Key message Analysis of phenotypic data for 20 drought tolerance traits in 1–7 seasons at 1–5 locations together with genetic mapping data for two mapping populations provided 9 QTL clusters of which one present on CaLG04 has a high potential to enhance drought tolerance in chickpea improvement. Abstract Chickpea (Cicer arietinum L.) is the second most important grain legume cultivated by resource poor farmers in the arid and semi-arid regions of the world. Drought is one of the major constraints leading up to 50 % production losses in chickpea. In order to dissect the complex nature of drought tolerance and to use genomics tools for enhancing yield of chickpea under drought conditions, two mapping populations—ICCRIL03 (ICC 4958 × ICC 1882) and ICCRIL04 (ICC 283 × ICC 8261) segregating for drought tolerance-related root traits were phenotyped for a total of 20 drought component traits in 1–7 seasons at 1–5 locations in India. Individual genetic maps comprising 241 loci and 168 loci for ICCRIL03 and ICCRIL04, respectively, and a consensus genetic map comprising 352 loci were constructed (http://cmap.icrisat.ac.in/cmap/sm/cp/varshney/). Analysis of extensive genotypic and precise phenotypic data revealed 45 robust main-effect QTLs (M-QTLs) explaining up to 58.20 % phenotypic variation and 973 epistatic QTLs (E-QTLs) explaining up to 92.19 % phenotypic variation for several target traits. Nine QTL clusters containing QTLs for several drought tolerance traits have been identified that can be targeted for molecular breeding. Among these clusters, one cluster harboring 48 % robust M-QTLs for 12 traits and explaining about 58.20 % phenotypic variation present on CaLG04 has been referred as “QTL-hotspot”. This genomic region contains seven SSR markers (ICCM0249, NCPGR127, TAA170, NCPGR21, TR11, GA24 and STMS11). Introgression of this region into elite cultivars is expected to enhance drought tolerance in chickpea.

Ambient temperatures are predicted to rise in the future owing to several reasons associated with global climate changes. These temperature increases can cause heat stress- a severe threat to crop production in most countries. Legumes are well-known for their impact on agricultural sustainability as well as their nutritional and health benefits. Heat stress imposes challenges for legume crops and has deleterious effects on the morphology, physiology and reproductive growth of plants. High-temperature stress during the reproductive stage is becoming a serious constraint to the productivity of grain legumes as their cultivation expands to warmer environments and temperature variability increases due to climate change. The reproductive period is vital in the life cycle of all plants and is susceptible to high-temperature stress as various metabolic processes are adversely impacted during this phase, which reduces crop yield. Food legumes exposed to high-temperature stress during reproduction show flower abortion, pollen and ovule infertility, impaired fertilization, and reduced seed filling, leading to smaller seeds and poor yields. Through various breeding techniques, heat tolerance in major legumes can be enhanced to improve performance in the field. Omics approaches unravel different mechanisms underlying thermotolerance, which is imperative to understand the processes of molecular responses towards high-temperature stress.

Chickpea (Cicer arietinum L.), in its reproductive stage, is sensitive to heat stress (32/20°C or higher as day/night temperatures) with consequent substantial loss of potential yields at high temperatures. The physiological mechanisms associated with reproductive failures have not been established: they constitute the basis of this study. Here, we initially screened a large core-collection of chickpea against heat stress and identified two heat-tolerant (ICC15614, ICCV. 92944) and two heat-sensitive (ICC10685, ICC5912) genotypes. These four genotypes were sown during the normal time of sowing (November–March) and also late (February–April) to expose them to heat stress during reproductive stage (>32/20°C). The genotypes were assessed for damage by heat stress to the leaves and reproductive organs using various indicators of stress injury and reproductive function. In the heat-stressed plants, phenology accelerated as days to flowering and podding, and biomass decreased significantly. The significant reduction in pod set (%) was associated with reduced pollen viability, pollen load, pollen germination (in vivo and in vitro) and stigma receptivity in all four genotypes. Heat stress inhibited pollen function more in the sensitive genotypes than in the tolerant ones, and consequently showed significantly less pod set. Heat stress significantly reduced stomatal conductance, leaf water content, chlorophyll, membrane integrity and photochemical efficiency with a larger effect on heat-sensitive genotypes. Rubisco (carbon-fixing enzyme) along with sucrose phosphate synthase (SPS) and sucrose synthase (SS) (sucrose-synthesising enzymes) decreased significantly in leaves due to heat stress leading to reduced sucrose content. Invertase, a sucrose-cleaving enzyme, was also inhibited along with SPS and SS. The inhibition of these enzymes was significantly greater in the heat-sensitive genotypes. Concurrently, the anthers of these genotypes had significantly less SPS and SS activity and thus, sucrose content. As a result, pollen had considerably lower sucrose levels, resulting in reduced pollen function, impaired fertilisation and poor pod set in heat-sensitive genotypes.

Summary: A set of 2486 single nucleotide polymorphisms (SNPs) were compiled in chickpea using four approaches, namely (i) Solexa/Illumina sequencing (1409), (ii) amplicon sequencing of tentative orthologous genes (TOGs) (604), (iii) mining of expressed sequence tags (ESTs) (286) and (iv) sequencing of candidate genes (187). Conversion of these SNPs to the cost‐effective and flexible throughput Competitive Allele Specific PCR (KASPar) assays generated successful assays for 2005 SNPs. These marker assays have been designated as Chickpea KASPar Assay Markers (CKAMs). Screening of 70 genotypes including 58 diverse chickpea accessions and 12 BC₃F₂ lines showed 1341 CKAMs as being polymorphic. Genetic analysis of these data clustered chickpea accessions based on geographical origin. Genotyping data generated for 671 CKAMs on the reference mapping population (Cicer arietinum ICC 4958 × Cicer reticulatum PI 489777) were compiled with 317 unpublished TOG‐SNPs and 396 published markers for developing the genetic map. As a result, a second‐generation genetic map comprising 1328 marker loci including novel 625 CKAMs, 314 TOG‐SNPs and 389 published marker loci with an average inter‐marker distance of 0.59 cM was constructed. Detailed analyses of 1064 mapped loci of this second‐generation chickpea genetic map showed a higher degree of synteny with genome of Medicago truncatula, followed by Glycine max, Lotus japonicus and least with Vigna unguiculata. Development of these cost‐effective CKAMs for SNP genotyping will be useful not only for genetics research and breeding applications in chickpea, but also for utilizing genome information from other sequenced or model legumes.