Phenotypic and genetic dissection of seed shape related traits in soybean (Glycine max L.)

Introduction Seed shape and hundred-seed weight (HSW) are yield-related traits, but the interrelationships between them and a systematic genetic analysis are lacking. Methods In this study, phenotypic evaluation of seed shape-related traits and HSW was performed in a recombinant inbred line (RIL) population derived from the cross between “ZD41” and “ZYD02878.” All seed shape-related traits (SW, seed width; SL, seed length; ST, seed thickness; SP, seed perimeter; SA, seed area; SLW, seed length-to-width ratio; SLT, seed length-to-thickness ratio; SWT, seed width to thickness ratio) were evaluated. Broad-sense heritability was calculated. Correlation analysis, path analysis, QTL mapping (using ICIM, EMMAX, and TASSEL), and genomic selection (using rrBLUP) were performed. Results All seed shape-related traits exhibited approximately normal distributions in the RIL population. The broad-sense heritability of seed shape-related traits ranged from 0.67 to 0.90, indicating that additive genes played a major role in expressing all studied traits. Correlation analysis revealed that SW showed the highest positive correlation with HSW (r = 0.86–0.87, P 0.001) among the three measured seed shape-related traits (SL, SW, and ST), which agrees with the finding that SW was the only trait showing a positive direct effect on HSW in path analysis. A total of 98 QTL corresponding to 59 unique regions were identified by ICIM, EMMAX, and TASSEL. Three genes, Glyma.02G255900, Glyma.02G270100 , and Glyma.02G275200 , were identified as candidates for seed shape regulation. Genomic selection for seed shape-related traits using rrBLUP revealed that the prediction accuracy of SL, SW, ST, SP, and SA reached 0.65, 0.68, 0.65, 0.67, and 0.68, respectively, based on genome-wide SNP markers. Discussion This study provided a systematic dissection of seed shape-related traits in terms of both phenotypic and genetic aspects, which laid a solid foundation for gene cloning and could be used in breeding programs in the future.