Data from Genome-Wide Association Mapping in Exotic x Canadian Elite Crosses: Mining Beneficial Alleles for Agronomic and Seed Composition Traits in Soybean

Phenotypic Data: The RIL populations along with their respective parents (n=294) were planted in three test environments over two years in Southwestern Ontario, Canada. The test environments included Chatham (42°23’58.5”N 82°07′17.1”W) and Palmyra (42°25′50.1″N 81°45′06.9″W) in 2022 and Ridgetown (42°27′14.8″N 81°52′48.0″W) in 2023. A randomized complete block design (RCBD) with two replicates was used in each field-testing location, where each plot consisted of five rows, 4.2 m long, with a row spacing of 43 cm. A total of 500 seeds were planted in each plot to achieve a plant density of 54 seeds per square meter (m²). The middle three rows were machine harvested at maturity for estimating yield performance and measuring seed quality traits. Seed yield (SY), plant height (PH), days to maturity (DTM), seed weight (SW) and seed composition traits, which included the seed concentration of protein, oil and sucrose on a dry seed basis. The agronomic traits including maturity (DTM,days) and plant height (PH,cm) were scored in the field at maturity. Seed yield (SY, kg/ha) and seed weight (SW, g/100 seeds) were measured for each harvested plot along with seed moisture and adjusted to 13% moisture. Seed composition traits were determined based on subsampling the total harvested plots on a dry basis (0% seed moisture) and measured as an average of three technical replicate readings. The seed composition traits were measured as percentage of dry seed weight using a Perten DA 7250 SD near-infrared reflectance (NIR) analyzer (Perten Instruments Canada, Winnipeg, MB).Genotypic Data: RIL marker data accquired from genotyping by sequencing (GBS) based on PE150 (pair-ended) library prep via BfaI restriction enzyme digest used for GWAS analysis. a marker score of 0 represents homozygous OAC Bruton allele, 1 represents heterozygous and 2 represents exotic parent allele. SNP List: positional information of markers in the genotypic data set. PCA Data: Top 5 principal components (PCs) used to plot principal component analysis (PCA) plot.表型数据：重组自交系（Recombinant Inbred Lines, RIL）群体及其各自亲本共计294份材料，于加拿大安大略省西南部的三个试验环境中开展两年的种植试验。2022年的试验地点为查塔姆（42°23′58.5"N 82°07′17.1"W）与帕尔迈拉（42°25′50.1"N 81°45′06.9"W），2023年的试验地点为里奇敦（42°27′14.8"N 81°52′48.0"W）。各田间试验点均采用随机完全区组设计（Randomized Complete Block Design, RCBD），设置2次重复；每个小区包含5行，行长4.2米，行距43厘米。每小区播种500粒种子，以达到每平方米54粒的种植密度。待作物成熟后，机械收获中间三行，用于评估产量表现并测定种子品质性状。 调查的性状包括种子产量（Seed Yield, SY）、株高（Plant Height, PH）、生育日数（Days to Maturity, DTM）、百粒重（Seed Weight, SW）以及以干种子为基准的蛋白质、油脂与蔗糖浓度组成的种子组成性状；农艺性状包括生育期（DTM，单位：天）与株高（PH，单位：厘米），均于田间成熟期进行调查。针对每个收获小区，测定种子产量（SY，单位：千克/公顷，kg/ha）与百粒重（SW，单位：克/100粒，g/100 seeds），同时测定种子含水量并校正至13%的标准含水量。种子组成性状通过采集总收获小区的干样品（种子含水量为0%）进行测定，取3次技术重复的平均值作为结果。种子组成性状以干种子重量百分比表示，采用Perten DA 7250 SD近红外反射光谱（Near-Infrared Reflectance, NIR）分析仪（加拿大Perten仪器公司，温尼伯，马尼托巴省）完成测定。 基因型数据：重组自交系（Recombinant Inbred Lines, RIL）的标记数据通过基于BfaI限制性酶切的PE150（双端）文库制备的测序分型（Genotyping by Sequencing, GBS）获得，用于全基因组关联分析（Genome-Wide Association Study, GWAS）。标记评分规则为：0代表纯合OAC Bruton等位基因，1代表杂合等位基因，2代表外来亲本等位基因。SNP列表：基因型数据集中标记的位置信息。 主成分分析数据：用于绘制主成分分析（Principal Component Analysis, PCA）图的前5个主成分（Principal Components, PCs）。