Infererence of the SNP effects on gene functions

2015 Fiscal Year Final Research Report

• Project/Area Number: 24510286
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Applied genomics
• Research Institution: Kazusa DNA Research Institute
• Principal Investigator: Hirakawa Hideki 公益財団法人かずさDNA研究所, 技術開発研究部, クループ長 (80372746)
• Project Period (FY): 2012-04-01 – 2016-03-31
• Keywords: SNP解析 / バイオインフォマティクス / データベース

Outline of Final Research Achievements

The SNP analysis pipeline for EST and NGS reads sequenced by ABI SOLiD, Illumina HiSeq and MiSeq platforms was constructed. The sequence data were respectively obtained from NCBI’s dbEST and SRA databases. Using the pipeline, SNPs on the tomato genome sequence were detected and classified into eight categories, and the effects of the SNPs on protein functions were inferred. The SNPs on the active site in the protein three-dimensional structure constructed by homology modeling were defined as ‘functional SNP’. SNPs on the genes related to disease resistances, stress tolerances and fruit color and aroma etc were investigated, and some SNPs were found in the genes related to sugar metabolism and so on. In future, the amount of data related to NGS, phenotypes, QTLs, and three-dimensional structures of protein would be increased in public database. By using these data, the accuracy of variety identification would be improved, and the increase of the breeding efficiency would be expected.

Free Research Field

バイオインフォマティクス