Unravelling the physiology and genetics of salinity tolerance in chickpea (Cicer arietinum L.)

Abstract

Chickpea (Cicer arietinum L.) is a nutritious legume predominantly grown in semi-arid environments under rain fed conditions, but is highly sensitive to soil salinity. Until recently, there has been slow progress in the application of molecular genetics in chickpea breeding. This is primarily because the available genetic variation in international chickpea germplasm collections has not been extensively characterised due to a lack of available genomics tools and high-throughput phenotyping resources. Molecular genetic approaches are needed to identify key loci with the potential to improve salinity tolerance in chickpea. In this project, genetic analysis was conducted on two populations: A recombinant inbred line (RIL) population of 200 individuals developed from a cross between Genesis836 and Rupali which are known to contrast in their tolerance to salinity and a diversity panel consisting of 245 chickpea accessions of diverse genetic background from ICRISAT. For phenotyping, an image-based high-throughput phenotyping platform was used. Data on growth rate, water use, plant senescence and necrosis, and agronomic traits were collected under both control and saline conditions (40 mM for diversity panel and 70 mM NaCl for RIL). In depth studies including differential metabolite accumulation and senescence detection were carried out to increase our understanding of the response of chickpea to salinity. Genesis836 and Rupali differentially accumulated metabolites associated with the TCA cycle, carbon and amino acid metabolism. Higher senescence scores were recorded in Rupali compared to Genesis836. On average, salinity reduced plant growth rate by 20%, plant height by 15% and shoot biomass by 28%. Additionally, salinity induced pod abortion and inhibited pod filling, which consequently reduced seed number and seed yield by 16% and 32%, respectively. Path analysis was utilised to understand the intricate relationship existing between the traits measured and aided in the identification of those most related to salinity tolerance. This analysis showed that seed number under salt was highly related to salinity tolerance in chickpea. To identify Quantitative Trait Loci (QTL) underlying salinity tolerance in chickpea, two complimentary genetic analysis approaches were used: genome-wide association studies (GWAS) and linkage mapping. Phenotypic data was combined with genotypic data from both the diversity panel (generated through whole-genome resequencing) and RIL population (from DArTseq). Linkage mapping and GWAS identified a total of 57 QTL and 54 marker-trait associations (MTAs), respectively. The loci identified were linked to growth rate, yield, yield components and ion accumulation. A novel major QTL for relative growth rate on chromosome 4 that explained 42.6% of genetic variation, was identified by both genetic analyses. This QTL co-located with several other QTL identified, including those associated with projected shoot area, water use, 100-seed weight, the number of filled pods, harvest index, seed number and seed yield under salt. Near-isogenic lines will be developed to allow for targeted fine mapping that will help identify candidate genes for molecular analysis. Molecular markers tightly linked to this QTL will be validated as a selection tool in breeding to improve salinity tolerance in chickpea.