Grain size is a core agronomic trait for breeders which influences grain yield. Previous studies have shown that histone acetylation modifications can affect grain size, but it is unclear how epigenetic mechanisms precisely target specific genes to regulate this trait.

Recently, Prof. LI Yunhai's team from the Institute of Genetics and Developmental Biology of the Chinese Academy of Sciences (CAS), Prof. ZHENG Leiying from the Institute of Botany of CAS and Prof. DIAO Xianmin from the Chinese Academy of Agricultural Sciences, revealed a novel epigenetic mechanism by which a complex formed by the histone-binding protein LARGE3 and the histone deacetylase OsHDT1 regulates grain size in rice by modulating histone H4 acetylation.

The researchers screened a rice mutant population. They identified large3-1 which produced significantly larger and heavier grains, and confirmed that the phenotype was caused by a mutation in the LARGE3 gene.

Further analyses revealed that LARGE3 was a nuclear protein that binds histones and directly interacts with OsHDT1, and that LARGE3 and OsHDT1 repressed the expression of an important grain size gene OsMKKK10 by decreasing its histone H4 acetylation level and increasing its nucleosome density.

Importantly, the researchers found that genome editing of the LARGE3 homolog in foxtail millet formed large grains and could increase grain yield, demonstrating that this module has the potential to improve the grain yield in key crops.

These findings, published in The Plant Cell, establish a novel link between epigenetic control of grain size and MAPK signaling. The study not only reveals a mechanistic framework but also provides a new target for precision breeding.