Wang, Yanyan;;Yang, Ziyi;;Xing, Meng;;Huang, Jingfen;;Ding, Yingbin;;Zhang, Lizhen;;Li, Fei;;Nie, Yamin;;Wang, Shizhuang;;Li, Yapeng;;Zhao, Mingchao;;Ge, Jinyue;;Lou, Danjing;;Liu, Ziran;;Fan, Weiya;;Guo, Wenlong;;Zheng, Xiaoming;;Qian, Qian;;Yang, Qingwen;;Qiao, Weihua

Plant Biotechnology Journal; 2023;  IF 13.80

DOI:10.1111/pbi.14014

ABSTRACT

Grain size and shape are determinants of grain yield and quality and have been selected during early rice domestication (Li et al., 2019). Most rice cultivars have larger seeds than their ancestral progenitor Oryza rufipogon. Previous studies have revealed that potential genes hidden in wild rice may be important for yield-related trait improvement (Huang et al., 2013). However, to date, positive regulation of grain length (GL) or yield by wild rice alleles has rarely been reported. To explore grain shape related genes in wild rice, we constructed a set of chromosome segment substitution lines using O. rufipogon (accession number CWR274) as the donor parent and the indica cultivar ‘9311’ as the receipt parent (Qiao et al., 2016). A major QTL associated with GL was identified on Chromosome 12 and further narrowed to a 15-kb genomic region using a fine mapping approach. Three genes were subsequently identified in this region. Only the LOC_Os12g39640 overexpression (OE) lines showed an increased GL phenotype. Therefore, the LOC_Os12g39640 gene was the most likely candidate gene and named GL12. According to the rice annotation database, LOC_Os12g39640/GL12 encodes a MYB transcription factor. Four nonsynonymous mutations in the coding region were detected between CWR274 and 9311, including three SNPs (+529 C>A; +2145 A>G, and +2190 T>C) and one 3-bp (GGA) insertion in the fifth exon, named as M1 to M4 (Figure 1a). We conducted a series of genetic modification verifications in the 9311 background. Compared with 9311, the near-isogenic line (NIL) of GL12w exhibited increases in GL (8.1%), and 1000- grain weight (TGW) (12.9%). Using CRISPR/Cas9 technology, we generated knock-out (ko) mutants of GL12w in the NIL background. As expected, the GL and TGW of the mutant plants decreased significantly. OE of GL12w increased GL and TGW by 5% and 6.8% in the 9311 genetic background, respectively. The GL129311-OE lines did not display obvious difference in grain traits. Correlation analyses showed that in both the NIL and GL12w-OE lines, GL and TGW were positively correlated.