基于重测序的陆地棉InDel标记开发与评价
|
摘要
碱基插入/缺失(InDel)是基因组中丰富的遗传变异形式。InDel以其密度高、易于基因型分型等优点成为分子标记开发的理想来源。本研究利用262份陆地棉品系重测序数据鉴定的InDel位点,在全基因组范围内设计了3206个InDel标记并挑选均匀分布的320个标记进行验证。320个标记筛选出87个多态性标记,多态性率为26.88%。利用多态性标记对不同地理来源的262份陆地棉种质资源进行基因分型,共检测到160个等位位点;多态性信息含量(PIC)为0.0836～0.3750,平均值为0.3073;基因多样性指数变异范围为0.0874～0.5000,平均值为0.3876,表明我国陆地棉遗传基础相对狭窄。群体结构分析将262份陆地棉品系大致划分为2个亚群,聚类分析和主成分分析的结果与之基本一致。采用混合线性模型(Mixed linear model)对6个纤维品质性状的关联分析检测到65个关联位点(P <0.01),各位点对表型变异贡献率为2.57%～8.12%。本研究旨在利用重测序数据开发全基因组范围的可用于凝胶检测的InDel标记,为棉花种质资源研究和分子标记辅助选择育种提供便捷工具。
Insertion and deletion(InDel) are abundant forms of genetic variation in the genome. InDel has been recognized as an ideal source for marker development due to its high-density distribution and genotyping efficiency. In this study, the whole genome re-sequencing data of 262 upland cotton accessions were applied to identify 3206 InDel markers, and 320 markers with uniform distribution across the genome were selected to be evaluated. Eighty-seven polymorphic markers were identified, accounting for 26.88% of screened markers. A total of 160 allelic loci were detected using the 87 polymorphic markers in the 262 upland cotton accessions with an average polymorphic information content(PIC) of 0.3073(ranging from 0.0836 to 0.3750) and an average genetic diversity of 0.3876(ranging from 0.0874 to 0.5000), indicating a relatively low genetic diversity. Population structure analysis revealed extensive admixture and identified two subgroups, clustering analysis and principal component analysis supported the subgroups identified by STRUCTURE. Association analysis were performed by MLM(Mixed linear model), and 65 marker loci were associated with fiber quality traits(P < 0.01), explaining 2.57%–8.12% of the phenotypic variation. Genome-wide and gel based In Del markers developed based on re-sequencing data in this study provide a facile tool for cotton germplasm resources research and molecular marker assisted selection breeding.
Insertion and deletion(InDel) are abundant forms of genetic variation in the genome. InDel has been recognized as an ideal source for marker development due to its high-density distribution and genotyping efficiency. In this study, the whole genome re-sequencing data of 262 upland cotton accessions were applied to identify 3206 InDel markers, and 320 markers with uniform distribution across the genome were selected to be evaluated. Eighty-seven polymorphic markers were identified, accounting for 26.88% of screened markers. A total of 160 allelic loci were detected using the 87 polymorphic markers in the 262 upland cotton accessions with an average polymorphic information content(PIC) of 0.3073(ranging from 0.0836 to 0.3750) and an average genetic diversity of 0.3876(ranging from 0.0874 to 0.5000), indicating a relatively low genetic diversity. Population structure analysis revealed extensive admixture and identified two subgroups, clustering analysis and principal component analysis supported the subgroups identified by STRUCTURE. Association analysis were performed by MLM(Mixed linear model), and 65 marker loci were associated with fiber quality traits(P < 0.01), explaining 2.57%–8.12% of the phenotypic variation. Genome-wide and gel based In Del markers developed based on re-sequencing data in this study provide a facile tool for cotton germplasm resources research and molecular marker assisted selection breeding.
引文
[1]喻树迅.中国棉花产业百年发展历程.农学学报,2018,(1):85-91.Yu S X.The development of cotton production in the recent hundred years of China.J Agric,2018,(1):85-91(in Chinese with English abstract).
[2]董承光,王娟,周小凤,马晓梅,李生秀,余渝,李保成.基于表型性状的陆地棉种质资源遗传多样性分析.植物遗传资源学报,2016,17:438-446.Dong C G,Wang J,Zhou X F,Ma X M,Li S X,Yu Y,Li B C.Evaluation on genetic diversity of cotton germplasm resources(Gossypium hirsutum L.)on morphological characters.J Plant Genet Resour,2016,17:438-446(in Chinese with English abstract).
[3]Dong C G,Wang J,Yu Y,Li B C,Chen Q J.Association mapping and favourable QTL alleles for fibre quality traits in Upland cotton(Gossypium hirsutum L.).J Genet,2018,97:e1-e12.
[4]Huang C,Shen C,Wen T W,Gao B,Zhu D,Li X,Ahmed M M,Li D,Lin Z X.SSR-based association mapping of fiber quality in upland cotton using an eight-way MAGIC population.Mol Genet Genomics,2018,293:793-805.
[5]Sahu P K,Mondal S,Sharma D,Vishwakarma G,Kumar V,Das B K.InDel marker based genetic differentiation and genetic diversity in traditional rice(Oryza sativa L.)landraces of Chhattisgarh,India.PLoS One,2017,12:e0188864.
[6]Liu J,Qu J T,Yang C,Tang D G,Li J W,Lan H,Rong T Z.Development of genome-wide insertion and deletion markers for maize,based on next-generation sequencing data.BMC Genomics,2015,16:601.
[7]Liu B,Wang Y,Zhai W,Deng J,Wang H,Cui Y,Cheng F,Wang X W,Wu J.Development of InDel markers for Brassica rapa based on whole-genome re-sequencing.Theor Appl Genet,2013,126:231-239.
[8]Zhang T,Hu Y,Jiang W,Fang L,Guan X,Chen J,Zhang J,Saski C A,Scheffler B E,Stelly D M.Sequencing of allotetraploid cotton(Gossypium hirsutum L.acc.TM-1)provides a resource for fiber improvement.Nat Biotechnol,2015,33:531-537.
[9]Wang M J,Tu L L,Min L,Lin Z X,Wang P C,Yang Q Y,Ye Z X,Shen C,Li J Y,Zhang X L.Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication.Nat Genet,2017,49:579-587.
[10]Huang C,Nie X H,Shen C,You C Y,Li W,Zhao W X,Zhang XL,Lin Z X.Population structure and genetic basis of the agronomic traits of upland cotton in China revealed by a genome-wide association study using high-density SNPs.Plant Biotechnol J,2017,15:1374-1386.
[11]Nie X H,Huang C,You C Y,Li W,Zhao W X,Shen C,Zhang BB,Wang H T,Yan Z H,Dai B S,Wang M J,Zhang X L,Lin Z X.Genome-wide SSR-based association mapping for fiber quality in nation-wide upland cotton inbreed cultivars in China.BMC Genomics,2016,17:352.
[12]Rozen S,Skaletsky H.Primer3 on the WWW for general users and for biologist programmers.Methods Mol Biol,2000,132:365-386.
[13]Li X M,Yuan D J,Wang H T,Chen X M,Wang B,Lin Z X,Zhang X L.Increasing cotton genome coverage with polymorphic SSRs as revealed by SSCP.Genome,2012,55:459-470.
[14]Botstein D,White R L,Skolnick M,Davis R W.Construction of a genetic linkage map in man using restriction fragment length polymorphisms.Am J Hum Genet,1980,32:314-331.
[15]Letunic I,Bork P.Interactive tree of life(iTOL)v3:an online tool for the display and annotation of phylogenetic and other trees.Nucl Acids Res,2016,44:W242-W245.
[16]Pritchard J K,Stephens M,Donnelly P.Inferences of population structure using multilocus genotype data.Genetics,2000,155:945-959.
[17]Earl D A,Vonholdt B M.STRUCTURE HARVESTER:a website and program for visualizing STRUCTURE output and implementing the Evanno method.Conserv Genet Resour,2012,4:359-361.
[18]Evanno G,Regnaut S,Goudet J.Detecting the number of clusters of individuals using the software STRUCTURE:a simulation study.Mol Ecol,2010,14:2611-2620.
[19]Bradbury P J,Zhang Z,Kroon D E,Casstevens T M,Ramdoss Y,Buckler E S.TASSEL:software for association mapping of complex traits in diverse samples.Bioinformatics,2007,23:2633-2635.
[20]Wu D H,Wu H P,Wang C S,Tseng H Y,Hwu K K.Genome-wide InDel marker system for application in rice breeding and mapping studies.Euphytica,2013,192:131-143.
[21]Wang H,Jin X,Zhang B,Shen C,Lin Z.Enrichment of an intraspecific genetic map of upland cotton by developing markers using parental RAD sequencing.DNA Res,2015,22:147-160.
[22]Lin Z X,Zhang Y X,Zhang X L,Guo X P.A high-density integrative linkage map for Gossypium hirsutum.Euphytica,2009,166:35-45.
[23]Liu R Z,Wang B H,Guo W Z,Qin Y S,Wang L G,Zhang Y M,Zhang T Z.Quantitative trait loci mapping for yield and its components by using two immortalized populations of a heterotic hybrid in Gossypium hirsutum L.Mol Breed,2012,29:297-311.
[24]Fang D D,Li P,Thyssen G,Hinze L L,Percy R G.A microsatellite-based genome-wide analysis of genetic diversity and linkage disequilibrium in Upland cotton(Gossypium hirsutum L.).Euphytica,2013,191:391-401.
[25]Wen T W,Wu M,Shen C,Gao B,Zhu D,Zhang X L,You C Y,Lin Z X.Linkage and association mapping reveals the genetic basis of brown fibre(Gossypium hirsutum).Plant Biotechnol J,2018,16:1654-1666.
[26]Ai X,Liang Y,Wang J,Zheng J,Gong Z,Guo J,Li X,Qu Y.Genetic diversity and structure of elite cotton germplasm(Gossypium hirsutum L.)using genome-wide SNP data.Genetica,2017,145:409-416.
[27]Tyagi P,Gore M A,Bowman D T,Campbell B T,Udall J A,Kuraparthy V.Genetic diversity and population structure in the US Upland cotton(Gossypium hirsutum L.).Theor Appl Genet,2014,127:283-295.
[28]Flint-Garcia S A,Thornsberry J M,Buckler E S.Structure of linkage disequilibrium in plants.Annu Rev Plant Biol,2003,54:357-374.
[29]Zhang Z W,Ersoz E,Lai C Q,Todhunter R J,Tiwari H K,Gore M A,Bradbury P J,Yu J M,Arnett D K,Ordovas J M,Buckler ES.Mixed linear model approach adapted for genome-wide association studies.Nat Genet,2010,4:355-360.
[30]Ma Z Y,He S P,Wang X F,Sun J L,Zhang Y,Zhang G Y,Wu LQ,Li Z K,Liu Z H,Sun G F,Du X M.Resequencing a core collection of upland cotton identifies genomic variation and loci influencing fiber quality and yield.Nat Genet,2018,50:803-813.
[31]Zhang S W,Feng L C,Xing L T,Yang B,Gao X,Zhu X F,Zhang T Z,Zhou B L.New QTLs for lint percentage and boll weight mined in introgression lines from two feral landraces into Gossypium hirsutum acc TM-1.Plant Breed,2016,135:90-101.
[32]Fang L,Wang Q,Hu Y,Jia Y H,Chen J D,Liu B L,Zhang Z Y,Guan X Y,Chen S Q,Zhou B L,Du X M.Genomic analyses in cotton identify signatures of selection and loci associated with fiber quality and yield traits.Nat Genet,2017,49:1089-1098.
[33]Islam M S,Thyssen G N,Jenkins J N,Zeng L,Delhom C D,McCarty J C,Deng D D,Hinchliffe D J,Jones D C,Fang D D.AMAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton.BMC Genomics,2016,17:903.
[34]Sun Z W,Wang X F,Liu Z W,Gu Q S,Zhang Y,Li Z K,Ke H F,Yang J,Wu J H,Wu L Q,Zhang G Y,Zhang C Y,Ma Z Y.Genome-wide association study discovered genetic variation and candidate genes of fibre quality traits in Gossypium hirsutum L.Plant Biotechnol J,2017,15:982-996.
[35]Liu Z H,Zhu L,Shi H Y,Chen Y,Zhang J M,Zheng Y,Li XB.Cotton GASL genes encoding putative gibberellinregulated proteins are involved in response to GA signaling in fiber development.Mol Biol Rep,2013,40:4561-4570.
[2]董承光,王娟,周小凤,马晓梅,李生秀,余渝,李保成.基于表型性状的陆地棉种质资源遗传多样性分析.植物遗传资源学报,2016,17:438-446.Dong C G,Wang J,Zhou X F,Ma X M,Li S X,Yu Y,Li B C.Evaluation on genetic diversity of cotton germplasm resources(Gossypium hirsutum L.)on morphological characters.J Plant Genet Resour,2016,17:438-446(in Chinese with English abstract).
[3]Dong C G,Wang J,Yu Y,Li B C,Chen Q J.Association mapping and favourable QTL alleles for fibre quality traits in Upland cotton(Gossypium hirsutum L.).J Genet,2018,97:e1-e12.
[4]Huang C,Shen C,Wen T W,Gao B,Zhu D,Li X,Ahmed M M,Li D,Lin Z X.SSR-based association mapping of fiber quality in upland cotton using an eight-way MAGIC population.Mol Genet Genomics,2018,293:793-805.
[5]Sahu P K,Mondal S,Sharma D,Vishwakarma G,Kumar V,Das B K.InDel marker based genetic differentiation and genetic diversity in traditional rice(Oryza sativa L.)landraces of Chhattisgarh,India.PLoS One,2017,12:e0188864.
[6]Liu J,Qu J T,Yang C,Tang D G,Li J W,Lan H,Rong T Z.Development of genome-wide insertion and deletion markers for maize,based on next-generation sequencing data.BMC Genomics,2015,16:601.
[7]Liu B,Wang Y,Zhai W,Deng J,Wang H,Cui Y,Cheng F,Wang X W,Wu J.Development of InDel markers for Brassica rapa based on whole-genome re-sequencing.Theor Appl Genet,2013,126:231-239.
[8]Zhang T,Hu Y,Jiang W,Fang L,Guan X,Chen J,Zhang J,Saski C A,Scheffler B E,Stelly D M.Sequencing of allotetraploid cotton(Gossypium hirsutum L.acc.TM-1)provides a resource for fiber improvement.Nat Biotechnol,2015,33:531-537.
[9]Wang M J,Tu L L,Min L,Lin Z X,Wang P C,Yang Q Y,Ye Z X,Shen C,Li J Y,Zhang X L.Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication.Nat Genet,2017,49:579-587.
[10]Huang C,Nie X H,Shen C,You C Y,Li W,Zhao W X,Zhang XL,Lin Z X.Population structure and genetic basis of the agronomic traits of upland cotton in China revealed by a genome-wide association study using high-density SNPs.Plant Biotechnol J,2017,15:1374-1386.
[11]Nie X H,Huang C,You C Y,Li W,Zhao W X,Shen C,Zhang BB,Wang H T,Yan Z H,Dai B S,Wang M J,Zhang X L,Lin Z X.Genome-wide SSR-based association mapping for fiber quality in nation-wide upland cotton inbreed cultivars in China.BMC Genomics,2016,17:352.
[12]Rozen S,Skaletsky H.Primer3 on the WWW for general users and for biologist programmers.Methods Mol Biol,2000,132:365-386.
[13]Li X M,Yuan D J,Wang H T,Chen X M,Wang B,Lin Z X,Zhang X L.Increasing cotton genome coverage with polymorphic SSRs as revealed by SSCP.Genome,2012,55:459-470.
[14]Botstein D,White R L,Skolnick M,Davis R W.Construction of a genetic linkage map in man using restriction fragment length polymorphisms.Am J Hum Genet,1980,32:314-331.
[15]Letunic I,Bork P.Interactive tree of life(iTOL)v3:an online tool for the display and annotation of phylogenetic and other trees.Nucl Acids Res,2016,44:W242-W245.
[16]Pritchard J K,Stephens M,Donnelly P.Inferences of population structure using multilocus genotype data.Genetics,2000,155:945-959.
[17]Earl D A,Vonholdt B M.STRUCTURE HARVESTER:a website and program for visualizing STRUCTURE output and implementing the Evanno method.Conserv Genet Resour,2012,4:359-361.
[18]Evanno G,Regnaut S,Goudet J.Detecting the number of clusters of individuals using the software STRUCTURE:a simulation study.Mol Ecol,2010,14:2611-2620.
[19]Bradbury P J,Zhang Z,Kroon D E,Casstevens T M,Ramdoss Y,Buckler E S.TASSEL:software for association mapping of complex traits in diverse samples.Bioinformatics,2007,23:2633-2635.
[20]Wu D H,Wu H P,Wang C S,Tseng H Y,Hwu K K.Genome-wide InDel marker system for application in rice breeding and mapping studies.Euphytica,2013,192:131-143.
[21]Wang H,Jin X,Zhang B,Shen C,Lin Z.Enrichment of an intraspecific genetic map of upland cotton by developing markers using parental RAD sequencing.DNA Res,2015,22:147-160.
[22]Lin Z X,Zhang Y X,Zhang X L,Guo X P.A high-density integrative linkage map for Gossypium hirsutum.Euphytica,2009,166:35-45.
[23]Liu R Z,Wang B H,Guo W Z,Qin Y S,Wang L G,Zhang Y M,Zhang T Z.Quantitative trait loci mapping for yield and its components by using two immortalized populations of a heterotic hybrid in Gossypium hirsutum L.Mol Breed,2012,29:297-311.
[24]Fang D D,Li P,Thyssen G,Hinze L L,Percy R G.A microsatellite-based genome-wide analysis of genetic diversity and linkage disequilibrium in Upland cotton(Gossypium hirsutum L.).Euphytica,2013,191:391-401.
[25]Wen T W,Wu M,Shen C,Gao B,Zhu D,Zhang X L,You C Y,Lin Z X.Linkage and association mapping reveals the genetic basis of brown fibre(Gossypium hirsutum).Plant Biotechnol J,2018,16:1654-1666.
[26]Ai X,Liang Y,Wang J,Zheng J,Gong Z,Guo J,Li X,Qu Y.Genetic diversity and structure of elite cotton germplasm(Gossypium hirsutum L.)using genome-wide SNP data.Genetica,2017,145:409-416.
[27]Tyagi P,Gore M A,Bowman D T,Campbell B T,Udall J A,Kuraparthy V.Genetic diversity and population structure in the US Upland cotton(Gossypium hirsutum L.).Theor Appl Genet,2014,127:283-295.
[28]Flint-Garcia S A,Thornsberry J M,Buckler E S.Structure of linkage disequilibrium in plants.Annu Rev Plant Biol,2003,54:357-374.
[29]Zhang Z W,Ersoz E,Lai C Q,Todhunter R J,Tiwari H K,Gore M A,Bradbury P J,Yu J M,Arnett D K,Ordovas J M,Buckler ES.Mixed linear model approach adapted for genome-wide association studies.Nat Genet,2010,4:355-360.
[30]Ma Z Y,He S P,Wang X F,Sun J L,Zhang Y,Zhang G Y,Wu LQ,Li Z K,Liu Z H,Sun G F,Du X M.Resequencing a core collection of upland cotton identifies genomic variation and loci influencing fiber quality and yield.Nat Genet,2018,50:803-813.
[31]Zhang S W,Feng L C,Xing L T,Yang B,Gao X,Zhu X F,Zhang T Z,Zhou B L.New QTLs for lint percentage and boll weight mined in introgression lines from two feral landraces into Gossypium hirsutum acc TM-1.Plant Breed,2016,135:90-101.
[32]Fang L,Wang Q,Hu Y,Jia Y H,Chen J D,Liu B L,Zhang Z Y,Guan X Y,Chen S Q,Zhou B L,Du X M.Genomic analyses in cotton identify signatures of selection and loci associated with fiber quality and yield traits.Nat Genet,2017,49:1089-1098.
[33]Islam M S,Thyssen G N,Jenkins J N,Zeng L,Delhom C D,McCarty J C,Deng D D,Hinchliffe D J,Jones D C,Fang D D.AMAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton.BMC Genomics,2016,17:903.
[34]Sun Z W,Wang X F,Liu Z W,Gu Q S,Zhang Y,Li Z K,Ke H F,Yang J,Wu J H,Wu L Q,Zhang G Y,Zhang C Y,Ma Z Y.Genome-wide association study discovered genetic variation and candidate genes of fibre quality traits in Gossypium hirsutum L.Plant Biotechnol J,2017,15:982-996.
[35]Liu Z H,Zhu L,Shi H Y,Chen Y,Zhang J M,Zheng Y,Li XB.Cotton GASL genes encoding putative gibberellinregulated proteins are involved in response to GA signaling in fiber development.Mol Biol Rep,2013,40:4561-4570.