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.