Indel-Seq: A Fast Forward Genetic Approach for Identification of Candidate Genomic Regions, an Example in Pigeonpea (Cajanus cajan)

Identification of candidate genomic regions through conventional methods of mapping target traits are challenging and time consuming. In recent years, a number of fast forward SNPs based mapping approaches have been developed and utilized for identification of causal genomic regions. However, in majority of these studies, Indels were largely ignored. For effective use of Indels in mapping target traits, we propose Indel-seq approach that is combination of whole genome re-sequencing and bulked segregant analysis. Deployment of Indel-seq approach has been used for identification of candidate genomic regions associated with fusarium wilt (FW) and sterility mosaic disease (SMD) resistance in pigeonpea. In brief, two candidate genes, one for FW resistance (probable receptor-like protein kinase) and one for SMD (copia like polyprotein) resistance have been identified. These candidate genes have also been validated on known resistance and susceptible genotypes for FW and SMD resistance. We believe that Indel-seq approach will facilitate quick and precise identification of candidate genomic regions for any target traits in any crop plants. Identified Indels can be easily converted into PCR based markers to facilitate genomics-assisted breeding in crops.