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.

Development of sequence-based markers for seed protein content in pigeonpea

“…(Color figure online) involve re-sequencing genomes of genotypes contrasting in trait phenotype together with detection of nonsynonymous sequence variants have been found to be efficient for rapid identification of potential candidate genes controlling complex traits in pigeonpea and other crops (Silva et al 2012;Xu et al 2014;Singh et al 2016aSingh et al , b, 2017. The results obtained from our previous NGS-based trait mapping studies (Singh et al 2016b(Singh et al , 2017) have encouraged us to use similar approach for identification of candidate genes/markers associated with SPC in pigeonpea.…”

Developing Climate-Resilient Chickpea Involving Physiological and Molecular Approaches With a Focus on Temperature and Drought Stresses

“…Similarly, non-coding RNA, including microRNA and long non-coding RNA (lncRNA), have received attention for their regulatory role in the expression of various genes controlling complex traits at the post-transcriptional level, including for drought stress in chickpea (Khandal et al, 2017;Singh et al, 2017). A microRNA (miRNA) profiling study of root apical meristem identified 284 unique miRNA sequences; of which 259 were differentially expressed under drought and salinity stress (Khandal et al, 2017).…”

The Peanut Genome

“…Another common trait mapping approach is bulked segregant analysis (BSA) where marker screening on the extreme bulks and parents provides trait-associated markers (see Semagn et al 2010). With the advantage of NGS technologies and draft genome sequence, rapid trait mapping has been performed for sterility mosaic disease (SMD) and fusarium wilt (FW) (Singh et al 2015(Singh et al , 2017. These approaches depend on extreme bulks and NGS to even provide markers for qualitative and quantitative traits.…”