Indel-seq: a fast-forward genetics approach for identification of trait-associated putative candidate genomic regions and its application in pigeonpea (Cajanus cajan )
| Autor: | Vikas K. Singh, Chanda Venkata Sameer Kumar, Rachit K. Saxena, Anuradha Ghanta, Annapurna Chitikineni, Vinay Kumar, Suryanarayana Vechalapu, Rajeev K. Varshney, Swathi Parupalli, Pallavi Sinha, K. N. Yamini, Mamta Sharma, Sonnappa Muniswamy, Sandip M. Kale, Aamir W. Khan |
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| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
Candidate gene Genotype Single-nucleotide polymorphism Plant Science whole‐genome resequencing Biology Polymorphism Single Nucleotide 03 medical and health sciences bulked segregant analysis Cajanus Fusarium INDEL Mutation Gene mapping SNP fusarium wilt Indel sterility mosaic disease Gene Research Articles Genetics Bulked segregant analysis food and beverages Forward genetics Indels 030104 developmental biology Agronomy and Crop Science Genome Plant Research Article Biotechnology |
| Zdroj: | Plant Biotechnology Journal |
| ISSN: | 1467-7644 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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