Indel‐seq: a fast‐forward genetics approach for identification of trait‐associated putative candidate genomic regions and its application in pigeonpea (Cajanus cajan) |
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| Authors: | Sandip M. Kale Swathi Parupalli Vinay Kumar Annapurna Chitikineni Suryanarayana Vechalapu Chanda Venkata Sameer Kumar Mamta Sharma Anuradha Ghanta Kalinati Narasimhan Yamini Sonnappa Muniswamy Rajeev K. Varshney |
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| Affiliation: | 1. International Crops Research Institute for the Semi‐Arid Tropics, Patancheru, Telangana State, India;2. Agricultural Research Station (ARS)‐Tandur, Professor Jayashankar Telangana State Agricultural University (PJTSAU), Hyderabad, Telangana State, India;3. Agricultural Research Station (ARS)‐Gulbarga, University of Agricultural Sciences (UAS), Raichur, Karnataka, India;4. School of Plant Biology and Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia |
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| 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. |
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| Keywords: | bulked segregant analysis fusarium wilt Indels sterility mosaic disease whole‐genome resequencing |
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