Natural variation of RGN1a regulates grain number per panicle in japonica rice

Quan Zhang; Jianyin Xie; Xueqiang Wang; Miaosong Liu; Xiaoyang Zhu; Tao Yang; Najeeb Ullah Khan; Chen Sun; Jinjie Li; Zhanying Zhang; Zichao Li; Hongliang Zhang

doi:10.3389/fpls.2022.1097622

Natural variation of RGN1a regulates grain number per panicle in japonica rice

Front Plant Sci. 2022 Dec 13:13:1097622. doi: 10.3389/fpls.2022.1097622. eCollection 2022.

Authors

Quan Zhang¹, Jianyin Xie^{1

2}, Xueqiang Wang¹, Miaosong Liu¹, Xiaoyang Zhu¹, Tao Yang¹, Najeeb Ullah Khan¹, Chen Sun¹, Jinjie Li¹, Zhanying Zhang¹, Zichao Li¹, Hongliang Zhang^{1

2}

Affiliations

¹ State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China.
² Sanya Institute of China Agricultural University, Sanya Nanfan Research Institute of Hainan University, Sanya, China.

Abstract

The grain number per panicle (GNP) is an important yield component. Identifying naturally favorable variations in GNP will benefit high-yield rice breeding. Here, we performed a genome-wide association study using a mini-core collection of 266 cultivated rice accessions with deep sequencing data and investigated the phenotype for three years. Three genes, i.e., TOTOU1 (TUT1), Grain height date 7 (Ghd7), and Days to heading 7/Grain height date 7.1/Pseudo-Response Regulator37 (DTH7/Ghd7.1/OsPRR37), which regulate GNP, were found in the quantitative trait loci (QTL) identified in this study. A stable QTL, qGNP1.3, which showed a strong correlation with variations in GNP, was repeatedly detected. After functional and transgenic phenotype analysis, we identified a novel gene, regulator of grain number 1a (RGN1a), which codes for protein kinase, controlling GNP in rice. The RGN1a mutation caused 37.2%, 27.8%, 51.2%, and 25.5% decreases in grain number, primary branch number per panicle, secondary branch number per panicle, and panicle length, respectively. Furthermore, breeding utilization analysis revealed that the additive effects of the dominant allelic variants of RGN1a and DTH7 played a significant role in increasing the grain number per panicle in japonica rice. Our findings enrich the gene pool and provide an effective strategy for the genetic improvement of grain numbers.

Keywords: GWAS; breeding; grain number per panicle; haplotype; rice.