Chinese Journal OF Rice Science >
Natural Variation of OsNF-YC10 and Its Correlation with Grain Width in Rice
Received date: 2024-07-17
Revised date: 2024-08-17
Online published: 2025-07-21
【Objective】 Grain width is an important determinant of grain type and grain weight, which can affect rice yield and appearance quality. So far, a large number of genes have been found to affect grain width, but only a limited number of genes have breeding value because mutations of other genes often have negative collateral effects. Hence, it is of great significance to explore new grain width genes and uncover natural variations that have no negative effects on quality and yield. DR610 is a small-grain indica rice and Hagengdao 7 (HG7) is a large-grain japonica rice. 【Method】 In this study, a QTL-seq was performed using the extreme grain weight individuals of the DR610×HG7 F2 population. Through the combined analysis of QTL-seq results and known genes affecting grain type, we found that a nonsense mutation of OsNF-YC10 in DR610 is likely to be the underlying genetic basis of its narrow grain. To determine the correlation between OsNF-YC10 variation and grain width, we analyzed the natural variation of OsNF-YC10 in more than 4000 rice germplasm accessions and its correlation with grain width. 【Result】 A total of 10 major OsNF-YC10 haplotypes were identified with HG7(Hap1) being the predominant haplotype (1464/1509) in japonica rice (1464 of 1509 accessions). The Hap5 (represented by DR610) contains a C(HapC)→T(HapT) nonsense mutation at nucleotide site 1048. The grain width of rice varieties with HapC (3.036 mm, n=1596) was significantly wider than that of HapT (2.938 mm, n= 309), indicating that this natural variation significantly affected the grain width. Further analysis showed that Hap1 and Hap5 are significantly differentiated between japonica and indica, with the latter mainly distributed in the low latitude regions. A molecular marker to distinguish C→T variants was developed using four tetra-primer ARMARMS-PCR, which can be used for marker-assisted selection of grain type. 【Conclusion】 In summary, this study determined the natural variation of OsNF-YC10, which is significantly correlated with the grain width. The finding is of importance to providing an important reference for breeding by design of grain type and weight in rice.
Key words： grain size; grain width; 1000-grain weight; QTL-seq; genotyping; tetra-primer ARMS-PCR
CHEN Jiale, YU Qingtao, ZHENG Chenfan, WANG Qing, TAN Yuanyuan, CHEN Baicui, LI Chengxin, JIANG Meng, SHU Qingyao . Natural Variation of OsNF-YC10 and Its Correlation with Grain Width in Rice[J]. Chinese Journal OF Rice Science, 2025 , 39(4) : 552 -562 . DOI: 10.16819/j.1001-7216.2025.240713
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