Genetic analysis and map-based delimitation of a major locus qSS3 for seed size in soybean

Seed size is a major determinant of grain yield in soybean, however their genetic basis remains largely unknown. In order to delimit map-based position of a major locus qSS3 , we evaluated three mapping populations, including RILs, NILs and a sub-F₂ in three environments for six seed size-related traits. For these traits, the kurtosis and skewness ranged between 0.0 and 1.16, while h²_b ranged from 0.75 to 0.96, indicating that this RIL population is suitable for QTL analysis. QTL analysis identified 12 loci which consist of 30 significant QTLs with PVE% and LOD values of 6.6%–26.2% and 2.50–5.61, respectively. Among them, qSS3 was a major and stable locus explaining 7.3%–26.2% of the variation in 5 of the 6 traits, with the respective LOD values falling in the range of 2.72–5.61. Additionally, qSS3 effects were confirmed in NILs and delimited to an interval of ~1,126 kb containing 123 annotated genes. Overall, this study may assist efforts aiming to improve soybean seed traits by identifying valuable genetic resources which can be used in future MAS breeding programmes.