iQTL-seq: Rapid identification of the gene controlling QTL by next generation sequencer

• Project/Area Number: 15H05611
• Research Category: Grant-in-Aid for Young Scientists (A)
• Allocation Type: Single-year Grants
• Research Field: Science in genetics and breeding
• Research Institution: Ishikawa Prefectural University (2016-2017); Iwate Biotechnology Research Center (2015)
• Principal Investigator: Takagi Hiroki 石川県立大学, 生物資源環境学部, 助教 (80616467)
• Project Period (FY): 2015-04-01 – 2018-03-31
• Project Status: Completed (Fiscal Year 2017)
• Budget Amount: ¥24,310,000 (Direct Cost: ¥18,700,000、Indirect Cost: ¥5,610,000); Fiscal Year 2017: ¥7,800,000 (Direct Cost: ¥6,000,000、Indirect Cost: ¥1,800,000); Fiscal Year 2016: ¥7,800,000 (Direct Cost: ¥6,000,000、Indirect Cost: ¥1,800,000); Fiscal Year 2015: ¥8,710,000 (Direct Cost: ¥6,700,000、Indirect Cost: ¥2,010,000)
• Keywords: 植物育種 / バイオインフォマティクス / 植物育種学 / 植物 / 育種学 / 遺伝学 / 植物遺伝学

Outline of Final Research Achievements

The identification of the gene controlling agronomically important trait is an important task for accelerating breeding speed. In this study, we tried to develop the next generation sequencer (NGS) based methods “iQTL-seq; identification of the gene in QTL controlling the phenotypic difference between cultivars/landraces”. iQTL-seq pipeline comprises three steps; 1) identification of the candidate genomic regions controlling the phenotypic difference by QTL-seq. 2) local de novo assembly for the identified region by using aligned sequences plus as well as short reads that were unmapped to the reference. 3) identification of the candidate gene located in the assembled contigs by comparing sequence depth between the bulked samples used for QTL-seq analysis in step 1. The developed pipeline was applied for identifying the resistance gene to rice blast disease. The pipeline is in preparation for opening to publicly available web site.