In silico identification and prediction of structural and functional effects of haplotypes found in OsGRAS-32 of rice (Oryza sativa l.) In 3KRG

Abstract

Rice (Oryza sativa L.) serves as the staple food for more than half of the world’s population. One important yield-related trait in rice is grain size. However, haplotypes in rice which may be associated with grain size, and their structural and functional effects, have not been characterized. Three haplotypes in OsGRAS-32 of rice in 3KRG were located and identified using the haplotype view function of SNP Query found in Rice SNP-Seek Database. hap3 was predicted to cause a change in the structure and function of OsGRAS-32. Five of its 16 SNPs were found in the coding region. This led to an amino acid change of proline to arginine at position 595. New candidate genes that are connected to the gene of interest were identified with the use of RiceNet. These were: LOC_Os09g36740, LOC_Os01g70560, LOC_Os02g15810, LOC_Os04g15800, LOC_Os03g07810, LOC_Os04g41900, LOC_Os04g40940, LOC_Os01g16650, LOC_Os03g39020, and LOC_Os07g32390. Thus, a new protein-protein interaction network is proposed. Protein-protein docking showed how the wild-type and the haplotype-bearing protein interacts with the protein products of the candidate genes. It was found that LOC_Os09g36740 + wild-type, LOC_Os01g70560 + wild-type, LOC_Os02g15810 + hap3, LOC_Os04g15800 + wild-type, LOC_Os03g07810 + wild-type, LOC_Os04g41900 + wild-type, LOC_Os04g40940 + hap3, LOC_Os01g16650 + hap3, LOC_Os03g39020 + wild-type, and LOC_Os07g32390 + hap3 protein-protein interactions are more favorable and spontaneous than the other interactions that were studied. Knowledge on the new protein-protein interactions may contribute to the understanding of mechanisms that affect grain size.