Chickpea Accessions Research Articles

The Development of a European and Mediterranean Chickpea Association Panel (EMCAP)

Association panels represent a useful tool for quantitative trait loci (QTL) mapping and pre-breeding. In this study, we report on the development of a European and Mediterranean chickpea association panel as a useful tool for gene discovery and breeding. Chickpea (Cicer arietinum L.) is one of the most important food legumes worldwide and a key crop in the Mediterranean environments. The selection of genotypes followed criteria aimed to build a set of materials representative of the genetic diversity of chickpea germplasm focusing on the European and Mediterranean environments, which have largely been ignored to date. This tool can help breeders to develop novel varieties adapted to European and Mediterranean agro-ecosystems. Initially, 1931 chickpea accessions were phenotypically evaluated in a field trial in central Italy. From these, an association panel composed by 480 genotypes derived from single-seed descent was identified and phenotypically evaluated. Current and future phenotypic data combined with the genotypic characterization of the association panel will allow to dissect the genetic architecture of important adaptive and quality traits and accelerate breeding. This information can be used to predict phenotypes of unexploited chickpea genetic resources available in genebanks for breeding.

Genome-wide association study for phosphate deficiency responsive root hair elongation in chickpea.

Root hairs (RHs) are single-celled elongated epidermal cells and play a vital role in nutrient absorption, particularly for immobile minerals like phosphorus (P). As an adaptive response to P deficiency, an increase in RH length enhances root-soil contact and absorptive area for P absorption. Genetic variations have been reported for RH length and its response to P deficiency in plants. However, only a few association studies have been conducted to identify genes and genetic loci associated with RH length. Here, we screened desi chickpea accessions for RH length and its plasticity under P deficiency. Further, the genome-wide association study (GWAS) was conducted to identify the genetic loci associated with RH length in P deficient and sufficient conditions. Although high variability was observed in terms of RH length in diverse genotypes, majority of the accessions showed typical response of increase in RH length in low P. Genome-wide association mapping identified many SNPs with significant associations with RH length in P-sufficient and P-deficient conditions. A few candidate genes for RH length in P deficient (SIZ1-like and HAD superfamily protein) and sufficient (RSL2-like and SMAP1-like) conditions were identified which have known roles in RH development and P deficiency response or both. Highly associated loci and candidate genes identified in this study would be useful for genomic-assisted breeding to develop P-efficient chickpea.

Multi-trait multi-locus SEM model discriminates SNPs of different effects

BackgroundThere is a plethora of methods for genome-wide association studies. However, only a few of them may be classified as multi-trait and multi-locus, i.e. consider the influence of multiple genetic variants to several correlated phenotypes.ResultsWe propose a multi-trait multi-locus model which employs structural equation modeling (SEM) to describe complex associations between SNPs and traits - multi-trait multi-locus SEM (mtmlSEM). The structure of our model makes it possible to discriminate pleiotropic and single-trait SNPs of direct and indirect effect. We also propose an automatic procedure to construct the model using factor analysis and the maximum likelihood method. For estimating a large number of parameters in the model, we performed Bayesian inference and implemented Gibbs sampling. An important feature of the model is that it correctly copes with non-normally distributed variables, such as some traits and variants.ConclusionsWe applied the model to Vavilov’s collection of 404 chickpea (Cicer arietinum L.) accessions with 20-fold cross-validation. We analyzed 16 phenotypic traits which we organized into five groups and found around 230 SNPs associated with traits, 60 of which were of pleiotropic effect. The model demonstrated high accuracy in predicting trait values.

Determination of the breeding value of collection chickpea (Cicer arietinum L.) accessions by cluster analysis.

Assessment of the genetic resources of chickpea (Cicer arietinum L.) in a zone that is atypical for its cultivation (eastern forest-steppe of Ukraine) gives an opportunity to identify valuable starting material for priority breeding areas. The article presents the results of a cluster analysis on chickpea accessions from the National Center for Plant Genetic Resources of Ukraine (NCPGRU) for a set of agronomic characteristics. In 2005–2017, 653 chickpea accessions from the NCPGRU’s core collection were studied: 369 kabuli accessions and 284 desi accessions. One hundred and fifty two sources of valuable traits were identified for 11 parameters: drought tolerance, resistance to Ascochyta leaf and pod spot, early ripening (vegetation period length), yield, performance, number of productive pods and seed number per plant, response to nitrogenization, protein content, seed size, and cooking quality. These accessions (77 kabuli accessions are light-colored and 75 desi ones are dark-colored) were grouped by a set of valuable economic characteristics using cluster analysis with the Euclidean distance as a measure. The study showed that this sample consisted of 4 clusters. Cluster 1 contained mainly kabuli accessions with optimal combinations of valuable traits: drought tolerance, resistance to Ascochyta leaf and pod spot, large seeds, high yield capacity and performance, pod and seed numbers as well as protein content in seeds. This cluster includes standards and most of reference varieties, which are well-adapted to the conditions of the eastern forest-steppe of Ukraine. The accessions of cluster 2 are characterized by high resistance to Ascochyta leaf and pod spot, late ripening, small seeds, low protein content, moderate response to nitrogenization, high performance attributed to a large number of productive pods and seeds per plant. Most of the accessions of this cluster are small-seeded late-ripening kabuli accessions. Cluster 3 consists of 3 accessions, which have large seeds and high protein content in them, give moderate yields, are highly responsive to nitrogenization and poorly resistant to Ascochyta leaf and pod spot. Cluster 4 comprises mainly desi accessions (63 %), which are mid-ripening, with small seeds, low performance, moderate yield capacity, medium protein content, poor cooking quality, moderate resistance to Ascochyta leaf and pod spot, and low drought tolerance. Representatives of this cluster are predominantly sources of one trait and may have restricted application in specialized breeding programs. Based on the data obtained, we concluded that the accessions of cluster 1 were preferable in breeding programs to develop chickpea varieties for the foreststeppe zone.

In Vitro and In Vivo Nutraceutical Characterization of Two Chickpea Accessions: Differential Effects on Hepatic Lipid Over-Accumulation.

Dietary habits are crucially important to prevent the development of lifestyle-associated diseases. Diets supplemented with chickpeas have numerous benefits and are known to improve body fat composition. The present study was undertaken to characterize two genetically and phenotypically distinct accessions, MG_13 and PI358934, selected from a global chickpea collection. Rat hepatoma FaO cells treated with a mixture of free fatty acids (FFAs) (O/P) were used as an in vitro model of hepatic steatosis. In parallel, a high-fat diet (HFD) animal model was also established. In vitro and in vivo studies revealed that both chickpea accessions showed a significant antioxidant ability. However, only MG_13 reduced the lipid over-accumulation in steatotic FaO cells and in the liver of HFD fed mice. Moreover, mice fed with HFD + MG_13 displayed a lower level of glycemia and aspartate aminotransferase (AST) than HFD mice. Interestingly, exposure to MG_13 prevented the phosphorylation of the inflammatory nuclear factor kappa beta (NF-kB) which is upregulated during HFD and known to be linked to obesity. To conclude, the comparison of the two distinct chickpea accessions revealed a beneficial effect only for the MG_13. These findings highlight the importance of studies addressing the functional characterization of chickpea biodiversity and nutraceutical properties.

Physiological and Biochemical Responses of Chickpea Accessions at Reproductive Stage Under Receding Moisture Conditions

The present study was conducted to assess the physiological and biochemical responses in the leaves of ten chickpea accessions trifurcated into moderately tolerant, intermittent and moderately sensitive on the basis of their yield losses via drought susceptibility index. Moderately sensitive accessions recorded higher decline in number of leaves and dehydrogenase activity and increased membrane permeability index (MPI) under receding moisture conditions. However, moderately tolerant genotypes, viz. GL 29078 and ICC 4958, maintained number of leaves and optimal dehydrogenase activity and lower MPI in leaves at reproductive stages by enhanced enzymatic activity of superoxide dismutase, catalase and ascorbate peroxidase that upregulated their antioxidative defense system at 75% moisture reduction levels. Furthermore, the tolerance capacity was maintained in moderately tolerant genotypes (IPCK-2009-165 and ICC 4958) due to increased proline level that acted as a positive loading variable component in principal component biplot analysis and lowered malondialdehyde content levels in leaves at receding moisture levels. Assessment of leaf tissue-specific response under lysimetric screening and its final correlation with yield adds to paramount importance and uniqueness to the current study.

Correlation and Path Coefficient Analysis Among Seed Yield and Yield Related Traits of Ethiopian Chickpea (Cicer arietinumL.) Landraces

An experiment was under taken on 202 new chickpea (Cicer arietinum L.) accessions and two released varieties to determine the association of different characters with seed yield, direct and indirect influence of characters towards yield and yield contributing traits. The experiment was planted at Sirinkaand Jari test stations under rain fed condition in 2016 using alpha lattice design with three replications. Data were collected on yield and yield related traits. Analysis of variance showed highly significant differences (P<0.001) among the tested genotypes. The correlation of grain yield with biomass (rg= 0.71 and rph= 0.72) and with harvest index (rg = 0.52 and rph= 0.54) was positive and highly significant both at genotypic and phenotypic levels. In addition, its association with pod filling period, plant height, secondary branches and hundred seed weight was positive but non-significant both at genotypic and phenotypic levels. Path coefficient analysis at genotypic level showed that among the fifteen causal (independent) traits; biomass (0.84), harvest index (0.69), pod length (9.73), days to pod setting (0.024), pod filing period (0.020), and number of pods per plant (0.019) had positive directly influence on grain yield. Despite the days to flowering, plant height and hundred seed weight had positive genotypic correlation with grain yield, and their direct effects on grain yield were negative. This implies that the observed positive correlations of these traits with grain yield were due to their indirect positive effects on grain yield through primary branches, number of seeds per pod, biomass, pod length, canopy width and harvest index. Therefore, future selection of chickpea genotypes should be focused on traits which had positive correlation and direct effect on grain yield at both genotypic and phenotypic levels for obtaining high yield in chickpea breeding program.

Long-term preservation of Cicer arietinum L. germplasm by in vitro propagation and cryopreservation

Chickpea (Cicer arietinum L.) is one of the most important pulse worldwide. This crop plays a significant role to maintain soil fertility through symbiotic N fixation, as well as in the Mediterranean diet for its important content of noble protein. In South Italy, particularly in the Puglia region, many traditional landraces are still cultivated in marginal areas, becoming therefore at strong risk of genetic erosion or even extinction. In vitro culture is a useful and innovative approach for the collection and the long-term preservation of threatened germplasm by means of the cryopreservation technology, as ex situ conservation strategy complementary to traditional ones. The aim of this study was to develop an efficient protocol for the multiplication and cryopreservation of two accessions of an Apulian black chickpea threatened landrace. Seeds of Apulian black chickpea were inoculated on agarized sucrose-free nutrient medium. The cotyledonary node and axillary buds were excised from the seedlings and then cultured on the same medium, supplemented with 6-benzylaminopurine and sucrose. After three subculture cycles, shoot tips from in vitro proliferated shoots were induced to rooting on IBA or used for germplasm conservation by comparing three cryopreservation techniques, i.e. PVS2-vitrification, droplet-vitrification and V-cryoplate. The results are very promising in terms of explant survival. However, the study should now progress to optimize a recovery medium, able to further improve shoot regrowth rates and plantlet formation in post-cryopreservation.

Genetic Diversity Analysis in Chickpea (Cicer arietinum L) Genotypes Grown in Northwestern Algeria using Microsatellite Markers (SSR)

The present study aimed to characterize a subset of 10 selected chickpea accessions (Cicer arietinum L.) using SSR. The result indicated a presence of a total of 59 alleles. The genetic diversity at the 15 microsatellites loci was varied from 0, 32 for TA22 to 0.78 for TA72 and TA117 with an average of 0.66. Polymorphic information content (PIC) values ranged from 0.27 to 0.74. This study also detected a high significant (P less than 0.01) positive correlation between alleles per locus, gene diversity (H) and polymorphism information content (PIC). In the dendrogram and on the PCoA bi-plots, chickpea genotypes were adjoined according to their geographic origin, type of chickpea (Kabuli/ Desi). Nevertheless, the distribution of the different grouping through the factorial correspondence analysis (AFC) is due to the genetic variability.

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

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

Variations in the antioxidant and free radical scavenging under induced heavy metal stress expressed as proline content in chickpea.

Thisstudy pertains to the effects of heavy metal salts viz., copper (Cu), manganese (Mn), lead (Pb) and zinc (Zn) on the chickpea accession ICC-4812. The salts were given as treatments to the chickpea seeds at various ascending levels of doses till proving toxic. The treatment of 24h soaked and swollen seeds were then extended to 7days duration from the date of treatment. Atomic absorption spectrophotometric analysis of bioassay tissue Cicer, showed maximum uptake of 9.41mg/g and minimum of 1.65mg/g tissue dry weight for Pb and Zn respectively. The study reveals that enhanced antioxidant responses are associated with substantial proline accumulation indicating induced stress. Ferric reducing antioxidant power assay measuring antioxidant activity was highest in the chickpea seedling treated with Zn, whereas, free radical scavenging activity was highest in the treatments with Mn. The total phenolic and flavonoid contents ranged between 0.24-0.97 and 0.27-1.00mg/g of dry matter content respectively. Higher Pb and Zn doses seem to elicit higher proline levels therefore, suggesting an extreme condition of induced abiotic stress. Dose dependent protein oxidation coupled with DNA degradation was observed in all treatments, depicting genotoxicity. Unweighted pair-group method arithmetic average analysis presented similarity coefficients between the treatments.

CLAVATA signaling pathway genes modulating flowering time and flower number in chickpea.

A combinatorial genomic strategy delineated functionally relevant natural allele of a CLAVATA gene and its marker (haplotype)-assisted introgression led to development of the early-flowering chickpea cultivars with high flower number and enhanced yield/productivity. Unraveling the genetic components involved in CLAVATA (CLV) signaling is crucial for modulating important shoot apical meristem (SAM) characteristics and ultimately regulating diverse SAM-regulated agromorphological traits in crop plants. A genome-wide scan identified 142 CLV1-, 28 CLV2- and 6 CLV3-like genes, and their comprehensive genomic constitution and phylogenetic relationships were deciphered in chickpea. The QTL/fine mapping and map-based cloning integrated with high-resolution association analysis identified SNP loci from CaCLV3_01 gene within a major CaqDTF1.1/CaqFN1.1 QTL associated with DTF (days to 50% flowering) and FN (flower number) traits in chickpea, which was further ascertained by quantitative expression profiling. Molecular haplotyping of CaCLV3_01 gene, expressed specifically in SAM, constituted two major haplotypes that differentiated the early-DTF and high-FN chickpea accessions from late-DTF and low-FN. Enhanced accumulation of transcripts of superior CaCLV3_01 gene haplotype and known flowering promoting genes was observed in the corresponding haplotype-introgressed early-DTF and high-FN near-isogenic lines (NILs) with narrow SAM width. The superior haplotype-introgressed NILs exhibited early-flowering, high-FN and enhanced seed yield/productivity without compromising agronomic performance. These delineated molecular signatures can regulate DTF and FN traits through SAM proliferation and differentiation and thereby will be useful for translational genomic study to develop early-flowering cultivars with enhanced yield/productivity.

Phenophasic development of wild Cicer species in relation to agroclimatic indices under rainfed and irrigated conditions

The field study was conducted on six wild chickpea accessions to evaluate the influence of agroclimatic indices viz., accumulated growing degree days (GDD), photo-thermal unit (PTU) and heliothermal unit (PTU) at various phenophases of chickpea under irrigated and rainfed conditions on yield of the plant. C pinnatifidum 212 witnessed highest accumulation of heat units at all stages of phenophasic development under irrigated and rainfed conditions. Agroclimatic indices depicted positive correlation with yield under rainfed conditions.Path coefficient analysis revealed that under irrigated conditions, yield attributes and agroclimatic indices showed strong positive correlation towards the final grain yield, though HTU at maturity indirectly affected yield via pods per plant (PPP) to the final yield in rainfed treatment. Among all the accessions, C pinnatifidum 212 performed better than other accessions by possessing high heat use efficiency (HUE) values, thus displaying their capacity of utilizing GDD and incorporating final yield.

Genome-wide generation and genotyping of informative SNPs to scan molecular signatures for seed yield in chickpea

We discovered 2150 desi and 2199 kabuli accessions-derived SNPs by cultivar-wise individual assembling of sequence-reads generated through genotyping-by-sequencing of 92 chickpea accessions. Subsequent large-scale validation and genotyping of these SNPs discovered 619 desi accessions-derived (DAD) SNPs, 531 kabuli accessions-derived (KAD) SNPs, 884 multiple accessions-derived (MAD) SNPs and 1083 two accessions (desi ICC 4958 and kabuli CDC Frontier)-derived (TAD) SNPs that were mapped on eight chromosomes. These informative SNPs were annotated in coding/non-coding regulatory sequence components of genes. The MAD-SNPs were efficient to detect high intra-specific polymorphic potential and wide natural allelic diversity level including high-resolution admixed-population genetic structure and precise phylogenetic relationship among 291 desi and kabuli accessions. This signifies their effectiveness in introgression breeding and varietal improvement studies targeting useful agronomic traits of chickpea. Six trait-associated genes with SNPs including quantitative trait nucleotides (QTNs) in combination explained 27.5% phenotypic variation for seed yield per plant (SYP). A pentatricopeptide repeat (PPR) gene with a synonymous-coding SNP/QTN significantly associated with SYP trait was found most-promising in chickpea. The essential information delineated can be of immense utility in genomics-assisted breeding applications to develop high-yielding chickpea cultivars.

Genome-wide association study between chickpea accessions from VIR collection and phenotypic data

Genome-wide association study between chickpea accessions from VIR collection and phenotypic data

Screening of chickpea accessions with a set of economically valuable features

Screening of chickpea accessions with a set of economically valuable features

Biochemical diversity evaluation in chickpea accessions employing mini-core collection.

The seeds of chickpea provide an exceptional source of dietary proteins and is one of the important legumes in both developed and developing countries over the world. The available germplasm of cultivated chickpea is deficient in desired biochemical signatures. To identify new sources of variations for breeding, reduced subsets of germplasm such as mini-core collection can be explored as an effective resource. In the present investigation, mini-core collections consisting of 215 accessions of chickpea were extensively evaluated for tapping biochemical diversity. Analysis included ten biochemical parameters comprising total protein, total free amino acids, phytic acid, tannin, total phenolics, total flavonoids, lectin, DPPH radical scavenging activity, in vitro digestibility of protein and starch. The spectrum of diversity was documented for total protein (4.60-33.90%), total free amino acids (0.092-9.33mg/g), phytic acid (0.009-4.06mg/g), tannin (0.232-189.63mg/g), total phenolics (0.15-0.81mg/g), total flavonoids (0.04-1.57mg/g), lectin (0.07-330.32 HU/mg), DPPH radical scavenging activity (26.74-49.11%), in vitro protein digestibility (59.45-76.22%) and in vitro starch digestibility (45.63-298.39mg of maltose/g). The principal component analysis revealed association of chickpea higher protein content to the lower level of total phenolics and flavonoid contents. The dendrogram obtained by unweighted pair group method using arithmetic average cluster analysis grouped the chickpea accessions into two major clusters. This is the first comprehensive report on biochemical diversity analysed in the mini-core chickpea accessions. The ultimate purpose of conducting such studies was to deliver information on nutritional characteristics for effective breeding programmes. Depending on the objectives of the breeding aforesaid accessions could be employed as a parent.

Easy strategy used to detect the genetic variability in chickpea (Cicer arietinum L.).

A priority in the management and use of elite plant materials for breeding has been based on molecular markers or DNA sequencing of entire genomes, in order to perform genetic differentiation which is still quite costly. Chickpea (Cicer arietinum) is one of the species with genomic monotony and very low polymorphism, and its detection even with DNA markers has not been easy. In germplasm banks, the genetic distinction is a priority in order to use properly selected lines. In this study, 57 chickpea accessions from a germplasm bank were analyzed by using nrRAMP (non-radioactive Random Amplified Microsatellite Polymorphism) markers, and their genetic variability was determined. Our results showed DNA polymorphisms, which are enough to differentiate between the accessions and between C. arietinum and Cicer reticulatum (out-group); this last wild species is closely related to chickpea. We concluded that the nrRAMP technique was an effective and a highly useful method to assess the genetic diversity and variability among closely related plants, such as chickpea; in addition, this technique can be easily implemented in laboratories.

Field evaluation of new Kabuli chickpeas lines for the production of canned seeds

There is an increased demand for canned chickpeas worldwide, which has also resulted in increased chickpea cultivation in Italy. The availability of Italian chickpea varieties, suitable for industrial transformation, is limited. The objective of the present study was to evaluate the field production of new Kabuli chickpea accessions and their suitability for industrial transformation. Thirteen accessions, provided by the International Centre for Agricultural Research of Turkey, together with ‘Blanco Sinaloa’, a commercial Mexican variety, were cultivated in Cesa, Tuscany, in 2016 and 2017. The average seed yield was 2.8 and 3.4 t ha-¹, respectively, in 2016 and 2017. Increased yield in 2017 was attributable to a more balanced rainfall pattern, compared to that in 2016 which induced increased vegetative growth. Based on production stability over the two-year trial, the varieties FLIP08-69C, FLIP-160C and FLIP05-157C turned out particularly suitable for cultivation. The climatic conditions in 2017 favored an increased presence of a Grade B seed classification [220-250 seeds per 100 g (caliber 8)] which is preferred by industry. Most varieties showed potential regarding seed dimension classification, however, of the varieties with a good production, FLIP05-157C was also characterized by seed gradation stability.

Application of DNA markers in determination of fusarium resistance and genetic diversity in chickpea

Genetic diversity and fusarium resistance of 50 cultivated chickpea genotypes was studied using ISSR and RAPD markers. The results of both marker systems were consistent with each other, but was somewhat higher for RAPDs. A total of 48 fragments were obtained with both markers together, 32.7% of which were polymorphic. Molecular characterisation through ISSR and RAPD data indicated low genetic variation (GDI=0.39; PIC=0.21) among local and introduced chickpea accessions. The genetic distance values ranged from 0 to 0.134, with a mean of 0.05. The low genetic diversity indicated that new genotypes must be introduced to increase the variability of chickpea germplasm in Azerbaijan. As a result of screening for resistance to fusarium most of genotypes were found to have 600 bp fragment of OPJ20 linked with Foc01 resistance gene, while none of them had resistance gene to Foc4. The results could provide information for future chickpea breeding activities and conservation.