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In rice, grain shape is an important quality trait that has a major impact on both the grain yield and the market values of grain products. A long, slender grain of rice is generally preferred by consumers in Southern China, the USA, and South and Southeast Asian countries, whereas consumers in Japan, Korea and Northern China prefer rice grain that is short and round. Grain length, length-to-width ratio and grain weight are three key components of grain yield that can vary dramatically depending upon the rice variety (Fig 1). These grain traits are controlled primarily by QTLs (Huang et al., 2013). The large grain size 1 (LGS1) mutant of rice was isolated in 1990s from M85, a cultivar with round-shape grain, and has been used extensively in rice breeding programs for development of improved rice cultivars with elongated rice grain, which is favored by consumers in South China and India. We conducted genetic mapping and gene cloning and demonstrated that the LGS1 gene encodes the GRF4 (Growth Regulating Factor 4) transcription factor (Jiang et al., 2018; Chen et al., 2019; Fig 2). We discovered that a missense mutation from nucleotides TT to AA in this gene leads to the substitution of a conserved Serine (S) residues by Lysine (K) in the GRF4 protein and also disrupts the pairing site of the LGS1 mRNA transcript by a microRNA (miR396), resulting in elevation of the LGS1 mRNA transcripts in the mutant rice and development of elongated grain (Fig 3). The mutant plants are found to be more resistant to cold stress, a highly desirable trait for rice growth in early spring.
Fig 1. Genetic basis of grain shape in rice.
(A) Domesticated rice varies from 3 to 11 mm in grain length and from 1.2 to 3.8 mm in grain width. (B) Grain Size 3 (GS3) is a major QTL regulating grain size in rice. The protein contains 4 motifs, among which the OSR motif acts as a negative regulator of grain length, while the V domain functions as a positive regulator of grain length (Fan et al., 2006; 2009; Mao et al., 2010).
Fig 2. LGS1 is a major regulator of grain length in rice.
(A-B) Ma85 is a rice cultivar with high grain quality and yield buthas round grains. It was subject to mutagenesis with γ-ray radiation. JF178 was isolated from the M1 generation and produces long rains. (C) The Long Grain Shape 1 (LGS1) locus was maintained in an near-isogenic line (NIL-LGS1) on the genetic background of Samba, a very short grain cultivar. (D) The LGS1 locus inherits as a semidominant maner and is fine mapped to the long arm of chromosome 2 between RM13838 and RM13840, where there is only one gene, LOC_Os02g47280, encoding growth-regulating factor 4 (GRF4), a transcription factor. (E) LGS1 is expressed in young vegetative tissues, pistil and stamens, and developing grain. (F) The TC to AA substitution occurs in exon 3 of LGS1.
Fig 3. LGS1 is a semi-dominant mutant.
(A). The two nucleotides, TC, in WT (lgs1) rice are substituted with AA in the mutant line JF178 (LGS1). (B) The two basepair mutation occurs in the priming site of miR396, a micro RNA that regulates the transcript level of GRF genes in plants. (C-D) The same mutation also leads to the amino acid change from serine to lysine (S163K), a highly conserved residue in the GRF proteins.
References
Chen X, Jiang L, Zheng J, Chen F, Wang T, Wang M, Tao y, Wang H, Hong Z, Huang Y, Huang Y (2019) A missense mutation in Large Grain Size 1 increases grain size and enhances cold tolerance in rice. J Exp Bot 70: 3851-3866
Fan C, Xing Y, Mao H, Lu T, Han B, Xu C, Li X, Zhang Q (2006) GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor Appl Genet 112: 1164-1171
Fan, C. Yu S, Wang C, Xing Y (2009) A causal C-A mutation in the second exon of GS3 highly associated with rice grain length and validated as a functional marker. Theor Appl Genet 118: 465–472
Fitzgerald MA, McCouch S, Hall R (2009) Not just a grain of rice: the quest for quality. Trends Plant Sci 14: 133-139
Huang R, Jiang L, Zheng J, Wang T, Wang H, Huang Y, Hong Z (2013) Genetic bases underlying rice grain shape: So many genes, so little known. Trends Plant Sci 18: 218-226
Jiang L, Zheng J, Zhang Z, Chen X, Chen F, Wang T, Huang Y, Wang H, Hong Z, Huang R (2018) Two independent grain-length mutants mapped to a single region on the long arm of chromosome 2 in rice. Bragantia 77: 452-465
Mao H, Sun S, Yao J, Zhang Q (2010) Linking differential domain functions of the GS3 protein to natural variation of grain size in rice. Proc Natl Acad Sci USA 107: 19579-19584
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