Advances in Chickpea Genomics

Abstract

Chickpea ( Cicer arietinum L.), the second largest consumed pulse crop of the world after common bean, is grown in over 50 countries and traded across 140 countries. After several decades of slow progress, the recent years have witnessed spectacular progress in development of genetic (mapping populations) and genomic resources (structural and functional molecular markers, integrated genetic map and mapping of genes/quantitative trait loci; QTLs) in this crop. QTLs associated with traits of interest including resistance against wilt, Ascochyta blight, Botrytis grey mould and rust; tolerance against salinity and drought and agronomic traits have been identifi ed and validated. A more than 30 genetic linkage maps available in this crop are useful resources for genetic analysis and marker assisted breeding. Genomic tools like bacterial artifi cial chromosome (BAC) libraries, expressed sequence tags (ESTs) and targeting induced local lesions in genome (TILLING) mutants have been developed in chickpea to facilitate the genome sequencing efforts in this crop. A major landmark in chickpea genomics has been the publication of 738 Mb draft whole genome sequence assembly of a kabuli variety, CDC Frontier. Now, chickpea is one of the most advanced grain legumes in terms of availability of genomic resources. Efforts have already begun on application of these genomics resources in chickpea improvement. This book chapter provides an update on the development of genetic and genomic resources for chickpea and their current and potential uses in chickpea improvement.

Chickpea

“…Molecular markers have been identifi ed for the genes/QTLs linked to resistance to several diseases, including Fusarium wilt (Sharma et al , 2005Cobos et al 2005 ;Gowda et al 2009 ;Garg Tosh 2012 ;Sabbavarapu et al 2013 ), Ascochyta blight (Millán et al 2003 ;Rakshit et al 2003 ;Collard et al 2003 ;Udupa and Baum 2003 ;Cho et al 2004 ;Iruela et al 2006 ;Lichitenzveiz et al 2006 ;Anbessa et al 2009 ;Kottapalli et al 2009 ;Aryamanesh et al 2010 ;Garg Tosh 2012 ;Sabbavarapu et al 2013 ), Botrytis grey mould (Anuradha et al 2011 ) and rust (Madrid et al 2008 ); salinity tolerance (Vadez et al 2012 ); traits related to drought tolerance Molina et al 2008 ;Rehman 2009 ;Rehman et al 2012 ; ICRISAT unpublished results), growth habit and podding Radhika et al 2007 ;Gowda et al 2009 ;Aryamanesh et al 2010 ;Garg Tosh et al 2012 ); phenology (Aryamanesh et al 2010 ;Rehman 2009 ;Rehman et al 2012 ); and seed characteristics (Gowda et al 2009 ). Several of these studies have been summarized in earlier reviews (Varshney et al 2007 ;Upadhyaya et al 2011 ;Gaur et al 2012bGaur et al , 2014b ).…”

“…Marker-assisted recurrent selection (MARS) has also been initiated in chickpea for the improvement of yield, particularly under moisture stress conditions. Two goodby-good crosses (JG 11 × ICCV 04112 and JG 130 × ICCV 05107) are being used at ICRISAT to implement MARS (Gaur et al 2014b ). QTLs were identifi ed specifi c to these crosses by genotyping in F 3 and phenotyping of F 3:5 progenies.…”

Genomics-assisted breeding for drought tolerance in chickpea

“…Details on the germplasm conserved and the genetic resources available in the case of chickpea have been extensively reviewed in recent publications Gaur et al 2013). For efficient and effective germplasm management and conservation, the concept of core and minicore collections have been advocated (Upadhyaya and Ortiz 2001), and trait-specific germplasm has been identified to aid breeding and genomics-assisted selection (Upadhyaya et al 2012).…”

“…Based on the evaluation of the minicore collection for terminal drought tolerance, germplasm lines with prolific root systems were identified and three recombinant inbred line mapping populations (Annigeri  ICC 4958, ICC 4958  ICC 1882 and ICC 283  ICC 8261) were developed at ICRISAT (see Gaur et al 2008). Similarly, several other mapping populations were also developed for gaining insights into most prevalent biotic and abiotic stresses (see Gaur et al 2013). Furthermore, for creating novel alleles and for functional validation of candidate drought-responsive genes, a 'target-induced local lesions in genome' (TILLING) population, comprising 3072 M2 chickpea lines, was also developed at ICRISAT.…”

Identification of QTLs for resistance to Fusarium wilt and Ascochyta blight in a recombinant inbred population of chickpea (Cicer arietinum L.)

“…In past, genomic resources have been deployed in chickpea to locate and tag the molecular markers linked to disease resistance (Gaur et al 2012b(Gaur et al , 2014. For FW, eight races (races 0, 1A, 1B/C, 2-6) have been identified and the genetics of resistance to six races has been reported as monogenic, digenic or quantitative (Singh et al 1987;Kumar 1998;Tullu et al 1999;Rubio et al 2003;Tekeoglu et al 2000;Sharma et al 2004Sharma et al , 2005.…”