王志鵬,景軍紅,周萌
(1.農(nóng)業(yè)部雞遺傳育種重點(diǎn)試驗(yàn)室,哈爾濱 150030;2.黑龍江省普通高等學(xué)校動(dòng)物遺傳育種與繁殖重點(diǎn)試驗(yàn)室,哈爾濱 150030;3.東北農(nóng)業(yè)大學(xué)動(dòng)物科學(xué)技術(shù)學(xué)院,哈爾濱 150030)
雞全基因組選擇信號(hào)篩選研究進(jìn)展
王志鵬1,2,3,景軍紅1,2,3,周萌1,2,3
(1.農(nóng)業(yè)部雞遺傳育種重點(diǎn)試驗(yàn)室,哈爾濱 150030;2.黑龍江省普通高等學(xué)校動(dòng)物遺傳育種與繁殖重點(diǎn)試驗(yàn)室,哈爾濱 150030;3.東北農(nóng)業(yè)大學(xué)動(dòng)物科學(xué)技術(shù)學(xué)院,哈爾濱 150030)
人工選擇對(duì)家雞馴化及品種形成具有重要作用,基因組上留有選擇痕跡。隨著基因組技術(shù)和選擇信號(hào)檢測(cè)方法完善,在基因組上檢測(cè)選擇信號(hào)成為進(jìn)化生物學(xué)領(lǐng)域研究熱點(diǎn)。文章主要描述選擇信號(hào)定義,總結(jié)檢測(cè)選擇信號(hào)的重要統(tǒng)計(jì)方法,分析雞基因組選擇信號(hào)檢測(cè)結(jié)果,以期為雞全基因組領(lǐng)域研究提供參考。
雞;基因組;選擇信號(hào)
王志鵬,景軍紅,周萌.雞全基因組選擇信號(hào)篩選研究進(jìn)展[J].東北農(nóng)業(yè)大學(xué)學(xué)報(bào),2016,47(10):100-106.
Wang Zhipeng,Jing Junhong,Zhou Meng.Genome-wide scan of selection signatures in chicken[J].Journal of Northeast Agricultural University,2016,47(10):100-106.(in Chinese with English abstract)
雞起源于雉科原雞屬,家雞簡(jiǎn)稱Gallus domes?ticus。研究表明,南亞、東南亞和我國(guó)北方地區(qū)是重要家雞起源地[1]。原雞經(jīng)長(zhǎng)期自然選擇和人工選擇已產(chǎn)生形態(tài)迥異、各具特色的品種,主要包括蛋用型、肉用型、兼用型、觀賞型、藥用型等。雞種選育歷史不同,體型、外貌、羽色及生產(chǎn)性狀方面差異顯著。由于人工或自然選擇干預(yù),生物群體在世代傳遞過程中,某種基因型個(gè)體比例變化,基因
組上會(huì)相應(yīng)留下明顯特征,即選擇信號(hào)。目前,利用高密度SNP標(biāo)記、重測(cè)序數(shù)據(jù)等DNA的多態(tài)信息已在雞基因組中篩選出多個(gè)存在選擇信號(hào)區(qū)域。本文主要描述選擇信號(hào)定義,總結(jié)檢測(cè)選擇信號(hào)的重要統(tǒng)計(jì)方法,分析已報(bào)道的雞基因組選擇信號(hào)檢測(cè)結(jié)果,歸納分析相關(guān)研究進(jìn)展,以期為雞全基因組領(lǐng)域研究提供參考。
中性進(jìn)化理論認(rèn)為,新突變需長(zhǎng)時(shí)間在群體中達(dá)到較高頻率,突變位點(diǎn)周圍的連鎖不平衡程度因重組發(fā)生衰減降解[2]。基因組上絕大多數(shù)未受選擇的位點(diǎn)始終處于隨機(jī)漂變狀態(tài),彼此間連鎖不平衡易衰減。但選擇作用下,群體有利等位基因頻率則在較短時(shí)間內(nèi)達(dá)到較高值,重組作用受一定程度抑制而不能對(duì)長(zhǎng)范圍單倍型實(shí)質(zhì)性降解。選擇作用下的連鎖不平衡造成選擇位點(diǎn)附近中性位點(diǎn)基因頻率增加,形成長(zhǎng)范圍單倍型純合。這種由選擇作用造成部分染色體片段多態(tài)性降低現(xiàn)象稱為選擇性掃除(Selective Sweep)[3]。受選擇作用的有利基因座位周圍中性位點(diǎn)由于連鎖關(guān)系其頻率迅速增加,這種現(xiàn)象稱為“搭車”效應(yīng)(Hitchhik?ing Effect)[4]。選擇性掃除和“搭車”效應(yīng)從不同角度反映選擇作用所致基因組變化?;谶x擇性掃除和“搭車”效應(yīng),篩選基因組選擇信號(hào),成為群體遺傳學(xué)領(lǐng)域研究熱點(diǎn)。
根據(jù)所用基因組信息來源差異,選擇信號(hào)檢測(cè)方法分為基因頻率譜方法、連鎖不平衡方法和基于群體分化方法等,各算法可檢測(cè)選擇事件、試驗(yàn)群體及算法簡(jiǎn)述見表1。
表1 選擇信號(hào)檢測(cè)方法Table 1Approaches for detecting genome-wide selection signatures
2.1 基于等位基因頻率譜檢測(cè)選擇信號(hào)方法
基因頻率譜是指各頻率等位基因占總等位基因數(shù)比例[5]。中性理論認(rèn)為基因組上存在廣泛遺傳多態(tài)位點(diǎn),當(dāng)突變發(fā)生時(shí),突變位點(diǎn)頻率維持在較低水平。當(dāng)基因組上出現(xiàn)有利突變時(shí),自然選擇發(fā)生作用,實(shí)現(xiàn)選擇性掃除或“搭車”效應(yīng)。早期經(jīng)典方法如Tajima's D檢測(cè)、Fay and Li's D檢測(cè)、Fay and Wu's H檢測(cè)等通過檢測(cè)等位基因在基因組上目標(biāo)區(qū)域內(nèi)出現(xiàn)的頻繁程度特征決定該基因是否受到選擇。
2.2 基于連鎖不平衡檢測(cè)選擇信號(hào)方法
研究表明,如群體經(jīng)歷正向選擇,則基因組上有利突變位點(diǎn)頻率很快提升,同時(shí)與該有利突變位點(diǎn)連鎖的周圍位點(diǎn)由于“搭車”效應(yīng),頻率也會(huì)在群體中增加。且由于經(jīng)歷時(shí)間短,位點(diǎn)間連鎖關(guān)系尚未被重組事件破壞,存在較長(zhǎng)LD區(qū)域。該區(qū)域長(zhǎng)度與正向選擇強(qiáng)度正相關(guān)[6]。這種特征為檢測(cè)基因組上是否發(fā)生正向選擇提供有效突破點(diǎn)?;诖耍蜒邪l(fā)多個(gè)檢測(cè)算法,如LRH[6],HS,iHS[7],LDD[8]等。
2.3 基于群體分化檢測(cè)選擇信號(hào)方法
選擇可使群體出現(xiàn)分化。特別是當(dāng)同種不同亞群間不同等位基因同時(shí)受到選擇時(shí),分化現(xiàn)象加速。F統(tǒng)計(jì)量(FST)是反映群體結(jié)構(gòu)變化統(tǒng)計(jì)量。主要基于遺傳多態(tài)性數(shù)據(jù),通過估計(jì)亞種群間與整個(gè)種群平均雜合性差異,刻畫群體結(jié)構(gòu)分化程度。FST受突變、遺傳漂變、近親交配、選擇作用或Wahlund效應(yīng)等因素影響。但在中性進(jìn)化條件下,F(xiàn)ST主要由遺傳漂變和遷移等因素影響,如種群中一個(gè)等位基因由于對(duì)特定環(huán)境適合度較高而經(jīng)歷適應(yīng)性選擇,其頻率升高增大種群分化水平,產(chǎn)生較高FST值。如果不同群體同一位點(diǎn)基因頻率差異顯著大于中性進(jìn)化條件下期望值,則認(rèn)為該位點(diǎn)存在選擇作用。目前,除FST統(tǒng)計(jì)量外,F(xiàn)LK檢測(cè)、hapFLK檢測(cè)等統(tǒng)計(jì)量已應(yīng)用于檢測(cè)群體分化。
上述選擇信號(hào)檢驗(yàn)統(tǒng)計(jì)量不同算法間相關(guān)程度不同。Grossman等認(rèn)為,假如每個(gè)選擇信號(hào)檢測(cè)方法揭示不同信息來源選擇性掃除,那么復(fù)合多個(gè)選擇信號(hào)檢測(cè)方法將有利于提高選擇信號(hào)檢測(cè)效力[9]。目前,已有多個(gè)研究通過復(fù)合多種選擇信號(hào)檢測(cè)方法在基因組范圍內(nèi)篩選出潛在選擇信號(hào),以期提高選擇信號(hào)檢測(cè)準(zhǔn)確性和精確度。Zeng等提出DH檢驗(yàn)即整合Tajima's D檢驗(yàn)和Fay and Wu's H檢驗(yàn)方法[10]。DH檢驗(yàn)可提高選擇檢測(cè)特異性,降低種群歷史等因素敏感度。Zeng等在DH基礎(chǔ)上,整合Ewens-Watterson算法(EW),提出DHEW檢驗(yàn),該算法對(duì)重組率變化不敏感[11]。Grossman等利用貝葉斯因子復(fù)合現(xiàn)有各選擇信號(hào)檢測(cè)方法,將該法定義為CMS[9]。Ma等在考慮各不同信號(hào)檢測(cè)方法相關(guān)性基礎(chǔ)上,提出去相關(guān)復(fù)合統(tǒng)計(jì)量法(DCMS)[12];Utsunomiya等合并統(tǒng)計(jì)量P值,提出meta-SS法[13];Randhawa等考慮統(tǒng)計(jì)量排序信息,提出CSS法[14]。
早期馴化和近現(xiàn)代育種實(shí)踐對(duì)雞種、體型外貌、行為習(xí)慣、生產(chǎn)性能影響顯著,基因組相應(yīng)變化。隨著芯片和重測(cè)序技術(shù)發(fā)展,可在基因組層面上檢測(cè)這種變化,揭示選育、基因與表型間關(guān)系。目前,已利用商用蛋雞、商用肉雞、雙向選擇品系雞、地方雞種等群體的12、60和600 k SNP數(shù)據(jù)和重測(cè)序數(shù)據(jù),在基因組上檢測(cè)選擇信號(hào)或基因。試驗(yàn)利用的群體、數(shù)據(jù)、檢測(cè)方法及檢測(cè)到的選擇信號(hào)均有差異,見表2。結(jié)合結(jié)構(gòu)基因組和功能基因組學(xué)研究結(jié)果對(duì)選擇信號(hào)區(qū)域注釋分析,發(fā)現(xiàn)這些選擇信號(hào)區(qū)域內(nèi)存在一些與外貌性狀、生長(zhǎng)性狀、體脂性狀、繁殖和蛋品質(zhì)性狀、抗病性狀等相關(guān)的重要基因。
3.1 外貌性狀相關(guān)基因
雞的羽色是確定雞品種重要特征。研究發(fā)現(xiàn)位于1號(hào)染色體SOX10(SRY(Sex determining region Y)-box 10)基因影響雞的羽色[27]。Gholami等在3個(gè)商品蛋雞中檢測(cè)發(fā)現(xiàn)SOX10基因受較強(qiáng)選擇作用[25]。雞膚色主要有黃色、白色、黑色等。Rubin等[15],Elferink等[21],Qanbari等[28]和Ma等[12]利用不同群體和不同檢測(cè)算法,均發(fā)現(xiàn)位于24號(hào)染色體上影響雞黃皮膚的BCDO2基因[29]受較強(qiáng)人工選擇。Ma等檢測(cè)到影響黑色素或色素沉積的MC1R(Melanocortin 1 receptor,位于11號(hào)染色體),DCT(Dopachrome tautomerase,位于1號(hào)染色體),TYR(Tyrosinase,位于1號(hào)染色體),OSTM1(Osteope?trosis associated transmembrane protein 1,位于3號(hào)染色體)基因受到選擇[12]。雞冠組織是雞皮膚的重要衍生物,起散熱等作用,根據(jù)形態(tài)差異可分為
單冠、玫瑰冠、豆冠、羽毛冠等。Qanbari等利用FST算法、iHS算法等通過檢測(cè)商業(yè)白殼蛋雞和褐殼蛋雞測(cè)序數(shù)據(jù),發(fā)現(xiàn)SOX5基因(SRY(Sex deter?mining region Y)-box 5,位于1號(hào)染色體)影響雞豆冠尺寸及形態(tài),且該基因在現(xiàn)代雞種中受極強(qiáng)人工選擇。GJD2基因(Gap junction protein delta 2,位于5號(hào)染色體)、SMPD3基因(Sphingomyelin phosphodiesterase 3,位于11號(hào)染色體)分別影響視力[30]和矮小形態(tài)[31],Qanbari等研究發(fā)現(xiàn)這些影響雞外貌特點(diǎn)基因均受較強(qiáng)人工選擇[28]。
表2 雞基因組上選擇信號(hào)篩選研究Table 2Summary of selection signatures surveys in chicken genome
3.2 生長(zhǎng)性狀相關(guān)基因
雞生長(zhǎng)性狀主要指雞體重等性狀?,F(xiàn)已培育出專門化商用雞品種。利用雞種和地方雞種為試驗(yàn)材料,在雞基因組上定位大量影響雞生長(zhǎng)性狀QTLs,并對(duì)多個(gè)重要候選基因展開功能研究。目前,已發(fā)現(xiàn)有很多基因影響雞體重,主要包括位于1號(hào)染色體的IGF1(Insulin-like growth factor 1),位于3號(hào)染色體的CAPN1(Calpain 1)、TGFB2(Transforming growth factor,beta 2),位于5號(hào)染色體的IGF2(Insulin-like growth factor 2),位于8號(hào)染色體LEPR(Leptin receptor gene),位于10號(hào)染色體的IGF-1R(Insulin-like growth factor 1 receptor),位于27號(hào)染色體的IGF2BP1(Insulin-like growth factor 2 mRNA binding protein 1)、IGFBP4(Insulin-like
growth factor binding protein 4)、STAT5B(Signal transducer and activator of transcription 5B),位于28號(hào)染色體的INSR(Insulin receptor)等基因。Qanbari等利用商用雞的重測(cè)序數(shù)據(jù),基于位點(diǎn)的雜合度發(fā)現(xiàn)IGF1、INSR、LEPR等基因受選擇影響[20];Rubin等也利用重測(cè)序數(shù)據(jù)檢測(cè)到IGF1和INSR在更多雞種基因組上留有選擇痕跡[15]。Gholami等利用原雞、多地雞種和商用雞種的600K SNP數(shù)據(jù)檢測(cè)到CAPN1、TGFB2、IGF2、IGF2BP1等基因受人工選擇[23]。Stainton等利用來源于Aviagen公司的9個(gè)肉雞專門化品系的12K SNP數(shù)據(jù)也檢測(cè)到IGF2BP1在基因組上存在選擇痕跡[24]。Gholami等利用原雞和商用雞的600K SNP數(shù)據(jù)檢測(cè)到IGF-1R、STAT5B等基因受較強(qiáng)選擇作用[25]。目前檢測(cè)到影響雞體重的部分QTL或基因受強(qiáng)烈人工選擇,由此推斷雞基因組會(huì)針對(duì)體重性狀所施加的人工選擇做出反應(yīng),并在基因組上留下選擇痕跡。
3.3 體脂性狀相關(guān)基因
隨著肉雞生長(zhǎng)速度和肉產(chǎn)量顯著提高,體脂性狀逐漸成為肉雞育種重點(diǎn)考慮性狀之一。利用QTL定位、基因芯片、全基因組關(guān)聯(lián)分析等技術(shù)平臺(tái)定位到眾多影響體脂性狀基因。通過QTLdb數(shù)據(jù)庫(kù)[34]檢索,截止目前,在雞上已定位380個(gè)與體脂性狀相關(guān)QTLs。利用GWAS平臺(tái)也定位到多個(gè)影響雞體脂性狀的遺傳標(biāo)記和重要基因。通過選擇信號(hào)檢測(cè)研究,發(fā)現(xiàn)多個(gè)通過上述定位方法篩選到的基因,也受較強(qiáng)選擇作用。Zhang等利用東北農(nóng)業(yè)大學(xué)腹脂雙向選擇系,在雞基因組上發(fā)現(xiàn)位于1號(hào)染色體的IGF1(Insulin-like growth factor 1)、TRPC4(Transient receptor potential cation channel, subfamily C,member 4)、RB1(Retinoblastoma 1)、MAOA(Monoamine oxidase A)、MAOB(Monoamine oxidase B)、MYO7A(Myosin VIIA),位于3號(hào)染色體的EHBP1(EH domain binding protein 1),位于4號(hào)染色體的BBS7(Bardet-Biedl syndrome 7)、LRP2BP(LRP2 binding protein),位于7號(hào)染色體的LRP1B(Low-density lipoprotein receptor-related protein 1B),位于10號(hào)染色體的MYO9A(Myosin IXA),位于11號(hào)染色體的ESRP2(Epithelial splic?ing regulatory protein 2)、FTO(Fat mass and obesity associated),位于18號(hào)染色體的PRPSAP1(Phos? phoribosyl pyrophosphate synthetase-associated pro?tein 1)和位于Z染色體的PCSK1(Proprotein conver?tase subtilisin/kexin type 1)基因等與脂肪組織代謝相關(guān)基因受較強(qiáng)選擇[18,19]。Fan等在2個(gè)中國(guó)雞種基因組上也檢測(cè)到ESRP2基因受到選擇[22]。LEPR(Leptin receptor,位于8號(hào)染色體)在食欲與能量消耗等生物學(xué)過程起重要作用。Twito等發(fā)現(xiàn)在LEPT基因上的SNP在蛋雞和肉雞群體間基因頻率差異顯著,與人工選擇相關(guān)[32]。MXD4(MAX di?merisation protein 4,位于4號(hào)染色體)是抑癌基因,GWAS研究發(fā)現(xiàn)該基因與雞腹脂重相關(guān)[33]。Stainton等在9個(gè)肉雞品系基因組上發(fā)現(xiàn)LEPR和MXD4基因受較強(qiáng)選擇作用[24]。Gholami等檢測(cè)到影響腹脂重PRKAB2(Protein kinase,AMP-activated,beta 2 non-catalytic subunit,位于8號(hào)染色體)基因受到選擇[23]。Roux等通過選擇信號(hào)篩選,發(fā)現(xiàn)受選擇作用的PARK2(Parkin RBR E3 ubiquitin protein li?gase,位于3號(hào)染色體)基因是促進(jìn)雞肥胖調(diào)控關(guān)鍵因子,JAG2(Jagged 2,位于5號(hào)染色體)基因是抑制雞肥胖調(diào)控關(guān)鍵因子[26]。
3.4 繁殖與蛋品質(zhì)性狀相關(guān)基因
繁殖性狀是雞重要經(jīng)濟(jì)性狀,產(chǎn)蛋量和蛋品質(zhì)等性狀是蛋用型雞育種重點(diǎn)。通過QTLdb數(shù)據(jù)庫(kù)[34]檢索,截至目前,在雞上已定位491個(gè)與繁殖和蛋品質(zhì)性狀相關(guān)的QTLs。已有研究表明PRL基因(Prolactin,位于2號(hào)染色體)影響雞產(chǎn)蛋量與就巢行為,Li等[17]和Qanbari等[20]發(fā)現(xiàn)該基因受到選擇作用。SPP1(Secreted phosphoprotein 1,位于4號(hào)染色體)與蛋殼質(zhì)量相關(guān)[35],Qanbari等[20]和Ghola?mi等[23]發(fā)現(xiàn)該基因也受到較強(qiáng)選擇作用。CALB1(Calbindin 1,位于2號(hào)染色體)與畸形蛋殼相關(guān);NCOA1(Nuclear receptor coactivator 1,位于3號(hào)染色體),SREBF2(Sterol regulatory element binding transcription factor 2,位于1號(hào)染色體)和RALGA?PA1(Ral GTPase activating protein,alpha subunit 1,位于5號(hào)染色體)分別與開產(chǎn)日齡,就巢性和產(chǎn)蛋量相關(guān)。Qanbari等[20]和Gholami等[23]在雞基因組上檢測(cè)到上述基因受到選擇。
3.5 抗病性狀相關(guān)基因
通過QTLdb數(shù)據(jù)庫(kù)[34]檢索,截止目前,在雞上已經(jīng)定位561個(gè)與抗病性狀相關(guān)QTLs。其中SLC11A1基因(Solute carrier family 11(Proton-cou?
pled divalent metal ion transporter),member 1,位于7號(hào)染色體)可抑制沙門氏桿菌傳染[36-37],Qanbari等在基因組上也檢測(cè)到該基因受較強(qiáng)選擇作用[20]。除上述區(qū)域外,通過檢測(cè)選擇信號(hào)在基因組上也定位到一些與雞疾病發(fā)生相關(guān)其他基因,如Li等在基因組上檢測(cè)到LHX2(LIM homeobox2,位于17號(hào)染色體)和SFRP1(Secreted frizzled-related protein 1,位于22號(hào)染色體)基因受選擇,且這些基因參與WNT信號(hào)通路,與癌癥發(fā)生相關(guān)[17]。
學(xué)者長(zhǎng)期重點(diǎn)針對(duì)雞生長(zhǎng)、體脂、繁殖、蛋品質(zhì)、抗病、飼料報(bào)酬性狀等開展高強(qiáng)度選育。在雞基因組上也遺留大量選擇痕跡。利用候選基因法、QTL定位及全基因組關(guān)聯(lián)等方法檢測(cè)到大量影響上述重要經(jīng)濟(jì)性狀的遺傳標(biāo)記、重要基因和QTL,且發(fā)現(xiàn)部分區(qū)域或基因的確受較強(qiáng)人工選擇作用。說明傳統(tǒng)依賴于表型數(shù)據(jù)選育的人工選擇在雞基因組進(jìn)化上具有重要作用,驗(yàn)證了傳統(tǒng)選擇方法在遺傳基礎(chǔ)上改良重要經(jīng)濟(jì)性狀的作用。隨著基因組測(cè)序技術(shù)快速發(fā)展,高效獲取海量雞基因組數(shù)據(jù),整合選擇信號(hào)分析、全基因組關(guān)聯(lián)分析和生物信息學(xué)分析將是篩選、鑒定影響重要經(jīng)濟(jì)性狀基因策略。由于目前所用選擇信號(hào)檢測(cè)方法在算法設(shè)計(jì)上使用的信息來源不一,檢測(cè)效率存在差異,如果在統(tǒng)計(jì)算法設(shè)計(jì)上充分利用群體各類信息源,完善檢測(cè)方法,檢測(cè)功效將顯著提高??傊?,在基因定位研究中引入選擇信號(hào)檢測(cè)分析結(jié)果,將更有利于篩選影響重要經(jīng)濟(jì)性狀的關(guān)鍵基因。
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Genome-wide scan of selection signatures in chicken
WANG Zhipeng1,2,3,
JING Junhong1,2,3,ZHOU Meng1,2,3(1.Key Laboratory of Chicken Genetics and Breeding,Ministry of Agriculture,Harbin 150030,China;2.Key Laboratory of Animal Genetics,Breeding and Reproduction,Education Department of Heilongjiang province,Harbin 150030,China;3.School of Animal Science and Technology,Northeast Agricultural University,Harbin 150030,China)
Artificial selection played an important role during chicken domestication and subsequent breed formation.So the imprints of selection episodes had been left within chicken genome.With the advances in genomics and the development of methods to detect selection signatures,the elucidation of these selection signatures had been of interest issue on the fields of evolutionary biology and population genetics.The aims of this review were to describe the definition of selection signatures on chicken genome, to present the main statistical methods used to detect selection signature,and to summarize some recent results on the selection footprint in chicken.This review should offer
to the researchers in the related fields.
chicken;genome-wide;selection signatures
S831;Q78
A
1005-9369(2016)10-0100-07
時(shí)間2016-10-28 13:22:52[URL]http://www.cnki.net/kcms/detail/23.1391.S.20161028.1322.006.html
2016-05-15
國(guó)家高技術(shù)研究發(fā)展計(jì)劃項(xiàng)目(863計(jì)劃)(2013AA102501);國(guó)家自然科學(xué)基金項(xiàng)目(31101709);東北農(nóng)業(yè)大學(xué)學(xué)術(shù)骨干項(xiàng)目(15XG14);東北農(nóng)業(yè)大學(xué)博士科研啟動(dòng)基金項(xiàng)目(2010RCB29)
王志鵬(1979-),男,副教授,博士,研究方向?yàn)閯?dòng)物分子數(shù)量遺傳學(xué)。E-mail:wangzhipeng@neau.edu.cn