Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, 1991 Buford Circle, Saint Paul, MN, 55108, USA.
Heredity (Edinb). 2022 Sep;129(3):155-160. doi: 10.1038/s41437-022-00548-8. Epub 2022 Jun 8.
The covariance between relatives is a tenet in quantitative genetics, but the covariance between nonrelatives in crops has not been studied. My objective was to determine if a covariance between nonrelatives is present in maize (Zea mays L.). The germplasm comprised 272 maize lines that were previously genotyped with 28,626 single nucleotide polymorphism (SNP) markers. Pairs of unrelated lines were identified on the basis of their membership probabilities in five subpopulations. The covariance between nonrelatives was assessed as the regression of phenotypic similarity on SNP similarity between unrelated lines. Out of 77 regressions, seven were significant at a 5% false discovery rate: anthesis and silking dates in unrelated B73 and Oh43 lines; plant height and ear height in unrelated Oh43 and PH207 lines; oil in unrelated A321 and Mo17 lines; starch in unrelated B73 and PH207 lines; and protein in unrelated B73 and Mo17 lines. The latter covariance was negative, and this negative covariance between nonrelatives was attributed to the subpopulations having different linkage phases between the markers and underlying causal variants. Overall, the results indicated that a covariance between nonrelatives in maize is not ubiquitous but is sometimes present for specific traits and for certain groups of unrelated individuals. I propose that the covariance between nonrelatives and the covariance between relatives be combined into a generalized covariance between individuals, thus giving a unified framework for expressing the resemblance regardless of the degree of relatedness.
亲属间的协方差是数量遗传学的一个基本原理，但作物中非亲属间的协方差尚未得到研究。我的目的是确定玉米（Zea mays L.）中非亲属间是否存在协方差。该种质由 272 条玉米系组成，这些系先前已通过 28626 个单核苷酸多态性（SNP）标记进行了基因型分析。根据其在五个亚群中的成员概率确定了非相关系对。非相关系之间的协方差评估为 SNP 相似性与非相关系之间表型相似性之间的回归。在 77 个回归中，有七个在 5%的假发现率下显著：非相关 B73 和 Oh43 系的开花期和吐丝期；非相关 Oh43 和 PH207 系的株高和穗位高；非相关 A321 和 Mo17 系的油分；非相关 B73 和 PH207 系的淀粉；以及非相关 B73 和 Mo17 系的蛋白质。后一种协方差为负，这种非相关个体之间的负协方差归因于标记和潜在因果变异之间的亚群具有不同的连锁相位。总体而言，结果表明，玉米中非亲属间的协方差并非普遍存在，但对于特定性状和某些非相关个体群体有时存在。我提出将非相关个体之间的协方差与相关个体之间的协方差结合为个体的广义协方差，从而为表达相似性提供一个统一的框架，而不论相关程度如何。
