Abstract
BackgroundAlthough chickpea (Cicer arietinum L.), an important food legume crop, is sensitive to salinity, considerable variation for salinity tolerance exists in the germplasm. To improve any existing cultivar, it is important to understand the genetic and physiological mechanisms underlying this tolerance.ResultsIn the present study, 188 recombinant inbred lines (RILs) derived from the cross ICCV 2 × JG 11 were used to assess yield and related traits in a soil with 0 mM NaCl (control) and 80 mM NaCl (salinity) over two consecutive years. Salinity significantly (P < 0.05) affected almost all traits across years and yield reduction was in large part related to a reduction in seed number but also a reduction in above ground biomass. A genetic map was constructed using 56 polymorphic markers (28 simple sequence repeats; SSRs and 28 single nucleotide polymorphisms; SNPs). The QTL analysis revealed two key genomic regions on CaLG05 (28.6 cM) and on CaLG07 (19.4 cM), that harboured QTLs for six and five different salinity tolerance associated traits, respectively, and imparting either higher plant vigour (on CaLG05) or higher reproductive success (on CaLG07). Two major QTLs for yield in the salinity treatment (explaining 12 and 17% of the phenotypic variation) were identified within the two key genomic regions. Comparison with already published chickpea genetic maps showed that these regions conferred salinity tolerance across two other populations and the markers can be deployed for enhancing salinity tolerance in chickpea. Based on the gene ontology annotation, forty eight putative candidate genes responsive to salinity stress were found on CaLG05 (31 genes) and CaLG07 (17 genes) in a distance of 11.1 Mb and 8.2 Mb on chickpea reference genome. Most of the genes were known to be involved in achieving osmoregulation under stress conditions.ConclusionIdentification of putative candidate genes further strengthens the idea of using CaLG05 and CaLG07 genomic regions for marker assisted breeding (MAB). Further fine mapping of these key genomic regions may lead to novel gene identification for salinity stress tolerance in chickpea.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0491-8) contains supplementary material, which is available to authorized users.
Highlights
Chickpea (Cicer arietinum L.), an important food legume crop, is sensitive to salinity, considerable variation for salinity tolerance exists in the germplasm
The combined unbalanced Analysis of variance (ANOVA) on two years data, for both of the treatments revealed that the traits days to 50% flowering (DF), Days to maturity (DM) and 100-seed weight were significantly influenced by both genotype and environment, but largely affected by the genetic potential rather than the environment
The present study has identified two potential genomic regions that harboured Quantitative trait loci (QTL) linked to salinity tolerance in chickpea and which can be used in marker assisted breeding (MAB)
Summary
Chickpea (Cicer arietinum L.), an important food legume crop, is sensitive to salinity, considerable variation for salinity tolerance exists in the germplasm. To improve any existing cultivar, it is important to understand the genetic and physiological mechanisms underlying this tolerance. In order to harness the complex phenomenon of salt tolerance, it is important to understand the genetic and physiological basis of salinity tolerance in order to improve existing crop cultivars. Several studies have been carried out to understand the molecular basis of salt tolerance in other crops and quantitative trait loci (QTLs) for traits associated to salinity tolerance have been identified in cereals like bread wheat [8], barley [9], and in legumes such as Medicago truncatula [10], and soybean [11]. Till date very few major QTLs were identified for yield components governing salinity tolerance. It becomes important to identify more number of additional QTLs governing salinity stress tolerance for yield and yield components that can be utilised effectively in marker-assisted genetic improvement of chickpea. Till date there is no report on putative candidate genes that would confer salinity tolerance in chickpea
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