title: Indel-seq: a fast-forward genetics approach for identification of trait-associated putative candidate genomic regions and its application in pigeonpea (Cajanus cajan).
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.
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana State, India.
authors.forename: Vikas K
authors.initials: VK
authors.lastname: Singh
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana State, India.
authors.forename: Aamir W
authors.initials: AW
authors.lastname: Khan
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana State, India.
authors.forename: Rachit K
authors.initials: RK
authors.lastname: Saxena
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana State, India.
authors.forename: Pallavi
authors.initials: P
authors.lastname: Sinha
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana State, India.
authors.forename: Sandip M
authors.initials: SM
authors.lastname: Kale
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana State, India.
authors.forename: Swathi
authors.initials: S
authors.lastname: Parupalli
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana State, India.
authors.forename: Vinay
authors.initials: V
authors.lastname: Kumar
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana State, India.
authors.forename: Annapurna
authors.initials: A
authors.lastname: Chitikineni
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana State, India.
authors.forename: Suryanarayana
authors.initials: S
authors.lastname: Vechalapu
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana State, India.
authors.forename: Chanda Venkata
authors.initials: CV
authors.lastname: Sameer Kumar
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana State, India.
authors.forename: Mamta
authors.initials: M
authors.lastname: Sharma
authors.affiliation: Agricultural Research Station (ARS)-Tandur, Professor Jayashankar Telangana State Agricultural University (PJTSAU), Hyderabad, Telangana State, India.
authors.forename: Anuradha
authors.initials: A
authors.lastname: Ghanta
authors.affiliation: Agricultural Research Station (ARS)-Tandur, Professor Jayashankar Telangana State Agricultural University (PJTSAU), Hyderabad, Telangana State, India.
authors.forename: Kalinati Narasimhan
authors.initials: KN
authors.lastname: Yamini
authors.affiliation: Agricultural Research Station (ARS)-Gulbarga, University of Agricultural Sciences (UAS), Raichur, Karnataka, India.
authors.forename: Sonnappa
authors.initials: S
authors.lastname: Muniswamy
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana State, India.|School of Plant Biology and Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia.
authors.forename: Rajeev K
authors.initials: RK
authors.lastname: Varshney
mesh_terms: D036561:Cajanus / Q000235:genetics* / Q000382:microbiology; D005670:Fusarium / Q000472:pathogenicity; D018745:Genome, Plant / Q000235:genetics*; D005838:Genotype; D054643:INDEL Mutation / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics
keywords: Indels; bulked segregant analysis; fusarium wilt; sterility mosaic disease; whole-genome resequencing