Haplotypes of qGL3 and their roles in grain size regulation with GS3 alleles in rice.

Grain size is an important trait that directly influences rice yield. The qGL3 and GS3 genes are two putative regulators that play a role in grain size determination. A single rare nucleotide substitution (C→A) at position 1092 in exon 10 of qGL3 might be responsible for variations in grain size. However, little is known about the haplotype variations of qGL3 and their interactions with GS3 during the regulation of grain length and grain weight. In this study, qGL3 haplotype variations were examined in 61 Indica varieties, and the effects of qGL3 and GS3 on grain trait variation in 110 lines were evaluated. Six qGL3 haplotypes were identified, and qGL3-2 was a major haplotype in Indica varieties. Moreover, qGL3-6, a reported key single nucleotide polymorphism, was validated. Our results showed that the mutants qgl3 and gs3 (loss-of-function mutation types of qGL3 and GS3, respectively) had significant effects on grain length and grain weight. However, no significant effects associated with differences in the regulation of grain thickness were observed. The genetic effects of qgl3 on grain phenotypes were stronger than those of gs3. In addition to increased grain length, qgl3 had an evident role in grain width increases. In contrast, gs3 played an opposite role in grain width regulation. These results provided novel insights into grain size control and the functions of qgl3 and gs3 in rice yield improvement.