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Abstract
Single nucleotide polymorphisms (SNPs) are widely used in functional genomics and genetics research work. The high-quality sequence of rice genome has provided a genome-wide SNP and proteome resource. However, the impact of SNPs on protein phosphorylation status in rice is not fully understood. In this paper, we firstly updated rice SNP resource based on the new rice genome Ver. 7.0, then systematically analyzed the potential impact of Non-synonymous SNPs (nsSNPs) on the protein phosphorylation status. There were 3,897,312 SNPs in Ver. 7.0 rice genome, among which 9.9% was nsSNPs. Whilst, a total 2,508,261 phosphorylated sites were predicted in rice proteome. Interestingly, we observed that 150,197 (39.1%) nsSNPs could influence protein phosphorylation status, among which 52.2% might induce changes of protein kinase (PK) types for adjacent phosphorylation sites. We constructed a database, SNP_rice, to deposit the updated rice SNP resource and phosSNPs information. It was freely available to academic researchers at http://bioinformatics.fafu.edu.cn. As a case study, we detected five nsSNPs that potentially influenced heterotrimeric G proteins phosphorylation status in rice, indicating that genetic polymorphisms showed impact on the signal transduction by influencing the phosphorylation status of heterotrimeric G proteins. The results in this work could be a useful resource for future experimental identification and provide interesting information for better rice breeding.
Highlights
IntroductionThe draft sequences of two main cultivated rice genomes, indica (93–11) and Japonica (Nipponbare), were all reported in 2002 [1,2]
Rice is one of the most important crops in the world
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Summary
The draft sequences of two main cultivated rice genomes, indica (93–11) and Japonica (Nipponbare), were all reported in 2002 [1,2]. With the development of high-throughput sequencing methods, more and more rice genotypes have been resequenced in recent years [4,5]. This will provide abundant information on the genetic variations of different rice genotype individuals, including copy number variations (CNVs) and single nucleotide polymorphisms (SNPs). SNPs are DNA sequence variations occurring when a single nucleotide in the genome differs between members of a biological species [6].
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