Abstract
Hypocotyl elongation is one of the key events during seed germination and seedling establishment, determining the field performance and yield of soybean. In this study, using a genome-wide association study (GWAS) method, we identified a candidate gene regulating soybean hypocotyl elongation, GmHE13 (HYPOCOTYL ELONGATION 13), which encodes an SNL histone deacetylase (HDAC)-binding protein. Knockout of GmHE13 led to over-elongated hypocotyls, while overexpression of GmHE13 suppressed hypocotyl elongation, confirming GmHE13 as an inhibitor of hypocotyl development. As an SNL protein, GmHE13 interacts with multiple HDACs and a Myb-like transcription factor (TF) GmRVE5 (REVEILLE5) to form HDAC complexes. These complexes remove H3K14 acetylation from hypocotyl growth-related genes, including expansins, thereby repressing their expression and inhibiting hypocotyl elongation. Furthermore, the lead SNP (single-nucleotide polymorphism) dividing GmHE13 into two major haplotypes was found to determine the binding activity of a light-responsive TF, GmOBP3, to GmHE13's promoter and lead to differential expression of GmHE13, resulting in differential hypocotyl elongation. Interestingly, the distribution of GmHE13 haplotypes displayed a latitudinal preference, with GmHE13(Hap1) being a target of artificial selection during soybean breeding. Taken together, our findings revealed a novel epigenetic mechanism regulating soybean hypocotyl elongation, providing a theoretical basis and gene loci for directional improvement of soybean varieties.