Validating genome-wide association candidates controlling quantitative variation in nodulation

Genome-wide association (GWA) studies offer the opportunity to identify genes that contribute to naturally occurring variation in quantitative traits. However, GWA relies exclusively on statistical association, so functional validation is necessary to make strong claims about gene function. We used a combination of gene-disruption platforms (Tnt1 retrotransposons, hairpin RNA-interference constructs, and CRISPR/Cas9 nucleases) together with randomized, well-replicated experiments to evaluate the function of genes that an earlier GWA study in Medicago truncatula had identified as candidates contributing to variation in the symbiosis between legumes and rhizobia. We evaluated ten candidate genes found in six clusters of strongly associated single nucleotide polymorphisms, selected on the basis of their strength of statistical association, proximity to annotated gene models, and root or nodule expression. We found statistically significant effects on nodule production for three candidate g...全基因组关联（Genome-wide association, GWA）研究为识别参与数量性状自然变异的基因提供了可能。然而，GWA研究仅依赖统计学关联，因此若要对基因功能作出严谨论断，必须开展功能验证。本研究结合基因敲除平台（包括Tnt1反转录转座子、发夹RNA干扰载体及CRISPR/Cas9核酸酶）与随机化、高重复实验，对蒺藜苜蓿早期一项GWA研究中鉴定出的候选基因进行功能评估，这些候选基因被认为与豆科植物与根瘤菌的共生性状变异相关。研究人员基于统计关联强度、与注释基因模型的邻近性以及根或根瘤的表达情况，筛选出6个强关联单核苷酸多态性（single nucleotide polymorphisms, SNPs）簇内的10个候选基因。最终发现3个候选基因对结瘤产量具有统计学意义上的显著影响……