Genome-wide association mapping for yield and other agronomic traits in an elite breeding population of tropical rice (Oryza sativa).
Genome-wide association mapping for yield and other agronomic traits in an elite breeding population of tropical rice (Oryza sativa).
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DOI：
10.1371/journal.pone.0119873
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发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
McCouch SR
中科院分区：
文献类型：
--
作者：
Begum H;Spindel JE;Lalusin A;Borromeo T;Gregorio G;Hernandez J;Virk P;Collard B;McCouch SR
全基因组关联作图研究（GWAS）是一种基于基因组间历史重组事件和连锁不平衡的QTL定位方法。通常，利用用高密度SNP组进行基因分型的多样性组，以测定广泛的等位基因和单倍型，并监测整个基因组的重组断点。相比之下，GWAS一般没有在育种群体中进行。在这项研究中，我们进行了关联映射的19个农艺性状，包括产量和产量构成因素的育种群体的精英灌溉热带水稻育种系，使其结果将更直接适用于育种比那些从多样性面板。使用测序基因分型（GBS）对群体进行了71，710个SNP的基因分型，并以加速育种计划中的选择为明确目标进行了GWAS。利用该育种面板共检测到11个农艺性状的52个QTL，其中包括开花时间和粒长/粒宽/粒长宽比的大效应QTL。我们还确定了单倍型，可用于选择植物在我们的人口中的身材矮小（株高），开花时间早，产量高，从而证明了实用的关联映射育种群体的育种决策。最后，我们探索如何利用新发现的显着的SNP和这些数量性状的遗传结构的见解，以建立基因组辅助选择模型。
Genome-wide association mapping studies (GWAS) are frequently used to detect QTL in diverse collections of crop germplasm, based on historic recombination events and linkage disequilibrium across the genome. Generally, diversity panels genotyped with high density SNP panels are utilized in order to assay a wide range of alleles and haplotypes and to monitor recombination breakpoints across the genome. By contrast, GWAS have not generally been performed in breeding populations. In this study we performed association mapping for 19 agronomic traits including yield and yield components in a breeding population of elite irrigated tropical rice breeding lines so that the results would be more directly applicable to breeding than those from a diversity panel. The population was genotyped with 71,710 SNPs using genotyping-by-sequencing (GBS), and GWAS performed with the explicit goal of expediting selection in the breeding program. Using this breeding panel we identified 52 QTL for 11 agronomic traits, including large effect QTLs for flowering time and grain length/grain width/grain-length-breadth ratio. We also identified haplotypes that can be used to select plants in our population for short stature (plant height), early flowering time, and high yield, and thus demonstrate the utility of association mapping in breeding populations for informing breeding decisions. We conclude by exploring how the newly identified significant SNPs and insights into the genetic architecture of these quantitative traits can be leveraged to build genomic-assisted selection models.
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影响因子：
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作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
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通讯作者：
Gardner CA