Identification of an adaptor protein 2σ gene for OsTGW12 to determine grain weight and potentiate quality breeding in rice.

Key message: This study identified an adaptor protein gene OsAP2σ (LOC_Os12g10560) as a causal gene for OsTGW12, a major QTL on rice chromosome to determine the thousand-grain weight (TGW), elucidated the role of a specific SNP (G266A) within this gene in determining grain size by affecting cell number, and the demonstrated interaction between OsAP2σ and OsSAMS1 suggested a novel regulatory mechanism linking clathrin-mediated endocytosis (CME) to S-adenosylmethionine metabolism in rice grain development. In rice, many quantitative trait loci/genes of thousand-grain weight (TGW) have been identified and applied to breed rice varieties with high yield. Here, we identified an allele OsAP2σ^89G from a small grain indica rice variety G1025, a causal gene for OsTGW12 on rice chromosome 12 to determine grain weight. AP2σ is an adaptor protein (AP) subunit 2σ involved in the clathrin-mediated endocytosis (CME) in eukaryotic cells. Moreover, overexpression of the allele K1561-OsAP2σ^89E but not the allele G1025-OsAP2σ^89G increased grain length, grain width and grain weight than the wild type G1025 whereas the RNAi-mediated OsAP2σ mutant showed the opposites. Co-immunoprecipitation mass spectrometry (Co-IP-MS), yeast two-hybrid (Y2H), and luciferase implementation (LUC) assays demonstrated the interaction between OsAP2σ and S-adenosylmethionine synthetase (OsSAMS1), a key enzyme involved in methionine metabolism pathway. In addition, both OsAP2σ and OsSAMS1 were localized into the plasma membrane (PM) and nucleus. Transcriptomic analysis revealed that OsAP2σ regulated the expressions of related genes to CME, mitogen activated protein kinase (MAPK) signaling, and auxin transport and transcriptional regulation during rice grain development. Thus, this study reveals a new role of OsAP2σ and provides a potential in further breeding programs of the quality improvement in rice.