Single-plant GWAS coupled with bulk segregant analysis allows rapid identification and corroboration of plant-height candidate SNPs
Single-plant GWAS coupled with bulk segregant analysis allows rapid identification and corroboration of plant-height candidate SNPs
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DOI：
10.1186/s12870-019-2000-y
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发表时间：
2019-10-08
影响因子：
5.3
通讯作者：
Beissinger, Timothy M.
中科院分区：
文献类型：
--
作者：
Gyawali, Abiskar;Shrestha, Vivek;Beissinger, Timothy M.
背景全基因组关联研究（GWAS）是鉴定与作物物种各种重要性状相关的数量性状基因座（QTL）和因果性单核苷酸多态性（SNP）/基因的有力工具。通常，作物中的GWAS使用一组近交系进行，其中测量相同近交系的多个重复，并将平均表型作为响应变量。在这里，我们描述和评估单株GWAS（SP-GWAS）进行GWAS对个别植物，这不需要一个协会小组的近交系。相反，sp-GWAS依赖于从随机交配群体中取样的个体植物的表型和基因型。重要的是，我们证明了如何SP-GWAS可以有效地结合了大量的分离分析（BSA）实验，以迅速证实证据显着SNPs.ResultsIn这项研究中，我们使用的Shoepeg玉米地方品种，收集作为一个开放授粉品种从一个农场在南密苏里州在20世纪60年代，评估sp-GWAS与BSA偶联是否可以有效和有力地用于检测SNP与植物高度（PH）的显著关联。植物在8个地点生长两年，总共768个个体进行了sp-GWAS的基因分型和表型。对768个个体的306 k个多态性标记进行关联分析，共检测到25个显著性差异（P
BackgroundGenome wide association studies (GWAS) are a powerful tool for identifying quantitative trait loci (QTL) and causal single nucleotide polymorphisms (SNPs)/genes associated with various important traits in crop species. Typically, GWAS in crops are performed using a panel of inbred lines, where multiple replicates of the same inbred are measured and the average phenotype is taken as the response variable. Here we describe and evaluate single plant GWAS (sp-GWAS) for performing a GWAS on individual plants, which does not require an association panel of inbreds. Instead sp-GWAS relies on the phenotypes and genotypes from individual plants sampled from a randomly mating population. Importantly, we demonstrate how sp-GWAS can be efficiently combined with a bulk segregant analysis (BSA) experiment to rapidly corroborate evidence for significant SNPs.ResultsIn this study we used the Shoepeg maize landrace, collected as an open pollinating variety from a farm in Southern Missouri in the 1960's, to evaluate whether sp-GWAS coupled with BSA can efficiently and powerfully used to detect significant association of SNPs for plant height (PH). Plant were grown in 8 locations across two years and in total 768 individuals were genotyped and phenotyped for sp-GWAS. A total of 306k polymorphic markers in 768 individuals evaluated via association analysis detected 25 significant SNPs (P