Genomic tools and germplasm diversity for chickpea improvement

Abstract

Chickpea is third most important grain legume grown in the arid and semi-arid regions of the world. In spite of vast germplasm accessions available in different genebanks, there has been very limited use of these accessions in genetic enhancement of chickpea. However, in recent years specialized germplasm sub sets like global composite collection, core collection, mini core collection and reference set have been developed. In parallel, significant genomic resources like molecular markers including simple sequence repeats (SSRs), single nucleotide polymorphsims (SNPs), Diversity Arrays Technologies (DArT) and transcript sequences e.g. expressed sequence tags (ESTs), short transcript reads have been developed. By using SSR, SNP and DArT markers, integrated genetic maps have been developed. It is anticipated that use of genomic resources and specialized germplasm sub sets such as mini core collection and reference set will facilitate identification of trait-specific germplasm, trait mapping and allele mining for resistance to biotic and abiotic stresses and for agronomic traits. Recent advances in genomics and bioinformatics offer the possibility of undertaking large scale sequencing of germplasm accessions so that modern breeding approaches such as genomic selection and breeding by design can be realized in near future for chickpea improvement.

Single Nucleotide Polymorphism Genotyping for Breeding and Genetics Applications in Chickpea and Pigeonpea using the BeadXpress Platform

“…Simple sequence repeat markers, being genome specific, codominant, highly polymorphic, and evenly distributed throughout the genome, have been the marker of choice for more than a decade. Chickpea and pigeonpea have more than 3000 SSR markers, which have been used for developing genetic maps (Nayak et al, 2010; Gujaria et al, 2011; Bohra et al, 2012; Choudhary et al, 2012; Saxena et al, 2012) and are being used in breeding application (see Upadhyaya et al, 2011b). Although SSR markers are being used in most of the ongoing marker‐assisted selection programs across the world, generating marker genotyping data is tedious and expensive compared to SNPs.…”

Pre-breeding for diversification of primary gene pool and genetic enhancement of grain legumes

“…Further, coordinated efforts have led to the development of large-scale genomic resources such as molecular markers, construction of comprehensive genetic maps, dense consensus maps and identification of marker-trait associations. Some recent reviews provide in-depth detail on quantity, source and development methods of these resources in these three legumes (see reviews Upadhyaya et al, 2011b; Varshney et al, 2012a, 2013a). Simple sequence repeat (SSR) or microsatellite and single nucleotide polymorphism (SNP) markers are the preferred marker systems especially for genetics and breeding applications.…”

Impact of Genomic Technologies on Chickpea Breeding Strategies

“…Efforts are being made to develop varieties with a vigorous and deeper root system to improve drought tolerance [28]. A large genetic variation for heat tolerance has been identified in chickpea [8,29]. A heat tolerant breeding line ICCV 92944 has been released for cultivation in Myanmar (Yezin 6) and India (JG 14).…”