Natural Variation in GmSL20 Improves Seed Size and Quality in Soybean

Seed size plays an important role in determining crop yield, yet the genetic mechanisms underlying the regulation of this agronomic trait remain incompletely understood in soybean. Here, we perform a genome-wide association study mapping with seed length variations and identify a major quantitative trait locus (QTL) on chromosome 20, named SL20 (Seed Length 20). GmSL20 encodes a TGA-type bZIP transcription factor that controls soybean seed size and weight in natural populations. Knockout of GmSL20 suppresses seed enlargement and lipid biosynthesis in soybean, whereas increased expression of GmSL20 improves seed size and oil content. Further functional investigations reveal that GmSL20 directly activates GmST05 and GmZF351, thus promoting carbon partitioning to seeds. A super allele that arose from domestication confers elevated capacity for DNA binding and transcriptional activation to GmSL20. It correlates with larger seed size in haplotype analysis and enhances seed size and weight in elite soybean variety; however, it has not been widely fixed and spread through modern breeding. The role of GmSL20 to promote yield and quality underscores its potential as a valuable resource for soybean breeding programs seeking to improve both traits simultaneously.