Genomics-assisted breeding for drought tolerance in chickpea

Abstract

Abstract.Terminal drought is one of the major constraints in chickpea (Cicer arietinum L.), causing more than 50% production losses. With the objective of accelerating genetic understanding and crop improvement through genomicsassisted breeding, a draft genome sequence has been assembled for the CDC Frontier variety. In this context, 544.73 Mb of sequence data were assembled, capturing of 73.8% of the genome in scaffolds. In addition, large-scale genomic resources including several thousand simple sequence repeats and several million single nucleotide polymorphisms, high-density diversity array technology (15 360 clones) and Illumina GoldenGate assay genotyping platforms, high-density genetic maps and transcriptome assemblies have been developed. In parallel, by using linkage mapping approach, one genomic region harbouring quantitative trait loci for several drought tolerance traits has been identified and successfully introgressed in three leading chickpea varieties (e.g. JG 11, Chefe, KAK 2) by using a marker-assisted backcrossing approach. A multilocation evaluation of these marker-assisted backcrossing lines provided several lines with 10-24% higher yield than the respective recurrent parents.Modern breeding approaches like marker-assisted recurrent selection and genomic selection are being deployed for enhancing drought tolerance in chickpea. Some novel mapping populations such as multiparent advanced generation intercross and nested association mapping populations are also being developed for trait mapping at higher resolution, as well as for enhancing the genetic base of chickpea. Such advances in genomics and genomics-assisted breeding will accelerate precision and efficiency in breeding for stress tolerance in chickpea.

Recent breeding programs enhanced genetic diversity in both desi and kabuli varieties of chickpea (Cicer arietinum L.)

“…We detected 310 regions spanning 2% of the chickpea genome that had been differentially selected between varieties released in RP1, RP2 and RP3. These regions include large number of known functional genes and loci associated with important agronomic traits like early flowering, disease resistance previously reported using both linkage and LD based trait mapping approaches4652. Identified CNVs and PAVs will become increasingly relevant for the chickpea breeding community as crop production expands to short hotter regions with poor soil moisture and accumulation of toxic metals and chemicals over years of intensive agriculture.…”

“…As a result, susceptibility of the crop has been aggravated to several biotic and abiotic stresses and production potential has been seriously hampered. To overcome these constraints, genomic approaches have been deployed in recent years to understand the genetic basis of such complex quantitative traits and for trait improvement in chickpea4. Several superior lines with enhanced drought tolerance and resistance to Fusarium wilt (FW; caused by Fusarium oxysporum fsp ciceris ) and Ascochyta blight (AB; caused by Ascochyta rabiei ), have been developed56.…”

Marker-trait association study for protein content in chickpea (Cicer arietinum L.)

“…Tremendous progress has been made in the area of chickpea genomics in the past five years, and this has resulted in the generation of few thousand molecular markers (Choudhary et al 2009;Hiremath et al 2012;Kujur et al 2013), several linkage maps (Nayak et al 2010;Thudi et al 2011; for a review, see Varshney et al 2013a), identification of marker-trait associations (MTAs) / quantitative trait loci (QTLs) (Varshney et al 2013a;Thudi et al 2014a) and the now available, majority of the breeding attempts made in chickpea have been, and are being, focussed on improving yield, resistance to diseases like Ascochyta blight and Fusarium wilt (Varshney et al 2014a) and on resistance to various abiotic stresses (Varshney et al 2013c(Varshney et al , 2014b; for a review, see Jha et al 2014;Thudi et al 2014b). However, there has been no impact of traditional breeding strategies in the improvement of the nutritional status of the chickpea.…”

Developing drought tolerant crops: hopes and challenges in an exciting journey

“…Drought adaptation is complex, likely to involve interaction among many genes and we interpret the reduction in papers offering transgenic solutions as an acceptance within the scientific community that there is no simple 'magic gene' solution for adaptation to drought. Instead, genomic selection has become an emerging breeding tool (Thudi et al 2014). Of course, the issues of GÂE interaction covered in the previous paragraph remind us of the complexity of drought adaptation and we suggest that genomic selection must be integrated with physiology, agronomy and other disciplines used to understand interactions in order to fulfil its potential.…”