Rice Science

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Genome-Wide Association Study of Brown Rice Weight Identifies an RNA-Binding Protein Antagonistically Regulating Grain Weight and Panicle Number

  1. State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization / Jiangsu Collaborative Innovation Center for Modern Crop Production / Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 211800, China; #These authors contributed equally to this work
  • Contact: ZHANG Hongsheng; CHEN Sunlu
  • Supported by:

    This study was supported by the National Natural Science Foundation of China (Grant Nos. 32000377, 32172037, and 32472211), the Biological Breeding-National Science and Technology Major Project, China (Grant No. 2023ZD04068), the Fundamental Research Funds for the Central Universities, China (Grant No. KJQN202103), the open funds of the State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, China (Grant No. ZW202401), and the Cyrus Tang Innovation Center for Crop Seed Industry, China. We thank Zhou Shoujun at Nanjing Agricultural University for field management. The CRISPR/Cas9 plasmids were a gift from Chen Qijun at China Agricultural University.

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Abstract: Rice grain yield is primarily determined by three key agronomic traits: panicle number, grain number per panicle, and grain weight (GW). However, the inherent tradeoffs among these yield components remain a persistent challenge in rice breeding programs. Notably, compared with GW, brown rice weight (BRW) provides a more direct metric associated with actual grain yield potential. In this study, we conducted a two-year replicated genome-wide association study to elucidate the genetic architecture of BRW and identify new loci regulating GW. Among seven consistently detected loci across experimental replicates, four were not co-localized with previously reported BRW/GW-related genes. BRW1.1, one of the four newly identified loci, was found to probably encode a novel RNA-binding protein. Functional characterization revealed that BRW1.1 acts as a negative regulator of BRW, potentially through modulation of mRNA translation processes. Intriguingly, through integrated analysis of mutant phenotypes and haplotype variations, we demonstrated that BRW1.1 mediates the physiological tradeoff between GW and panicle number. This study not only delineates the genetic determinants of BRW but also identifies BRW1.1 as a promising molecular target for breaking the yield component tradeoff in precision rice breeding.

Key words: GWAS, brown rice weight, RNA-binding protein, tradeoff, grain weight, panicle number