Key messageAnalysis 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.AbstractChickpea (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.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-013-2230-6) contains supplementary material, which is available to authorized users.

SummaryExtensive and deep root systems have been recognized as one of the most important traits for improving chickpea (Cicer arietinum L.) productivity under progressively receding soil moisture conditions. However, available information on the range of variation for root traits is still limited. Genetic variability for the root traits was investigated using a cylinder culture system during two consecutive growth seasons in the mini-core germplasm collection of ICRISAT plus several wild relatives of chickpea. The largest genetic variability was observed at 35 days after sowing for root length density (RLD) (heritability, h 2 = 0.51 and 0.54) across seasons, and followed by the ratio of plant dry weight to root length density with h 2 of 0.37 and 0.47 for first and second season, respectively. The root growth of chickpea wild relatives was relatively poor compared to C. arietinum, except in case of C. reticulatum. An outstanding genotype, ICC 8261, which had the largest RLD and one of the deepest root system, was identified in chickpea mini-core germplasm collection. The accession ICC 4958 which was previously characterized as a source for drought avoidance in chickpea was confirmed as one with the most prolific and deep root system, although many superior accessions were also identified. The chickpea landraces collected from the Mediterranean and the west Asian region showed a significantly larger RLD than those from the south Asian region. In addition, the landraces originating from central Asia (former Soviet Union), characterized by arid agro-climatic conditions, also showed relatively larger RLD. As these regions are underrepresented in the chickpea collection, they might be interesting areas for further germplasm exploration to identify new landraces with large RLD. The information on the genetic variability of chickpea root traits provides valuable baseline knowledge for further progress on the selection and breeding for drought avoidance root traits in chickpea.

The importance of root systems in acquiring water has long been recognized as crucial to cope with drought conditions. This investigation was conducted to: (i) evaluate the variability on root length density (RLD) of chickpea in the vegetative growth stage; (ii) estimate the effect of RLD on seed yield under terminal drought conditions; and (iii) set up a procedure to facilitate the screening of chickpea genotypes with large RLD. Twelve diverse chickpea genotypes were grown in tall PVC cylinders with two different soil water treatments in 2000 and 2001, and in field under water deficit conditions during 2000/2001 and 2001/2002. In field trials, the mean RLD at 35 days after sowing showed a significant positive correlation with seed yield in both years. Similarly, the RLD in the 15-30 cm soil depth had significant positive effects to the seed yield in both years. The importance of the root trait was particularly relevant in 2001/2002, a more severe drought year, when the RLD in deeper soil layer, 30-60 cm depth, showed a significant positive relationship with seed yield. Also, the RLD at deeper soil layer, 30-60 cm depth, was higher in 2001/2002 than in 2000/2001, in particular in tolerant genotypes. The PVC cylinder trials were set up to facilitate the screening of chickpea genotypes with large RLD. RLD of plants grown in cylinders with 70% field capacity was correlated with RLD in the field trials (r = 0.731; p = 0.01). This work highlights the importance of roots in coping with terminal drought in chickpea. The cylinder system offers a much easier procedure to screen chickpea genotypes with large RLD.

BackgroundChickpea (Cicer arietinum L.), an important grain legume crop of the world is seriously challenged by terminal drought and salinity stresses. However, very limited number of molecular markers and candidate genes are available for undertaking molecular breeding in chickpea to tackle these stresses. This study reports generation and analysis of comprehensive resource of drought- and salinity-responsive expressed sequence tags (ESTs) and gene-based markers.ResultsA total of 20,162 (18,435 high quality) drought- and salinity- responsive ESTs were generated from ten different root tissue cDNA libraries of chickpea. Sequence editing, clustering and assembly analysis resulted in 6,404 unigenes (1,590 contigs and 4,814 singletons). Functional annotation of unigenes based on BLASTX analysis showed that 46.3% (2,965) had significant similarity (≤1E-05) to sequences in the non-redundant UniProt database. BLASTN analysis of unique sequences with ESTs of four legume species (Medicago, Lotus, soybean and groundnut) and three model plant species (rice, Arabidopsis and poplar) provided insights on conserved genes across legumes as well as novel transcripts for chickpea. Of 2,965 (46.3%) significant unigenes, only 2,071 (32.3%) unigenes could be functionally categorised according to Gene Ontology (GO) descriptions. A total of 2,029 sequences containing 3,728 simple sequence repeats (SSRs) were identified and 177 new EST-SSR markers were developed. Experimental validation of a set of 77 SSR markers on 24 genotypes revealed 230 alleles with an average of 4.6 alleles per marker and average polymorphism information content (PIC) value of 0.43. Besides SSR markers, 21,405 high confidence single nucleotide polymorphisms (SNPs) in 742 contigs (with ≥ 5 ESTs) were also identified. Recognition sites for restriction enzymes were identified for 7,884 SNPs in 240 contigs. Hierarchical clustering of 105 selected contigs provided clues about stress- responsive candidate genes and their expression profile showed predominance in specific stress-challenged libraries.ConclusionGenerated set of chickpea ESTs serves as a resource of high quality transcripts for gene discovery and development of functional markers associated with abiotic stress tolerance that will be helpful to facilitate chickpea breeding. Mapping of gene-based markers in chickpea will also add more anchoring points to align genomes of chickpea and other legume species.