Mapping quantitative trait loci for seed size traits in soybean (Glycine max L. Merr.)

Seed size traits in soybean-length, width and thickness-and their corresponding ratios-length-to-width, length-to-thickness and width-to-thickness-play a crucial role in determining seed appearance, quality and yield. In this study, an attempt was made to detect quantitative trait loci (QTL) for the aforementioned seed size traits in F-2:3, F-2:4 and F-2:5 populations from the direct and reciprocal crosses of Lishuizhongzihuang with Nannong 493-1, using multi-QTL joint analysis (MJA) along with composite interval mapping (CIM). A total of 121 main-effect QTL (M-QTL), six environmental effects, eight environment-by-QTL interactions, five cytoplasmic effects and 92 cytoplasm-by-QTL interactions were detected. Fifty-two common M-QTL across MJA and CIM, 21 common M-QTL in more than two populations and 5 M-QTL in all three populations showed the stability of the results. Five M-QTL had higher heritability, greater than 20%. In addition, 28 cytoplasm-by-QTL and 4 environment-by-QTL interactions were confirmed by CIM. Most M-QTL were clustered in eight chromosomal regions. Our results provide a good foundation for fine mapping, cloning and designed molecular breeding of favorable genes related to soybean seed size traits.