高密度SNP标记法解析两个玉米重组自交系穗夹角的遗传基础
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摘要
为了探究控制玉米穗夹角的遗传基础,本试验以BYD和MX两个玉米重组自交系群体为材料,采用高密度SNP和连锁分析,对调控玉米穗夹角性状的基因进行QTL定位和可能的功能基因分析。结果表明,穗夹角性状具有较高的遗传性,受基因型和环境的影响。穗夹角经过多环境的调查表明,在两个分离群体中均呈正态分布;共定位到调控穗夹角性状27个QTL,包括5个主效QTL,分别位于2号、4号和7号染色体上,两个来自BYD群体,3个来自MX群体,穗夹角性状QTL的表型贡献率从5.7%(qBYDEA2)到6.9%(qMXEA2-2);进一步通过bin图谱法缩进主效QTL区间,共发掘7个穗夹角性状候选基因,它们主要编码转录调控和代谢的酶。本研究结果首次揭示了玉米穗夹角的遗传基础,并有助于未来通过分子育种应用从而提高玉米优良穗夹角的品种。
In order to reveal the genetic basis on controlling maize panicle angle, two recombined maize inbred lines, BYD and MX were used as materials in this study to carry out QTL location and possible functional gene analysis for the genes regulating maize panicle angle by high density SNP markers and linkage studies. The results showed that maize panicle angle trait was highly hereditary and affected by both genotypes and environments. The multi-environmental survey of panicle angles showed a normal distribution in the two RIL populations. Besides,27 QTLs controlling the panicle angle trait were co-located, including five major QTLs, located on the 2 nd, 4 thand7 thchromosomes, respectively. Furthermore, two QTLs were from the BYD population and the other three were from the MX population, and the phenotypic contribution rate of the QTLs for maize panicle angle trait was from5.7%(qBYDEA2) to 6.9%(q MXEA2-2). Bin mapping method was used to further narrow the major QTL intervals,a total of seven candidate genes for maize panicle trait were identified, which mainly encoded enzymes related to transcriptional regulation and metabolism. The results first revealed the genetic basis of the corn panicle angles,which would help improve the varieties of excellent maize panicle angles through molecular breeding applications in the future.
In order to reveal the genetic basis on controlling maize panicle angle, two recombined maize inbred lines, BYD and MX were used as materials in this study to carry out QTL location and possible functional gene analysis for the genes regulating maize panicle angle by high density SNP markers and linkage studies. The results showed that maize panicle angle trait was highly hereditary and affected by both genotypes and environments. The multi-environmental survey of panicle angles showed a normal distribution in the two RIL populations. Besides,27 QTLs controlling the panicle angle trait were co-located, including five major QTLs, located on the 2 nd, 4 thand7 thchromosomes, respectively. Furthermore, two QTLs were from the BYD population and the other three were from the MX population, and the phenotypic contribution rate of the QTLs for maize panicle angle trait was from5.7%(qBYDEA2) to 6.9%(q MXEA2-2). Bin mapping method was used to further narrow the major QTL intervals,a total of seven candidate genes for maize panicle trait were identified, which mainly encoded enzymes related to transcriptional regulation and metabolism. The results first revealed the genetic basis of the corn panicle angles,which would help improve the varieties of excellent maize panicle angles through molecular breeding applications in the future.
引文
Dai G.L.,Cai Y.L.,Xu D.L.,Lv X.G.,Wang G.Q.,Wang J.G.,and Sun H.Y.,2009,QTL mapping for ear traits in maize(Zea mays L.),Xinan Shifan Daxue Xuebao(Journal of Southwest China Normal University(Natural Science Edition)),34(5):133-138(代国丽,蔡一林,徐德林,吕学高,王国强,王久光,孙海艳,2009,玉米穗部性状的QTL定位,西南师范大学学报(自然科学版),34(5):133-138)
De S.,Bouchez M.,Chabrier P.,Milan D.,and Schiex T.,2005,CARHTA GENE:multipopula tion integrated genetic and radiation hybrid mapping,Bioinformatics,21(8):1703-1704
Ding J.,Zhang L.,Chen J.,Li X.,Li Y.,Cheng H.,Huang R.,Zhou B.,Li Z.,Wang J.,and Wu J.,2015,Genomic dissec tion of leaf angle in mazie(Zea mays L.)using a four-way cross mapping population,PLoS One,10(10):e0141619
Ganal M.W.,Durstewitz G.,Polley A.,Bérard A.,Buckler E.S.,Charcosset A.,Clarke J.D.,Graner E.M.,Hansen M.,Joets J.,Le P.M.C.,Mc M.M.D.,Montalent P.,Rose M.,Schon C.C.,Sun Q.,Walter H.,Martin O.C.,and Falque M.,2011,Alarge maize(Zea mays L.)SNP genotyping array:development and germplasm genotyping,and genetic mapping to compare with the B73 reference genome,PLoS One,6(12):e28334
Goldman I.L.,Rocheford T.R.,and Dudley J.W.,1993,Quantitative trait loci influencing protein and starch concentration in the Illinois long term selection maize strains,Theor.Appl.Genet.,87(1-2):217-224
Guo J.,Su G.,Zhang J.,and Wang G.,2008,Genetic analysis and QTL mapping of maize yield and associate agronomic traits under semi-arid land condition,African J.Biotechnol.,7(12):1829-1838
Knapp S.J.,Stroup W.W.,and Ross W.M.,1985,Exact confidence-intervals for heritability on a progeny mean basis,Crop Sci.,25(1):192-194
Koch K.,2004,Sucrose metabolism:regulatory mechanisms and pivotal roles in sugar sensing and plant development,Curr.Opin.Plant Biol.,7(3):235-246
Kramer E.M.,and Ackelsberg E.M.,2015,Auxin metabolism rates and implications for plant development,Front Plant Sci.,6(17):150
Ku L.X.,Zhang J.,Guo S.L.,Liu H.Y.,Zhao R.F.,and Chen Y.H.,2012,Integrated multiple population analysis of leaf architecture traits in maize(Zea mays L.),J.Exp.Bot.,63(1):261-274
Ku L.X.,Zhao W.M.,Zhang J.,Wu L.C.,Wang P.A.,Zhang W.Q.,and Chen Y.H.,2010,Quantitative trait loci mapping of leaf angle and leaf orientation value in maize(Zea mays L.),Theor.Appl.Genet.,121(5):951-959
Li C.,Li Y.,Shi Y.,Song Y.,Zhang D.,Buckler E.S.,Zhang Z.,Wang T.,and Li Y.,2015,Genetic control of the leaf angle and leaf orientation value as revealed by ultra-high density maps in three connected maize populations,PLoS One,10(3):e0121624
Li Q.,Yang X.H.,Xu S.,Cai Y.,Zhang D.L.,Han Y.J.,Li L.,Zhang Z.,Gao S.,Li J.,and Yan J.B.,2012,Genome-wide association studies identified three independent polymorphisms association withα-tocopherol content in maize kernels,PLoS One,7(5):e36807
Mendes-Moreira P.,Alves M.L.,Satovic Z.,Dos Santos J.P.,Santos J.N.,Souza J.C.,Pêgo S.E.,Hallauer A.R.,and Vaz Patto M.C.,2015,Genetic architecture of ear fasciation in mazie(Zea mays)under QTL scrutiny,PLo S One,10(4):e0124543
Mickelson S.M.,Stuber C.S.,Senior L.,and Kaeppler M.S.,2002,Quantitative trait loci controlling leaf and tassel traits in a B73×Mo17 population of maize,Crop Sci.,42(6):1902-1909
Pan Q.,Li L.,Yang X.,Tong H.,Xu S.,Li Z.,Li W.,Muehlbauer G.J.,Li J.,and Yan J.,2016,Genome-wide recombination dynamics are associated with phenotypic variation in maize,New Phytol.,210(3):1083-1094
Robinson H.F.,Comstock R.E.,and Harvey P.H.,1951,Genotype and phenotypic correlations in corn and their implications in selection,Agronomy Journal,43(6):477-483
Song J.J.,Liu J.L.,Zhou B.M.,Cui M.Y.,Liu R.Q.,and Li G.,2006,Studies on the relationship between yield and traits of corn ears,Jilin Nongye Kexue(Journal of Jilin Agricultural Sciences),31(4):11-13(宋继娟,柳金来,周柏明,崔明元,刘荣清,李刚,2006,玉米穗部性状与产量关系的研究,吉林农业科学,31(4):11-13)
Tang H.,Yan J.B.,Huang Y.Q.,Zheng Y.L.,and Li J.S.,2005,QTL mapping of five agronomic traits in maize,Yichuan Xuebao(Journal of Genetics and Genomics),32(2):203-209(汤华,严建兵,黄益勤,郑用琏,李建生,2005,玉米5个农艺性状的QTL定位,遗传学报,32(2):203-209)
Tang J.,Yan J.,Ma X.,Teng W.,Wu W.,Dai J.,Dhillion B.S.,Melchinger A.E.,and Li J.,2010,Dissection of the genetic basis of heterosis in an elite maize hybrid by QTL mapping in an immortalized F2population,Theor.Appl.Genet.,120(2):333-340
Tang J.H.,Yan J.B.,Ma X.Q.,Teng W.T.,Meng Y.J.,Dai J.R.,and Li J.S.,2007,Genetic dissection for grain yield and its components using an"immortalized F2population"in maize,Zuowu Xuebao(Acta Agronomica Sinica),33(8):1299-1303(汤继华,严建兵,马西青,滕文禄,孟义江,戴景瑞,李建生,2007,利用“永久F2”群体剖析玉米产量及其相关性的遗传机制,作物学报,33(8):1299-1303)
Tepperman J.M.,Hwang Y.S.,and Quail P.H.,2006,PhyA dominates in transduction of red-light signals to rapidly responding genes at the initiation of arabidopsis seeding de-etiolation,Plant J.,48(5):728-742
Van Os H.,Stam P.,Visser R.G.F.,and Van Eck H.J.,2015,RECORD:a novel method for ordering loci on a genetic linkage map,Theor.Appl.Genet.,112(1):30-40
Veldboom L.R.,and Lee M.,1994,Molecular-marker-facilitated studies of morphological traits in maize:Ⅱdetermination of QTLs for grain yield and yield components,Theor.Appl.Genet.,89(4):451-458
Wang P.,Kelly S.,Fouracre J.P.,and Langdale J.A.,2013,Genome-wide transcript analysis of early maize leaf development reveals gene cohorts associated with the differentiation of C4 kranz anatomy,Plant J.,75(4):656-670
Wang T.,Min W.,Hu S.,Xiao Y.,Hao T.,Pan Q.,Xue J.,Yan J.,Li J.,and Yang X.,2015,Genetic basis of maize kernel starch content revealed by high-density single nucleotide polymorphism markers in a recombinant inbred line population,BMC Plant Biology,15:288
Wang W.,Hao Q.,Tian F.,Li Q.,and Wang W.,2016,The staygreen phenotype of wheat mutant tasg1 is associated with altered cytokinin metabolism,Plant Cell Rep.,35(3):585-599
Wen B.Q.,Xing M.Q.,Zhang H.,Dai C.,and Xue H.W.,2011,Rice homeobox transcription factor HOX1a positively regulates gibberellin responses by directly suppressing EL1,J.Integr.Plant Biol.,53(11):869-878
Yu J.M.,and Buckler E.S.,2006,Genetic association mapping and genome organization of maize,Curr.Opin.Biotechnol.,17(2):155-160
Zhang J.,Ku L.X.,Han Z.P.,Guo S.L.,Liu H.J.,Zhang Z.Z.,Cao L.R.,Cui X.J.,and Chen Y.H.,2014,The ZmCLA4 gene in the qLA4-1 QTL controls leaf angle in maize(Zea mays L.),J.Exp.Bot.,65(17):5063-5076
Zou G.H.,Zhai G.W.,Feng Q.,Yan S.,Wang A.H.,Zhao Q.,Shao J.,Zou J.,Han B.,and Tao Y.,2012,Identification of QTLs for eight agronomically important traits using ultra-high-density map based on SNPs generated from highthroughput sequencing in sorghum under contrasting photoperiods,J.Exp.Bot.,63(15):5451-5462
De S.,Bouchez M.,Chabrier P.,Milan D.,and Schiex T.,2005,CARHTA GENE:multipopula tion integrated genetic and radiation hybrid mapping,Bioinformatics,21(8):1703-1704
Ding J.,Zhang L.,Chen J.,Li X.,Li Y.,Cheng H.,Huang R.,Zhou B.,Li Z.,Wang J.,and Wu J.,2015,Genomic dissec tion of leaf angle in mazie(Zea mays L.)using a four-way cross mapping population,PLoS One,10(10):e0141619
Ganal M.W.,Durstewitz G.,Polley A.,Bérard A.,Buckler E.S.,Charcosset A.,Clarke J.D.,Graner E.M.,Hansen M.,Joets J.,Le P.M.C.,Mc M.M.D.,Montalent P.,Rose M.,Schon C.C.,Sun Q.,Walter H.,Martin O.C.,and Falque M.,2011,Alarge maize(Zea mays L.)SNP genotyping array:development and germplasm genotyping,and genetic mapping to compare with the B73 reference genome,PLoS One,6(12):e28334
Goldman I.L.,Rocheford T.R.,and Dudley J.W.,1993,Quantitative trait loci influencing protein and starch concentration in the Illinois long term selection maize strains,Theor.Appl.Genet.,87(1-2):217-224
Guo J.,Su G.,Zhang J.,and Wang G.,2008,Genetic analysis and QTL mapping of maize yield and associate agronomic traits under semi-arid land condition,African J.Biotechnol.,7(12):1829-1838
Knapp S.J.,Stroup W.W.,and Ross W.M.,1985,Exact confidence-intervals for heritability on a progeny mean basis,Crop Sci.,25(1):192-194
Koch K.,2004,Sucrose metabolism:regulatory mechanisms and pivotal roles in sugar sensing and plant development,Curr.Opin.Plant Biol.,7(3):235-246
Kramer E.M.,and Ackelsberg E.M.,2015,Auxin metabolism rates and implications for plant development,Front Plant Sci.,6(17):150
Ku L.X.,Zhang J.,Guo S.L.,Liu H.Y.,Zhao R.F.,and Chen Y.H.,2012,Integrated multiple population analysis of leaf architecture traits in maize(Zea mays L.),J.Exp.Bot.,63(1):261-274
Ku L.X.,Zhao W.M.,Zhang J.,Wu L.C.,Wang P.A.,Zhang W.Q.,and Chen Y.H.,2010,Quantitative trait loci mapping of leaf angle and leaf orientation value in maize(Zea mays L.),Theor.Appl.Genet.,121(5):951-959
Li C.,Li Y.,Shi Y.,Song Y.,Zhang D.,Buckler E.S.,Zhang Z.,Wang T.,and Li Y.,2015,Genetic control of the leaf angle and leaf orientation value as revealed by ultra-high density maps in three connected maize populations,PLoS One,10(3):e0121624
Li Q.,Yang X.H.,Xu S.,Cai Y.,Zhang D.L.,Han Y.J.,Li L.,Zhang Z.,Gao S.,Li J.,and Yan J.B.,2012,Genome-wide association studies identified three independent polymorphisms association withα-tocopherol content in maize kernels,PLoS One,7(5):e36807
Mendes-Moreira P.,Alves M.L.,Satovic Z.,Dos Santos J.P.,Santos J.N.,Souza J.C.,Pêgo S.E.,Hallauer A.R.,and Vaz Patto M.C.,2015,Genetic architecture of ear fasciation in mazie(Zea mays)under QTL scrutiny,PLo S One,10(4):e0124543
Mickelson S.M.,Stuber C.S.,Senior L.,and Kaeppler M.S.,2002,Quantitative trait loci controlling leaf and tassel traits in a B73×Mo17 population of maize,Crop Sci.,42(6):1902-1909
Pan Q.,Li L.,Yang X.,Tong H.,Xu S.,Li Z.,Li W.,Muehlbauer G.J.,Li J.,and Yan J.,2016,Genome-wide recombination dynamics are associated with phenotypic variation in maize,New Phytol.,210(3):1083-1094
Robinson H.F.,Comstock R.E.,and Harvey P.H.,1951,Genotype and phenotypic correlations in corn and their implications in selection,Agronomy Journal,43(6):477-483
Song J.J.,Liu J.L.,Zhou B.M.,Cui M.Y.,Liu R.Q.,and Li G.,2006,Studies on the relationship between yield and traits of corn ears,Jilin Nongye Kexue(Journal of Jilin Agricultural Sciences),31(4):11-13(宋继娟,柳金来,周柏明,崔明元,刘荣清,李刚,2006,玉米穗部性状与产量关系的研究,吉林农业科学,31(4):11-13)
Tang H.,Yan J.B.,Huang Y.Q.,Zheng Y.L.,and Li J.S.,2005,QTL mapping of five agronomic traits in maize,Yichuan Xuebao(Journal of Genetics and Genomics),32(2):203-209(汤华,严建兵,黄益勤,郑用琏,李建生,2005,玉米5个农艺性状的QTL定位,遗传学报,32(2):203-209)
Tang J.,Yan J.,Ma X.,Teng W.,Wu W.,Dai J.,Dhillion B.S.,Melchinger A.E.,and Li J.,2010,Dissection of the genetic basis of heterosis in an elite maize hybrid by QTL mapping in an immortalized F2population,Theor.Appl.Genet.,120(2):333-340
Tang J.H.,Yan J.B.,Ma X.Q.,Teng W.T.,Meng Y.J.,Dai J.R.,and Li J.S.,2007,Genetic dissection for grain yield and its components using an"immortalized F2population"in maize,Zuowu Xuebao(Acta Agronomica Sinica),33(8):1299-1303(汤继华,严建兵,马西青,滕文禄,孟义江,戴景瑞,李建生,2007,利用“永久F2”群体剖析玉米产量及其相关性的遗传机制,作物学报,33(8):1299-1303)
Tepperman J.M.,Hwang Y.S.,and Quail P.H.,2006,PhyA dominates in transduction of red-light signals to rapidly responding genes at the initiation of arabidopsis seeding de-etiolation,Plant J.,48(5):728-742
Van Os H.,Stam P.,Visser R.G.F.,and Van Eck H.J.,2015,RECORD:a novel method for ordering loci on a genetic linkage map,Theor.Appl.Genet.,112(1):30-40
Veldboom L.R.,and Lee M.,1994,Molecular-marker-facilitated studies of morphological traits in maize:Ⅱdetermination of QTLs for grain yield and yield components,Theor.Appl.Genet.,89(4):451-458
Wang P.,Kelly S.,Fouracre J.P.,and Langdale J.A.,2013,Genome-wide transcript analysis of early maize leaf development reveals gene cohorts associated with the differentiation of C4 kranz anatomy,Plant J.,75(4):656-670
Wang T.,Min W.,Hu S.,Xiao Y.,Hao T.,Pan Q.,Xue J.,Yan J.,Li J.,and Yang X.,2015,Genetic basis of maize kernel starch content revealed by high-density single nucleotide polymorphism markers in a recombinant inbred line population,BMC Plant Biology,15:288
Wang W.,Hao Q.,Tian F.,Li Q.,and Wang W.,2016,The staygreen phenotype of wheat mutant tasg1 is associated with altered cytokinin metabolism,Plant Cell Rep.,35(3):585-599
Wen B.Q.,Xing M.Q.,Zhang H.,Dai C.,and Xue H.W.,2011,Rice homeobox transcription factor HOX1a positively regulates gibberellin responses by directly suppressing EL1,J.Integr.Plant Biol.,53(11):869-878
Yu J.M.,and Buckler E.S.,2006,Genetic association mapping and genome organization of maize,Curr.Opin.Biotechnol.,17(2):155-160
Zhang J.,Ku L.X.,Han Z.P.,Guo S.L.,Liu H.J.,Zhang Z.Z.,Cao L.R.,Cui X.J.,and Chen Y.H.,2014,The ZmCLA4 gene in the qLA4-1 QTL controls leaf angle in maize(Zea mays L.),J.Exp.Bot.,65(17):5063-5076
Zou G.H.,Zhai G.W.,Feng Q.,Yan S.,Wang A.H.,Zhao Q.,Shao J.,Zou J.,Han B.,and Tao Y.,2012,Identification of QTLs for eight agronomically important traits using ultra-high-density map based on SNPs generated from highthroughput sequencing in sorghum under contrasting photoperiods,J.Exp.Bot.,63(15):5451-5462