98份谷子材料穗部性状的全基因组SNP关联分析
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摘要
调查98份谷子材料的穗长、穗粗、穗码数、穗质量、穗粒质量、千粒质量6个穗部性状,并进行基因组重测序。基因组重测序共开发了4 482 208个SNP标记;与穗长、穗粗、穗码数、穗质量、穗粒质量、千粒质量关联的SNP位点数分别为118、83、97、13、54、458个,其中与穗长、穗码数、穗粒质量、千粒质量关联的SNP在谷子9条染色体上均有分布,与穗质量关联的SNP分布在除1、2、5号染色体以外的其他6条染色体上,与穗粗关联的SNP分布在除6号染色体以外的其他8条染色体上。
In this study, six panicle traits of 98 foxtail millet cultivars were investigated and genome re-sequencing was performed for the 98 foxtail millet cultivars. Totally 4 482 208 SNPs were developed by re-sequencing of the 98 foxtail millet cultivars. Genome-wide association analysis between SNPs and panicle traits showed that 118, 83, 97, 13, 54 and 458 SNPs were associated with panicle length, panicle diameter, branch number per panicle, panicle weight, grain weight per panicle and 1 000-grain weight respectively. The SNPs associated with panicle length, branch number per panicle, grain weight per panicle and 1 000-grain weight distributed on all of the nine chromosomes, while the SNPs associated with panicle weight distributed on the six chromosomes except Chr.1, Chr.2 and Chr.5 and the SNPs associated with panicle diameter distributed on the eight chromosomes except Chr.6.
In this study, six panicle traits of 98 foxtail millet cultivars were investigated and genome re-sequencing was performed for the 98 foxtail millet cultivars. Totally 4 482 208 SNPs were developed by re-sequencing of the 98 foxtail millet cultivars. Genome-wide association analysis between SNPs and panicle traits showed that 118, 83, 97, 13, 54 and 458 SNPs were associated with panicle length, panicle diameter, branch number per panicle, panicle weight, grain weight per panicle and 1 000-grain weight respectively. The SNPs associated with panicle length, branch number per panicle, grain weight per panicle and 1 000-grain weight distributed on all of the nine chromosomes, while the SNPs associated with panicle weight distributed on the six chromosomes except Chr.1, Chr.2 and Chr.5 and the SNPs associated with panicle diameter distributed on the eight chromosomes except Chr.6.
引文
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[17]GUPTA S,KUMARI K,MUTHAMILARASAN M,et al.Population structure and association mapping of yield contributing agronomic traits in foxtail millet[J].Plant Cell Reports,2014,33(6):881-893.
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[21]LI J,CHU H W,ZHANG Y H,et al.The rice HGW gene encodes a ubiquitin-associated(UBA)domain protein that regulates heading date and grain weight[J].PLoS One,2012,7(3):e34231.
[2]王晓宇,刁现民,王节之,等.谷子SSR分子图谱构建及主要农艺性状QTL定位[J].植物遗传资源学报,2013,14(5):871-878.
[3]FANG X M,DONG K J,WANG X Q,et al.A high density genetic map and QTL for agronomic and yield traits in foxtail millet[Setaria italica(L.)P.Beauv.][J].Bmc Genomics,2016,17:336.
[4]WANG J,WANG Z L,DU X F,et al.A high-density genetic map and QTL analysis of agronomic traits in foxtail millet[Setaria italica(L.)P.Beauv.]using RAD-seq[J].PLoS One,2017,12(6):e0179717.
[5]ZHANG K,FAN G Y,ZHANG X X,et al.Identification of QTLs for 14 agronomically important traits in Setaria italica based on SNPs generated from high-throughput sequencing[J].G3:GENES,GENOMES,GENETICS,2017,7(5):1587-1594.
[6]杨小红,严建兵,郑艳萍,等.植物数量性状关联分析研究进展[J].作物学报,2007,33(4):523-530.
[7]ARANZANA M J,KIM S,ZHAO K Y,et al.Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes[J].PLoS Genetics,2005,1(5):e60.
[8]OLSEN K M,HALLDORSDOTTIR S S,Stinchcombe JR,et al.Linkage disequilibrium mapping of Arabidopsis CRY2 flowering time alleles[J].Genetics,2004,167(3):1361-1369.
[9]BRESEGHELLO F,SORRELLS M E.Association mapping of kernel size and milling quality in wheat(Triticum aestivum L.)cultivars[J].Genetics,2006,172(2):1165-1177.
[10]HUANG X H,WEI X H,SANG T,et al.Genome-wide association studies of 14 agronomic traits in rice landraces[J].Nature Genetics,2010,42(11):961-967.
[11]陈广凤,陈建省,田纪春.小麦株高相关性状与SNP标记全基因组关联分析[J].作物学报,2015,41(10):1500-1509.
[12]高宝祯,刘博,李石开,等.白菜类作物开花时间的全基因组关联分析[J].中国农业科学,2017,50(17):3375-3385.
[13]周庆红,周灿,郑伟,等.甘蓝型油菜角果长度全基因组关联分析[J].中国农业科学,2017,50(2):228-239.
[14]邓敏.玉米籽粒氨基酸全基因组关联分析与连锁分析及玉米和水稻代谢组的比较分析[D].武汉:华中农业大学,2017.
[15]BENNETZEN J L,SCHMUTZ J,WANG H,et al.Reference genome sequence of the model plant Setaria[J].Nature Biotechnology,2012,30(6):555-561.
[16]ZHANG G Y,LIU X,QUAN Z W,et al.Genome sequence of foxtail millet(Setaria italica)provides insights into grass evolution and biofuel potential[J].Nature Biotechnology,2012,30(6):549-554.
[17]GUPTA S,KUMARI K,MUTHAMILARASAN M,et al.Population structure and association mapping of yield contributing agronomic traits in foxtail millet[J].Plant Cell Reports,2014,33(6):881-893.
[18]JIA G Q,HUANG X H,ZHI H,et al.A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet(Setaria italica)[J].Nature Genetics,2013,45(8):957-961.
[19]DUAN P G,RAO Y C,ZENG D L,et al.SMALLGRAIN 1,which encodes a mitogen-activated protein kinase kinase 4,influences grain size in rice[J].The Plant Journal,2014,77(4):547-557.
[20]HU J,WANG Y X,FANG Y X,et al.A rare allele of GS2enhances grain size and grain yield in rice[J].Molecular Plant,2015,8(10):1455-1465.
[21]LI J,CHU H W,ZHANG Y H,et al.The rice HGW gene encodes a ubiquitin-associated(UBA)domain protein that regulates heading date and grain weight[J].PLoS One,2012,7(3):e34231.