An Intronic Structural Variant in GhEBS1 Drives Cotton Fruit Size Divergence by Modulating Chromatin Accessibility and Gene Expression

Abstract

ABSTRACT Fruit size is not only a crucial fitness trait in plant evolution but also an important agronomic target in crop domestication and improvement, yet its regulatory mechanisms remain poorly characterized. Here, we identified an F‐box E3 ubiquitin ligase gene, GhEBS1 (ENLARGED BOLL SIZE 1), as a positive regulator of cotton boll size via map‐based cloning. An 845‐bp structural variant in the promoter‐proximal intronic region of GhEBS1 alters local chromatin accessibility and histone modifications, specifically H3K27 and H3K9 methylation levels and acetylation, thereby modulating GhEBS1 expression and driving boll size divergence. Overexpression or heterologous expression of GhEBS1 in cotton (capsule), tomato (berry) and Arabidopsis (silique) promoted fruit enlargement, indicating its functional conservation. Further analysis showed that GhEBS1 interacts with GhPPD1/2 and GhKIX8/9 to modulate downstream cell proliferation‐related genes to control cell number and boll size. Breeding evaluations confirm that the elite GhEBS1 L allele significantly increases boll size, seed size and boll weight. Haplotype analysis reveals that GhEBS1 L originated from Gossypium hirsutum race latifolium and underwent artificial selection during cotton domestication. Our findings provide new insights into the regulation of plant fruit size and present a valuable genetic locus for crop yield improvement.