Development of genome-wide informative simple sequence repeat markers for large-scale genotyping applications in chickpea and development of web resource.

Swarup K Parida,Supriya Ambawat,Rohini Garg,Santosh K Yadav,Mohit Verma,Shouvik Das,Mukesh Jain

doi:10.3389/fpls.2015.00645

Abstract

Development of informative polymorphic simple sequence repeat (SSR) markers at a genome-wide scale is essential for efficient large-scale genotyping applications. We identified genome-wide 1835 SSRs showing polymorphism between desi and kabuli chickpea. A total of 1470 polymorphic SSR markers from diverse coding and non-coding regions of the chickpea genome were developed. These physically mapped SSR markers exhibited robust amplification efficiency (73.9%) and high intra- and inter-specific polymorphic potential (63.5%), thereby suggesting their immense use in various genomics-assisted breeding applications. The SSR markers particularly derived from intergenic and intronic sequences revealed high polymorphic potential. Using the mapped SSR markers, a wider functional molecular diversity (16–94%, mean: 68%), and parentage- and cultivar-specific admixed domestication pattern and phylogenetic relationships in a structured population of desi and kabuli chickpea genotypes was evident. The intra-specific polymorphism (47.6%) and functional molecular diversity (65%) potential of polymorphic SSR markers developed in our study is much higher than that of previous documentations. Finally, we have developed a user-friendly web resource, Chickpea Microsatellite Database (CMsDB; http://www.nipgr.res.in/CMsDB.html), which provides public access to the data and results reported in this study. The developed informative SSR markers can serve as a resource for various genotyping applications, including genetic enhancement studies in chickpea.

Highlights

CDC Frontier; Varshney et al, 2013) chickpea genomes were obtained from Chickpea Genome Analysis Project1 and International Chickpea Genetics & Genomics Consortium2, respectively
The overall frequency of compound simple sequence repeat (SSR) identified in desi (2563, 0.005 SSRs/kb) and kabuli (2470, 0.004 SSRs/kb) chickpea was almost comparable with each other
The class I and class II di-nucleotide repeat-motifs were present in maximum fraction varying from 49.1 (18537) to 62.3% (25568) in desi and kabuli chickpea (Figure 1A)

Summary

Introduction

A significant progress has been made concerning the development of numerous genomic and transcript-derived simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers at a genome-wide scale and their deployment in multi-dimensional genomicsassisted breeding applications in chickpea (Winter et al, 2000; Abbo et al, 2005; Millan et al, 2010; Nayak et al, 2010; Gujaria et al, 2011; Thudi et al, 2011; Gaur et al, 2012; Hiremath et al, 2012; Roorkiwal et al, 2013; Deokar et al, 2014; Jaganathan et al, 2014). The length polymorphism in the functional domain of transcription factor genes, and alteration of secondary structure of proteins and functional domain sites have been proposed to control seed weight/seed size in chickpea (Kujur et al, 2013) These studies have suggested the utility of coding and non-CDS-based SSR markers for rapidly establishing marker-trait linkages and identifying genes/QTLs for many useful agronomic traits in crop plants. The SSR markers derived from the nonCDS components of genes with moderate selection pressure are expected to reveal high intra-specific polymorphism in contrast to highly constrained CDS-based markers (Cho et al, 2000; Chabane et al, 2005; Parida et al, 2010; Kujur et al, 2013)

Objectives

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Conclusion