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

Giriraj Kumawat,Donghe Xu

doi:10.3389/fgene.2021.646102

Abstract

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 R2 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.

Highlights

Soybean [Glycine max (L.) Merr.] is one of the world’s most economically important food and oil crops
Fendou 16 seeds are larger with trait values 21.5% (SSW), 29.3% (SL), 30.7% (SLW), 36.7% (SLT), and 8.7% (SWT) higher compared to K099, which has an ST value 11.3% higher than Fendou 16
We have identified six stable Quantitative trait locus (QTL) for seed size and shape traits accounting for significant phenotypic contributions across multiple years, besides identifying several other environmentspecific QTLs

Summary

Introduction

Soybean [Glycine max (L.) Merr.] is one of the world’s most economically important food and oil crops It is a rich source of edible oil and protein, and provides substrate for several food and industrially important products (Lam et al, 2010; Kumawat et al, 2016). Seed size is highly correlated with seed weight, and a primary breeding target to improve seed yield (Xu et al, 2011; Li et al, 2019). Seed size traits such as length (SL), width (SW), thickness (ST), and single seed weight (SSW), and seed shape traits such as length-to-width (SLW), length-to-thickness (SLT) and width-to-thickness

Methods

Results

Discussion

Conclusion