When handling a structured population in association mapping, group-specific allele effects may be observed at quantitative trait loci (QTLs) for several reasons: (i) a different linkage disequilibrium (LD) between SNPs and QTLs across groups, (ii) group-specific genetic mutations in QTL regions, and/or (iii) epistatic interactions between QTLs and other loci that have differentiated allele frequencies between groups. We present here a new genome-wide association (GWAS) approach to identify QTLs exhibiting such group-specific allele effects. We developed genetic materials including admixed progeny from different genetic groups with known genome-wide ancestries (local admixture). A dedicated statistical methodology was developed to analyze pure and admixed individuals jointly, allowing one to disentangle the factors causing the heterogeneity of allele effects across groups. This approach was applied to maize by developing an inbred “Flint-Dent” panel including admixed individuals that was evaluated for flowering time. Several associations were detected revealing a wide range of configurations of allele effects, both at known flowering QTLs (Vgt1, Vgt2 and Vgt3) and new loci. We found several QTLs whose effect depended on the group ancestry of alleles while others interacted with the genetic background. Our GWAS approach provides useful information on the stability of QTL effects across genetic groups and can be applied to a wide range of species.

当在关联作图中处理结构化群体时，由于多种原因，可能会在数量性状位点 (QTL) 处观察到群体特异性等位基因效应：(i) 群体间 SNP 和 QTL 之间存在不同的连锁不平衡 (LD)，(ii) 群体- QTL 区域中的特定基因突变，和/或 (iii) QTL 与其他基因座之间的上位相互作用，这些基因座在群体之间具有不同的等位基因频率。我们在此提出了一种新的全基因组关联（GWAS）方法来识别表现出此类群体特异性等位基因效应的 QTL。我们开发了遗传材料，包括来自具有已知全基因组祖先的不同遗传群体的混合后代（局部混合物）。开发了一种专门的统计方法来共同分析纯个体和混合个体，从而使人们能够理清导致群体间等位基因效应异质性的因素。通过开发近交“Flint-Dent”小组，将这种方法应用于玉米，其中包括评估开花时间的混合个体。检测到的几种关联揭示了多种等位基因效应的配置，包括已知的开花 QTL（Vgt1、Vgt2和Vgt3）和新基因座。我们发现了几个 QTL，其影响取决于等位基因的群体祖先，而其他 QTL 则与遗传背景相互作用。我们的 GWAS 方法提供了有关跨遗传群体 QTL 效应稳定性的有用信息，并且可应用于广泛的物种。