大豆三粒荚数QTL定位及上位性效应分析
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摘要
大豆的三粒荚数与单株荚数密切相关,是重要的产量影响因素之一。为定位大豆三粒荚数QTL位点及分析位点间上位性互作关系,本研究利用一套高世代重组自交系群体对三粒荚数进行连续4年表型数据调查,结合SLAF-seq高密度遗传图谱对大豆三粒荚数进行QTL分析及位点互作效应分析。结果显示,共获得了17个QTL位点分布于GM02、17、18及19连锁群,其中位于GM02连锁群上有3个主效QTL,加性效应值为-7.02～-3.12,表型贡献率为11.03%～12.75%;GM17、GM18连锁群各有2个主效QTL、GM19连锁群有1个主效QTL;共检测到14对上位性互作QTLs,贡献率较高的互作对有QNThSP01-3和QNThSP15-1、QNThSP03-1和QNThSP05-1、QNThSP12-2和QNThSP15-1以及QNThSP15-1和QNThSP19-3,其中QNThSP15-1在所有互作对中参与互作的频率为50%,可能是影响大豆三粒荚数的重要QTL位点。因此对大豆三粒荚数进行QTL定位及上位性互作研究具有重要意义。
The number of three seeded-pod, closely related to the number of pods per plant was one of important factors to soybean yield. The purpose of this study was to localize the QTL locus of three pod number in soybean and analyze the epistatic interection of QTLs for the number of three seeded-pod. The identification and epistatic effects of QTLs for the number of three seeded-pod was meaningful on soybean. In order to find out these results, a RIL population were used for phenotype data collection in four years in a row, and a high density genetic map from specific-length amplified fragment sequencing was used to detect the QTLs. The results showed that a total of seventeen QTLs were distributed in GM02, GM17, GM18 and GM19 linkage group. There were three main effected QTL located on GM02 linkage group, which had the additive effects range-7.02 to-3.12 and the phenotypic variance explanation range from 11.03% to 12.75%. Another four main effected QTLs distributed in GM17 and GM18, one lie in GM19, respectively. There were fourteen pair of epistatic effects QTLs were detected. Four of these had higher phenotypic variance explanation, QNThSP01-3 and QNThSP15-1, QNThSP03-1 and QNThSP05-1, QNThSP12-2 and QNThSP15-1, QNThSP15-1 and QNThSP19-3. The QTL of QNThSP15-1 participated in a half of all epistatic effects QTLs, which might be a important QTL for the number of three seeded-pod in soybena. So it might be significant meaningful to locate the QTLs and analyze the epistatic effects of QTLs for the number of three seeded-pod.
The number of three seeded-pod, closely related to the number of pods per plant was one of important factors to soybean yield. The purpose of this study was to localize the QTL locus of three pod number in soybean and analyze the epistatic interection of QTLs for the number of three seeded-pod. The identification and epistatic effects of QTLs for the number of three seeded-pod was meaningful on soybean. In order to find out these results, a RIL population were used for phenotype data collection in four years in a row, and a high density genetic map from specific-length amplified fragment sequencing was used to detect the QTLs. The results showed that a total of seventeen QTLs were distributed in GM02, GM17, GM18 and GM19 linkage group. There were three main effected QTL located on GM02 linkage group, which had the additive effects range-7.02 to-3.12 and the phenotypic variance explanation range from 11.03% to 12.75%. Another four main effected QTLs distributed in GM17 and GM18, one lie in GM19, respectively. There were fourteen pair of epistatic effects QTLs were detected. Four of these had higher phenotypic variance explanation, QNThSP01-3 and QNThSP15-1, QNThSP03-1 and QNThSP05-1, QNThSP12-2 and QNThSP15-1, QNThSP15-1 and QNThSP19-3. The QTL of QNThSP15-1 participated in a half of all epistatic effects QTLs, which might be a important QTL for the number of three seeded-pod in soybena. So it might be significant meaningful to locate the QTLs and analyze the epistatic effects of QTLs for the number of three seeded-pod.
引文
Chase K.,Adler F.R.,and Lark K.G.,1997,Epistat:A computer program for identifying and testing in teractions between pairs of quantitative trait loci,Theor.Appl.Genet.,94:724-730
Chen Q.,Yan L.,Deng Y.Y.,Xiao E.N.,Liu B.Q.,Yang C.Y.,and Zhang M.C.,2016,Mapping quantitative trait loci for seed size and shape traits in soybean,Zuowu Xuebao(Acta Agronomica Sinica),42(9):1309-1318(陈强,闫龙,邓莹莹,肖二宁,刘兵强,杨春燕,张孟臣,2016,大豆籽粒大小与形状性状的QTL定位,作物学报,42(9):1309-1318)
Chen Q.S.,Zhang Z.C.,Liu C.Y.,Wang W.Q.,and Li W.B.,2005,Construction and analysis of soybean genetic map using recombinant inbred line of Charleston×Dongnong 594,Zhongguo Nongye Kexue(Scientia Agricultura Sinica),38(7):1312-1316(陈庆山,张忠臣,刘春燕,王伟权,李文滨,2005,应用Charleston×东农594重组自交系群体构建SSR大豆遗传图谱,中国农业科学,38(7):1312-1316)
Choi I.Y.,Hyten D.L.,Matukumalli L.K.,Song Q.J.,and Chaky J.M.,Quigley C.V.,Chase K.,Lark K.G.,Reiter R.S.,Yoon M.S.,Hwang E.Y.,Yi S.I.,Young N.D.,Shoemaker R.C.,van Tassell C.P.,Specht J.E.,and Cregan P.B.,2007,A soybean transcript map:gene distribution,haplotype and single-nucleotide polymorphism analysis,Genetics,176(1):685-696
Cooper R.L.,Martin R.J.,and Martin S.K.,1995,Registration of'Charleston'soybean,Crop Sci.,35(2):592
Cregan P.B.,Jarvik T.,Bush A.L.,Shoemaker R.C.,Lark K.G.,Kahler A.L.,Kaya N.,VanToai T.T.,Lohnes D.G.,Chung J.,and Specht J.E.,1999,An integrated genetic linkage map of the soybean genome,Crop Sci.,39:1464-1490
Gao J.Y.,Liu CY.,Jiang H.W.,Hu G.H.,and Chen Q.S.,2012,QTL analysis of pod number per plant in soybean under multiple locations,Zhongguo Youliao Zuowu Xuebao(Chinese Journal of Oil Crop Sciences),34(1):1-7(高静瑶,刘春燕,蒋洪蔚,胡国华,陈庆山,2012,多环境下大豆单株荚数性状的QTL分析,中国油料作物学报,34(1):1-7)
Hyten D.L.,Choi I.Y.,Song Q.,Specht J.E.,Carter T.E.,Shoemaker R.C.,Hwang E.Y.,Matukumalli L.K.,and Cregan P.B.,2010,A high density integrated genetic linkage map of soybean and the development of a 1536 universal soy linkage panel for quantitative trait locus mapping,Crop Sci.,50(3):960-968
Kulwal P.,Kumar N.,Kumar A.,Gupta R.K.,Balyan H.S.,and Gupta P.K.,2005,Gene networks in hexaploid wheat:interacting quantitative trait loci for grain protein content,Funct.Integr.Genomics,5(4):254-259
Liang H.Z.,Yu Y.L.,Yang H.Q.,Zhang H.Y.,Dong W.,Li C.Y.,Du H.,Gong P.T.,Liu X.Y.,and Fang X.J.,2014,Epistatic effects and QTL×environment interaction effects of QTLs for yield and agronomic traits in soybean,Zuowu Xuebao(Acta Agronomica Sinica),40(1):37-44(梁慧珍,余永亮,杨红旗,张海洋,董薇,李彩云,杜华,巩鹏涛,刘学义,方宣钧,2014,大豆产量及主要农艺性状QTL的上位性互作和环境互作分析,作物学报,40(1):37-44)
Liang H.Z.,Yu Y.L.,Yang H.Q.,Zhang H.Y.,Dong W.,Li C.Y.,Gong P.T.,Liu X.Y.,and Fang X.J.,2012,Genetic analysis and QTL mapping of pod-seed traits in soybean under different environments,Zhongguo Nongye Kexue(Scientia Agricultura Sinica),45(13):2568-2579(梁慧珍,余永亮,杨红旗,张海洋,董薇,李彩云,巩鹏涛,刘学义,方宣钧,2012,不同环境下大豆荚粒性状的遗传与QTL分析,中国农业科学,45(13):2568-2579)
Oz M.,Karasu O.M.,Goksoy A.T.,and Turan Z.M.,2009,Interrelationships of agronomical characteristics in soybean(Glycine max)grown in different environments,Inter.J.A-gric.Biol.,11(1):85-88
Qi Z.M.,Huang L.,Zhu R.S.,Xin D.W.,Liu C.Y.,Han X.,Jiang H.W.,Hong W.,Hu G.H.,Zheng H.,and Chen Q.S.,2014,Ahigh-density genetic map for soybean based on specific length amplified fragment sequencing,PLoS One,9(8):e104871
Song Q.J.,Marek L.F.,Shoemaker R.C.,Lark K.G.,Concibido V.C.,Delannay X.,Specht J.E.,and Cregan P.B.,2004,A new integrated genetic linkage map of the soybean,Theor.Appl.Genet.,109(1):122-128
Wlia H.,Wilson C.,Condamine P.,Liu X.,Ismail A.M.,Zeng L.H.,Wanamaker S.I.,Mandal J.,Xu J.,Cui X.P.,and Close T.J.,2005,Comparative transcriptional profiling of two contrasting rice genotypes under salinity stress during the vegetative growth stage,Plant Physiol.,139(2):822-835
Yang Z.,Pei Y.F.,Xie S.N.,Liu C.Y.,Jiang H.W.,Han X.,Xin D.W.,Chen Q.S.,and Hu G.H.,2012,Epistatic effects and QE interaction effects of QTLs for two-seed pod length and width in soybean,Zhongguo Nongye Kexue(Scientia Agricultura Sinica),45(12):2346-2356(杨振,裴宇峰,谢圣男,刘春燕,蒋洪蔚,韩雪,辛大伟,陈庆山,胡国华,2012,大豆二粒荚长、宽相关QTL间上位效应和QE互作效应分析,中国农业科学,45(12):2346-2356)
Yang Z.,Sun Y.N.,Qi Z.M.,Xin D.W.,Jiang H.W.,He L.,Luan H.H.,Liu C.Y.,Zhong P.,Liu L.J.,Hu G.H.,Chen Q.S.,and Wang F.Y.,2013,Analysis of additive effect,epistatic and QE interaction effect for QTL of pod number traits in soybean,Zhongguo Nongye Daxue(Journal of China Agricultural University),8(3):1-13(杨喆,孙亚男,齐照明,辛大伟,蒋洪蔚,何琳,栾怀海,刘春燕,钟鹏,刘丽君,胡国华,陈庆山,王凤义,2013,大豆荚数性状相关QTL的加性、上位性及QE互作效应分析,中国农业大学学报,8(3):1-13)
Yang Z.,Xin D.W.,Liu C.Y.,Jiang H.W.,Han X.,Sun Y.N.,Qi Z.M.,Hu G.H.,and Chen Q.S.,2013,Identification of QTLs for seed and pod traits in soybean and analysis for additive effects and epistatic effects of QTLs among multiple environments,Mol.Genet.Genomics,288:651-667
Zhang W.Y.,Wang J.X.,Zong C.M.,Fu C.X.,Wang M.Q.,Sun Y.J.,Hu G.H.,and Chen Q.S.,2012,QTL analysis of seed and pod traits in soybean,Dadou Kexue(Soybean Science),31(2):193-197(张维耀,王金星,宗春美,付春旭,王茂青,孙艳杰,胡国华,陈庆山,2012,大豆荚粒性状的QTL分析,大豆科学,31(2):193-197)
Zhou X.A.,Wang X.Z.,Cai S.P.,Wu X.J.,Sha A.H.,Qiu D.Z.,and Zhang X.J.,2005,Relation of three-seed and four-seed pods with yield of RILs in soybeans,Zhongguo Youliao Zuowu Xuebao(Chinese Journal of Oil Crop Science),27(4):22-25(周新安,王贤智,蔡淑平,吴学军,沙爱华,邱德珍,张晓娟,2005,大豆重组自交系群体三、四粒荚变异及其与产量的关系,中国油料作物学报,27(4):22-25)
Chen Q.,Yan L.,Deng Y.Y.,Xiao E.N.,Liu B.Q.,Yang C.Y.,and Zhang M.C.,2016,Mapping quantitative trait loci for seed size and shape traits in soybean,Zuowu Xuebao(Acta Agronomica Sinica),42(9):1309-1318(陈强,闫龙,邓莹莹,肖二宁,刘兵强,杨春燕,张孟臣,2016,大豆籽粒大小与形状性状的QTL定位,作物学报,42(9):1309-1318)
Chen Q.S.,Zhang Z.C.,Liu C.Y.,Wang W.Q.,and Li W.B.,2005,Construction and analysis of soybean genetic map using recombinant inbred line of Charleston×Dongnong 594,Zhongguo Nongye Kexue(Scientia Agricultura Sinica),38(7):1312-1316(陈庆山,张忠臣,刘春燕,王伟权,李文滨,2005,应用Charleston×东农594重组自交系群体构建SSR大豆遗传图谱,中国农业科学,38(7):1312-1316)
Choi I.Y.,Hyten D.L.,Matukumalli L.K.,Song Q.J.,and Chaky J.M.,Quigley C.V.,Chase K.,Lark K.G.,Reiter R.S.,Yoon M.S.,Hwang E.Y.,Yi S.I.,Young N.D.,Shoemaker R.C.,van Tassell C.P.,Specht J.E.,and Cregan P.B.,2007,A soybean transcript map:gene distribution,haplotype and single-nucleotide polymorphism analysis,Genetics,176(1):685-696
Cooper R.L.,Martin R.J.,and Martin S.K.,1995,Registration of'Charleston'soybean,Crop Sci.,35(2):592
Cregan P.B.,Jarvik T.,Bush A.L.,Shoemaker R.C.,Lark K.G.,Kahler A.L.,Kaya N.,VanToai T.T.,Lohnes D.G.,Chung J.,and Specht J.E.,1999,An integrated genetic linkage map of the soybean genome,Crop Sci.,39:1464-1490
Gao J.Y.,Liu CY.,Jiang H.W.,Hu G.H.,and Chen Q.S.,2012,QTL analysis of pod number per plant in soybean under multiple locations,Zhongguo Youliao Zuowu Xuebao(Chinese Journal of Oil Crop Sciences),34(1):1-7(高静瑶,刘春燕,蒋洪蔚,胡国华,陈庆山,2012,多环境下大豆单株荚数性状的QTL分析,中国油料作物学报,34(1):1-7)
Hyten D.L.,Choi I.Y.,Song Q.,Specht J.E.,Carter T.E.,Shoemaker R.C.,Hwang E.Y.,Matukumalli L.K.,and Cregan P.B.,2010,A high density integrated genetic linkage map of soybean and the development of a 1536 universal soy linkage panel for quantitative trait locus mapping,Crop Sci.,50(3):960-968
Kulwal P.,Kumar N.,Kumar A.,Gupta R.K.,Balyan H.S.,and Gupta P.K.,2005,Gene networks in hexaploid wheat:interacting quantitative trait loci for grain protein content,Funct.Integr.Genomics,5(4):254-259
Liang H.Z.,Yu Y.L.,Yang H.Q.,Zhang H.Y.,Dong W.,Li C.Y.,Du H.,Gong P.T.,Liu X.Y.,and Fang X.J.,2014,Epistatic effects and QTL×environment interaction effects of QTLs for yield and agronomic traits in soybean,Zuowu Xuebao(Acta Agronomica Sinica),40(1):37-44(梁慧珍,余永亮,杨红旗,张海洋,董薇,李彩云,杜华,巩鹏涛,刘学义,方宣钧,2014,大豆产量及主要农艺性状QTL的上位性互作和环境互作分析,作物学报,40(1):37-44)
Liang H.Z.,Yu Y.L.,Yang H.Q.,Zhang H.Y.,Dong W.,Li C.Y.,Gong P.T.,Liu X.Y.,and Fang X.J.,2012,Genetic analysis and QTL mapping of pod-seed traits in soybean under different environments,Zhongguo Nongye Kexue(Scientia Agricultura Sinica),45(13):2568-2579(梁慧珍,余永亮,杨红旗,张海洋,董薇,李彩云,巩鹏涛,刘学义,方宣钧,2012,不同环境下大豆荚粒性状的遗传与QTL分析,中国农业科学,45(13):2568-2579)
Oz M.,Karasu O.M.,Goksoy A.T.,and Turan Z.M.,2009,Interrelationships of agronomical characteristics in soybean(Glycine max)grown in different environments,Inter.J.A-gric.Biol.,11(1):85-88
Qi Z.M.,Huang L.,Zhu R.S.,Xin D.W.,Liu C.Y.,Han X.,Jiang H.W.,Hong W.,Hu G.H.,Zheng H.,and Chen Q.S.,2014,Ahigh-density genetic map for soybean based on specific length amplified fragment sequencing,PLoS One,9(8):e104871
Song Q.J.,Marek L.F.,Shoemaker R.C.,Lark K.G.,Concibido V.C.,Delannay X.,Specht J.E.,and Cregan P.B.,2004,A new integrated genetic linkage map of the soybean,Theor.Appl.Genet.,109(1):122-128
Wlia H.,Wilson C.,Condamine P.,Liu X.,Ismail A.M.,Zeng L.H.,Wanamaker S.I.,Mandal J.,Xu J.,Cui X.P.,and Close T.J.,2005,Comparative transcriptional profiling of two contrasting rice genotypes under salinity stress during the vegetative growth stage,Plant Physiol.,139(2):822-835
Yang Z.,Pei Y.F.,Xie S.N.,Liu C.Y.,Jiang H.W.,Han X.,Xin D.W.,Chen Q.S.,and Hu G.H.,2012,Epistatic effects and QE interaction effects of QTLs for two-seed pod length and width in soybean,Zhongguo Nongye Kexue(Scientia Agricultura Sinica),45(12):2346-2356(杨振,裴宇峰,谢圣男,刘春燕,蒋洪蔚,韩雪,辛大伟,陈庆山,胡国华,2012,大豆二粒荚长、宽相关QTL间上位效应和QE互作效应分析,中国农业科学,45(12):2346-2356)
Yang Z.,Sun Y.N.,Qi Z.M.,Xin D.W.,Jiang H.W.,He L.,Luan H.H.,Liu C.Y.,Zhong P.,Liu L.J.,Hu G.H.,Chen Q.S.,and Wang F.Y.,2013,Analysis of additive effect,epistatic and QE interaction effect for QTL of pod number traits in soybean,Zhongguo Nongye Daxue(Journal of China Agricultural University),8(3):1-13(杨喆,孙亚男,齐照明,辛大伟,蒋洪蔚,何琳,栾怀海,刘春燕,钟鹏,刘丽君,胡国华,陈庆山,王凤义,2013,大豆荚数性状相关QTL的加性、上位性及QE互作效应分析,中国农业大学学报,8(3):1-13)
Yang Z.,Xin D.W.,Liu C.Y.,Jiang H.W.,Han X.,Sun Y.N.,Qi Z.M.,Hu G.H.,and Chen Q.S.,2013,Identification of QTLs for seed and pod traits in soybean and analysis for additive effects and epistatic effects of QTLs among multiple environments,Mol.Genet.Genomics,288:651-667
Zhang W.Y.,Wang J.X.,Zong C.M.,Fu C.X.,Wang M.Q.,Sun Y.J.,Hu G.H.,and Chen Q.S.,2012,QTL analysis of seed and pod traits in soybean,Dadou Kexue(Soybean Science),31(2):193-197(张维耀,王金星,宗春美,付春旭,王茂青,孙艳杰,胡国华,陈庆山,2012,大豆荚粒性状的QTL分析,大豆科学,31(2):193-197)
Zhou X.A.,Wang X.Z.,Cai S.P.,Wu X.J.,Sha A.H.,Qiu D.Z.,and Zhang X.J.,2005,Relation of three-seed and four-seed pods with yield of RILs in soybeans,Zhongguo Youliao Zuowu Xuebao(Chinese Journal of Oil Crop Science),27(4):22-25(周新安,王贤智,蔡淑平,吴学军,沙爱华,邱德珍,张晓娟,2005,大豆重组自交系群体三、四粒荚变异及其与产量的关系,中国油料作物学报,27(4):22-25)
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