An efficient computational method for screening functional SNPs in plants

Granule Bound Starch Synthase I (GBSSI), which influences the grain quality of cereals and, particularly, rice, is one of the most important plant genes. Using GBSSI as a model plant gene in this study, we examined a number of different computational algorithm tools and programs to explore the functional SNPs of this important rice gene and the possible relationships between genetic mutation and phenotypic variation. A total of 51 SNPs/indels were retrieved from databases, including three important coding non-synonymous SNPs, namely those in exons 6, 9 and 10. Sorting Intolerant from Tolerant (SIFT) results showed that a candidate [C/A] SNP (ID: OryzaSNP2) in exon 6 (coordinate 2494) is the most important non-synonymous SNP with the highest phenotypic impact on waxy protein. This SNP can alter a tyrosine to serine residue at position 224 of waxy protein. Computational simulation of GBSSI protein with the Geno3D suggested that this mutant SNP creates a bigger loop on the surface of waxy protein and results in a shape different from that of native GBSSI. Here, we suggest a potential transcriptional binding factor site (TBF8) which has one [C/T] SNP [rs53176842] at coordinate 2777 in boundary site of intron 7/exon 8, according to Transcriptional Factor (TF) search analysis. This SNP might potentially have a major effect on regulation and function of GBSSI. Combining SNP mining data and in silico structural analysis of waxy protein led us to prepare an efficient computational pathway which can be applied for other plant genes.