University of São Paulo, Luiz de Queiroz College of Agriculture, Department of Genetics, Piracicaba, São Paulo, Brazil.
Institute of Quantitative Health Sciences and Engineering, Michigan State University, East Lansing, Michigan, United States of America.
PLoS One. 2020 Feb 7;15(2):e0228724. doi: 10.1371/journal.pone.0228724. eCollection 2020.
Genome-wide association studies (GWAS) is one of the most popular methods of studying the genetic control of traits. This methodology has been intensely performed on inbred genotypes to identify causal variants. Nonetheless, the lack of covariance between the phenotype of inbred lines and their offspring in cross-pollinated species (such as maize) raises questions on the applicability of these findings in a hybrid breeding context. To address this topic, we incorporated previously reported parental lines GWAS information into the prediction of a low heritability trait in hybrids. This was done by marker-assisted selection based on significant markers identified in the lines and by genomic prediction having these markers as fixed effects. Additive-dominance GWAS of hybrids, a non-conventional procedure, was also performed for comparison purposes. Our results suggest that incorporating information from parental inbred lines GWAS led to decreases in the predictive ability of hybrids. Correspondingly, inbred lines and hybrids-based GWAS yielded different results. These findings do not invalidate GWAS on inbred lines for selection purposes, but mean that it may not be directly useful for hybrid breeding.
全基因组关联研究（GWAS）是研究性状遗传控制的最流行方法之一。这种方法在近交基因型上进行了深入研究，以鉴定因果变异。然而，在异花授粉物种（如玉米）中，近交系与其后代的表型之间缺乏协方差，这使得这些发现是否适用于杂种繁殖背景受到质疑。为了解决这个问题，我们将先前报道的亲本系 GWAS 信息纳入了杂种低遗传力性状的预测中。这是通过基于在线性中鉴定到的显著标记的标记辅助选择和将这些标记作为固定效应的基因组预测来完成的。还进行了杂种的加性-显性 GWAS 分析，作为比较目的的非常规程序。我们的结果表明，整合来自亲本近交系 GWAS 的信息会降低杂种的预测能力。相应地，基于近交系和杂种的 GWAS 产生了不同的结果。这些发现并不否定 GWAS 对选择目的的近交系的有效性，但意味着它可能对杂种繁殖没有直接的用处。
