Fine mapping and candidate gene analysis of qGSN5, a novel quantitative trait locus coordinating grain size and grain number in rice

• Published in: Theoretical and applied genetics Vol. 135; no. 1; pp. 51 - 64
• Main Authors: Yuan, Hua, Gao, Peng, Hu, Xiaoling, Yuan, Min, Xu, Zhengyan, Jin, Mengya, Song, Wencheng, Zhan, Shijie, Zhu, Xiaobo, Tu, Bin, Li, Ting, Wang, Yuping, Ma, Bingtian, Qin, Peng, Chen, Weilan, Li, Shigui
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01.01.2022; Springer; Springer Nature B.V
• Subjects: Agricultural research; Agriculture; Biochemistry; Biomedical and Life Sciences; Biotechnology; Cell proliferation; Chromosome 5; Chromosome Mapping; Chromosomes, Plant; Cloning; Crop yields; Edible Grain - genetics; Gene mapping; Genes, Plant; Genetic analysis; Genetic aspects; Genetic Association Studies; Genetic engineering; Grain size; Life Sciences; Original Article; Oryza - genetics; Phenotype; Phenotypes; Physiological aspects; Plant Biochemistry; Plant breeding; Plant Breeding/Biotechnology; Plant Genetics and Genomics; Quantitative Trait Loci; Rice; Seeds - anatomy & histology; Seeds - genetics; China
• ISSN: 0040-5752; 1432-2242
• DOI: 10.1007/s00122-021-03951-7

Key message qGSN5 , a novel quantitative trait locus coordinating grain size and grain number in rice, was fine-mapped to an 85.60-kb region. GS3 may be a suppressor of qGSN5 . Grain size and grain number are two factors that directly determine rice grain yield; however, the underlying genetic mechanisms are complicated and remain largely unclear. In this study, a chromosome segment substitution line (CSSL), CSSL28, which showed increased grain size and decreased grain number per panicle, was identified in a set of CSSLs derived from a cross between 93-11 (recipient) and Nipponbare (donor). Four substitution segments were identified in CSSL28, and the substitution segment located on chromosome 5 was responsible for the phenotypes of CSSL28. Thus, we defined this quantitative trait locus (QTL) as grain size and grain number 5 ( qGSN5 ). Cytological and quantitative PCR analysis showed that qGSN5 regulates the development of the spikelet hull by affecting cell proliferation. Genetic analysis showed that qGSN5 is a semi-dominant locus regulating grain size and grain number. Through map-based cloning and overlapping substitution segment analysis, qGSN5 was finally delimited to an 85.60-kb region. Based on sequence and quantitative PCR analysis, Os05g47510 , which encodes a P-type pentatricopeptide repeat protein, is the most likely candidate gene for qGSN5 . Pyramiding analysis showed that the effect of qGSN5 was significantly lower in the presence of a functional GS3 gene, indicating that GS3 may be a suppressor of qGSN5 . In addition, we found that qGSN5 could improve the grain shape of hybrid rice. Together, our results lay the foundation for cloning a novel QTL coordinating grain size and grain number in rice and provide a good genetic material for long-grain hybrid rice breeding.