Development of exome mutation database in the micro-tom mutant population

2016 Fiscal Year Final Research Report

• Project/Area Number: 15H06071
• Research Category: Grant-in-Aid for Research Activity Start-up
• Allocation Type: Single-year Grants
• Research Field: Science in genetics and breeding
• Research Institution: University of Tsukuba
• Principal Investigator: YANO Ryoichi 筑波大学, 生命環境系, 助教 (00443044)
• Co-Investigator(Renkei-kenkyūsha): EZURA Hiroshi 筑波大学, 生命環境系, 教授 (00332552) ; ARIIZUMI Toru 筑波大学, 生命環境系, 准教授 (70575381) ; HOSHIKAWA Ken 筑波大学, 生命環境系, 助教 (70634715)
• Project Period (FY): 2015-08-28 – 2017-03-31
• Keywords: トマト / 誘発変異集団 / エクソームシークエンシング / 次世代シークエンス / 変異情報データベース / webアプリケーション / ゲノムワイド変異検索システム

Outline of Final Research Achievements

Exome sequencing (ES) is a cost-effective next-generation sequencing (NGS) method for rapid identification of genome-wide exon mutations at a population scale. In this study, a 96-plex ES library preparation method was newly developed in the model tomato cultivar'Micro-Tom'. When exome NGS data was obtained by the Illumina Hiseq paired-end sequencing platform and further subjected to a bioinformatics pipeline using bowtie2, samtools, and GATK, over 240,000 mutations were identified in 95 Micro-Tom mutant individuals. Of these, over 70,000 mutations were expected to affect protein function because they cause amino acid substitution, premature stop codons, or frameshift in the deduced protein amino acid sequences. A web-application system was also developed based on the mutation dataset to enable in silico one-click search of specific mutations or mutants.

Free Research Field

ゲノム情報科学、園芸育種科学、バイオインフォマティクス