Singh, V K and Khan, A W and Saxena, R K and Sinha, P and Kale, S M and Parupalli, S and Kumar, V and Chitikineni, A and Vechalapu, S and Sameer Kumar, C V and Sharma, M and Ghanta, A and Yamini, K N and Muniswamy, S and Varshney, R K (2017) 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. pp. 1-9. ISSN 1467-7644
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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.
| Item Type: | Article |
|---|---|
| Divisions: | Research Program : Genetic Gains |
| CRP: | CGIAR Research Program on Grain Legumes |
| Uncontrolled Keywords: | Bulked segregant analysis, fusarium wilt, Indels, sterility mosaic disease, whole-genome resequencing, pigeonpea, Indel-seq approach |
| Subjects: | Mandate crops > Pigeonpea Others > Genetics and Genomics |
| Depositing User: | Mr Ramesh K |
| Date Deposited: | 13 Apr 2017 04:30 |
| Last Modified: | 13 Apr 2017 04:31 |
| URI: | http://oar.icrisat.org/id/eprint/9955 |
| Official URL: | http://dx.doi.org/10.1111/pbi.12685 |
| Projects: | UNSPECIFIED |
| Funders: | UNSPECIFIED |
| Acknowledgement: | Authors are thankful to the United States Agency for International Development (USAID); Biotechnology Industry Partnership Programme (BIPP) and Department of Biotechnology of Government of India; Ministry of Agriculture, Government of Karnataka state of India for funding various projects related to pigeonpea genomics. This work has been undertaken as part of the CGIAR Research Program on Grain Legumes. ICRISAT is a member of CGIAR Consortium. |
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