 RSDW LNE1 BS00074787_51 4B 7564601 3.68E-04 0.1263889 RSDW LNE1 BS00077411_51 4B 7564601 1.73E-07 0.264344202 RSDW LNE1 BobWhite_c17457_89 4B 7564601 1.98E-06 0.218706362 RSDW LNE1 Excalibur_c56741_119 4B 7564601 1.98E-06 0.218706362 RSDW LNE1 IACX9010 4B 7564601 3.68E-04 0.1263889 RSDW HNAV BS00040305_51 4B 6039137 3.66E-04 0.100603001 RSDW HNE1 BS00040305_51 4B 6039137 1.84E-05 0.148555916 RSNC LNAV RAC875_c24098_141 4B 2987866 7.57E-04 0.115114568 RSNC LNAV BobWhite_c44691_648 4B 5950715 6.73E-04 0.117125091

RSNC LNAV wsnp_Ex_c5769_10136243 4B 7090614 2.80E-04 0.132070475 RSNC LNAV RFL_Contig5498_1000 4B 7146136 7.50E-04 0.115278212 RSNC LNAV BS00022181_51 4B 7191375 4.69E-04 0.123262666 RSNC LNAV Ku_c24961_1176 4B 7191375 5.38E-04 0.120905311 RSNC LNAV BS00022125_51 4B 7252380 6.53E-04 0.117620543 RSNC LNAV wsnp_JD_c13364_13377722 4B 7252380 6.53E-04 0.117620543 RSNC LNAV BobWhite_c17457_89 4B 7564601 5.38E-04 0.120905311 RSNC LNAV Excalibur_c56741_119 4B 7564601 5.38E-04 0.120905311 RSNC LNAV Kukri_c7241_322 4B 8128725 4.29E-04 0.124791846 RSNC LNE1 RAC875_c24098_141 4B 2987866 2.32E-07 0.270020218 RSNC LNE1 BobWhite_c44691_648 4B 5950715 1.77E-07 0.275475107 RSNC LNE1 Jagger_c1432_289 4B 6657411 1.62E-04 0.146264734 RSNC LNE1 wsnp_Ex_c5769_10136243 4B 7090614 6.50E-04 0.121570678 RSNC LNE1 RFL_Contig5498_1000 4B 7146136 7.32E-05 0.160581485 RSNC LNE1 BS00022181_51 4B 7191375 1.96E-07 0.273380625 RSNC LNE1 RAC875_c39226_131 4B 7213652 1.40E-04 0.148835958 RSNC LNE1 BS00022125_51 4B 7252380 2.33E-07 0.269962155 RSNC LNE1 wsnp_JD_c13364_13377722 4B 7252380 2.33E-07 0.269962155 RSNC LNE1 Kukri_c7241_322 4B 8128725 2.97E-04 0.135406607 RSNC HNAV BS00040305_51 4B 6039137 1.26E-04 0.11739612 RSNC HNE1 BS00040305_51 4B 6039137 6.18E-05 0.135289928 RNCe LNE1 wsnp_Ex_rep_c67296_65839761 4D 8067651 3.77E-04 0.125988348 RSNC HNE2 Excalibur_c55675_178 4D 8842797 9.61E-04 0.085778873 RDW HNAV Excalibur_c92705_94 5A 9914468 9.46E-04 0.110475159 RDW HNE2 Ra_c10762_1137 5A 1560869 6.95E-04 0.115648694 RDW HNE2 RAC875_c15713_943 5A 4973212 4.42E-04 0.123286643 RNC CKE1 CAP8_rep_c4852_130 5A 11120022 3.17E-04 0.128933573 RNC CKE1 RAC875_c59520_130 5A 11128611 2.12E-04 0.109118804 RNC HNE2 RAC875_c15713_943 5A 4973212 5.08E-04 0.120930742 RNCe LNAV Ku_c19858_2078 5A 8870493 3.55E-04 0.127017438 RNCe LNE1 BS00057293_51 5A 1560869 7.74E-04 0.11384222 RNCe HNAV BS00015653_51 5A 5346502 6.98E-04 0.090650174 RNCe HNAV BobWhite_c13238_386 5A 5560011 6.89E-04 0.1157886 RNCe HNAV BobWhite_rep_c61813_322 5A 5647491 1.41E-04 0.115577172 RNCe HNAV Kukri_c14275_674 5A 5647491 1.41E-04 0.115577172 RNCe HNAV wsnp_JD_rep_c49046_33288885 5A 5647491 1.41E-04 0.115577172 RNCe HNAV wsnp_Ku_c14275_22535576 5A 5647491 2.92E-04 0.130306183 RNCe HNAV wsnp_Ku_c14275_22535693 5A 5647491 2.92E-04 0.130306183 RNCe HNAV BobWhite_c40643_370 5A 8816766 9.61E-05 0.121703571 RNCe HNAV BobWhite_rep_c63332_67 5A 12519912 4.89E-04 0.121564067 RNCe HNAV Kukri_c75091_220 5A 12568246 7.39E-04 0.114627972 RNCe HNAV wsnp_Ex_c23795_33033010 5A 12568246 7.39E-04 0.114627972 RNCe HNAV Tdurum_contig42962_2138 5A 12600002 6.72E-04 0.116221743 RNCe HNAV wsnp_Ex_c2505_4679749 5A 13142462 9.45E-04 0.110488275 RNCe HNE2 BS00021660_51 5A 4326694 5.07E-04 0.120967323 RNCe HNE2 BS00078654_51 5A 4326694 5.07E-04 0.120967323 RNCe HNE2 Kukri_rep_c107435_940 5A 4326694 6.21E-04 0.117540484 RNCe HNE2 wsnp_Ra_c11420_18529863 5A 4326694 5.07E-04 0.120967323 RNCe HNE2 wsnp_Ex_c2718_5038582 5A 4337879 5.07E-04 0.120967323 RNCe HNE2 BobWhite_rep_c63332_67 5A 12519912 3.25E-04 0.128494383 RNCe HNE2 Kukri_c75091_220 5A 12568246 4.17E-04 0.124285035

RNCe HNE2 wsnp_Ex_c23795_33033010 5A 12568246 4.17E-04 0.124285035 RNCe HNE2 wsnp_Ex_c23795_33033150 5A 12568246 4.14E-04 0.124389725 RNCe HNE2 wsnp_Ex_c2505_4679749 5A 13142462 4.51E-04 0.122940692 RNCe HNE2 BS00021684_51 5A 14174853 8.78E-04 0.111734067 RNUE HNAV BS00022500_51 5A 4937461 5.32E-04 0.121116029 RNUE HNE2 RAC875_c15713_943 5A 4973212 8.47E-04 0.11233468 RNUE HNE2 Tdurum_contig81510_198 5A 4973212 2.99E-04 0.129911578 RSNC LNAV wsnp_BE500291A_Ta_2_1 5A 1560869 3.35E-04 0.128984429 RSNC LNAV wsnp_Ex_rep_c104290_89051908 5A 1570456 3.42E-04 0.128631313 RSNC LNAV wsnp_Ex_c62818_62296773 5A 8901650 8.08E-04 0.114025857 RSNC LNE1 wsnp_BE500291A_Ta_2_1 5A 1560869 1.09E-07 0.285147838 RSNC LNE1 wsnp_Ex_rep_c104290_89051908 5A 1570456 2.32E-07 0.270078039 RSNC LNE1 IAAV2080 5A 4607311 7.21E-04 0.119748089 RSNC LNE1 wsnp_Ku_c5071_9050628 5A 4607311 7.21E-04 0.119748089 RSNC LNE1 GENE-3189_377 5A 7030005 8.85E-04 0.116180627 RSNC LNE1 Ex_c21738_1175 5A 7680916 5.73E-04 0.123783435 RSNC LNE1 wsnp_Ex_c62818_62296773 5A 8901650 2.31E-07 0.270146004 RSNC LNE2 BS00022500_51 5A 4937461 3.66E-04 0.127508011 RSNC HNAV Kukri_s112978_54 5A 7030005 6.53E-04 0.116697476 RSNC HNAV Excalibur_c49297_159 5A 12519912 8.77E-05 0.150991005 RSNC HNE2 Excalibur_c49297_159 5A 12519912 3.61E-04 0.126721257 SDW LNE2 BobWhite_c40643_370 5A 8816766 3.84E-04 0.099871155 TNCe HNAV BobWhite_c13238_386 5A 5560011 8.36E-04 0.112550882 TNCe HNAV BobWhite_rep_c61813_322 5A 5647491 9.84E-04 0.085422138 TNCe HNAV Kukri_c14275_674 5A 5647491 9.84E-04 0.085422138 TNCe HNAV wsnp_JD_rep_c49046_33288885 5A 5647491 9.84E-04 0.085422138 TNCe HNAV BobWhite_c40643_370 5A 8816766 1.32E-04 0.116656474 TNCe HNAV BobWhite_rep_c63332_67 5A 12519912 7.21E-04 0.115034772 TNCe HNAV CAP8_c3064_95 5A 12519912 8.59E-04 0.112084793 TNCe HNE2 BS00021684_51 5A 14174853 4.79E-04 0.121932085 RDW CKAV BS00050709_51 5B 3849523 8.26E-04 0.112745911 RDW CKE1 BS00078203_51 5B 1747881 9.92E-04 0.085304611 RDW LNAV wsnp_Ex_c12431_19823475 5B 4134720 7.62E-04 0.089308498 RDW LNAV GENE-3101_854 5B 5115851 3.78E-04 0.125945167 RDW LNE1 BS00041704_51 5B 5115851 1.93E-04 0.137380324 RDW LNE1 Excalibur_c2433_324 5B 5115851 6.60E-04 0.116520959 RDW LNE1 GENE-3101_854 5B 5115851 2.17E-11 0.447959506 RDW LNE1 IAAV4074 5B 5115851 1.81E-04 0.138508447 RDW LNE1 Kukri_c57830_63 5B 5115851 1.66E-04 0.139939258 RDW LNE1 wsnp_Ex_c3817_6937184 5B 5115851 1.61E-04 0.140492154 RDW LNE1 RAC875_c25756_279 5B 5174758 8.61E-04 0.112060401 RDW LNE1 Excalibur_c97559_331 5B 5783136 2.65E-04 0.131995999 RDW LNE1 Excalibur_rep_c110067_199 5B 5783136 4.33E-04 0.123611808 RDW HNE2 Tdurum_contig10268_1000 5B 10064319 7.08E-04 0.115338796 RNC LNAV BobWhite_c4852_323 5B 4037830 3.65E-04 0.100647564 RNC LNAV RAC875_rep_c81986_877 5B 4056500 5.88E-04 0.093278981 RNC LNAV wsnp_Ex_c18519_27369737 5B 4056500 5.88E-04 0.093278981 RNC LNAV Excalibur_c15838_305 5B 4060041 5.61E-04 0.094015232 RNC LNAV Kukri_c47551_513 5B 4060041 8.12E-04 0.08835242 RNC LNAV wsnp_Ku_c61976_63270478 5B 4060041 5.61E-04 0.094015232 RNC LNAV wsnp_Ex_c12431_19823475 5B 4134720 6.98E-05 0.126848437

RNC LNAV BS00065390_51 5B 4606616 5.89E-04 0.118427741 RNC LNAV GENE-3101_854 5B 5115851 1.93E-04 0.137345344 RNC LNE1 Excalibur_c15838_305 5B 4060041 7.69E-04 0.089179636 RNC LNE1 Kukri_c47551_513 5B 4060041 6.59E-04 0.091536279 RNC LNE1 wsnp_Ku_c61976_63270478 5B 4060041 7.69E-04 0.089179636 RNC LNE1 wsnp_Ex_c12431_19823475 5B 4134720 4.24E-04 0.098317499 RNC LNE1 BS00041704_51 5B 5115851 4.56E-04 0.122761146 RNC LNE1 GENE-3101_854 5B 5115851 1.01E-10 0.41461532 RNC HNE2 BS00050709_51 5B 3849523 6.19E-04 0.117600297 RNCe LNAV RAC875_c51548_403 5B 4056500 2.04E-04 0.136478447 RNCe LNE1 RAC875_c51548_403 5B 4056500 4.15E-04 0.124357604 RNCe LNE1 Excalibur_c4623_876 5B 14354836 9.57E-04 0.110291165 RNCe HNAV Excalibur_c97559_331 5B 5783136 9.20E-04 0.110939563 RNCe HNE1 IAAV6876 5B 6836372 1.52E-05 0.186308269 RNUE LNAV GENE-3101_854 5B 5115851 1.09E-04 0.14718097 RNUE LNE1 BS00041704_51 5B 5115851 4.78E-04 0.121964459 RNUE LNE1 Ex_c66350_301 5B 5115851 7.02E-04 0.11548471 RNUE LNE1 Excalibur_c2433_324 5B 5115851 1.03E-04 0.148172556 RNUE LNE1 GENE-3101_854 5B 5115851 2.56E-13 0.548469486 RNUE LNE1 IAAV4074 5B 5115851 5.00E-05 0.160773417 RNUE LNE1 Kukri_c57830_63 5B 5115851 2.19E-04 0.135247067 RNUE LNE1 wsnp_Ex_c3817_6937184 5B 5115851 4.71E-05 0.161816595 RNUE LNE1 RAC875_c25756_279 5B 5174758 8.22E-04 0.11282837 RNUE LNE1 Excalibur_c97559_331 5B 5783136 2.40E-04 0.133646493 RNUE LNE1 Excalibur_rep_c110067_199 5B 5783136 2.79E-04 0.131113647 RNUE HNE2 wsnp_Ex_rep_c75281_72691771 5B 5115851 1.69E-04 0.139633101 RSDW LNAV BS00041704_51 5B 5115851 5.70E-04 0.118999143 RSDW LNAV GENE-3101_854 5B 5115851 2.06E-10 0.399558434 RSDW LNE1 BS00028183_51 5B 5103619 3.34E-04 0.128048004 RSDW LNE1 BS00041704_51 5B 5115851 8.66E-06 0.191850837 RSDW LNE1 GENE-3101_854 5B 5115851 5.03E-17 0.761865926 RSDW LNE1 Kukri_c57830_63 5B 5115851 2.21E-05 0.175114044 RSDW LNE1 Excalibur_c97559_331 5B 5783136 4.61E-07 0.245749757 RSNC LNAV Kukri_rep_c101776_81 5B 2766029 5.43E-04 0.120767572 RSNC LNAV BobWhite_c7400_194 5B 2834915 7.61E-04 0.115043512 RSNC LNAV wsnp_Ku_c35090_44349517 5B 2962384 2.65E-04 0.133008803 RSNC LNAV wsnp_Ku_c11988_19476255 5B 4056500 3.96E-04 0.126133195 RSNC LNAV BobWhite_c4383_143 5B 4189442 4.36E-04 0.124512738 RSNC LNAV BS00065390_51 5B 4606616 1.66E-05 0.181742994 RSNC LNAV RAC875_c33387_1102 5B 5824017 2.23E-04 0.136003566 RSNC LNAV Excalibur_c44034_1785 5B 6836372 3.21E-04 0.129721032 RSNC LNAV BobWhite_c6633_179 5B 7194961 5.38E-04 0.120915071 RSNC LNAV BS00067744_51 5B 10064319 8.41E-04 0.113351075 RSNC LNE1 Kukri_rep_c101776_81 5B 2766029 2.27E-07 0.270442463 RSNC LNE1 BobWhite_c7400_194 5B 2834915 2.33E-07 0.269958812 RSNC LNE1 wsnp_Ku_c35090_44349517 5B 2962384 1.60E-07 0.277512525 RSNC LNE1 wsnp_Ku_c11988_19476255 5B 4056500 2.33E-07 0.269999503 RSNC LNE1 BobWhite_c4383_143 5B 4189442 1.60E-07 0.277486003 RSNC LNE1 BS00065390_51 5B 4606616 1.03E-07 0.286357051 RSNC LNE1 RAC875_c33387_1102 5B 5824017 2.32E-07 0.270080517 RSNC LNE1 Excalibur_c44034_1785 5B 6836372 2.04E-07 0.27260849

RSNC LNE1 RAC875_c38382_625 5B 6919098 1.42E-04 0.148626541 RSNC LNE1 BobWhite_c6633_179 5B 7194961 1.11E-07 0.284730752 RSNC LNE1 BS00087696_51 5B 9343599 1.91E-04 0.143299474 RSNC LNE1 Excalibur_c56310_57 5B 9343599 2.67E-04 0.137332998 RSNC LNE1 BS00067744_51 5B 10064319 7.32E-05 0.160568413 RSNC LNE1 RAC875_rep_c109097_771 5B 12573478 7.04E-04 0.120179022 SDW LNE2 Kukri_c54078_114 5B 8297124 4.54E-04 0.097276633 SDW LNE2 wsnp_Ku_c3102_5810751 5B 8297124 4.57E-04 0.097178753 SNUE LNE2 Kukri_c54078_114 5B 8297124 5.63E-04 0.094703322 SNUE LNE2 wsnp_Ku_c3102_5810751 5B 8297124 4.66E-04 0.097630514 TDW LNE2 Kukri_c54078_114 5B 8297124 2.78E-04 0.104886248 TDW LNE2 wsnp_Ku_c3102_5810751 5B 8297124 1.95E-04 0.110454546 TNCe HNE1 IAAV6876 5B 6836372 1.81E-04 0.144308254 TNUE LNE2 wsnp_Ku_c3102_5810751 5B 8297124 5.54E-04 0.094938329 RNUE LNE1 BS00023151_51 5D 20732863 3.41E-04 0.127680067 RNUE HNAV wsnp_Ex_c23618_32855041 5D 19080122 2.48E-04 0.134146638 RNUE HNAV BS00023151_51 5D 20732863 8.82E-04 0.112553034 RNUE HNE2 wsnp_Ex_c23618_32855041 5D 19080122 2.41E-04 0.133618319 RSDW LNAV BS00023151_51 5D 20732863 9.80E-04 0.109895952 RSDW LNE1 BS00021727_51 5D 20732863 7.37E-05 0.154003139 RSDW LNE1 BS00023151_51 5D 20732863 3.05E-04 0.129566097 RSDW HNE1 IAAV1320 5D 19597675 4.69E-04 0.122289071 RSNC LNAV RAC875_c26265_117 5D 6749211 7.86E-04 0.114483184 RSNC LNAV RAC875_c26265_146 5D 6913161 7.86E-04 0.114483184 RSNC LNE1 RAC875_c26265_117 5D 6749211 6.01E-05 0.164150433 RSNC LNE1 RAC875_c26265_146 5D 6913161 6.01E-05 0.164150433 RDW LNAV Tdurum_contig30273_182 6A 7423762 4.81E-04 0.121850121 RDW LNE1 Kukri_rep_c104648_106 6A 5491248 1.40E-04 0.142868672 RDW LNE1 Excalibur_c8399_398 6A 5850322 5.42E-05 0.159361238 RDW LNE1 Excalibur_c8399_516 6A 5850322 5.42E-05 0.159361238 RDW LNE1 wsnp_Ex_c15378_23639387 6A 6369815 1.30E-05 0.18459283 RDW LNE1 RAC875_c27962_61 6A 6927543 4.59E-06 0.203324979 RDW LNE1 BS00021747_51 6A 7123703 2.70E-04 0.131643887 RDW LNE1 Kukri_c22149_276 6A 7123703 9.32E-05 0.149922828 RDW LNE1 RAC875_c28637_1004 6A 7123703 4.01E-04 0.124929082 RDW LNE1 RAC875_rep_c73850_589 6A 7123703 1.00E-05 0.189205629 RDW LNE1 Tdurum_contig83190_441 6A 7123703 2.70E-04 0.131643887 RDW LNE1 tplb0052b07_577 6A 7123703 2.83E-04 0.130862697 RDW LNE1 wsnp_Ex_c12141_19415226 6A 7123703 6.58E-05 0.15598979 RDW LNE1 wsnp_Ex_c14192_22135363 6A 7123703 2.70E-04 0.131643887 RDW LNE1 wsnp_Ex_rep_c66433_64661643 6A 7123703 2.70E-04 0.131643887 RDW LNE1 Excalibur_rep_c82397_137 6A 7172743 1.04E-04 0.147976414 RDW LNE1 Tdurum_contig55124_310 6A 7172743 5.96E-05 0.157711656 RDW LNE1 IACX6453 6A 7423762 8.90E-04 0.111505481 RDW LNE1 TA004558-1018 6A 7423762 3.26E-04 0.128456385 RDW LNE1 Tdurum_contig30273_182 6A 7423762 2.76E-11 0.442735632 RDW HNE2 BobWhite_c26503_61 6A 9904030 1.73E-04 0.13930291 RDW HNE2 Tdurum_contig54311_256 6A 9943511 3.75E-04 0.126084052 RNC CKE2 Ex_c8890_2497 6A 9904030 9.84E-04 0.085414474 RNC LNAV Tdurum_contig30273_182 6A 7423762 3.52E-04 0.127134706 RNC LNE1 Kukri_rep_c104648_106 6A 5491248 6.99E-04 0.115556712

RNC LNE1 Excalibur_c8399_398 6A 5850322 1.71E-04 0.139418842 RNC LNE1 Excalibur_c8399_516 6A 5850322 1.71E-04 0.139418842 RNC LNE1 wsnp_Ex_c15378_23639387 6A 6369815 4.22E-04 0.124071774 RNC LNE1 RAC875_c27962_61 6A 6927543 5.46E-06 0.20018461 RNC LNE1 BS00021747_51 6A 7123703 8.54E-04 0.1121908 RNC LNE1 Kukri_c22149_276 6A 7123703 6.43E-04 0.11694469 RNC LNE1 RAC875_c28637_1004 6A 7123703 6.98E-04 0.115577143 RNC LNE1 RAC875_rep_c73850_589 6A 7123703 5.19E-05 0.160133882 RNC LNE1 Tdurum_contig83190_441 6A 7123703 8.54E-04 0.1121908 RNC LNE1 tplb0052b07_577 6A 7123703 7.61E-04 0.114117245 RNC LNE1 wsnp_Ex_c12141_19415226 6A 7123703 3.08E-04 0.12941924 RNC LNE1 wsnp_Ex_c14192_22135363 6A 7123703 8.54E-04 0.1121908 RNC LNE1 wsnp_Ex_rep_c66433_64661643 6A 7123703 8.54E-04 0.1121908 RNC LNE1 Excalibur_rep_c82397_137 6A 7172743 7.01E-04 0.115513454 RNC LNE1 Tdurum_contig55124_310 6A 7172743 1.18E-04 0.145866153 RNC LNE1 Tdurum_contig30273_182 6A 7423762 1.36E-10 0.408381855 RNCe CKAV wsnp_Ku_c27273_37219950 6A 7907514 9.94E-04 0.085264092 RNCe CKAV wsnp_Ra_rep_c100410_86374467 6A 7907514 9.94E-04 0.085264092 RNCe LNE1 Kukri_c52953_562 6A 2552580 2.24E-04 0.134815852 RNCe HNE2 Tdurum_contig78006_158 6A 8009750 7.99E-04 0.113301147 RNUE LNAV Tdurum_contig30273_182 6A 7423762 1.60E-04 0.14063318 RNUE LNE1 Kukri_rep_c104648_106 6A 5491248 2.52E-05 0.172829298 RNUE LNE1 Excalibur_c8399_398 6A 5850322 8.82E-05 0.150892241 RNUE LNE1 Excalibur_c8399_516 6A 5850322 8.82E-05 0.150892241 RNUE LNE1 wsnp_Ex_c15378_23639387 6A 6369815 1.54E-05 0.18155693 RNUE LNE1 RAC875_c27962_61 6A 6927543 1.72E-06 0.221310353 RNUE LNE1 BS00021747_51 6A 7123703 6.59E-05 0.155945971 RNUE LNE1 CAP7_c2381_149 6A 7123703 1.03E-04 0.148265959 RNUE LNE1 Kukri_c22149_276 6A 7123703 2.75E-05 0.171301738 RNUE LNE1 RAC875_c28637_1004 6A 7123703 1.88E-04 0.137859528 RNUE LNE1 RAC875_rep_c73850_589 6A 7123703 6.95E-06 0.19582608 RNUE LNE1 Tdurum_contig16290_156 6A 7123703 3.22E-04 0.128644884 RNUE LNE1 Tdurum_contig83190_441 6A 7123703 6.59E-05 0.155945971 RNUE LNE1 tplb0052b07_577 6A 7123703 2.41E-04 0.133609518 RNUE LNE1 wsnp_Ex_c12141_19415226 6A 7123703 4.16E-05 0.164011626 RNUE LNE1 wsnp_Ex_c14192_22135363 6A 7123703 6.59E-05 0.155945971 RNUE LNE1 wsnp_Ex_rep_c66433_64661643 6A 7123703 6.59E-05 0.155945971 RNUE LNE1 Excalibur_rep_c82397_137 6A 7172743 3.11E-05 0.169102893 RNUE LNE1 Tdurum_contig55124_310 6A 7172743 3.07E-05 0.169330746 RNUE LNE1 IAAV583 6A 7423762 5.42E-04 0.119828122 RNUE LNE1 IACX6453 6A 7423762 3.56E-04 0.126928144 RNUE LNE1 Kukri_c16463_584 6A 7423762 7.49E-04 0.114400542 RNUE LNE1 Kukri_c7794_1247 6A 7423762 7.49E-04 0.114400542 RNUE LNE1 RFL_Contig2605_672 6A 7423762 5.42E-04 0.119828122 RNUE LNE1 TA004558-1018 6A 7423762 1.32E-04 0.143951461 RNUE LNE1 Tdurum_contig30273_182 6A 7423762 2.76E-13 0.546683709 RNUE HNAV BobWhite_c26503_61 6A 9904030 1.39E-04 0.144227264 RNUE HNAV Tdurum_contig54311_256 6A 9943511 1.30E-04 0.145298863 RNUE HNE2 BobWhite_c26503_61 6A 9904030 2.85E-05 0.170669025 RNUE HNE2 Tdurum_contig54311_256 6A 9943511 7.69E-05 0.15325663 RNUE HNE2 Excalibur_c51068_220 6A 13685108 3.92E-04 0.12533368

RSDW LNAV Kukri_rep_c104648_106 6A 5491248 5.10E-05 0.160427924 RSDW LNAV Excalibur_c8399_398 6A 5850322 4.56E-04 0.122764789 RSDW LNAV Excalibur_c8399_516 6A 5850322 4.56E-04 0.122764789 RSDW LNAV wsnp_Ex_c15378_23639387 6A 6369815 6.50E-05 0.156185144 RSDW LNAV RAC875_c27962_61 6A 6927543 1.13E-04 0.146596781 RSDW LNAV RAC875_rep_c73850_589 6A 7123703 6.66E-04 0.116356478 RSDW LNAV BS00046964_51 6A 7361423 3.38E-04 0.127851124 RSDW LNAV Tdurum_contig30273_182 6A 7423762 1.54E-10 0.405661742 RSDW LNE1 Kukri_rep_c104648_106 6A 5491248 5.29E-05 0.159783681 RSDW LNE1 Excalibur_c8399_344 6A 5850322 8.27E-04 0.112736204 RSDW LNE1 Excalibur_c8399_398 6A 5850322 2.70E-06 0.212989081 RSDW LNE1 Excalibur_c8399_516 6A 5850322 2.70E-06 0.212989081 RSDW LNE1 wsnp_Ex_c15378_23639387 6A 6369815 6.79E-06 0.196246949 RSDW LNE1 RAC875_c27962_61 6A 6927543 1.43E-05 0.182852586 RSDW LNE1 RAC875_c28637_1004 6A 7123703 2.70E-05 0.171634126 RSDW LNE1 RAC875_rep_c73850_589 6A 7123703 2.62E-05 0.172148307 RSDW LNE1 tplb0052b07_577 6A 7123703 3.24E-04 0.128547801 RSDW LNE1 wsnp_Ex_c12141_19415226 6A 7123703 1.43E-06 0.224719865 RSDW LNE1 BS00021999_51 6A 7172743 6.22E-04 0.11750727 RSDW LNE1 RAC875_c4632_1681 6A 7172743 6.22E-04 0.11750727 RSDW LNE1 Tdurum_contig55124_310 6A 7172743 1.52E-04 0.141526693 RSDW LNE1 Excalibur_c30324_564 6A 7289525 5.88E-04 0.118450487 RSDW LNE1 BS00046964_51 6A 7361423 1.50E-04 0.141728035 RSDW LNE1 IACX6453 6A 7423762 4.00E-04 0.124951086 RSDW LNE1 Kukri_c62705_73 6A 7423762 4.70E-04 0.122233566 RSDW LNE1 Tdurum_contig30273_182 6A 7423762 4.73E-17 0.763480471 RSDW LNE1 wsnp_Ex_c3913_7100986 6A 7423762 6.19E-04 0.117603141 RSDW LNE1 BS00041481_51 6A 7742523 3.83E-04 0.125718524 RSNC LNAV Excalibur_c35324_183 6A 4511277 5.68E-05 0.159829717 RSNC LNE1 D_GBUVHFX02I5C26_339 6A 4511277 3.10E-04 0.134624 RSNC LNE1 Excalibur_c35324_183 6A 4511277 5.53E-08 0.298929124 SDW CKE2 wsnp_Ku_c1765_3452586 6A 14086572 6.09E-04 0.092744225 SDW LNAV wsnp_Ku_c1765_3452586 6A 14086572 1.39E-04 0.115795761 SDW LNE1 wsnp_Ku_c1765_3452586 6A 14086572 6.95E-04 0.090715054 SNC LNAV wsnp_Ku_c1765_3452586 6A 14086572 8.31E-05 0.125026447 TDW CKE2 wsnp_Ku_c1765_3452586 6A 14086572 9.30E-04 0.086274429 TDW LNAV wsnp_Ku_c1765_3452586 6A 14086572 5.57E-04 0.094123941 TNC LNAV wsnp_Ku_c1765_3452586 6A 14086572 2.15E-04 0.113404124 TNCe HNE2 Tdurum_contig12045_246 6A 1345279 5.06E-04 0.120990627 RDW LNAV Excalibur_c100270_78 6B 3668872 2.77E-05 0.171155325 RDW LNAV BS00060838_51 6B 6408376 4.72E-04 0.122162524 RDW LNAV Excalibur_c16961_85 6B 6408376 5.74E-04 0.118864271 RDW LNAV BS00049942_51 6B 6636180 5.83E-04 0.118596487 RDW LNE1 BS00033641_51 6B 2842278 3.81E-07 0.249330019 RDW LNE1 Excalibur_c100270_78 6B 3668872 2.22E-08 0.304127685 RDW LNE1 RAC875_c31280_122 6B 4275276 4.48E-05 0.162689696 RDW LNE1 IAAV7556 6B 4802036 6.43E-04 0.116944469 RDW LNE1 wsnp_CAP7_c399_215824 6B 4802036 6.43E-04 0.116944469 RDW LNE1 BS00060838_51 6B 6408376 1.97E-11 0.450079909 RDW LNE1 BS00076093_51 6B 6408376 4.80E-04 0.121897242 RDW LNE1 Excalibur_c16961_85 6B 6408376 2.77E-11 0.442637705

RDW LNE1 BS00049942_51 6B 6636180 1.75E-11 0.452716942 RDW LNE1 Kukri_c50603_164 6B 6636180 8.90E-04 0.111500367 RDW HNE2 Excalibur_rep_c69865_157 6B 11899094 1.95E-05 0.17737488 RNC LNAV Excalibur_c100270_78 6B 3668872 1.65E-05 0.180380779 RNC LNAV BS00060838_51 6B 6408376 3.55E-04 0.127004966 RNC LNAV Excalibur_c16961_85 6B 6408376 3.44E-04 0.127505585 RNC LNAV BS00049942_51 6B 6636180 3.53E-04 0.127108606 RNC LNE1 BS00033641_51 6B 2842278 1.78E-06 0.22067797 RNC LNE1 Excalibur_c100270_78 6B 3668872 2.99E-08 0.298212135 RNC LNE1 RAC875_c31280_122 6B 4275276 8.14E-05 0.152279979 RNC LNE1 BS00060838_51 6B 6408376 1.26E-10 0.40995091 RNC LNE1 Excalibur_c16961_85 6B 6408376 1.37E-10 0.40824359 RNC LNE1 BS00049942_51 6B 6636180 1.23E-10 0.410423199 RNCe LNAV Tdurum_contig28405_288 6B 5707395 9.33E-04 0.110713097 RNCe LNAV wsnp_Ex_c9948_16379867 6B 6456982 3.34E-04 0.128050975 RNCe LNE1 wsnp_Ex_c9948_16379867 6B 6456982 2.97E-04 0.130014647 RNCe LNE1 wsnp_Ex_c3940_7144946 6B 6956218 9.89E-04 0.109738638 RNCe HNAV Kukri_c58961_76 6B 8300495 3.73E-04 0.126177004 RNCe HNE1 Kukri_c58961_76 6B 8300495 7.00E-09 0.335721708 RNCe HNE2 Excalibur_c6566_745 6B 11367064 9.78E-04 0.109922607 RNUE LNAV BS00033641_51 6B 2842278 7.68E-04 0.113963864 RNUE LNAV Excalibur_c100270_78 6B 3668872 5.43E-06 0.200262779 RNUE LNAV BS00060838_51 6B 6408376 1.28E-04 0.144405135 RNUE LNAV Excalibur_c16961_85 6B 6408376 1.42E-04 0.142618131 RNUE LNAV BS00049942_51 6B 6636180 1.59E-04 0.140714062 RNUE LNE1 wsnp_Ex_c7191_12352173 6B 2110553 4.77E-04 0.12199671 RNUE LNE1 BS00033641_51 6B 2842278 3.08E-08 0.297679877 RNUE LNE1 Excalibur_c100270_78 6B 3668872 2.01E-09 0.352263789 RNUE LNE1 RAC875_c31280_122 6B 4275276 1.32E-05 0.184332519 RNUE LNE1 IAAV7556 6B 4802036 3.38E-04 0.127823813 RNUE LNE1 wsnp_CAP7_c399_215824 6B 4802036 3.38E-04 0.127823813 RNUE LNE1 Kukri_c38732_225 6B 5915874 4.93E-04 0.12142129 RNUE LNE1 BS00045761_51 6B 6408376 5.43E-04 0.119794191 RNUE LNE1 BS00047254_51 6B 6408376 9.89E-04 0.109734231 RNUE LNE1 BS00060838_51 6B 6408376 1.55E-13 0.56018536 RNUE LNE1 BS00076093_51 6B 6408376 6.48E-05 0.156252962 RNUE LNE1 Excalibur_c16961_85 6B 6408376 2.76E-13 0.546735221 RNUE LNE1 Kukri_c25377_240 6B 6408376 6.90E-04 0.115781489 RNUE LNE1 BS00049942_51 6B 6636180 1.40E-13 0.562620599 RNUE LNE1 Kukri_c50603_164 6B 6636180 2.18E-04 0.135320232 RNUE LNE1 BS00106588_51 6B 6724022 2.93E-04 0.130234553 RNUE HNAV Ra_c5942_955 6B 7190171 5.92E-05 0.159122506 RNUE HNAV Excalibur_c11769_2154 6B 11367064 3.62E-04 0.101568725 RNUE HNAV Excalibur_c32219_491 6B 11367064 3.16E-04 0.103739285 RNUE HNAV Excalibur_rep_c69865_157 6B 11899094 6.17E-05 0.158375253 RNUE HNE2 Ra_c5942_955 6B 7190171 3.53E-05 0.16688083 RNUE HNE2 Excalibur_rep_c69865_157 6B 11899094 8.10E-06 0.193056865 RSDW LNAV BS00033641_51 6B 2842278 1.66E-06 0.221880197 RSDW LNAV Excalibur_c100270_78 6B 3668872 1.49E-08 0.311929258 RSDW LNAV RAC875_c31280_122 6B 4275276 1.26E-04 0.144713097 RSDW LNAV IAAV7556 6B 4802036 1.61E-04 0.140510934

RSDW LNAV wsnp_CAP7_c399_215824 6B 4802036 1.61E-04 0.140510934 RSDW LNAV BS00045761_51 6B 6408376 7.51E-04 0.114344898 RSDW LNAV BS00060838_51 6B 6408376 2.48E-10 0.395654705 RSDW LNAV Excalibur_c16961_85 6B 6408376 2.30E-10 0.397215217 RSDW LNAV BS00049942_51 6B 6636180 2.48E-10 0.395648233 RSDW LNE1 wsnp_Ex_c7191_12352173 6B 2110553 2.29E-05 0.174492943 RSDW LNE1 BS00033641_51 6B 2842278 1.27E-10 0.409743761 RSDW LNE1 Excalibur_c100270_78 6B 3668872 3.63E-08 0.294458333 RSDW LNE1 RAC875_c31280_122 6B 4275276 1.05E-06 0.230371075 RSDW LNE1 BS00074183_51 6B 4696333 9.68E-05 0.149269864 RSDW LNE1 IAAV7556 6B 4802036 1.05E-06 0.23038934 RSDW LNE1 wsnp_CAP7_c399_215824 6B 4802036 1.05E-06 0.23038934 RSDW LNE1 BS00087190_51 6B 5698026 5.12E-05 0.160348658 RSDW LNE1 Ex_c102862_798 6B 5698026 5.78E-04 0.118756204 RSDW LNE1 Ra_c10469_616 6B 6328439 6.79E-04 0.116050947 RSDW LNE1 BS00021686_51 6B 6408376 1.35E-04 0.143562446 RSDW LNE1 BS00022226_51 6B 6408376 1.35E-04 0.143562446 RSDW LNE1 BS00045761_51 6B 6408376 2.80E-05 0.170969678 RSDW LNE1 BS00060838_51 6B 6408376 5.72E-17 0.758463826 RSDW LNE1 BS00076093_51 6B 6408376 3.99E-04 0.12499571 RSDW LNE1 BobWhite_c17750_568 6B 6408376 1.35E-04 0.143562446 RSDW LNE1 Excalibur_c16961_85 6B 6408376 5.30E-17 0.760487113 RSDW LNE1 IAAV8065 6B 6482163 8.63E-05 0.151274861 RSDW LNE1 BS00049942_51 6B 6636180 5.72E-17 0.758456251 RSDW LNE1 Tdurum_contig13698_141 6B 6655798 3.86E-04 0.125595635 RSDW LNE1 RAC875_rep_c71463_98 6B 10550132 4.69E-04 0.122290764 RSNC LNAV Excalibur_c100270_78 6B 3668872 2.23E-05 0.176381001 RSNC LNAV RAC875_c29042_1124 6B 4802036 7.46E-04 0.115366514 RSNC LNAV wsnp_Ra_c18735_27835674 6B 5819541 7.93E-04 0.11434258 RSNC LNAV Excalibur_c22998_621 6B 6724022 6.11E-04 0.118744135 RSNC LNAV wsnp_Ex_c13896_21759905 6B 6956218 4.00E-04 0.125962755 RSNC LNAV Kukri_c4834_1883 6B 7176409 5.03E-04 0.122072876 RSNC LNAV BobWhite_c28409_271 6B 7341845 4.47E-04 0.124090512 RSNC LNAV wsnp_Ku_c4910_8793327 6B 9913569 7.88E-04 0.114453837 RSNC LNAV Excalibur_c27139_516 6B 11133111 6.19E-04 0.118527353 RSNC LNAV BobWhite_c13202_399 6B 12208592 1.92E-04 0.138628364 RSNC LNE1 Excalibur_c100270_78 6B 3668872 5.81E-04 0.123555117 RSNC LNE1 RAC875_c29042_1124 6B 4802036 2.15E-07 0.27161021 RSNC LNE1 RAC875_c25672_473 6B 5819541 3.43E-04 0.132842136 RSNC LNE1 wsnp_Ra_c18735_27835674 6B 5819541 2.30E-07 0.270199584 RSNC LNE1 Excalibur_c22998_621 6B 6724022 1.77E-07 0.275391819 RSNC LNE1 wsnp_Ex_c13896_21759905 6B 6956218 2.30E-07 0.270250739 RSNC LNE1 Kukri_c4834_1883 6B 7176409 2.32E-07 0.270033993 RSNC LNE1 BobWhite_c28409_271 6B 7341845 1.70E-07 0.2762655 RSNC LNE1 wsnp_Ku_c4910_8793327 6B 9913569 2.33E-07 0.269979925 RSNC LNE1 Excalibur_c27139_516 6B 11133111 2.09E-07 0.272143952 RSNC LNE1 BobWhite_c13202_399 6B 12208592 2.32E-07 0.270046278 SNC LNE2 tplb0060j17_1061 6B 3668872 2.64E-05 0.173392297 SNCe LNAV tplb0060j17_1061 6B 3668872 3.85E-08 0.295800156 SNCe LNE2 tplb0060j17_1061 6B 3668872 2.01E-14 0.615040965 SNUE LNE2 BS00066799_51 6B 5819541 4.77E-04 0.097269899

RSNC LNE1 BS00098482_51 7A 18930326 6.10E-04 0.122687959 RSNC LNE1 BS00080311_51 7A 21636313 2.19E-07 0.271232503 RSNC HNAV BS00023003_51 7A 22434214 2.15E-04 0.135567042 SDW LNE1 BS00035033_51 7A 11667480 4.89E-04 0.121556441 SNCe LNAV Tdurum_contig17020_550 7A 12679927 8.43E-04 0.113294491 SNCe LNE2 RAC875_c81356_688 7A 12679927 1.54E-05 0.183060708 SNCe LNE2 Tdurum_contig17020_550 7A 12679927 1.17E-04 0.147143521 TDW CKE1 wsnp_BE445506A_Ta_2_2 7A 21958811 7.84E-04 0.113629561 TNC LNE2 BS00023128_51 7A 15053880 9.01E-04 0.112183081 TNCe LNE2 RAC875_c81356_688 7A 12679927 7.57E-04 0.115132204 TNCe HNAV Kukri_c33620_129 7A 21266138 1.70E-04 0.139563376 TNCe HNE1 Kukri_c33620_129 7A 21266138 5.15E-06 0.20989613 TNUE CKE1 wsnp_BE445506A_Ta_2_2 7A 21958811 9.51E-04 0.111278591 TNUE LNAV Excalibur_c11047_424 7A 15230283 8.92E-04 0.116073701 RNC LNE2 tplb0039c07_334 7B 8078553 9.00E-04 0.086776312 RNCe LNE1 BS00063208_51 7B 9195819 9.21E-04 0.110923241 RNCe LNE1 wsnp_Ex_c22955_32173776 7B 10118494 1.10E-04 0.147131885 RNCe LNE1 wsnp_BE605194B_Ta_2_1 7B 10279352 8.51E-04 0.112259239 RNCe LNE1 wsnp_BE605194B_Ta_2_7 7B 10279352 8.10E-04 0.113080407 RNCe HNE2 BobWhite_c12256_96 7B 8912833 5.69E-04 0.09379532 RNUE LNE1 Tdurum_contig30677_66 7B 2726792 2.46E-04 0.133262964 RNUE LNE2 Ra_c10804_1595 7B 9252042 4.31E-04 0.098087901 RSDW CKAV BS00022498_51 7B 6251008 3.73E-04 0.126172232 RSDW CKE1 Excalibur_c25719_238 7B 7166186 6.47E-04 0.091813861 RSDW CKE2 BS00022498_51 7B 6251008 3.25E-04 0.1284898 RSDW HNE2 BS00022498_51 7B 6251008 5.32E-04 0.120145671 RSDW HNE2 Tdurum_contig51087_573 7B 6747328 5.32E-04 0.094814048 RSNC CKAV BS00109317_51 7B 13067678 8.64E-04 0.087395463 RSNC CKE1 Ku_c5789_1180 7B 12081285 9.77E-04 0.086208324 RSNC LNAV Tdurum_contig5352_556 7B 1006070 6.27E-04 0.118326708 RSNC LNAV Excalibur_c3423_1170 7B 2405074 5.54E-04 0.120435267 RSNC LNAV BobWhite_rep_c50229_413 7B 7132765 3.51E-04 0.128210312 RSNC LNAV Kukri_c67810_105 7B 7630646 7.33E-04 0.115666704 RSNC LNAV wsnp_BQ171683B_Ta_2_1 7B 7630959 7.80E-04 0.114609782 RSNC LNAV Tdurum_contig47317_100 7B 11316971 5.31E-04 0.121151901 RSNC LNE1 Tdurum_contig5352_556 7B 1006070 2.33E-07 0.269978396 RSNC LNE1 Excalibur_c3423_1170 7B 2405074 1.90E-07 0.274065126 RSNC LNE1 Excalibur_c573_259 7B 7002204 2.17E-05 0.182883323 RSNC LNE1 BobWhite_rep_c50229_413 7B 7132765 1.86E-07 0.274405899 RSNC LNE1 Kukri_c67810_105 7B 7630646 2.19E-07 0.27115476 RSNC LNE1 wsnp_BQ171683B_Ta_2_1 7B 7630959 2.23E-07 0.270797728 RSNC LNE1 CAP8_c665_242 7B 10118494 2.99E-04 0.135289598 RSNC LNE1 Tdurum_contig47317_100 7B 11316971 1.56E-07 0.277984811 RSNC LNE1 BS00083578_51 7B 13359098 6.80E-05 0.161900593 RSNC LNE1 BS00066920_51 7B 16316091 2.31E-04 0.139848964 SDW CKE1 RAC875_c57326_85 7B 13374090 5.78E-04 0.118736924 SDW CKE2 Ku_c5789_1180 7B 12081285 7.53E-04 0.089486415 SDW CKE2 Excalibur_c90713_226 7B 12977409 7.16E-04 0.115146121 SDW LNAV BS00067599_51 7B 6444351 6.26E-04 0.11740753 SDW HNAV Excalibur_c90713_226 7B 12977409 8.56E-04 0.112156099 SNC CKE1 RAC875_c57326_85 7B 13374090 2.63E-04 0.133163147

SNC CKE2 Ku_c5789_1180 7B 12081285 7.75E-04 0.090482554 SNC LNAV BS00067599_51 7B 6444351 3.03E-04 0.130750547 SNCe LNE2 BS00111247_51 7B 16316091 1.38E-04 0.144333644 SNCe LNE2 BS00052146_51 7B 16739946 9.03E-04 0.112151755 SNUE CKE2 Ku_c5789_1180 7B 12081285 9.53E-04 0.087273001 SNUE CKE2 Excalibur_c90713_226 7B 12977409 1.84E-04 0.140483097 SNUE CKE2 BS00109317_51 7B 13067678 8.28E-04 0.089448416 SNUE HNAV Excalibur_c90713_226 7B 12977409 4.17E-04 0.124251552 TDW HNAV Excalibur_c90713_226 7B 12977409 4.78E-04 0.121943192 TNC CKE1 RAC875_c57326_85 7B 13374090 3.99E-04 0.126032838 TNC CKE2 Ku_c5789_1180 7B 12081285 7.54E-04 0.090908236 TNC LNAV BS00067599_51 7B 6444351 6.56E-04 0.121454532 TNCe LNAV BS00052146_51 7B 16739946 6.10E-04 0.12267095 TNCe LNE1 Excalibur_c17078_400 7B 7338602 2.40E-04 0.139162116 TNUE CKE2 Excalibur_c90713_226 7B 12977409 4.63E-04 0.125501946 RDW HNE2 Excalibur_c100965_80 7D 18452173 5.09E-04 0.120889943 RNC HNAV Kukri_c80931_147 7D 2633251 8.33E-04 0.112618533 RNC HNE2 BobWhite_c12316_383 7D 2633251 3.15E-04 0.129008479 RNC HNE2 Excalibur_c88899_626 7D 2633251 1.30E-04 0.144163577 RNC HNE2 Kukri_c80931_147 7D 2633251 1.65E-04 0.1401172 RNUE HNE2 Excalibur_c100965_80 7D 18452173 4.88E-04 0.121604465 RNUE HNE2 D_contig70255_308 7D 19107326 7.53E-04 0.114313118 RNUE HNE2 D_contig22976_123 7D 19320442 7.53E-04 0.114313118 RSNC LNAV D_contig78519_72 7D 2284679 7.56E-04 0.115146395 RSNC LNAV D_contig18045_60 7D 19194017 2.04E-04 0.137516141 RSNC LNE1 D_contig78519_72 7D 2284679 1.51E-07 0.278616028 RSNC LNE1 Ku_c47803_245 7D 14886538 6.49E-04 0.12159293 RSNC LNE1 Kukri_c15768_68 7D 14996708 5.67E-04 0.123969236 RSNC LNE1 D_contig18045_60 7D 19194017 4.50E-04 0.128053403

Genome-wide association analysis for yield and nitrogen efficiency related traits of wheat at seedling stage

ZHANG PengXia1, ZHOU XiuWen1, LIANG Xue2, GUO Ying1, ZHAO Yan1, LI SiShen1, KONG FanMei1

1Shandong Agricultural University/State Key Laboratory of Crop Biology/National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai’an 271018, Shandong;2Caoxian soil fertilizer workstation of Shandong province, Caoxian 274400, Shandong

【】To identify and locate the molecular markers which were stable and significantly correlated to the traits of biomass and N efficiency under different N nutrition levels will help to provide reference for cloning and characterization of the related genes.【】A group of 134 wheat varieties (or lines) were used in a two-years (2013 and 2014) hydroponic experiments, in which three treatments applying normal level N, low level N and high level N were set up. Fourteen traits related to biomass and N efficiency were measured, as the respective average values of each treatment in one year and two years. Genome-wide association analysis using 90K SNP molecular markers was carried out for the tested traits by MLM+K+Q mixed linear model. 【】Compared with normal nitrogen treatments, roots, shoots, and plant nitrogen content and nitrogen accumulation were significantly reduced in low nitrogen treatments, while root biomass and root and plant nitrogen efficiency were significantly increased. In high nitrogen treatments, almost all traits are significantly increased. The heritability of all the tested traits were above 40%. According to genome-wide association analysis on the 9 329 SNPs, a total of 838 molecular marker sites were identified associating with 14 traits significantly (≤0.001). These markers located on 21 chromosomes, among which 435 (51.91%) molecular marker sites were detected in only one environment, 403 and 8 environment stable sites were identified in at least two or three environments, two environmental stable SNP marker sites were identified in at least four environments. The two stable markers (Kukri_c65481_121 and tplb0025f09_1052) were significantly related to total nitrogen use efficiency of plant (TNUE) and root nitrogen use efficiency (RNUE), respectively. Five multi-trait co-location SNP marker sites which simultaneously associated with at least six traits were located on chromosomes 1A, 1B(2), and 2A(2). Furtherly, candidate gene prediction was conducted in the 214 kb genomic region of 5 SNP sites co-located with 6 traits (biomass and N efficiency traits) and 2 SNP sites associated with multiple environments (4 environments). According to the genome annotation and LD attenuation level, a total of 84 candidate genes were determined. Gene function annotations of these genes were performed using the coding protein types of known cloned nitrogen efficiency genes, candidate gene function annotation information and the use of plant comparative genomics resource library protein sequence homology analysis, 3 candidate genes were initially determined. 【】Different N treatments significantly affected the phenotypic traits of biomass, N efficiency and the expression of related QTLs at seedling stage of wheat. Most SNPs were detected in only one N environment, but there were some locations with relatively strong environmental stability. There was a significant correlation between biomass and N efficiency related traits, and they might be partly controlled by the same QTL/gene.The functions of related candidate genes related to N efficiency and biomass of wheat selected in this paper needed to be further verified.

wheat; GWAS; biomass; nitrogen efficiency

10.3864/j.issn.0578-1752.2021.21.001

2021-02-07；

2021-04-14

山東省重大科技創(chuàng)新工程項目（2018YFJH0602）

張鵬霞，E-mail：zhangpengxia0824@163.com。通信作者孔凡美，E-mail：fmkong@sdau.edu.cn

（責(zé)任編輯 李莉）