ArticlePlant biotechnology journal2017
Indel-seq: a fast-forward genetics approach for identification of trait-associated putative candidate genomic regions and its application in pigeonpea (Cajanus cajan).
Article in Plant biotechnology journal, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31 citing papers in PubMed.
- Article
- Review
- A 294 kb deletion causes reduced leaflet size and biomass in pigeonpea.Plant cell reports · 2025Article
- Molecular breeding of tomato: Advances and challenges.Journal of integrative plant biology · 2025Review
- Mapping and characterization of a novel powdery mildew resistance locus (PM2) inFrontiers in plant science · 2025Article
- Mapping of a novel locus Ra conferring extreme resistance against potato virus A in cultivated potato (Solanum tuberosum L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Extreme trait GWAS (Et-GWAS): Unraveling rare variants in the 3,000 rice genome.Life science alliance · 2024Article
- Article
- Major-effect quantitative trait locus qLKR4.1 encodes a phospholipase Dδ protein associated with low-KTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Identification and characterization analysis of candidate genes controlling mushroom leaf development in Chinese kale by BSA-seq.Molecular breeding : new strategies in plant improvement · 2023Article
- Bulk segregant linkage mapping for rodent and human malaria parasites.Parasitology international · 2022Review
- OsWRKY115 on qCT7 links to cold tolerance in rice.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
- Function Analysis of theInternational journal of molecular sciences · 2022Article
- Review
- Comparative transcriptomic profiling of susceptible and resistant cultivars of pigeonpea demonstrates early molecular responses during Fusarium udum infection.Scientific reports · 2021Article
- Genomic Approaches to Identify Molecular Bases of Crop Resistance to Diseases and to Develop Future Breeding Strategies.International journal of molecular sciences · 2021Review
- A diagnostic marker kit for Fusarium wilt and sterility mosaic diseases resistance in pigeonpea.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
- Discovery of genomic regions and candidate genes for grain weight employing next generation sequencing based QTL-seq approach in rice (Oryza sativa L.).Molecular biology reports · 2020Article
- A mutation in the intron splice acceptor site of a GA3ox gene confers dwarf architecture in watermelon (Citrullus lanatus L.).Scientific reports · 2020Article
- 5Gs for crop genetic improvement.Current opinion in plant biology · 2020Review
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15 authors.
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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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