Phenotypic and marker data for statistical genetic analysis of Minnesota maize lines

Publicly available maize lines are a resource for studying quantitative genetic variation in plants. This dataset includes cluster or subpopulation information, phenotypic data, and single nucleotide polymorphism (SNP) data for 272 maize lines developed by the University of Minnesota, other universities, and seed companies. The lines were evaluated at multiple locations in Minnesota in 2011 and 2012 for different phenological, morphological, and kernel composition traits. The lines were genotyped for 56,110 SNP loci on the Maize SNP50 Beadchip (Illumina). Filtering for SNP data quality led to data for 28,626 SNP loci for the 272 maize lines. Population structure analysis showed that the maize lines clustered into five subpopulations (A321 or Minnesota 13, B73, Mo17, Oh43, and PH207 or Iodent) that represented most of the U.S. Corn Belt diversity (Schaefer and Bernardo 2013a, Crop Science 53:1529-1536). Genomewide association mapping revealed marker-trait associations for male flowering date, female flowering date, plant height, ear height, and kernel concentration for oil, protein, and starch (Schaefer and Bernardo 2013b, Crop Science 53:2518-2529). The covariance between relatives is a tenet in quantitative genetics, but such classical theory has ignored any resemblance between individuals unrelated by pedigree. Analysis of this maize dataset showed that a covariance between nonrelatives in maize is not ubiquitous but it is sometimes rpesent for specific traits and for certain groups of unrelated individuals (Bernardo 2022, Heredity).

公开获取的玉米自交系是开展植物数量遗传变异研究的宝贵资源。本数据集涵盖了由明尼苏达大学、其他高校及种子公司培育的272份玉米自交系的聚类/亚群体信息、表型数据与单核苷酸多态性（Single Nucleotide Polymorphism, SNP）数据。2011年与2012年，研究人员在明尼苏达州多个试验点对这些自交系开展了物候学、形态学及籽粒组成相关性状的表型鉴定。这些自交系通过Illumina公司的玉米SNP50基因分型芯片（Maize SNP50 Beadchip）对56110个SNP位点进行了基因分型；经过SNP数据质量过滤后，最终得到272份玉米自交系的28626个SNP位点的有效分型数据。群体结构分析表明，这批玉米自交系可划分为5个亚群体：A321（亦称明尼苏达13）、B73、Mo17、Oh43以及PH207（亦称Iodent），这些亚群体涵盖了美国玉米带的绝大多数遗传多样性（Schaefer与Bernardo，2013a，《作物科学》（Crop Science），53卷：1529-1536）。全基因组关联定位分析鉴定出了雄花开花期、雌花开花期、株高、穗位高以及籽粒油分、蛋白质与淀粉含量相关的标记-性状关联位点（Schaefer与Bernardo，2013b，《作物科学》，53卷：2518-2529）。亲属间的协方差是数量遗传学的核心原理之一，但经典数量遗传理论并未考虑无系谱关联个体间的遗传相似性。对本玉米数据集的分析表明，玉米无关联个体间的协方差并非普遍存在，但针对特定性状以及部分无关联自交系群体，该协方差确实存在（Bernardo，2022，《遗传》（Heredity））。