Genetic dissection of drought tolerance in chickpea (Cicer arietinum L.).

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. 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.

Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits.

We report a map of 4.97 million single-nucleotide polymorphisms of the chickpea from whole-genome resequencing of 429 lines sampled from 45 countries. We identified 122 candidate regions with 204 genes under selection during chickpea breeding. Our data suggest the Eastern Mediterranean as the primary center of origin and migration route of chickpea from the Mediterranean/Fertile Crescent to Central Asia, and probably in parallel from Central Asia to East Africa (Ethiopia) and South Asia (India). Genome-wide association studies identified 262 markers and several candidate genes for 13 traits. Our study establishes a foundation for large-scale characterization of germplasm and population genomics, and a resource for trait dissection, accelerating genetic gains in future chickpea breeding.

Genotypic variation in soil water use and root distribution and their implications for drought tolerance in chickpea.

Chickpeas are often grown under receding soil moisture and suffer ~50% yield losses due to drought stress. The timing of soil water use is considered critical for the efficient use of water under drought and to reduce yield losses. Therefore the root growth and the soil water uptake of 12 chickpea genotypes known for contrasts in drought and rooting response were monitored throughout the growth period both under drought and optimal irrigation. Root distribution reduced in the surface and increased in the deep soil layers below 30cm in response to drought. Soil water uptake was the maximum at 45-60cm soil depth under drought whereas it was the maximum at shallower (15-30 and 30-45cm) soil depths when irrigated. The total water uptake under drought was 1-fold less than optimal irrigation. The amount of water left unused remained the same across watering regimes. All the drought sensitive chickpea genotypes were inferior in root distribution and soil water uptake but the timing of water uptake varied among drought tolerant genotypes. Superiority in water uptake in most stages and the total water use determined the best adaptation. The water use at 15-30cm soil depth ensured greater uptake from lower depths and the soil water use from 90-120cm soil was critical for best drought adaptation. Root length density and the soil water uptake across soil depths were closely associated except at the surface or the ultimate soil depths of root presence.

Correction: Genetic Dissection of Drought and Heat Tolerance in Chickpea through Genome-Wide and Candidate Gene-Based Association Mapping Approaches.

[This corrects the article DOI: 10.1371/journal.pone.0096758.].

Transcriptome analyses reveal genotype- and developmental stage-specific molecular responses to drought and salinity stresses in chickpea.

Drought and salinity are the major factors that limit chickpea production worldwide. We performed whole transcriptome analyses of chickpea genotypes to investigate the molecular basis of drought and salinity stress response/adaptation. Phenotypic analyses confirmed the contrasting responses of the chickpea genotypes to drought or salinity stress. RNA-seq of the roots of drought and salinity related genotypes was carried out under control and stress conditions at vegetative and/or reproductive stages. Comparative analysis of the transcriptomes revealed divergent gene expression in the chickpea genotypes at different developmental stages. We identified a total of 4954 and 5545 genes exclusively regulated in drought-tolerant and salinity-tolerant genotypes, respectively. A significant fraction (~47%) of the transcription factor encoding genes showed differential expression under stress. The key enzymes involved in metabolic pathways, such as carbohydrate metabolism, photosynthesis, lipid metabolism, generation of precursor metabolites/energy, protein modification, redox homeostasis and cell wall component biogenesis, were affected by drought and/or salinity stresses. Interestingly, transcript isoforms showed expression specificity across the chickpea genotypes and/or developmental stages as illustrated by the AP2-EREBP family members. Our findings provide insights into the transcriptome dynamics and components of regulatory network associated with drought and salinity stress responses in chickpea.

Plant growth promoting rhizobia: challenges and opportunities.

Modern agriculture faces challenges, such as loss of soil fertility, fluctuating climatic factors and increasing pathogen and pest attacks. Sustainability and environmental safety of agricultural production relies on eco-friendly approaches like biofertilizers, biopesticides and crop residue return. The multiplicity of beneficial effects of microbial inoculants, particularly plant growth promoters (PGP), emphasizes the need for further strengthening the research and their use in modern agriculture. PGP inhabit the rhizosphere for nutrients from plant root exudates. By reaction, they help in (1) increased plant growth through soil nutrient enrichment by nitrogen fixation, phosphate solubilization, siderophore production and phytohormones production (2) increased plant protection by influencing cellulase, protease, lipase and ß-1,3 glucanase productions and enhance plant defense by triggering induced systemic resistance through lipopolysaccharides, flagella, homoserine lactones, acetoin and butanediol against pests and pathogens. In addition, the PGP microbes contain useful variation for tolerating abiotic stresses like extremes of temperature, pH, salinity and drought; heavy metal and pesticide pollution. Seeking such tolerant PGP microbes is expected to offer enhanced plant growth and yield even under a combination of stresses. This review summarizes the PGP related research and its benefits, and highlights the benefits of PGP rhizobia belonging to the family Rhizobiaceae, Phyllobacteriaceae and Bradyrhizobiaceae.

The extent of variation in salinity tolerance of the minicore collection of finger millet (Eleusine coracana L. Gaertn.) germplasm.

Finger millet (Eleusine coracana L. Gaertn.) ranks third in production among the dry land cereals. It is widely cultivated in Africa and South Asia where soil salinization is a major production constraint. It is a potential crop for salt affected soils. To identify salt tolerant germplasm, the minicore finger millet germplasm (n=80) was screened for grain yield performance in a soil saturated with NaCl solution of 100 or 125mM. Genotype effect was significant for most traits, while salinity×genotype interaction was significant only in one year. Salinity delayed phenology, marginally reduced shoot biomass and grain yield. There was a large range of genotypic variation in grain yield under salinity and other traits. The yield loss was higher in accessions with prolific growth and yield potential was associated with saline yields. Based on saline yields, accessions were grouped in to four groups and the top tolerant group had 22 accessions with IE 4797 remaining at the top. Salinity had no adverse impact on grain yield of five accessions. Root anatomy in selected genotype of pearl and finger millet showed presence of porous cortex and well fortified endodermis in finger millet that can exclude Na(+) and enhance N absorption.

Genomics-assisted breeding for drought tolerance in chickpea.

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 genomics-assisted breeding, a draft genome sequence has been assembled for the CDC Frontier variety. In this context, 544.73Mb 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 (15360 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.

Genetic dissection of drought and heat tolerance in chickpea through genome-wide and candidate gene-based association mapping approaches.

To understand the genetic basis of tolerance to drought and heat stresses in chickpea, a comprehensive association mapping approach has been undertaken. Phenotypic data were generated on the reference set (300 accessions, including 211 mini-core collection accessions) for drought tolerance related root traits, heat tolerance, yield and yield component traits from 1-7 seasons and 1-3 locations in India (Patancheru, Kanpur, Bangalore) and three locations in Africa (Nairobi, Egerton in Kenya and Debre Zeit in Ethiopia). Diversity Array Technology (DArT) markers equally distributed across chickpea genome were used to determine population structure and three sub-populations were identified using admixture model in STRUCTURE. The pairwise linkage disequilibrium (LD) estimated using the squared-allele frequency correlations (r2; when r2<0.20) was found to decay rapidly with the genetic distance of 5 cM. For establishing marker-trait associations (MTAs), both genome-wide and candidate gene-sequencing based association mapping approaches were conducted using 1,872 markers (1,072 DArTs, 651 single nucleotide polymorphisms [SNPs], 113 gene-based SNPs and 36 simple sequence repeats [SSRs]) and phenotyping data mentioned above employing mixed linear model (MLM) analysis with optimum compression with P3D method and kinship matrix. As a result, 312 significant MTAs were identified and a maximum number of MTAs (70) was identified for 100-seed weight. A total of 18 SNPs from 5 genes (ERECTA, 11 SNPs; ASR, 4 SNPs; DREB, 1 SNP; CAP2 promoter, 1 SNP and AMDH, 1SNP) were significantly associated with different traits. This study provides significant MTAs for drought and heat tolerance in chickpea that can be used, after validation, in molecular breeding for developing superior varieties with enhanced drought and heat tolerance.

Variation in carbon isotope discrimination and its relationship with harvest index in the reference collection of chickpea germplasm.

Terminal drought is a major constraint to chickpea productivity. Carbon isotope discrimination (Δ13C), an integrator of plant behaviour influencing transpiration efficiency (TE), is an important component of yield under drought. The variation in Δ13C and its association with yield was assessed in the reference collection of chickpea germplasm. Drought stress reduced shoot biomass by 36-39% and grain yield by 23%. Mean Δ13C was low and the range of genetic variation was high under drought stress. Largely, high Δ13C accessions were early in flowering (40-50 days), moderate in shoot biomass, high in seed yields and high in harvest index (HI). Δ13C was positively correlated with seed yield in both the years under drought stress, only in 2008-09 under optimal irrigation. This positive association was very close with HI. Among the yield components, Δ13C was closely associated with pod numbers per unit area and seed size under drought stress. Path coefficients showed no direct association of Δ13C with grain yield but an indirect negative association through shoot biomass at maturity and a close positive association through HI. The closest association of HI or shoot biomass was seen in the maturity group of accessions that experienced the optimum terminal drought stress.