Analysis of Genes Associated with Grain Shape Traits in japonica Rice Cultivar ‘Daeribbyeo 1’

Grain size controlled by quantitative trait loci (QTL) has a great impact on grain yield and quality in rice. ‘Daeribbyeo 1’ with large grain is widely used as genetic materials to develop varieties with diverse grain size. This study was conducted to identify genes controlling grain size traits of Daeribbyeo 1. An F_2:3 population derived from a cross between two japonica cultivars, ‘Boseogheugchal’ and ‘Daeribbyeo 1’, was used to identify QTL controlling grain shape traits. 284 F₂ plants were measured for grain length (GL), grain width (GW), grain thickness (GT), 1000 grain weight (TGW), and two morphological traits, pericarp color and waxy endosperm. 60 F₃ lines were selected based on the grain shape traits and SSR marker genotypes and evaluated for grain shape traits. SSR markers tightly linked to five known grain size genes and two QTLs were selected and used for genotyping. A total of 11 QTLs detected on chromosomes 2, 3, 4 and 6 explained phenotypic variation from 5.3% to 59.3%. qTGW2, qGW2 and qGT2 were detected in the same region between RM12811-RM12837 that are tightly linked with GW2 gene. qTGW3 and qGL3 were detected near GS3 gene. To know whether Daeribbyeo 1 has the same mutation in GW2 and GS3 as the various grain-size genotypes, GW2 and GS3 of two parents were sequenced. Daeribbyeo 1 had the same one base (A) deletion at a position 316 as ‘WY3’ in GW2 which results in the loss of function of GW2 gene. Boseogheugchal showed a C-to-A nonsense mutation in the second exon of GS3 gene. Interaction between GW2 and GS3 was not significant indicating that two genes controlled grain-size traits in an additive way. The results from this study indicate that at least four genes, GW2, qGT4 , qSW5 and qGL6 are associated with the grain size variation in Daeribbyeo 1 with GW2 as the major QTL..