Journal article
Indel-seq: a fast-forward genetics approach for identification of trait-associated putative candidate genomic regions and its application in pigeonpea (Cajanus cajan)
Plant Biotechnology Journal, Vol.15(7), pp.906-914
2017
Abstract
Identification of candidate genomic regions associated with target traits using conventional mapping methods is challenging and time-consuming. In recent years, a number of single nucleotide polymorphism (SNP)-based mapping approaches have been developed and used for identification of candidate/putative genomic regions. However, in the majority of these studies, insertion–deletion (Indel) were largely ignored. For efficient use of Indels in mapping target traits, we propose Indel-seq approach, which is a combination of whole-genome resequencing (WGRS) and bulked segregant analysis (BSA) and relies on the Indel frequencies in extreme bulks. Deployment of Indel-seq approach for identification of candidate genomic regions associated with fusarium wilt (FW) and sterility mosaic disease (SMD) resistance in pigeonpea has identified 16 Indels affecting 26 putative candidate genes. Of these 26 affected putative candidate genes, 24 genes showed effect in the upstream/downstream of the genic region and two genes showed effect in the genes. Validation of these 16 candidate Indels in other FW- and SMD-resistant and FW- and SMD-susceptible genotypes revealed a significant association of five Indels (three for FW and two for SMD resistance). Comparative analysis of Indel-seq with other genetic mapping approaches highlighted the importance of the approach in identification of significant genomic regions associated with target traits. Therefore, the Indel-seq approach can be used for quick and precise identification of candidate genomic regions for any target traits in any crop species.
Details
- Title
- Indel-seq: a fast-forward genetics approach for identification of trait-associated putative candidate genomic regions and its application in pigeonpea (Cajanus cajan)
- Authors/Creators
- V.K. Singh (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsA.W. Khan (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsR.K. Saxena (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsP. Sinha (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsS.M. Kale (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsS. Parupalli (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsV. Kumar (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsA. Chitikineni (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsS. Vechalapu (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsC.V. Sameer Kumar (Author/Creator)M. Sharma (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsA. Ghanta (Author/Creator) - Professor Jayashankar Telangana State Agricultural UniversityK.N. Yamini (Author/Creator) - Professor Jayashankar Telangana State Agricultural UniversityS. Muniswamy (Author/Creator) - University of Agricultural Sciences RaichurR.K. Varshney (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
- Publication Details
- Plant Biotechnology Journal, Vol.15(7), pp.906-914
- Publisher
- Blackwell Publishing Inc.
- Identifiers
- 991005541570107891
- Copyright
- © 2016 The Authors.
- Murdoch Affiliation
- Murdoch University
- Language
- English
- Resource Type
- Journal article
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- Collaboration types
- Domestic collaboration
- International collaboration
- Citation topics
- 3 Agriculture, Environment & Ecology
- 3.4 Crop Science
- 3.4.96 QTL
- Web Of Science research areas
- Biotechnology & Applied Microbiology
- Plant Sciences
- ESI research areas
- Plant & Animal Science