The SNL Histone Deacetylase-Binding Factor GmHE13 Is a Novel Regulator of Soybean Hypocotyl Elongation

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.