Indel-seq: a fast-forward genetics approach for identification of trait-associated putative candidate genomic regions and its application in pigeonpea (Cajanus cajan).

Vikas K Singh,Rajeev K Varshney,Aamir W Khan,Pallavi Sinha,Suryanarayana Vechalapu,Rachit K Saxena,Anuradha Ghanta,Kalinati Narasimhan Yamini,Sonnappa Muniswamy,Annapurna Chitikineni,Chanda Venkata Sameer Kumar,Mamta Sharma,Vinay Kumar,Swathi Parupalli,Sandip M Kale

doi:10.1111/pbi.12685

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.

Highlights

Conventional trait mapping methods are generally expensive and take much time in generating and analysing genotyping data on segregating populations
This study reports a novel approach called ‘Indel-seq’, which is a combination of whole-genome resequencing (WGRS) and bulked segregant analysis (BSA), for the identification of Indels associated with target traits
Indel-seq combines WGRS and BSA to identify the genomic regions associated with the target traits

Summary

Introduction

Conventional trait mapping methods are generally expensive and take much time in generating and analysing genotyping data on segregating populations. Trait mapping becomes more timeconsuming if genotyping is performed using low-throughput marker systems such as simple sequence repeat (SSR) markers Visual scoring in such marker systems adds to the possibility of discovering spurious marker–trait associations (MTAs). Meeting the increasing demand of nutritious food under anticipated climate change scenario along with everdecreasing agricultural lands and limited water resources is a challenging task (Khoury et al, 2014). It requires sophisticated rapid genome mapping and targeted GAB approaches to produce better and high-yielding crop varieties in faster manner (Godfray, 2010; Varshney et al, 2005)

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Conclusion