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Tillage and crop residue management play an imperative role in soil physico-chemical properties that eventually affects crop productivity. The objective of the study to find out a compatible combination of tillage and crop residue management for achieving sustainable food production by improving soil properties, providing favorable environment to crop plants. Secondly, managing crop residues effectively to reduce environmental pollution arising due to crop residue burning. With this aim, a field experiment was conducted on six years continued running experiment under conservation agricultural practices during rabi season of 2019-20 on chickpea. The experiment was comprised of five tillage operations with or without crop residue in main plot and three levels of nutrients in sub plots laid out in split plot design with three replications. Reduced Tillage with 60cm residue height (RT60) was recorded higher growth and yield attributes over conventional tillage practice that attributed to economic yield enhancement. The percent yield increment under NT and RT with 30 and 60cm height residue retention varied from 6.91% to 9.67% over conventional tillage. Maximum grain (2380 kg ha-1) and biological output (5762 kg ha-1) was recorded under RT60 (T4), which ascribed to higher net return (Rs 60551 ha-1) and benefit-cost ratio (2.97). The augmentation in net monetary benefit among tillage systems was lies between 24.32% to 37.78% over conventional tillage. The seed protein content ranged between 20.38 to 21.69% among the treatments. Moreover, total N uptake was maximum under RT60, while total P and K uptake was higher in No Tillage with 30cm residue height (T1). No-Tillage with 60cm residue height (NT60) recorded relatively higher soil moisture content (SMC) (22.71 and 15.40%). Treatment NT30 accrued relatively higher value of soil bulk density (1.42 Mg m-3) followed by NT60 and RT60 in comparison to conventional tillage (1.34 Mg m-3). In conclusion, NT and RT with 60cm residue height along with STCR (N3) nutrient dose was found effective for sustainable food production.

Present investigation was conducted at the Research Farm of Indian Institute of Soil Science, Bhopal during 2017–18 and 2018–19 to study the performance of chickpea crop under various nutrient management modules in a Vertisol. The field experiment was set up in a randomized block design with three replications of twelve different INM modules. During the rabi seasons of 2017–18 and 2018–19, the chickpea (cv. JG-315) was grown with a set of treatments. The crop’s performance was evaluated in terms of growth, yield (grain and straw), nutritional content, and nutrient uptake under different treatments. At crop harvest, the physic-chemical characteristics of the soil were also evaluated. Finally, the relationship between the numerous examined parameters was determined. The results showed that integrated nutrient management modules had a positive impact on chickpea crop performance and productivity when compared to using only inorganic fertilizer. The INM modules dramatically increased soil organic carbon and improved soil health in terms of physical and chemical qualities, in addition to higher crop performance. Among the various modules, (1) application of 75% STCR dose + FYM @ 5t ha-1to maize followed by 100% P only to chickpea and (2) application of FYM @ 20t ha-1to maize followed by FYM @ 5t ha-1 to chickpea increased the productivity and nutrient uptake in chickpea, improved soil physico-chemical properties and reflected as viable technique in improving soil nutrient availability on sustainable basis.

Unravelling the genetic architecture underlying yield components and agronomic traits is important for enhancing crop productivity. Here, a recombinant inbred line (RIL) population, developed from ICC 4958 and DCP 92-3 cross, was used for constructing linkage map and QTL mapping analysis. The RIL population was genotyped using a high-throughput Axiom®CicerSNP array, which enabled the development of a high-density genetic map consisting of 3,818 SNP markers and spanning a distance of 1064.14 cM. Analysis of phenotyping data for yield, yield components and agronomic traits measured across three years together with genetic mapping data led to the identification of 10 major-effect QTLs and six minor-effect QTLs explaining up to 59.70% phenotypic variance. The major-effect QTLs identified for 100-seed weight, and plant height possessed key genes, such as C3HC4 RING finger protein, pentatricopeptide repeat (PPR) protein, sugar transporter, leucine zipper protein and NADH dehydrogenase, amongst others. The gene ontology studies highlighted the role of these genes in regulating seed weight and plant height in crop plants. The identified genomic regions for yield, yield components, and agronomic traits, and the closely linked markers will help advance genetics research and breeding programs in chickpea.

Evaluation of the genetic diversity and an understanding of the genetic structure and relationships of chickpea genotypes are valuable to design efficient germplasm conservation strategies and crop breeding programs. Information is limited, in these regards, for Ethiopian chickpea germplasms. Therefore, the present study was carried out to estimate the genetic diversity, population structure, and relationships of 152 chickpea genotypes using simple sequence repeats (SSR) markers. Twenty three SSR markers exhibited polymorphism producing a total of 133 alleles, with a mean of 5.8 alleles per locus. Analyses utilizing various genetic-based statistics included pairwise population Nei's genetic distance, heterozygosity, Shannon's information index, polymorphic information content, and percent polymorphism. These analyses exemplified the existence of high genetic variation within and among chickpea genotypes. The 152 genotypes were divided into two major clusters based on Nei's genetic distances. The exotic genotypes were grouped in one cluster exclusively showing that these genotypes are distinct to Ethiopian genotypes, while the patterns of clustering of Ethiopian chickpea genotypes based on their geographic region were not consistent because of the seed exchange across regions. Model-based population structure clustering identified two discrete populations. These finding provides useful insight for chickpea collections and ex-situ conservation and national breeding programs for widening the genetic base of chickpea.

Cicer arietinum is the 3rd most important cool season legume crop growing in vast arid and semi-arid regions of the world. A lab experiment was designed using hydrothermal time model (HTT) to investigate the chickpea seed germination (SG) behavior, cardinal temperatures and germination responses across fluctuating temperatures (Ts) and water potentials (Ψs). Seeds of chickpea var. NIFA 1995 were germinated at six constant Ts (7, 14, 21, 28, 35 and 42°C) each having the following five water potentials: 0, -0.2, -0.4-0.6 and -0.8 MPa. Germination percentage (G%) decreased significantly at (*P ≤ 0.05) from 86.7% at 28°C in -0.2 MPa to 10% in -0.2 MPa at 7°C. The germination rate (GR = 1/t50) against different T percentiles exhibited that linear increase was observed in the GR pattern above and below the To. Based on the confidence intervals of the model coefficients and (R2: 0.96), the average cardinal temperatures were 4.7, 23 and 44.2°C for the base (Tb), optimal (To) and ceiling (Tc) temperatures respectively. θT1 value was observed maximum at 28°C in -0.2 MPa and decreases with decreasing Ψ (-0.8 MPa). In comparison with control, the θT2 value was also highest in -0.2 MPa at 28°C. The thermal time (TT) concept is well fitted to germination fraction data in distilled water with an R2 value increasing 0.972. The hydro time constant (θH) increased with an increase in T to To and then decreased when T>To. The ѱb(50) irregularly varied with increasing T, σΨb was also recorded lowest (0.166 MPa) at 28°C and highest (0.457 MPa) at 7°C. Based on the statistical analysis, cardinal temperatures, hydrothermal time constant (θHTT) and germination findings the HTT gives an insight into the interactive effect of T and Ψ on seed germination time courses under varying environmental conditions.

This study is the first report on the biosynthesized iron oxide nanoparticles (IONPs) which mediate in-vitro callus induction and shoot regeneration in economically important recalcitrant chickpea crop (Cicer arietinum L.). Here, we used leaf extract of Cymbopogon jwarancusa for the synthesis of IONPs in order to achieve a better biocompatibility. The bioactive compounds in C. jwarancusa leaf extract served as both reducing and capping agents in the fabrication process of IONPs. Field emission scanning electron microscopy (FE-SEM) revealed rods like surface morphology of IONPs with an average diameter of 50±0.2 nm. Energy-dispersive X-ray spectroscopy (EDS) depicted formation of pure IONPs with 69.84% Fe and 30.16% O2. X-ray diffractometry (XRD) and attenuated total reflectance-fourier transform infrared (ATR-FTIR) validate the crystalline structure, chemical analysis detect the presence of various biomolecular fingerprints in the as synthesized IONPs. UV-visible absorption spectroscopy depicts activity of IONPs under visible light. Thermo-gravimetric analysis (TGA) displayed thermal loss of organic capping around 500°C and confirmed their stabilization. The biosynthesized IONPs revealed promising results in callus induction, shoot regeneration and root induction of chickpea plants. Both chickpea varieties Punjab-Noor 09 and Bittle-98 explants, Embryo axes (EA) and Embryo axes plus adjacent part of cotyledon (EXC) demonstrated dose-dependent response. Among all explants, EXC of Punjab-Noor variety showed the highest callogenesis (96%) and shoot regeneration frequency (88%), while root induction frequency was also increased to 83%. Iron content was quantified in regenerated chickpea varieties through inductively coupled plasma-optical emission spectrometry. The quantity of iron is significantly increased in Punjab-Noor regenerated plants (4.88 mg/g) as compare to control treated plants (2.42 mg/g). We found that IONPs enhance chickpea growth pattern and keep regenerated plantlets infection free by providing an optimum environment for rapid growth and development. Thus, IONPs synthesized through green process can be utilized in tissue culture studies in other important recalcitrant legumes crops.

The ever-increasing industrial activities over the decades have generated high toxic metal such as chromium (Cr) that hampers the crop productivity. This study evaluated the effect of Cr on two chickpea (Cicer arietinum L.) varieties, Pusa 2085 and Pusa Green 112, in hydroponic and pot-grown conditions. First, growth parameters (seed germination, seedling growth, and biomass production) and physio-biochemical parameters (oxidative stress and the content of antioxidants and proline) were measured to evaluate the performance of both varieties grown hydroponically for 21 days at concentrations of 0, 30, 60, 90 and 120 μM Cr in the form of potassium dichromate (K2Cr2O7). In both varieties, significantly deleterious effects on germination and seedling growth parameters were observed at 90 and 120 μM, while growth was stimulated at 30 μM Cr. Significant increases in malondialdehyde and hydrogen peroxide content and electrolyte leakage demonstrated enhanced oxidative injury to seedlings caused by higher concentrations of Cr. Further, increasing concentrations of Cr positively correlated with increased proline content, superoxide dismutase activity, and peroxide content in leaves. There was also an increase in peroxisomal ascorbate peroxidase and catalase in the leaves of both varieties at lower Cr concentrations, whereas a steep decline was recorded at higher Cr concentrations. In the pot experiments conducted over two consecutive years, growth, yield, yield attributes, grain protein, and Cr uptake and accumulation were measured at different Cr concentrations. Pusa Green 112 showed a significant reduction in plant growth, chlorophyll content, grain protein, pod number, and grain yield per plant when compared with Pusa 2085. Overall, our results indicate that Pusa 2085 has a higher Cr tolerance than Pusa Green 112. Therefore, Pusa 2085 could be used to further elucidate the mechanisms of Cr tolerance in plants and in breeding programmes to produce Cr-resistant varieties.

Tillage and crop residue management play an imperative role in soil physico-chemical properties that eventually affects crop productivity. The objective of the study to find out a compatible combination of tillage and crop residue management for achieving sustainable food production by improving soil properties, providing favorable environment to crop plants. Secondly, managing crop residues effectively to reduce environmental pollution arising due to crop residue burning. With this aim, a field experiment was conducted on six years continued running experiment under conservation agricultural practices during rabi season of 2019-20 on chickpea. The experiment was comprised of five tillage operations with or without crop residue in main plot and three levels of nutrients in sub plots laid out in split plot design with three replications. Reduced Tillage with 60cm residue height (RT60) was recorded higher growth and yield attributes over conventional tillage practice that attributed to economic yield enhancement. The percent yield increment under NT and RT with 30 and 60cm height residue retention varied from 6.91% to 9.67% over conventional tillage. Maximum grain (2380 kg ha-1) and biological output (5762 kg ha-1) was recorded under RT60 (T4), which ascribed to higher net return (Rs 60551 ha-1) and benefit-cost ratio (2.97). The augmentation in net monetary benefit among tillage systems was lies between 24.32% to 37.78% over conventional tillage. The seed protein content ranged between 20.38 to 21.69% among the treatments. Moreover, total N uptake was maximum under RT60, while total P and K uptake was higher in No Tillage with 30cm residue height (T1). No-Tillage with 60cm residue height (NT60) recorded relatively higher soil moisture content (SMC) (22.71 and 15.40%). Treatment NT30 accrued relatively higher value of soil bulk density (1.42 Mg m-3) followed by NT60 and RT60 in comparison to conventional tillage (1.34 Mg m-3). In conclusion, NT and RT with 60cm residue height along with STCR (N3) nutrient dose was found effective for sustainable food production., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2022 Singh et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Chickpea has a profound nutritional and economic value in vegetarian society. Continuous decline in chickpea productivity is attributed to insufficient genetic variability and different environmental stresses. Chickpea like several other legumes is highly susceptible to terminal drought stress. Multiple genes control drought tolerance and ASR gene plays a key role in regulating different plant stresses. The present study describes the molecular characterization and functional role of Abscissic acid and stress ripening (ASR) gene from chickpea (Cicer arietinum) and the gene sequence identified was submitted to NCBI Genbank (MK937569). Molecular analysis using MUSCLE software proved that the ASR nucleotide sequences in different legumes show variations at various positions though ASR genes are conserved in chickpea with only few variations. Sequence similarity of ASR gene to chickpea putative ABA/WDS induced protein mRNA clearly indicated its potential involvement in drought tolerance. Physiological screening and qRT-PCR results demonstrated increased ASR gene expression under drought stress possibly enabled genotypes to perform better under stress. Conserved domain search, protein structure analysis, prediction and validation, network analysis using Phyre2, Swiss-PDB viewer, ProSA and STRING analysis established the role of hypothetical ASR protein NP_001351739.1 in mediating drought responses. NP_001351739.1 might have enhanced the ASR gene activity as a transcription factor regulating drought stress tolerance in chickpea. This study could be useful in identification of new ASR genes that play a major role in drought tolerance and also develop functional markers for chickpea improvement.

Plant growth regulators (PGRs) and plant growth promoting rhizobacteria (PGPRs) play an important role in mitigating abiotic stresses. However, little is known about the parallel changes in physiological processes coupled with metabolic changes induced by PGRs and PGPRs that help to cope with drought stress in chickpeas. The present investigation was carried out to study the integrative effects of PGRs and PGPRs on the physiological and metabolic changes, and their association with drought tolerance in two chickpea genotypes. Inoculated seeds of two chickpea genotypes, Punjab Noor-2009 (drought sensitive) and 93127 (drought tolerance), were planted in greenhouse condition at the University of Florida. Prior to sowing, seeds of two chickpea varieties were soaked for 3 h in 24 h old cultures of PGPRs (Bacillus subtilis, Bacillus thuringiensis, and Bacillus megaterium), whereas, some of the seeds were soaked in distilled water for the same period of time and were treated as control. Plant growth regulators, salicylic acid (SA) and putrescine (Put), were applied on 25 days old seedlings just prior to the induction of drought stress. Drought stress was imposed by withholding the supply of water on 25-day-old seedlings (at the three-leaf stage) and continued for the next 25 days until the soil water content reached 14%. Ultrahigh-performance liquid chromatography-high resolution mass spectrometry (UPLC-HRMS) analysis concomitant with physiological parameters were carried out in chickpea leaves at two-time points i.e. 14 and 25 d after imposition of drought stress. The results showed that both genotypes, treated with PGRs and PGPRs (consortium), performed significantly better under drought condition through enhanced leaf relative water content (RWC), greater biomass of shoot and root, higher Fv/FM ratio and higher accumulation of protein, sugar and phenolic compounds. The sensitive genotype was more responsive than tolerant one. The results revealed that the accumulation of succinate, leucine, disaccharide, saccharic acid and glyceric acid was consistently higher in both genotypes at both time points due to PGRs and PGPRs treatment. Significant accumulation of malonate, 5-oxo-L-proline, and trans-cinnamate occurred at both time points only in the tolerant genotype following the consortium treatment. Aminoacyl-tRNA, primary and secondary metabolite biosynthesis, amino acid metabolism or synthesis pathways, and energy cycle were significantly altered due to PGRs and PGPRs treatment. It is inferred that changes in different physiological and metabolic parameters induced by PGRs and PGPRs treatment could confer drought tolerance in chickpeas.

This study was focused on analyzing the effects of dietary inclusion of raw chickpea seed as a replacement of soybean meal as a primary protein source on bone structure in broiler chickens. Broiler chickens (n = 160) received in their diet either soybean meal (SBM) or raw chickpea seeds (CPS) as a primary protein source throughout the whole rearing period (n = 80 in each group). On the 42th day randomly selected chickens from each group (n = 8) were slaughtered. Collected tibiotarsus were subjected to examination of the biomechanical characteristics of bone mid-diaphysis, microstructure of the growth plate and articular cartilages; the analysis of mineral content and crystallinity of mineral phase, and the measurements of thermal stability of collagen in hyaline cartilage were also carried out. The inclusion of chickpea seeds resulted in increase of bone osteometric parameters (weight, length and mid-diaphysis cross-sectional area) and mechanical endurance (yield load, ultimate load, stiffness, Young modulus). However, when loads were adjusted to bone shape (yield and ultimate stress) both groups did not differ. Mineral density determined by means of densitometric measurements did not differ between groups, however the detailed analysis revealed the differences in the macro- and microelements composition. The results of FT-IR and XRD analyses showed no effect of diet type on mineral phase crystallinity and hydroxyapatite nanocrystallites size. In trabecular bone, the increase of real bone volume (BV/TV) and number of trabeculae was observed in the CPS group. Total thickness of articular cartilage was the same in both groups, save the transitional zone, which was thicker in the SBM group. The total thickness of the growth plate cartilage was significantly increased in the CPS group. The area of the most intense presence of proteoglycans was wider in the SBM group. The structural analysis of fibrous components of bone revealed the increase of fraction of thin, immature collagen content in articular cartilage, trabeculae and compact bone in the CPS group. The dietary inclusion of CPS affected the thermal stability of collagen, as decrease of net denaturation enthalpy was observed. This study showed a beneficial effect of CPS on the skeletal development, improving the overall bone development and the microarchitecture of cancellous bone. It suggests that CPS can be a promising replacement for SBM in broilers feeding in the aspect of animal welfare related to the development of the skeletal system.

Drought is the most important constraint that effects chickpea production globally. RNA-Seq has great potential to dissect the molecular mechanisms of tolerance to environmental stresses. Transcriptome profiles in roots and shoots of two contrasting Iranian kabuli chickpea genotypes (Bivanij and Hashem) were investigated under water-limited conditions at early flowering stage using RNA-Seq approach. A total of 4,572 differentially expressed genes (DEGs) were identified. Of these, 261 and 169 drought stress responsive genes were identified in the shoots and the roots, respectively, and 17 genes were common in the shoots and the roots. Gene Ontology (GO) analysis revealed several sub-categories related to the stress, including response to stress, defense response and response to stimulus in the tolerant genotype Bivanij as compared to the sensitive genotype Hashem under drought stress. In addition, several Transcription factors (TFs) were identified in major metabolic pathways such as, ABA, proline and flavonoid biosynthesis. Furthermore, a number of the DEGs were observed in "QTL-hotspot" regions which were reported earlier in chickpea. Drought tolerance dissection in the genotypes revealed that the genes and the pathways involved in shoots of Bivanij were the most important factor to make a difference between the genotypes for drought tolerance. The identified TFs in the experiment, particularly those which were up-regulated in shoots of Bivanij during drought stress, were potential candidates for enhancing tolerance to drought.

Present investigation was conducted at the Research Farm of Indian Institute of Soil Science, Bhopal during 2017-18 and 2018-19 to study the performance of chickpea crop under various nutrient management modules in a Vertisol. The field experiment was set up in a randomized block design with three replications of twelve different INM modules. During the rabi seasons of 2017-18 and 2018-19, the chickpea (cv. JG-315) was grown with a set of treatments. The crop's performance was evaluated in terms of growth, yield (grain and straw), nutritional content, and nutrient uptake under different treatments. At crop harvest, the physic-chemical characteristics of the soil were also evaluated. Finally, the relationship between the numerous examined parameters was determined. The results showed that integrated nutrient management modules had a positive impact on chickpea crop performance and productivity when compared to using only inorganic fertilizer. The INM modules dramatically increased soil organic carbon and improved soil health in terms of physical and chemical qualities, in addition to higher crop performance. Among the various modules, (1) application of 75% STCR dose + FYM @ 5t ha-1to maize followed by 100% P only to chickpea and (2) application of FYM @ 20t ha-1to maize followed by FYM @ 5t ha-1 to chickpea increased the productivity and nutrient uptake in chickpea, improved soil physico-chemical properties and reflected as viable technique in improving soil nutrient availability on sustainable basis., Competing Interests: The authors have declared that no competing interests exist.

Cicer arietinum is the 3rd most important cool season legume crop growing in vast arid and semi-arid regions of the world. A lab experiment was designed using hydrothermal time model (HTT) to investigate the chickpea seed germination (SG) behavior, cardinal temperatures and germination responses across fluctuating temperatures (Ts) and water potentials (Ψs). Seeds of chickpea var. NIFA 1995 were germinated at six constant Ts (7, 14, 21, 28, 35 and 42°C) each having the following five water potentials: 0, -0.2, -0.4-0.6 and -0.8 MPa. Germination percentage (G%) decreased significantly at (*P ≤ 0.05) from 86.7% at 28°C in -0.2 MPa to 10% in -0.2 MPa at 7°C. The germination rate (GR = 1/t50) against different T percentiles exhibited that linear increase was observed in the GR pattern above and below the To. Based on the confidence intervals of the model coefficients and (R2: 0.96), the average cardinal temperatures were 4.7, 23 and 44.2°C for the base (Tb), optimal (To) and ceiling (Tc) temperatures respectively. θT1 value was observed maximum at 28°C in -0.2 MPa and decreases with decreasing Ψ (-0.8 MPa). In comparison with control, the θT2 value was also highest in -0.2 MPa at 28°C. The thermal time (TT) concept is well fitted to germination fraction data in distilled water with an R2 value increasing 0.972. The hydro time constant (θH) increased with an increase in T to To and then decreased when T>To. The ѱb(50) irregularly varied with increasing T, σΨb was also recorded lowest (0.166 MPa) at 28°C and highest (0.457 MPa) at 7°C. Based on the statistical analysis, cardinal temperatures, hydrothermal time constant (θHTT) and germination findings the HTT gives an insight into the interactive effect of T and Ψ on seed germination time courses under varying environmental conditions., Competing Interests: The authors have declared that no competing interests exist.

Evaluation of the genetic diversity and an understanding of the genetic structure and relationships of chickpea genotypes are valuable to design efficient germplasm conservation strategies and crop breeding programs. Information is limited, in these regards, for Ethiopian chickpea germplasms. Therefore, the present study was carried out to estimate the genetic diversity, population structure, and relationships of 152 chickpea genotypes using simple sequence repeats (SSR) markers. Twenty three SSR markers exhibited polymorphism producing a total of 133 alleles, with a mean of 5.8 alleles per locus. Analyses utilizing various genetic-based statistics included pairwise population Nei's genetic distance, heterozygosity, Shannon's information index, polymorphic information content, and percent polymorphism. These analyses exemplified the existence of high genetic variation within and among chickpea genotypes. The 152 genotypes were divided into two major clusters based on Nei's genetic distances. The exotic genotypes were grouped in one cluster exclusively showing that these genotypes are distinct to Ethiopian genotypes, while the patterns of clustering of Ethiopian chickpea genotypes based on their geographic region were not consistent because of the seed exchange across regions. Model-based population structure clustering identified two discrete populations. These finding provides useful insight for chickpea collections and ex-situ conservation and national breeding programs for widening the genetic base of chickpea., Competing Interests: The authors declare there are no competing interests.

The CCCH zinc finger is a group of proteins characterised by a typical motif consisting of three cysteine residues and one histidine residue. These proteins have been reported to play important roles in regulation of plant growth, developmental processes and environmental responses. In the present study, genome wide analysis of the CCCH zinc finger gene family was carried out in the available chickpea genome. Various bioinformatics tools were employed to predict 58 CCCH zinc finger genes in chickpea (designated CarC3H1-58), which were analysed for their physio-chemical properties. Phylogenetic analysis classified the proteins into 12 groups in which members of a particular group had similar structural organization. Further, the numbers as well as the types of CCCH motifs present in the CarC3H proteins were compared with those from Arabidopsis and Medicago truncatula. Synteny analysis revealed valuable information regarding the evolution of this gene family. Tandem and segmental duplication events were identified and their Ka/Ks values revealed that the CarC3H gene family in chickpea had undergone purifying selection. Digital, as well as real time qRT-PCR expression analysis was performed which helped in identification of several CarC3H members that expressed preferentially in specific chickpea tissues as well as during abiotic stresses (desiccation, cold, salinity). Moreover, molecular characterization of an important member CarC3H45 was carried out. This study provides comprehensive genomic information about the important CCCH zinc finger gene family in chickpea. The identified tissue specific and abiotic stress specific CCCH genes could be potential candidates for further characterization to delineate their functional roles in development and stress.

A hallmark trait of chickpea (Cicer arietinum L.), like other legumes, is the capability to convert atmospheric nitrogen (N2) into ammonia (NH3) in symbiotic association with Mesorhizobium ciceri. However, the complexity of molecular networks associated with the dynamics of nodule development in chickpea need to be analyzed in depth. Hence, in order to gain insights into the chickpea nodule development, the transcriptomes of nodules at early, middle and late stages of development were sequenced using the Roche 454 platform. This generated 490.84 Mb sequence data comprising 1,360,251 reads which were assembled into 83,405 unigenes. Transcripts were annotated using Gene Ontology (GO), Cluster of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways analysis. Differential expression analysis revealed that a total of 3760 transcripts were differentially expressed in at least one of three stages, whereas 935, 117 and 2707 transcripts were found to be differentially expressed in the early, middle and late stages of nodule development respectively. MapMan analysis revealed enrichment of metabolic pathways such as transport, protein synthesis, signaling and carbohydrate metabolism during root nodulation. Transcription factors were predicted and analyzed for their differential expression during nodule development. Putative nodule specific transcripts were identified and enriched for GO categories using BiNGO which revealed many categories to be enriched during nodule development, including transcription regulators and transporters. Further, the assembled transcriptome was also used to mine for genic SSR markers. In conclusion, this study will help in enriching the transcriptomic resources implicated in understanding of root nodulation events in chickpea.

Unravelling the genetic architecture underlying yield components and agronomic traits is important for enhancing crop productivity. Here, a recombinant inbred line (RIL) population, developed from ICC 4958 and DCP 92-3 cross, was used for constructing linkage map and QTL mapping analysis. The RIL population was genotyped using a high-throughput Axiom®CicerSNP array, which enabled the development of a high-density genetic map consisting of 3,818 SNP markers and spanning a distance of 1064.14 cM. Analysis of phenotyping data for yield, yield components and agronomic traits measured across three years together with genetic mapping data led to the identification of 10 major-effect QTLs and six minor-effect QTLs explaining up to 59.70% phenotypic variance. The major-effect QTLs identified for 100-seed weight, and plant height possessed key genes, such as C3HC4 RING finger protein, pentatricopeptide repeat (PPR) protein, sugar transporter, leucine zipper protein and NADH dehydrogenase, amongst others. The gene ontology studies highlighted the role of these genes in regulating seed weight and plant height in crop plants. The identified genomic regions for yield, yield components, and agronomic traits, and the closely linked markers will help advance genetics research and breeding programs in chickpea., Competing Interests: The authors have declared that no competing interests exist.

The ever-increasing industrial activities over the decades have generated high toxic metal such as chromium (Cr) that hampers the crop productivity. This study evaluated the effect of Cr on two chickpea (Cicer arietinum L.) varieties, Pusa 2085 and Pusa Green 112, in hydroponic and pot-grown conditions. First, growth parameters (seed germination, seedling growth, and biomass production) and physio-biochemical parameters (oxidative stress and the content of antioxidants and proline) were measured to evaluate the performance of both varieties grown hydroponically for 21 days at concentrations of 0, 30, 60, 90 and 120 μM Cr in the form of potassium dichromate (K2Cr2O7). In both varieties, significantly deleterious effects on germination and seedling growth parameters were observed at 90 and 120 μM, while growth was stimulated at 30 μM Cr. Significant increases in malondialdehyde and hydrogen peroxide content and electrolyte leakage demonstrated enhanced oxidative injury to seedlings caused by higher concentrations of Cr. Further, increasing concentrations of Cr positively correlated with increased proline content, superoxide dismutase activity, and peroxide content in leaves. There was also an increase in peroxisomal ascorbate peroxidase and catalase in the leaves of both varieties at lower Cr concentrations, whereas a steep decline was recorded at higher Cr concentrations. In the pot experiments conducted over two consecutive years, growth, yield, yield attributes, grain protein, and Cr uptake and accumulation were measured at different Cr concentrations. Pusa Green 112 showed a significant reduction in plant growth, chlorophyll content, grain protein, pod number, and grain yield per plant when compared with Pusa 2085. Overall, our results indicate that Pusa 2085 has a higher Cr tolerance than Pusa Green 112. Therefore, Pusa 2085 could be used to further elucidate the mechanisms of Cr tolerance in plants and in breeding programmes to produce Cr-resistant varieties., Competing Interests: The authors have declared that no competing interests exist.

This study is the first report on the biosynthesized iron oxide nanoparticles (IONPs) which mediate in-vitro callus induction and shoot regeneration in economically important recalcitrant chickpea crop (Cicer arietinum L.). Here, we used leaf extract of Cymbopogon jwarancusa for the synthesis of IONPs in order to achieve a better biocompatibility. The bioactive compounds in C. jwarancusa leaf extract served as both reducing and capping agents in the fabrication process of IONPs. Field emission scanning electron microscopy (FE-SEM) revealed rods like surface morphology of IONPs with an average diameter of 50±0.2 nm. Energy-dispersive X-ray spectroscopy (EDS) depicted formation of pure IONPs with 69.84% Fe and 30.16% O2. X-ray diffractometry (XRD) and attenuated total reflectance-fourier transform infrared (ATR-FTIR) validate the crystalline structure, chemical analysis detect the presence of various biomolecular fingerprints in the as synthesized IONPs. UV-visible absorption spectroscopy depicts activity of IONPs under visible light. Thermo-gravimetric analysis (TGA) displayed thermal loss of organic capping around 500°C and confirmed their stabilization. The biosynthesized IONPs revealed promising results in callus induction, shoot regeneration and root induction of chickpea plants. Both chickpea varieties Punjab-Noor 09 and Bittle-98 explants, Embryo axes (EA) and Embryo axes plus adjacent part of cotyledon (EXC) demonstrated dose-dependent response. Among all explants, EXC of Punjab-Noor variety showed the highest callogenesis (96%) and shoot regeneration frequency (88%), while root induction frequency was also increased to 83%. Iron content was quantified in regenerated chickpea varieties through inductively coupled plasma-optical emission spectrometry. The quantity of iron is significantly increased in Punjab-Noor regenerated plants (4.88 mg/g) as compare to control treated plants (2.42 mg/g). We found that IONPs enhance chickpea growth pattern and keep regenerated plantlets infection free by providing an optimum environment for rapid growth and development. Thus, IONPs synthesized through green process can be utilized in tissue culture studies in other important recalcitrant legumes crops., Competing Interests: The authors have declared that no competing interests exist.

Considering the economic importance of chickpea (C. arietinum L.) seeds, it is important to understand the mechanisms underlying seed development for which a cDNA library was constructed from 6 day old chickpea embryos. A total of 8,186 ESTs were obtained from which 4,048 high quality ESTs were assembled into 1,480 unigenes that majorly encoded genes involved in various metabolic and regulatory pathways. Of these, 95 ESTs were found to be involved in ubiquitination related protein degradation pathways and 12 ESTs coded specifically for putative F-box proteins. Differential transcript accumulation of these putative F-box genes was observed in chickpea tissues as evidenced by quantitative real-time PCR. Further, to explore the role of F-box proteins in chickpea seed development, two F-box genes were selected for molecular characterization. These were named as CarF-box_PP2 and CarF-box_LysM depending on their C-terminal domains, PP2 and LysM, respectively. Their highly conserved structures led us to predict their target substrates. Subcellular localization experiment revealed that CarF-box_PP2 was localized in the cytoplasm and CarF-box_LysM was localized in the nucleus. We demonstrated their physical interactions with SKP1 protein, which validated that they function as F-box proteins in the formation of SCF complexes. Sequence analysis of their promoter regions revealed certain seed specific cis-acting elements that may be regulating their preferential transcript accumulation in the seed. Overall, the study helped in expanding the EST database of chickpea, which was further used to identify two novel F-box genes having a potential role in seed development.

Calcium ion (Ca2+) is a ubiquitous second messenger that transmits various internal and external signals including stresses and, therefore, is important for plants' response process. Calcineurin B-like proteins (CBLs) are one of the plant calcium sensors, which sense and convey the changes in cytosolic Ca2+-concentration for response process. A search in four leguminous plant (soybean, Medicago truncatula, common bean and chickpea) genomes identified 9 to 15 genes in each species that encode CBL proteins. Sequence analyses of CBL peptides and coding sequences (CDS) suggested that there are nine original CBL genes in these legumes and some of them were multiplied during whole genome or local gene duplication. Coding sequences of chickpea CBL genes (CaCBL) were cloned from their cDNAs and sequenced, and their annotations in the genome assemblies were corrected accordingly. Analyses of protein sequences and gene structures of CBL family in plant kingdom indicated its diverse origin but showed a remarkable conservation in overall protein structure with appearance of complex gene structure in the course of evolution. Expression of CaCBL genes in different tissues and in response to different stress and hormone treatment were studied. Most of the CaCBL genes exhibited high expression in flowers. Expression profile of CaCBL genes in response to different abiotic stresses and hormones related to development and stresses (ABA, auxin, cytokinin, SA and JA) at different time intervals suggests their diverse roles in development and plant defence in addition to abiotic stress tolerance. These data not only contribute to a better understanding of the complex regulation of chickpea CBL gene family, but also provide valuable information for further research in chickpea functional genomics.

Chickpea has a profound nutritional and economic value in vegetarian society. Continuous decline in chickpea productivity is attributed to insufficient genetic variability and different environmental stresses. Chickpea like several other legumes is highly susceptible to terminal drought stress. Multiple genes control drought tolerance and ASR gene plays a key role in regulating different plant stresses. The present study describes the molecular characterization and functional role of Abscissic acid and stress ripening (ASR) gene from chickpea (Cicer arietinum) and the gene sequence identified was submitted to NCBI Genbank (MK937569). Molecular analysis using MUSCLE software proved that the ASR nucleotide sequences in different legumes show variations at various positions though ASR genes are conserved in chickpea with only few variations. Sequence similarity of ASR gene to chickpea putative ABA/WDS induced protein mRNA clearly indicated its potential involvement in drought tolerance. Physiological screening and qRT-PCR results demonstrated increased ASR gene expression under drought stress possibly enabled genotypes to perform better under stress. Conserved domain search, protein structure analysis, prediction and validation, network analysis using Phyre2, Swiss-PDB viewer, ProSA and STRING analysis established the role of hypothetical ASR protein NP_001351739.1 in mediating drought responses. NP_001351739.1 might have enhanced the ASR gene activity as a transcription factor regulating drought stress tolerance in chickpea. This study could be useful in identification of new ASR genes that play a major role in drought tolerance and also develop functional markers for chickpea improvement., Competing Interests: No authors have competing interests

A comprehensive transcriptome assembly of chickpea has been developed using 134.95 million Illumina single-end reads, 7.12 million single-end FLX/454 reads and 139,214 Sanger expressed sequence tags (ESTs) from >17 genotypes. This hybrid transcriptome assembly, referred to as Cicer arietinumTranscriptome Assembly version 2 (CaTA v2, available at http://data.comparative-legumes.org/transcriptomes/cicar/lista_cicar-201201), comprising 46,369 transcript assembly contigs (TACs) has an N50 length of 1,726 bp and a maximum contig size of 15,644 bp. Putative functions were determined for 32,869 (70.8%) of the TACs and gene ontology assignments were determined for 21,471 (46.3%). The new transcriptome assembly was compared with the previously available chickpea transcriptome assemblies as well as to the chickpea genome. Comparative analysis of CaTA v2 against transcriptomes of three legumes - Medicago, soybean and common bean, resulted in 27,771 TACs common to all three legumes indicating strong conservation of genes across legumes. CaTA v2 was also used for identification of simple sequence repeats (SSRs) and intron spanning regions (ISRs) for developing molecular markers. ISRs were identified by aligning TACs to the Medicago genome, and their putative mapping positions at chromosomal level were identified using transcript map of chickpea. Primer pairs were designed for 4,990 ISRs, each representing a single contig for which predicted positions are inferred and distributed across eight linkage groups. A subset of randomly selected ISRs representing all eight chickpea linkage groups were validated on five chickpea genotypes and showed 20% polymorphism with average polymorphic information content (PIC) of 0.27. In summary, the hybrid transcriptome assembly developed and novel markers identified can be used for a variety of applications such as gene discovery, marker-trait association, diversity analysis etc., to advance genetics research and breeding applications in chickpea and other related legumes.

Chickpea (Cicer arietinum L.) is the third most important cool season food legume, cultivated in arid and semi-arid regions of the world. The goal of this study was to develop novel molecular markers such as microsatellite or simple sequence repeat (SSR) markers from bacterial artificial chromosome (BAC)-end sequences (BESs) and diversity arrays technology (DArT) markers, and to construct a high-density genetic map based on recombinant inbred line (RIL) population ICC 4958 (C. arietinum)×PI 489777 (C. reticulatum). A BAC-library comprising 55,680 clones was constructed and 46,270 BESs were generated. Mining of these BESs provided 6,845 SSRs, and primer pairs were designed for 1,344 SSRs. In parallel, DArT arrays with ca. 15,000 clones were developed, and 5,397 clones were found polymorphic among 94 genotypes tested. Screening of newly developed BES-SSR markers and DArT arrays on the parental genotypes of the RIL mapping population showed polymorphism with 253 BES-SSR markers and 675 DArT markers. Segregation data obtained for these polymorphic markers and 494 markers data compiled from published reports or collaborators were used for constructing the genetic map. As a result, a comprehensive genetic map comprising 1,291 markers on eight linkage groups (LGs) spanning a total of 845.56 cM distance was developed (http://cmap.icrisat.ac.in/cmap/sm/cp/thudi/). The number of markers per linkage group ranged from 68 (LG 8) to 218 (LG 3) with an average inter-marker distance of 0.65 cM. While the developed resource of molecular markers will be useful for genetic diversity, genetic mapping and molecular breeding applications, the comprehensive genetic map with integrated BES-SSR markers will facilitate its anchoring to the physical map (under construction) to accelerate map-based cloning of genes in chickpea and comparative genome evolution studies in legumes.

Reactive oxygen species are known to play pivotal roles in pathogen perception, recognition and downstream defense signaling. But, how these redox alarms coordinate in planta into a defensive network is still intangible. Present study illustrates the role of Fusarium oxysporum f.sp ciceri Race1 (Foc1) induced redox responsive transcripts in regulating downstream defense signaling in chickpea. Confocal microscopic studies highlighted pathogen invasion and colonization accompanied by tissue damage and deposition of callose degraded products at the xylem vessels of infected roots of chickpea plants. Such depositions led to the clogging of xylem vessels in compatible hosts while the resistant plants were devoid of such obstructions. Lipid peroxidation assays also indicated fungal induced membrane injury. Cell shrinkage and gradual nuclear adpression appeared as interesting features marking fungal ingress. Quantitative real time polymerase chain reaction exhibited differential expression patterns of redox regulators, cellular transporters and transcription factors during Foc1 progression. Network analysis showed redox regulators, cellular transporters and transcription factors to coordinate into a well orchestrated defensive network with sugars acting as internal signal modulators. Respiratory burst oxidase homologue, cationic peroxidase, vacuolar sorting receptor, polyol transporter, sucrose synthase, and zinc finger domain containing transcription factor appeared as key molecular candidates controlling important hubs of the defense network. Functional characterization of these hub controllers may prove to be promising in understanding chickpea-Foc1 interaction and developing the case study as a model for looking into the complexities of wilt diseases of other important crop legumes.

Plant growth regulators (PGRs) and plant growth promoting rhizobacteria (PGPRs) play an important role in mitigating abiotic stresses. However, little is known about the parallel changes in physiological processes coupled with metabolic changes induced by PGRs and PGPRs that help to cope with drought stress in chickpeas. The present investigation was carried out to study the integrative effects of PGRs and PGPRs on the physiological and metabolic changes, and their association with drought tolerance in two chickpea genotypes. Inoculated seeds of two chickpea genotypes, Punjab Noor-2009 (drought sensitive) and 93127 (drought tolerance), were planted in greenhouse condition at the University of Florida. Prior to sowing, seeds of two chickpea varieties were soaked for 3 h in 24 h old cultures of PGPRs (Bacillus subtilis, Bacillus thuringiensis, and Bacillus megaterium), whereas, some of the seeds were soaked in distilled water for the same period of time and were treated as control. Plant growth regulators, salicylic acid (SA) and putrescine (Put), were applied on 25 days old seedlings just prior to the induction of drought stress. Drought stress was imposed by withholding the supply of water on 25-day-old seedlings (at the three-leaf stage) and continued for the next 25 days until the soil water content reached 14%. Ultrahigh-performance liquid chromatography-high resolution mass spectrometry (UPLC-HRMS) analysis concomitant with physiological parameters were carried out in chickpea leaves at two-time points i.e. 14 and 25 d after imposition of drought stress. The results showed that both genotypes, treated with PGRs and PGPRs (consortium), performed significantly better under drought condition through enhanced leaf relative water content (RWC), greater biomass of shoot and root, higher Fv/FM ratio and higher accumulation of protein, sugar and phenolic compounds. The sensitive genotype was more responsive than tolerant one. The results revealed that the accumulation of succinate, leucine, disaccharide, saccharic acid and glyceric acid was consistently higher in both genotypes at both time points due to PGRs and PGPRs treatment. Significant accumulation of malonate, 5-oxo-L-proline, and trans-cinnamate occurred at both time points only in the tolerant genotype following the consortium treatment. Aminoacyl-tRNA, primary and secondary metabolite biosynthesis, amino acid metabolism or synthesis pathways, and energy cycle were significantly altered due to PGRs and PGPRs treatment. It is inferred that changes in different physiological and metabolic parameters induced by PGRs and PGPRs treatment could confer drought tolerance in chickpeas., Competing Interests: The authors have declared that no competing interests exist.

This study was focused on analyzing the effects of dietary inclusion of raw chickpea seed as a replacement of soybean meal as a primary protein source on bone structure in broiler chickens. Broiler chickens (n = 160) received in their diet either soybean meal (SBM) or raw chickpea seeds (CPS) as a primary protein source throughout the whole rearing period (n = 80 in each group). On the 42th day randomly selected chickens from each group (n = 8) were slaughtered. Collected tibiotarsus were subjected to examination of the biomechanical characteristics of bone mid-diaphysis, microstructure of the growth plate and articular cartilages; the analysis of mineral content and crystallinity of mineral phase, and the measurements of thermal stability of collagen in hyaline cartilage were also carried out. The inclusion of chickpea seeds resulted in increase of bone osteometric parameters (weight, length and mid-diaphysis cross-sectional area) and mechanical endurance (yield load, ultimate load, stiffness, Young modulus). However, when loads were adjusted to bone shape (yield and ultimate stress) both groups did not differ. Mineral density determined by means of densitometric measurements did not differ between groups, however the detailed analysis revealed the differences in the macro- and microelements composition. The results of FT-IR and XRD analyses showed no effect of diet type on mineral phase crystallinity and hydroxyapatite nanocrystallites size. In trabecular bone, the increase of real bone volume (BV/TV) and number of trabeculae was observed in the CPS group. Total thickness of articular cartilage was the same in both groups, save the transitional zone, which was thicker in the SBM group. The total thickness of the growth plate cartilage was significantly increased in the CPS group. The area of the most intense presence of proteoglycans was wider in the SBM group. The structural analysis of fibrous components of bone revealed the increase of fraction of thin, immature collagen content in articular cartilage, trabeculae and compact bone in the CPS group. The dietary inclusion of CPS affected the thermal stability of collagen, as decrease of net denaturation enthalpy was observed. This study showed a beneficial effect of CPS on the skeletal development, improving the overall bone development and the microarchitecture of cancellous bone. It suggests that CPS can be a promising replacement for SBM in broilers feeding in the aspect of animal welfare related to the development of the skeletal system., Competing Interests: The authors have declared that no competing interests exist.

Drought is the most important constraint that effects chickpea production globally. RNA-Seq has great potential to dissect the molecular mechanisms of tolerance to environmental stresses. Transcriptome profiles in roots and shoots of two contrasting Iranian kabuli chickpea genotypes (Bivanij and Hashem) were investigated under water-limited conditions at early flowering stage using RNA-Seq approach. A total of 4,572 differentially expressed genes (DEGs) were identified. Of these, 261 and 169 drought stress responsive genes were identified in the shoots and the roots, respectively, and 17 genes were common in the shoots and the roots. Gene Ontology (GO) analysis revealed several sub-categories related to the stress, including response to stress, defense response and response to stimulus in the tolerant genotype Bivanij as compared to the sensitive genotype Hashem under drought stress. In addition, several Transcription factors (TFs) were identified in major metabolic pathways such as, ABA, proline and flavonoid biosynthesis. Furthermore, a number of the DEGs were observed in "QTL-hotspot" regions which were reported earlier in chickpea. Drought tolerance dissection in the genotypes revealed that the genes and the pathways involved in shoots of Bivanij were the most important factor to make a difference between the genotypes for drought tolerance. The identified TFs in the experiment, particularly those which were up-regulated in shoots of Bivanij during drought stress, were potential candidates for enhancing tolerance to drought., Competing Interests: The authors have declared that no competing interests exist.

The CCCH zinc finger is a group of proteins characterised by a typical motif consisting of three cysteine residues and one histidine residue. These proteins have been reported to play important roles in regulation of plant growth, developmental processes and environmental responses. In the present study, genome wide analysis of the CCCH zinc finger gene family was carried out in the available chickpea genome. Various bioinformatics tools were employed to predict 58 CCCH zinc finger genes in chickpea (designated CarC3H1-58), which were analysed for their physio-chemical properties. Phylogenetic analysis classified the proteins into 12 groups in which members of a particular group had similar structural organization. Further, the numbers as well as the types of CCCH motifs present in the CarC3H proteins were compared with those from Arabidopsis and Medicago truncatula. Synteny analysis revealed valuable information regarding the evolution of this gene family. Tandem and segmental duplication events were identified and their Ka/Ks values revealed that the CarC3H gene family in chickpea had undergone purifying selection. Digital, as well as real time qRT-PCR expression analysis was performed which helped in identification of several CarC3H members that expressed preferentially in specific chickpea tissues as well as during abiotic stresses (desiccation, cold, salinity). Moreover, molecular characterization of an important member CarC3H45 was carried out. This study provides comprehensive genomic information about the important CCCH zinc finger gene family in chickpea. The identified tissue specific and abiotic stress specific CCCH genes could be potential candidates for further characterization to delineate their functional roles in development and stress.

A hallmark trait of chickpea (Cicer arietinum L.), like other legumes, is the capability to convert atmospheric nitrogen (N2) into ammonia (NH3) in symbiotic association with Mesorhizobium ciceri. However, the complexity of molecular networks associated with the dynamics of nodule development in chickpea need to be analyzed in depth. Hence, in order to gain insights into the chickpea nodule development, the transcriptomes of nodules at early, middle and late stages of development were sequenced using the Roche 454 platform. This generated 490.84 Mb sequence data comprising 1,360,251 reads which were assembled into 83,405 unigenes. Transcripts were annotated using Gene Ontology (GO), Cluster of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways analysis. Differential expression analysis revealed that a total of 3760 transcripts were differentially expressed in at least one of three stages, whereas 935, 117 and 2707 transcripts were found to be differentially expressed in the early, middle and late stages of nodule development respectively. MapMan analysis revealed enrichment of metabolic pathways such as transport, protein synthesis, signaling and carbohydrate metabolism during root nodulation. Transcription factors were predicted and analyzed for their differential expression during nodule development. Putative nodule specific transcripts were identified and enriched for GO categories using BiNGO which revealed many categories to be enriched during nodule development, including transcription regulators and transporters. Further, the assembled transcriptome was also used to mine for genic SSR markers. In conclusion, this study will help in enriching the transcriptomic resources implicated in understanding of root nodulation events in chickpea. [ABSTRACT FROM AUTHOR]

Calcium ion (Ca2+) is a ubiquitous second messenger that transmits various internal and external signals including stresses and, therefore, is important for plants' response process. Calcineurin B-like proteins (CBLs) are one of the plant calcium sensors, which sense and convey the changes in cytosolic Ca2+-concentration for response process. A search in four leguminous plant (soybean, Medicago truncatula, common bean and chickpea) genomes identified 9 to 15 genes in each species that encode CBL proteins. Sequence analyses of CBL peptides and coding sequences (CDS) suggested that there are nine original CBL genes in these legumes and some of them were multiplied during whole genome or local gene duplication. Coding sequences of chickpea CBL genes (CaCBL) were cloned from their cDNAs and sequenced, and their annotations in the genome assemblies were corrected accordingly. Analyses of protein sequences and gene structures of CBL family in plant kingdom indicated its diverse origin but showed a remarkable conservation in overall protein structure with appearance of complex gene structure in the course of evolution. Expression of CaCBL genes in different tissues and in response to different stress and hormone treatment were studied. Most of the CaCBL genes exhibited high expression in flowers. Expression profile of CaCBL genes in response to different abiotic stresses and hormones related to development and stresses (ABA, auxin, cytokinin, SA and JA) at different time intervals suggests their diverse roles in development and plant defence in addition to abiotic stress tolerance. These data not only contribute to a better understanding of the complex regulation of chickpea CBL gene family, but also provide valuable information for further research in chickpea functional genomics.

Considering the economic importance of chickpea (C. arietinum L.) seeds, it is important to understand the mechanisms underlying seed development for which a cDNA library was constructed from 6 day old chickpea embryos. A total of 8,186 ESTs were obtained from which 4,048 high quality ESTs were assembled into 1,480 unigenes that majorly encoded genes involved in various metabolic and regulatory pathways. Of these, 95 ESTs were found to be involved in ubiquitination related protein degradation pathways and 12 ESTs coded specifically for putative F-box proteins. Differential transcript accumulation of these putative F-box genes was observed in chickpea tissues as evidenced by quantitative real-time PCR. Further, to explore the role of F-box proteins in chickpea seed development, two F-box genes were selected for molecular characterization. These were named as CarF-box_PP2 and CarF-box_LysM depending on their C-terminal domains, PP2 and LysM, respectively. Their highly conserved structures led us to predict their target substrates. Subcellular localization experiment revealed that CarF-box_PP2 was localized in the cytoplasm and CarF-box_LysM was localized in the nucleus. We demonstrated their physical interactions with SKP1 protein, which validated that they function as F-box proteins in the formation of SCF complexes. Sequence analysis of their promoter regions revealed certain seed specific cis-acting elements that may be regulating their preferential transcript accumulation in the seed. Overall, the study helped in expanding the EST database of chickpea, which was further used to identify two novel F-box genes having a potential role in seed development.

A comprehensive transcriptome assembly of chickpea has been developed using 134.95 million Illumina single-end reads, 7.12 million single-end FLX/454 reads and 139,214 Sanger expressed sequence tags (ESTs) from >17 genotypes. This hybrid transcriptome assembly, referred to as Cicer arietinumTranscriptome Assembly version 2 (CaTA v2, available at http://data.comparative-legumes.org/transcriptomes/cicar/lista_cicar-201201), comprising 46,369 transcript assembly contigs (TACs) has an N50 length of 1,726 bp and a maximum contig size of 15,644 bp. Putative functions were determined for 32,869 (70.8%) of the TACs and gene ontology assignments were determined for 21,471 (46.3%). The new transcriptome assembly was compared with the previously available chickpea transcriptome assemblies as well as to the chickpea genome. Comparative analysis of CaTA v2 against transcriptomes of three legumes - Medicago, soybean and common bean, resulted in 27,771 TACs common to all three legumes indicating strong conservation of genes across legumes. CaTA v2 was also used for identification of simple sequence repeats (SSRs) and intron spanning regions (ISRs) for developing molecular markers. ISRs were identified by aligning TACs to the Medicago genome, and their putative mapping positions at chromosomal level were identified using transcript map of chickpea. Primer pairs were designed for 4,990 ISRs, each representing a single contig for which predicted positions are inferred and distributed across eight linkage groups. A subset of randomly selected ISRs representing all eight chickpea linkage groups were validated on five chickpea genotypes and showed 20% polymorphism with average polymorphic information content (PIC) of 0.27. In summary, the hybrid transcriptome assembly developed and novel markers identified can be used for a variety of applications such as gene discovery, marker-trait association, diversity analysis etc., to advance genetics research and breeding applications in chickpea and other related legumes.

Chickpea (Cicer arietinum L.) is the third most important cool season food legume, cultivated in arid and semi-arid regions of the world. The goal of this study was to develop novel molecular markers such as microsatellite or simple sequence repeat (SSR) markers from bacterial artificial chromosome (BAC)-end sequences (BESs) and diversity arrays technology (DArT) markers, and to construct a high-density genetic map based on recombinant inbred line (RIL) population ICC 4958 (C. arietinum) ×PI 489777 (C. reticulatum). A BAC-library comprising 55,680 clones was constructed and 46,270 BESs were generated. Mining of these BESs provided 6,845 SSRs, and primer pairs were designed for 1,344 SSRs. In parallel, DArT arrays with ca. 15,000 clones were developed, and 5,397 clones were found polymorphic among 94 genotypes tested. Screening of newly developed BES-SSR markers and DArT arrays on the parental genotypes of the RIL mapping population showed polymorphism with 253 BES-SSR markers and 675 DArT markers. Segregation data obtained for these polymorphic markers and 494 markers data compiled from published reports or collaborators were used for constructing the genetic map. As a result, a comprehensive genetic map comprising 1,291 markers on eight linkage groups (LGs) spanning a total of 845.56 cM distance was developed (http://cmap.icrisat.ac.in/cmap/sm/cp/thudi/). The number of markers per linkage group ranged from 68 (LG 8) to 218 (LG 3) with an average inter-marker distance of 0.65 cM. While the developed resource of molecular markers will be useful for genetic diversity, genetic mapping and molecular breeding applications, the comprehensive genetic map with integrated BES-SSR markers will facilitate its anchoring to the physical map (under construction) to accelerate map-based cloning of genes in chickpea and comparative genome evolution studies in legumes. [ABSTRACT FROM AUTHOR]