Domesticated Chickpea Research Articles

A Genome-wide Combinatorial Strategy Dissects Complex Genetic Architecture of Seed Coat Color in Chickpea.

The study identified 9045 high-quality SNPs employing both genome-wide GBS- and candidate gene-based SNP genotyping assays in 172, including 93 cultivated (desi and kabuli) and 79 wild chickpea accessions. The GWAS in a structured population of 93 sequenced accessions detected 15 major genomic loci exhibiting significant association with seed coat color. Five seed color-associated major genomic loci underlying robust QTLs mapped on a high-density intra-specific genetic linkage map were validated by QTL mapping. The integration of association and QTL mapping with gene haplotype-specific LD mapping and transcript profiling identified novel allelic variants (non-synonymous SNPs) and haplotypes in a MATE secondary transporter gene regulating light/yellow brown and beige seed coat color differentiation in chickpea. The down-regulation and decreased transcript expression of beige seed coat color-associated MATE gene haplotype was correlated with reduced proanthocyanidins accumulation in the mature seed coats of beige than light/yellow brown seed colored desi and kabuli accessions for their coloration/pigmentation. This seed color-regulating MATE gene revealed strong purifying selection pressure primarily in LB/YB seed colored desi and wild Cicer reticulatum accessions compared with the BE seed colored kabuli accessions. The functionally relevant molecular tags identified have potential to decipher the complex transcriptional regulatory gene function of seed coat coloration and for understanding the selective sweep-based seed color trait evolutionary pattern in cultivated and wild accessions during chickpea domestication. The genome-wide integrated approach employed will expedite marker-assisted genetic enhancement for developing cultivars with desirable seed coat color types in chickpea.

Genetic Relationship in Cicer Sp. Expose Evidence for Geneflow between the Cultigen and Its Wild Progenitor.

There is a debate concerning mono- or poly-phyletic origins of the Near Eastern crops. In parallel, some authors claim that domestication was not possible within the natural range of the wild progenitors due to wild alleles flow into the nascent crops. Here we address both, the mono- or poly-phyletic origins and the domestications within or without the natural range of the progenitor, debates in order to understand the relationship between domesticated chickpea (Cicer arietinum L.) and its wild progenitor (C. reticulatum Ladizinsky) with special emphasis on its domestication centre in southeastern Turkey. A set of 103 chickpea cultivars and landraces from the major growing regions alongside wild accessions (C. reticulatum, C. echinospermum P.H Davis and C. bijugum K.H. Rech) sampled across the natural distribution range in eastern Turkey were genotyped with 194 SNPs markers. The genetic affinities between and within the studied taxa were assessed. The analysis suggests a mono-phyletic origin of the cultigen, with several wild accession as likely members of the wild stock of the cultigen. Clear separation between the wild and domesticated germplasm was apparent, with negligible level of admixture. A single C. reticulatum accession shows morphological and allelic signatures of admixture, a likely result of introgression. No evidence of geneflow from the wild into domesticated germplasm was found. The traditional farming systems of southeaster Turkey are characterized by occurrence of sympatric wild progenitor—domesticated forms of chickpea (and likewise cereals and other grain legumes). Therefore, both the authentic crop landraces and the wild populations native to the area are a unique genetic resource. Our results grant support to the notion of domestication within the natural distribution range of the wild progenitor, suggesting that the Neolithic domesticators were fully capable of selecting the desired phenotypes even when facing rare wild-domesticated introgression events.

Deploying QTL-seq for rapid delineation of a potential candidate gene underlying major trait-associated QTL in chickpea.

A rapid high-resolution genome-wide strategy for molecular mapping of major QTL(s)/gene(s) regulating important agronomic traits is vital for in-depth dissection of complex quantitative traits and genetic enhancement in chickpea. The present study for the first time employed a NGS-based whole-genome QTL-seq strategy to identify one major genomic region harbouring a robust 100-seed weight QTL using an intra-specific 221 chickpea mapping population (desi cv. ICC 7184 × desi cv. ICC 15061). The QTL-seq-derived major SW QTL (CaqSW1.1) was further validated by single-nucleotide polymorphism (SNP) and simple sequence repeat (SSR) marker-based traditional QTL mapping (47.6% R2 at higher LOD >19). This reflects the reliability and efficacy of QTL-seq as a strategy for rapid genome-wide scanning and fine mapping of major trait regulatory QTLs in chickpea. The use of QTL-seq and classical QTL mapping in combination narrowed down the 1.37 Mb (comprising 177 genes) major SW QTL (CaqSW1.1) region into a 35 kb genomic interval on desi chickpea chromosome 1 containing six genes. One coding SNP (G/A)-carrying constitutive photomorphogenic9 (COP9) signalosome complex subunit 8 (CSN8) gene of these exhibited seed-specific expression, including pronounced differential up-/down-regulation in low and high seed weight mapping parents and homozygous individuals during seed development. The coding SNP mined in this potential seed weight-governing candidate CSN8 gene was found to be present exclusively in all cultivated species/genotypes, but not in any wild species/genotypes of primary, secondary and tertiary gene pools. This indicates the effect of strong artificial and/or natural selection pressure on target SW locus during chickpea domestication. The proposed QTL-seq-driven integrated genome-wide strategy has potential to delineate major candidate gene(s) harbouring a robust trait regulatory QTL rapidly with optimal use of resources. This will further assist us to extrapolate the molecular mechanism underlying complex quantitative traits at a genome-wide scale leading to fast-paced marker-assisted genetic improvement in diverse crop plants, including chickpea.

Phylogenetic diversity of Mesorhizobium in chickpea.

Crop domestication, in general, has reduced genetic diversity in cultivated gene pool of chickpea (Cicer arietinum) as compared with wild species (C. reticulatum, C. bijugum). To explore impact of domestication on symbiosis, 10 accessions of chickpeas, including 4 accessions of C. arietinum, and 3 accessions of each of C. reticulatum and C. bijugum species, were selected and DNAs were extracted from their nodules. To distinguish chickpea symbiont, preliminary sequences analysis was attempted with 9 genes (16S rRNA, atpD, dnaJ, glnA, gyrB, nifH, nifK, nodD and recA) of which 3 genes (gyrB, nifK and nodD) were selected based on sufficient sequence diversity for further phylogenetic analysis. Phylogenetic analysis and sequence diversity for 3 genes demonstrated that sequences from C. reticulatum were more diverse. Nodule occupancy by dominant symbiont also indicated that C. reticulatum (60 percent) could have more various symbionts than cultivated chickpea (80 percent). The study demonstrated that wild chickpeas (C. reticulatum) could be used for selecting more diverse symbionts in the field conditions and it implies that chickpea domestication affected symbiosis negatively in addition to reducing genetic diversity.

Market integration of grain legumes in India: the case of the chickpea market

The present study assesses the market integration of chickpea in India from 2003 to 2010. The month end prices of chickpea for twelve markets in north India were used for the study. Out of twelve markets, only three markets are cointegrated, indicating weak integration of chickpea markets in India. However, the terminal markets located in major consuming (Delhi) and export/import locations (Dohad/Gujarat) clearly play an important role in price discovery and influences other domestic markets indicating the relevance of the import prices and large consuming centres on local market prices. Error correction terms indicate that the adjustment process from short-term disequilibrium in prices to long run price equilibrium is very slow. Overall, there is evidence of weak cointegration in the chickpea markets in North India and imports and major consuming centres are playing an important role in price discovery in domestic chickpea markets.DOI: http://dx.doi.org/10.3329/sja.v10i2.18320 SAARC J. Agri., 10(2): 11-29 (2012)

Functionally Relevant Microsatellite Markers From Chickpea Transcription Factor Genes for Efficient Genotyping Applications and Trait Association Mapping

We developed 1108 transcription factor gene-derived microsatellite (TFGMS) and 161 transcription factor functional domain-associated microsatellite (TFFDMS) markers from 707 TFs of chickpea. The robust amplification efficiency (96.5%) and high intra-specific polymorphic potential (34%) detected by markers suggest their immense utilities in efficient large-scale genotyping applications, including construction of both physical and functional transcript maps and understanding population structure. Candidate gene-based association analysis revealed strong genetic association of TFFDMS markers with three major seed and pod traits. Further, TFGMS markers in the 5′ untranslated regions of TF genes showing differential expression during seed development had higher trait association potential. The significance of TFFDMS markers was demonstrated by correlating their allelic variation with amino acid sequence expansion/contraction in the functional domain and alteration of secondary protein structure encoded by genes. The seed weight-associated markers were validated through traditional bi-parental genetic mapping. The determination of gene-specific linkage disequilibrium (LD) patterns in desi and kabuli based on single nucleotide polymorphism-microsatellite marker haplotypes revealed extended LD decay, enhanced LD resolution and trait association potential of genes. The evolutionary history of a strong seed-size/weight-associated TF based on natural variation and haplotype sharing among desi, kabuli and wild unravelled useful information having implication for seed-size trait evolution during chickpea domestication.

Temperature-stratified screening of chickpea ( Cicer arietinum L.) genetic resource collections reveals very limited reproductive chilling tolerance compared to its annual wild relatives

Low reproductive chilling tolerance in chickpea impairs ovule fertilization, delaying pod set, exposing the crop to terminal drought throughout much of its distribution range. Despite this realization, little progress has been made because of the limited genetic variation available to breeders. To address this issue a wide range of domesticated ( n = 1762) and wild Cicer ( n = 200) germplasm collected from sites stratified by flowering phase temperature was extensively field evaluated, and compared with Lupinus angustifolius, a well-adapted Mediterranean winter annual. Chilling tolerance was estimated by regressing the time interval between pod set and first flower against mean post-anthesis temperature. Field screening was augmented by smaller scale experiments evaluating the effects of contrasting post-anthesis temperature regimes on plant growth and productivity, pollen function and subsequent pod set in temperature-controlled cabinets. Chickpea was less chilling tolerant than its wild relatives, the flower-pod interval increasing curvi-linearly as sites became cooler, with a strong effects between 11 and 16 °C, tailing off after 17.5 °C, but remaining statistically significant. There is little useful variation for chilling tolerance within domesticated chickpea. Small, albeit statistically significant differences in pod set delay in chickpea collected from contrasting flowering phase habitats, were marginal compared to more tolerant species such as Cicer bijugum, Cicer judaicum and L. angustifolius, and to a lesser extent Cicer reticulatum, Cicer pinnatifidum, and Cicer echinospermum. No differences were observed between desi and kabuli types. Field screening identified robust chilling tolerance in a C. echinospermum accession that commenced podding earlier, at lower temperatures (10.0 °C), and yielded 5 times more than Rupali, the most productive chickpea. Controlled temperature experiments confirmed that in contrast to chickpea, pollen germination, viability, frequency on the stigma surface and subsequent pod set were unaffected by low post-anthesis temperatures (13/7 °C) in C. echinospermum and L. angustifolius. Our results indicate that chickpea is even more chilling sensitive than previously thought. Because C. echinospermum is inter-fertile with chickpea, it has considerable potential both as a donor of robust chilling tolerance and as an agent for investigating resistance mechanisms.

Aggressiveness of eight Didymella rabiei isolates from domesticated and wild chickpea native to Turkey and Israel, a case study

Ascochyta blight, caused by Didymella rabiei, affects both domesticated chickpea and its congeneric wild relatives. The aim of this study was to compare the aggressiveness of D. rabiei isolates from wild and domesticated Cicer spp. in Turkey and Israel on wild and domesticated hosts from both countries. A total of eight isolates of D. rabiei sampled from C. pinnatifidum, C. judaicum and C. arietinum in Turkey and Israel was tested on two domesticated chickpea cultivars and two wild Cicer accessions from Turkey and Israel. Using cross-inoculation experiments, we compared pathogen aggressiveness across the different pathogen and host origin combinations. Two measures of aggressiveness were used, incubation period and relative area under the disease progress curve. The eight tested isolates infected all of the host plants, but were more aggressive on their original hosts with one exception; Turkish domesticated isolates were less aggressive on their domesticated host in comparison to the aggressiveness of Israeli domesticated isolates on Turkish domesticated chickpea. C. judaicum plants were highly resistant against all of the isolates from different origins except for their own isolates. Regardless of the country of origin, the wild isolates were highly aggressive on domesticated chickpea while the domesticated isolates were less aggressive on the wild hosts compared with the wild isolates. These results suggest that the aggressiveness pattern of D. rabiei on different hosts could have been shaped by adaptation to the distinct ecological niches of wild vs. domesticated chickpea.

A comparative study of Turkish and Israeli populations of Didymella rabiei, the ascochyta blight pathogen of chickpea

The Fertile Crescent is the centre of domestication of chickpea (Cicer arietinum) and also the place of origin of its pathogens. Agrosystems provide different environments to natural eco‐systems, thus imposing different types of selection on pathogens. Here, the genetic structure and in vitro temperature growth response of the chickpea pathogen Didymella rabiei from domesticated chickpea (59 isolates from Turkey and 31 from Israel) and wild Cicer spp. (three isolates from Turkish C. pinnatifidum and 35 from Israeli C. judaicum) were studied. Six sequence‐tagged microsatellite site (STMS) primer pairs were used to determine the genetic structure of the 128 D. rabiei isolates. Turkish isolates exhibited the highest genetic diversity (H = 0·69). Turkish and Israeli D. rabiei from domesticated chickpea were genetically closer to each other than isolates from the wild Cicer spp. Analysis of molecular variance showed that 54% of the genetic variation resided between isolates from wild and domesticated origins. EF1‐α sequences distinguished between D. rabiei isolates from domesticated and wild Cicer spp. by four polymorphic sites. Nevertheless, a certain degree of mixing between isolates from wild and domesticated origin was demonstrated using the Bayesian algorithm as well as with principal coordinates analysis. Isolates sampled from domesticated chickpea from both countries were better adapted to temperatures typical of Levantine spring and had a significantly larger colony area at 25°C than at 15°C (typical Levantine winter temperature). These observations were in accordance to the heritability values of the temperature growth response.

Stress gradients select for ecotype formation in Cicer judaicum Boiss., a wild relative of domesticated chickpea

The investigation of plant adaptive strategies has been enhanced by the advent of high resolution climate models facilitating greatly improved fine-scale habitat characterization. We have used this approach in the evaluation of C. judaicum Boiss., an annual wild relative of chickpea. 54 accessions from 12 Israeli populations representing three separate habitats differing in temperature and terminal drought stress intensity were evaluated in a common garden experiment, measuring phenology and growth. The results indicate that C. judaicum formed distinct ecotypes along environmental stress gradients, with stress avoidance as a key adaptive strategy: (1) germination is delayed with increasing collection site altitude and associated decreasing temperatures; (2) flowering date and productivity (as estimated by mainstem length) are inversely related to habitat stress, as defined by site climate or soil type. Populations from stressful sites escape drought stress through early flowering at the likely cost of biomass production. We conclude that precise habitat characterization facilitates the study of specific adaptation over relatively short geographic distances. This is particularly pertinent today because many of the key crop production system stresses (i.e., terminal drought, the impact of climate change) can be modelled climatically to identify potentially-adapted germplasm from ex situ and in situ collections.

A note on the evolution of kabuli chickpeas as shown by induced mutations in Cicer reticulatum Ladizinsky

Two distinct chickpeas of the domestic chickpea, C. arietinum L., exist and are referred to as ‘desi’ or microsperma and ‘kabuli’ or macrosperma. Cicer reticulatum Ladiz. is considered to be the wild progenitor of the domestic chickpea. However, the morphological variation in 18 original accessions of C. reticulatum is narrower than those of the domestic chickpeas. The aim of the study is to increase the variability in C. reticulatum. In M2 generation, a mutant with white flower color was isolated despite of the fact that the parent has the pink flower. Although seed coat color of the parent was dark brown, the mutant was cream like ‘kabuli’ chickpea. It is commonly accepted that the large seeded domestic ‘kabuli’ chickpeas originated from the small seeded ‘desi’ chickpeas, but the induced mutants (white flower and cream seed coat color) of C. reticulatum may suggest an additional path for the evolution of ‘kabuli’ chickpea. ‘Kabuli’ chickpeas could have originated from spontaneous mutants of C. reticulatum. In M3 generation, multipinnate leaf, erect growth habit, green seed and double-podded chickpeas were isolated. Among these progenies, morphologic variability increased and approached domesticated chickpea. Based on historical records and the induced mutants obtained from this study, the domestic ‘kabuli’ chickpea could have directly emerged from C. reticulatum in ancient Eastern Turkey.

Sympatric ascochyta complex of wild Cicer judaicum and domesticated chickpea

The aim of this study was to isolate, identify and characterize ascochyta blight pathogens from Cicer judaicum, a wild annual Cicer species which grows in Israel and other Mediterranean countries in sympatric distribution with legume crops, and determine their virulence and aggressiveness to other wild and domesticated legumes. Native C. judaicum plants exhibited symptoms resembling ascochyta diseases of grain legume crops. Two distinct pathogens were isolated and identified as Phoma pinodella and Didymella rabiei using morphological and molecular tools; their infectivity was verified using Koch's postulates. The virulence of these pathogens was examined on 13 legume species, of which P. pinodella was virulent to Pisum sativum, P. fulvum, C. judaicum, C. arietinum, C. reticulatum, C. pinnatifidum and C. bijugum. Didymella rabiei infected all these Cicer species, but not the other legume species tested. Aggressiveness of the pathogens was tested on wild and domesticated chickpea and pea. Didymella rabiei isolated from C. judaicum had significantly higher (P < 0·001) aggressiveness than P. pinodella from C. judaicum on both wild and domesticated chickpea. Disease severity on the former species ranged from 62·5% to 70% and on the latter from 41% to 56%. Phoma pinodella isolates from C. judaicum were more aggressive on C. arietinum and P. sativum than on C. judaicum and P. fulvum. Results of the current study suggest that C. judaicum may serve as an alternative host to ascochyta pathogens that endanger chickpea and possibly other crops and wild species growing in close proximity.

Chickpea domestication in the Neolithic Levant through the nutritional perspective

An alternative approach to the process of selection and domestication of grain crops in early history based on nutritional value is proposed. Selection by a long trial and error process among a number of wild large seeded legumes gave rise to a nutritionally superior domesticated chickpea among the selected “founder crops” of the Neolithic Near Eastern agriculture. We found considerably higher free tryptophan levels in cultivated stocks (44 desi and 29 kabuli types from 25 countries; 1.10 mg/g seed dry weight), compared with the wild progenitor Cicer reticulatum (15 accessions; 0.33 mg/g seed dry weight). Dietary tryptophan determines brain serotonin synthesis, which in turn affects certain brain functions and human behaviour. We suggest that these nutritive facts may explain the decision of prehistoric farmers to choose this rare species and struggle to keep such an agronomically complicated crop under domestication.

RAPD and seed coat morphology variation in annual and perennial species of the genus Cicer L.

Molecular and morphological variation of six perennial and five annual species including domesticated chickpea, C. arietinum, were inferred on the basis of RAPD and S.E.M. seed coat features using three outgroup taxa (Lens ervoides, Lathyrus japonica and Pisum sativum). Of the 66 decamer arbitrary primers tested, eight primers revealed 87 informative fragments. Neighbor-joining cluster analysis using Jaccard's coefficient of similarity on the basis of polymorphic fragments indicated a narrow variation in C. arietinum and recognized two major clusters in the genus Cicer. The first one included four species of sect. Monocicer: C. echinospermum, C. arietinum, C. reticulatum and Iranian material of C. bijugum. The second cluster contained annual and perennial species belonging to sections Chamaecicer, Polycicer and Acanthocicer. The character state of morphological and ecological traits on the RAPD phenogram indicated no monophyletic incision. Our results suggested that the high genetic difference between annual and perennial species might be regarded as a rapid speciation of section Monocicer. Reconsideration of traditional classification of sections Polycicer and Acanthocicer is necessary. The ‘Desi’ and ‘Kabuli’ types of C. arietinum could not be separately grouped at the DNA level, and the low level of genetic variation of C. arietinum may result from a bottleneck during the domestication process.

The chickpea, summer cropping, and a new model for pulse domestication in the ancient near east.

The widely accepted models describing the emergence of domesticated grain crops from their wild type ancestors are mostly based upon selection (conscious or unconscious) of major features related either to seed dispersal (nonbrittle ear, indehiscent pod) or free germination (nondormant seeds, soft seed coat). Based on the breeding systems (self-pollination) and dominance relations between the allelomorphs of seed dispersal mode and seed dormancy, it was postulated that establishment of the domesticated forms and replacement of the wild ancestral populations occurred in the Near East within a relatively short time. Chickpea (Cicer arietinum L.), however, appears as an exception among all other "founder crops" of Old World agriculture because of its ancient conversion into a summer crop. The chickpea is also exceptional because its major domestication trait appears to be vernalization insensitivity rather than pod indehiscence or free germination. Moreover, the genetic basis of vernalization response in wild chickpea (Cicer reticulatum Ladiz.) is polygenic, suggesting that a long domestication process was imperative due to the elusive phenotype of vernalization nonresponsiveness. There is also a gap in chickpea remains in the archaeological record between the Late Prepottery Neolithic and the Early Bronze Age. Contrary to the common view that Levantine summer cropping was introduced relatively late (Early Bronze Age), we argue for an earlier (Neolithic) Levantine origin of summer cropping because chickpea, when grown as a common winter crop, was vulnerable to the devastating pathogen Didymella rabiei, the causal agent of Ascochyta blight. The ancient (Neolithic) conversion of chickpea into a summer crop required seasonal differentiation of agronomic operation from the early phases of the Neolithic revolution. This topic is difficult to deal with, as direct data on seasonality in prehistoric Old World field crop husbandry are practically nonexistent. Consequently, this issue was hardly dealt with in the literature. Information on the seasonality of ancient (Neolithic, Chalcolithic, and Early Bronze Age, calibrated 11,500 to 4,500 years before present) Near Eastern agriculture may improve our understanding of the proficiency of early farmers. This in turn may provide a better insight into Neolithic agrotechniques and scheduling. It is difficult to fully understand chickpea domestication without a Neolithic seasonal differentiation of agronomic practice because the rapid establishment of the successful Near Eastern crop package which included wheats, barley, pea, lentil, vetches, and flax, would have preempted the later domestication of this rare wild legume.

Transformation Studies on Chickpea Embryo Axis

In vitro regeneration was achieved in chickpea mature and immature decapitated embryo axis. The cultivars used were BG384, Avrodhi and Anupam. Of the three cultivars used, BG384 gave best response in terms of regeneration efficiency and transformation efficiency using either mature or immature decapitated embryo axes. Mature decapitated embryo axes of the above three cultivars were used for transformation by Agrobacterium tumefaciens (LBA4404) having the binary plasmid pBl121. Transformation via electroporation was also performed using plasmid pBl221. The expression of uidA (GUS) gene was checked in the transformants by the histochemical assay. The positive results obtained indicate the suitability of such type of explants for transformation studies in domestic chickpea cultivars.