Genomic prediction (GP), which could predict the breeding value of crop plants genotyped with molecular markers, has been carried out in multiple species. Prediction accuracy (PA) of GP depends on various factors, including genetic relatedness and genetic basis. In this study, we examined the rationale for the low PA of GP when the training and validation populations were distinct using 170 temperate inbred lines and 210 tropical and subtropical inbred lines, respectively. All inbred lines were evaluated for 17 traits and genotyped with 550K high‐density markers. The results show that: (a) the influences of heritability and marker number on PA reflected variations in phenotypic variance captured by the genetic information; (b) the low PA of GP when the training and validation populations represent structured subpopulation is related to the ratio of subpopulation‐common alleles (RSCA) and the genetic relatedness between the two subpopulations; (c) RSCA and PA increased with the increase of genetic relatedness, suggesting that these three factors were related. Our findings would provide references when performing GP, and guidance when designing breeding populations.

中文翻译：

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遗传相关性和亚种群常见等位基因的比例与玉米结构化亚种群的基因组预测有关

基因组预测（GP）可以预测使用分子标记进行基因分型的农作物的育种价值，已在多个物种中进行。GP的预测准确性（PA）取决于多种因素，包括遗传相关性和遗传基础。在这项研究中，我们分别使用170个温带自交系和210个热带及亚热带自交系来检验当训练和验证人群不同时GP低PA的基本原理。评价了所有自交系的17个性状，并用550K高密度标记进行了基因分型。结果表明：（a）遗传力和标记数对PA的影响反映了遗传信息捕获的表型变异的变化；（b）当训练和验证人群代表结构化亚群时GP的低PA与亚群常见等位基因（RSCA）的比例以及两个亚群之间的遗传相关性有关; （c）RSCA和PA随着遗传相关性的增加而增加，表明这三个因素是相关的。我们的发现将为进行全科医生提供参考，并为设计繁殖种群提供指导。