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Seed size and shape traits are important determinants of seed yield and appearance quality in soybean [ Glycine max  (L.) Merr.]. Understanding the genetic architecture of these traits is important to enable their genetic improvement through efficient and targeted selection in soybean breeding, and for the identification of underlying causal genes. To map seed size and shape traits in soybean, a recombinant inbred line (RIL) population developed from K099 (small seed size) × Fendou 16 (large seed size), was phenotyped in three growing seasons. A genetic map of the RIL population was developed using 1,485 genotyping by random amplicon sequencing-direct (GRAS-Di) and 177 SSR markers. Quantitative trait locus (QTL) mapping was conducted by inclusive composite interval mapping. As a result, 53 significant QTLs for seed size traits and 27 significant QTLs for seed shape traits were identified. Six of these QTLs ( qSW8.1, qSW16.1, qSLW2.1, qSLT2.1, qSWT1.2 , and  qSWT4.3 ) were identified with LOD scores of 3.80–14.0 and  R  2  of 2.36%–39.49% in at least two growing seasons. Among the above significant QTLs, 24 QTLs were grouped into 11 QTL clusters, such as, three major QTLs ( qSL2.3 ,  qSLW2.1 , and  qSLT2.1 ) were clustered into a major QTL on Chr.02, named as  qSS2 . The effect of  qSS2  was validated in a pair of near isogenic lines, and its candidate genes ( Glyma.02G269400, Glyma.02G272100, Glyma.02G274900, Glyma.02G277200 , and  Glyma.02G277600 ) were mined. The results of this study will assist in the breeding programs aiming at improvement of seed size and shape traits in soybean.

A Major and Stable Quantitative Trait Locus qSS2 for Seed Size and Shape Traits in a Soybean RIL Population