Chickpea Landraces Research Articles

Integrating multilocus genome-wide association studies in chickpea landraces to discern the genetics of drought tolerance

In chickpea breeding, drought is a major concern and a complex trait controlled by several genes. To develop drought-tolerant varieties, it is essential to use the available germplasm and genomic resources. Over the years, the landraces have proven to be a good source for the dissection of genes for different yield and yield-related traits. The present investigation for marker–trait associations (MTAs) and candidate gene identification was conducted by studying 125 chickpea landraces collected from the West Asia and North Africa (WANA) region, along with 4 varieties suitable for irrigated and rainfed environments. This study analyzed 13 physio-morphological traits in 2 consecutive years at two isolated locations (IARI, New Delhi, and Dharwad). A strong correlation coefficient was observed between the trait seed yield (SY) and biological yield (BY) under both conditions. The Drought Susceptibility Index (DSI) ranged from 0.02 to 1.84 and 0.10 to 2.04 at the IARI, New Delhi and Dharwad locations, respectively. The genotypic data of 6,367 single nucleotide polymorphisms (SNPs) distributed across the genome were used for genetic diversity study, population structure, and genome-wide association study (GWAS). The average polymorphic information content (PIC) value observed was 0.25, and the average linkage disequilibrium (LD) decay distance was 152,269 bp across the genome. A total of four subgroups were observed within the population for genotypic data. Fixed and random model Circulating Probability Unification (FarmCPU) was used for the GWAS analysis, which considered both fixed- and random-effect models. A total of 52 significant SNPs were reported in both irrigated and rainfed conditions at low locations; 7 SNPs were associated with more than one trait, which may have pleiotropic effects. Significant SNPs were annotated in the pulse database. The identified genomic region found in or near MTA under rainfed conditions encodes for guard cell hydrogen peroxide-resistant1 (GHR1), late embryogenesis-abundant, E3 ubiquitin-protein ligase, walls are thin1 (WAT1), and beta-galactosidase that are known to be associated with drought tolerance.

Genome-wide association analysis in chickpea landraces and cultivars

Chickpea (Cicer arientinum) is an important leguminous crop, which is widely grown especially in the Near East. In wet weather conditions, the susceptibility of chickpeas to fungal diseases such as Ascochyta blight and Fusarium blight increases. Thus, selection of disease-resistant and early-ripening varieties is critically needed. The present study was conducted to investigate genome associations in 171 samples of chickpea plants, grown in two experimental stations in Krasnodar (Kuban experimental station) and Astrakhan (Astrakhan experimental station), examine relationship between genes and 12 phenotypic traits as well as explore the association between genes and 3 hallmarks of resistance to pathogenes: Fusarium blight, Ascochyta blight and Noctuidae. Variants associated with different phenotypic traits were identified using a genome-wide association study (GWAS).

Untapped Genetic Resources for Breeding Acidic Soil-Adapted Chickpea (Cicer arietinum L.) Cultivars

Globally, more than half of potentially arable land is acidic, and aluminum (Al) is the primary factor limiting plant growth and crop productivity on acidic soils worldwide. The development and utilization of Al-tolerant crops is a sustainable approach to enhancing crop production on acidic soils. For this purpose, screening available genetic resources under Al-stressed conditions is a crucial initial step. Hence, the present study aimed to evaluate the Al tolerance of 264 Ethiopian chickpea landraces under hydroponic conditions without Al (control) and with 120 µM Al (Al treatment). Significant (p < 0.001) variations were detected among the genotypes for all studied traits under control (0 µM Al) and 120 µM Al concentration. The relative growth values for the 120 µM Al/0 µM Al ratio was also significant, indicating the presence of a considerable amount of genetic variation in Ethiopian chickpea landraces in terms of Al tolerance. Based on relative root growth (RRG) as an Al-tolerance parameter, the genotypes were grouped into five distinct (p < 0.001) classes. The highest RRG value (1.59) was obtained for genotype ETC_209008, followed by ETC_41184 and ETC_212589, while ETC_208995 had the lowest RRG value of 0.27. Of the total landraces screened, 35% had higher RRG values than the tolerant genotype ETC_WL_1_2016 used as a reference, indicating the presence of adequate genotypes capable of outperforming the reference genotype on acidic soils. The genotypes identified in the present study may serve as sources of novel alleles in genes regulating Al tolerance in chickpea that can be utilized in breeding programs to improve the crop’s adaptation to acidic soils, thus contributing to smallholder farmers’ increased nutritional and food security.

A Multi-Model Based Stability Analysis Employing Multi-Environmental Trials (METs) Data for Discerning Heat Tolerance in Chickpea (Cicer arietinum L.) Landraces.

Identifying a congenially targeted production environment and understanding the effects of genotype by environmental interactions on the adaption of chickpea genotypes is essential for achieving an optimal yield stability. Different models like additive main effect and multiplicative interactions (AMMI 1, AMM2), weighted average absolute scores of BLUPs (WAASB), and genotype plus genotype-environment (GGE) interactions were used to understand their suitability in the precise estimation of variance and their interaction. Our experiment used genotypes that represent the West Asia-North Africa (WANA) region. This trial involved two different sowing dates, two distinct seasons, and three different locations, resulting in a total of 12 environments. Genotype IG 5871(G1) showed a lower heat susceptibility index (HSI) across environments under study. The first four interactions principal component axis (IPCA) explain 93.2% of variations with significant genotype-environment interactions. Considering the AMMI stability value (ASV), the genotypes IG5862(G7), IG5861(G6), ILC239(G40), IG6002(G26), and ILC1932(G39), showing ASV scores of 1.66, 1.80, 2.20, 2.60, and 2.84, respectively, were ranked as the most stable and are comparable to the weighted average absolute scores of BLUPs (WAASB) ranking of genotypes. The which-won-where pattern of genotype plus genotype-environment (GGE) interactions suggested that the target environment consists of one mega environment. IG5866(G10), IG5865(G9), IG5884(G14), and IG5862(G7) displayed higher stability, as they were nearer to the origin. The genotypes that exhibited a superior performance in the tested environments can serve as ideal parental lines for heat-stress tolerance breeding programs. The weighted average absolute scores of BLUPs (WAASB) serve as an ideal tool to discern the variations and identify the stable genotype among all methods.

Multi-block approach for the characterization and discrimination of Italian chickpeas landraces

An untargeted characterization was carried out to attempt the geographical discrimination of three high-valued Italian chickpeas (Cicer arietinum L.), harvested in 2019 in three traditional and relatively close production areas: Navelli (Abruzzo, Central Italy), Cicerale (Campania, South Italy), and Valentano (Lazio, Central Italy). The present study aimed to develop and validate a potentially non-destructive and routine-compatible method for the geographical traceability of chickpea landraces of high traditional value. The outer part of 146 kernels belonging to the three varieties was analysed by Attenuated Total Reflectance-Fourier Transform-Mid Infrared (ATR-FT-MIR) and FT-Near Infrared (NIR) spectroscopies. Eventually, each sample was cut in two, and the cross-sections (the internal and external parts) were analysed by the two spectroscopic techniques. Spectral information was organized in four data blocks (MIRout, MIRin, NIRout, and NIRin), and single-block Partial Least Squares-Linear Discriminant Analysis (PLS-LDA) was applied. Accurate results were obtained from the single-block-processing of the spectroscopic profiles for the outer kernel part (MIRout and NIRout) that, combined with interesting outcomes from a preliminary class modelling approach suggest the real possibility of implementing a non-destructive authentication method. Notwithstanding, Sequential and Orthogonalized (SO)-PLS-LDA and SO-Covariance selection (Covsel)-LDA were applied to interpret better the information in the four collected data blocks. In this context, VIP (Variable Importance in Projection) analysis was performed to identify the significant variables, leading to a direct chemical interpretation of the classification models.

Evaluation of chickpea (Cicer arietinum L.) in response to salinity stress

Soil salinity is a severe and expanding soil degradation problem that affects 80 million ha of arable lands globally. Chickpea (Cicer arietinum L.) is very sensitive to saline conditions; the most susceptible genotypes may die in just 25 mM NaCl in hydroponics. Approximately 8–10% yield loss in chickpea production is estimated due to salinity stress. However, it is still not established why chickpea is so susceptible to salt affection. Salinity (NaCl) impedes germination of seeds, though chickpea varieties considerably differ from one another in this respect. Some chickpea genotypes are more tolerant in the stage of germination, tolerating even 320 mM NaCl. The reasons of this variation are unrevealed; there is a shortage of knowledge about the germination abilities of chickpea genotypes in saline conditions. Nevertheless, the effect of salt stress on vegetative growth can be analysed in hydroponics, in pot or field conditions, regardless the experimental environment, the ranking of genotypes regarding salt resistance is coherent. Chickpea genotypes can be different in their ability to retain water, maybe under salt affection; the more salt tolerant lines can maintain higher water content in the shoots, while the more sensitive ones cannot. The identification of salt tolerant chickpea landraces based on developing genetic variability is a suitable strategy to combat against salinity problems arising in arid and semi-arid areas.

Historical routes for diversification of domesticated chickpea inferred from landrace genomics.

According to archaeological records, chickpea (Cicer arietinum) was first domesticated in the Fertile Crescent about 10k years BP. Its subsequent diversification in Middle East, South Asia, Ethiopia, and the Western Mediterranean, however, remains obscure and cannot be resolved using only archeological and historical evidence. Moreover, chickpea has two market types: 'desi' and 'kabuli', for which the geographic origin is a matter of debate. To decipher chickpea history, we took the genetic data from 421 chickpea landraces unaffected by the green revolution and tested complex historical hypotheses of chickpea migration and admixture on two hierarchical spatial levels: within and between major regions of cultivation. For chickpea migration within regions, we developed popdisp, a Bayesian model of population dispersal from a regional representative center towards the sampling sites, that considers geographical proximities between sites. This method confirmed that chickpea spreads within each geographical region along optimal geographical routes rather than by simple diffusion and estimated representative allele frequencies for each region. For chickpea migration between regions, we developed another model, migadmi, that takes allele frequencies of populations and evaluates multiple and nested admixture events. Applying this model to desi populations, we found both Indian and Middle Eastern traces in Ethiopian chickpea, suggesting the presence of a seaway from South Asia to Ethiopia. As for the origin of kabuli chickpeas, we found significant evidence for its origin from Turkey rather than Central Asia.

Siphoning novel sources of seedling salinity tolerance from the diverse chickpea landraces

Context Chickpea (Cicer arietinum L.) are highly sensitive to elevated salinity, particularly at initial seedling establishment stage. Seedling screening would be an effective means to identify novel sources of donors for salt tolerance. Aim This study aimed to identify salt stress tolerant genotypes at seedling stage from 50 chickpea accessions. Methods The screening of 50 chickpea accessions was done under two salinity conditions including salt stress (8 dS m−1) and control (no salt stress). Accessions were studied for morphological traits, root system architectural analysis, and CSTI (Cumulative salt tolerance index). Further, principal component analysis was conducted to validate these results for more accuracy and reliability. Key results For morphological traits, a high degree of genetic variation was seen among genotypes, and root traits were found to be the better indicators of salt stress tolerance. CSTI was used to classify the accessions; 22 (44%) were identified as salt sensitive, 21 (42%) were found to be moderately salt tolerant, and 7 (14%) had moderate to high salt tolerance. The most salt tolerant and salt sensitive genotypes were found to be ICCV10 and ILC5595, respectively. Conclusions Early seedling screening has a great potential to identify genotypes with robust root systems, which can withstand salinity. Implications We used a novel approach to classify chickpea landraces based on the combination of CSTI and principal component analysis methods. By choosing suitable donors and prospective genotypes at early growth stages, the knowledge gathered from this study may aid scientists and chickpea breeders in developing salt tolerant cultivars.

Exploring the Amino-Acid Composition, Secondary Structure, and Physicochemical and Functional Properties of Chickpea Protein Isolates.

This study examined the amino-acid profile, secondary structure, and physicochemical and functional properties of proteins isolated from Anatolian chickpea landraces. Secondary objective of the study was to determine whether a relationship exists between the amino-acid composition and physicochemical and functional properties. Aspartic acid and glutamic acid were the dominant amino acids, while the isolates were deficient in methionine. Secondary structures were determined by Fourier transform infrared spectroscopy, where the β-sheet was shown to be dominant. The denaturation temperature of the isolates was between 87 and 145 °C, and the highest net surface charge (≃28.6 mV) and solubility (∼95.0%) were observed at pH 9.0-10.0. The isolates' water-holding capacity varied between 2.1 and 2.7 g water/g protein, whereas their oil-holding capacity ranged between 3.4 and 4.4 g oil/g protein. Emulsion capacity, emulsifying activity, and the stability indices of isolates were found to be between 401.2 and 469.1 g oil/g protein, 14.5 and 25.7 m2/g, and 45.7 and 146.9 min, respectively. Isolates of Hisar and Erzincan chickpeas exhibited good emulsifying properties. The Yasa isolate had a relatively high hydrophobic amino-acid content and delivered the best gelation performance. Overall, significant differences in the characteristics of proteins were observed among the different chickpea landraces studied.

Evaluation of Ethiopian chickpea (Cicer arietinum L.) genotypes for frost tolerance

Frost stress is one of the most significant abiotic factors affecting chickpea (Cicer arietinum L.) production in the Ethiopian highlands. To investigate the frost tolerance of chickpea, 673 genotypes were characterized using an augmented design at Bakelo, Debre Berhan, Ethiopia for two years. A significant (p < 0.01) variability amongst genotypes was recorded for all agronomic traits considered. A considerable number of accessions better performing over the frost susceptible genotypes were identified for agronomic traits. Stem/leaf pigmented genotypes showed a better reaction for frost stress than non-pigmented genotypes. The majority of black seeded chickpea adapted well under frost stress when compared to with brown and white seeded genotypes. According to the freezing tolerance rate (FTR) and plant survival rate (SR), 83 (12.3 %) and 85 (12.6 %) genotypes were identified as frost tolerant. There was a strong correlation (p < 0.01) in grain yield with FTR, SR, seed shriveling score, stem/leaf pigmentation and seed color. Based on our findings, Ethiopian chickpea landraces has a good genetic potential for frost resistance traits for use in breeding programs.

A Genomic Analysis of Historic Chickpea Landraces

The collection of seeds and living plants at the N.I. Vavilov All Russian Institute of Plant Genetic Resources (VIR) contains historic chickpea landraces sampled from major historic centers of chickpea cultivation and secondary diversification. In this work, we analyze the results obtained from phenotype characterization of 407 historic chickpea landraces grown in the trial fields of Kuban experimental station in 2017. GWAS analysis identified three single nucleotide polymorphisms on chromosomes 2, 7 and 8 that were highly associated with the days to flowering phenotype trait. These single nucleotide polymorphisms and the regions of genome near to these single nucleotide polymorphisms were identified in previous studies. Estimation of the Genotype–Environment interaction for phenotypic traits coincident with plant seeds led to identification of the best genotypes in the environments. These genotypes have an alternative homozygote at loci Ca7:30930779 which shows similar phenotypic traits that were described during phenotype characterization of seeds grown in the trial fields of the Kuban experimental station in 2016 and with the period of flowering typical of phenotype characterization of the plants in 2017. These results can accelerate the search for the seed samples that are the most promising for cultivation of chickpea landraces.

Identification of stable drought tolerant landraces of chickpea (Cicer arietinum) under multiple environments

Drought is a major constraint to chickpea production leading to maximum crop loss. Further the narrow genetic base of chickpea (Cicer arietinum L.) can be widened by crossing them to landraces and wild species of which landraces provide valuable sources for abiotic and biotic stresses. The present investigation identifies highly stable drought tolerant landraces using AMMI analysis and GGE biplot techniques. The 42 chickpea genotypes (38 chickpea landraces obtained from West Asia and North Africa (WANA) and 4 known varieties) were evaluated at two locations under randomized block design in irrigated and rainfed condition in two seasons. Additive main effects and multiplicative interaction (AMMI) and Genotype main effect and genotype × environment interaction (GGE) were employed in the evaluation of genotype. AMMI analyses decomposes SS for GEI in to 3 Interaction Principal Components(PC) of which PC1(79.6%) and PC2(17.8%) explains most of the variability. From AMMI Stability Value (ASV) the genotype G35 (IL184) and G23 (IG5895) were found most stable landraces while Yield Stability Value (YSI) ranking identified G8 (IG5856) as the best genotype, based on stability and mean yield. From GGE biplot analyses the PC1 explains 80.0% and PC2 explains 18.9% of variability. G8(IG5856) performs well under across all the environments with high mean yield. Drought Susceptible Index (DSI) indicated G8 (IG5856) and G2 (ICC4958) to have the lowest DSI at both the locations. From the above investigation the landrace IG 5856 from Jordan was found to be most drought tolerant.

Genomic Analysis of Vavilov's Historic Chickpea Landraces Reveals Footprints of Environmental and Human Selection.

A defining challenge of the 21st century is meeting the nutritional demands of the growing human population, under a scenario of limited land and water resources and under the specter of climate change. The Vavilov seed bank contains numerous landraces collected nearly a hundred years ago, and thus may contain ‘genetic gems’ with the potential to enhance modern breeding efforts. Here, we analyze 407 landraces, sampled from major historic centers of chickpea cultivation and secondary diversification. Genome-Wide Association Studies (GWAS) conducted on both phenotypic traits and bioclimatic variables at landraces sampling sites as extended phenotypes resulted in 84 GWAS hits associated to various regions. The novel haploblock-based test identified haploblocks enriched for single nucleotide polymorphisms (SNPs) associated with phenotypes and bioclimatic variables. Subsequent bi-clustering of traits sharing enriched haploblocks underscored both non-random distribution of SNPs among several haploblocks and their association with multiple traits. We hypothesize that these clusters of pleiotropic SNPs represent co-adapted genetic complexes to a range of environmental conditions that chickpea experienced during domestication and subsequent geographic radiation. Linking genetic variation to phenotypic data and a wealth of historic information preserved in historic seed banks are the keys for genome-based and environment-informed breeding intensification.

The Signatures of Ecological Adaptation in the Genomes of Chickpea Landraces

Abstract—The seed bank of the Vavilov All-Russia Institute of Plant Genetic Resources (VIR) contains a wide range of landraces that were collected almost 100 years ago, in which natural selection might leave signatures through crop diversification. In this study, we analyzed 407 landraces sampled at centers of the origin of the chickpea and at sites of secondary diversity. We hypothesize that a fraction of single nucleotide polymorphisms might have exhibited strong selection to a range of environmental conditions that chickpea experienced during domestication and subsequent geographic distribution. Using the BayPass package we identified 13 polymorphisms; these assort by environmental conditions and are strong candidates for local adaptation.

Regression Model for Time to Flowering of Chickpea Landraces

Regression models for time to flowering had been developed for VIR chickpea landraces collected in Turkey and Ethiopia. Predicted flowering time coincides closely with experimental data. The difference between models is statistically significant. The impact of the temperature to the model for Ethiopia landraces is weaker than that for Turkey landraces, 48 and 60% respectively. The impact of precipitation on phenotype is more than 80%. The obtained results are in agreement with climate characteristics at collection sites.

Genetic Diversity Analysis and SDS-PAGE Protein Profile in Landraces of Chickpea Grown in Yavatmal District (Maharashtra)

Four chick pea landraces viz. LC1, LC2, LC3 and LC4 collected from Savana, Wai, Kapara and Wakodi villages of Yavatmal district were used for RAPD analysis for assessment of genetic diversity by using five RAPD primers. The SDS-PAGE protein pattern profile was also resolved. Twenty amplicons were found to be amplified from which 55% were polymorphic and 45% were monomorphic across the local cultivar. The electrophoresis pattern of protein fractions were found to be directly related to the genetic background of the proteins and can be used to identify genetic makeup. Total 26 bands were expressed with different intensity. The 110 KDa and 41 KDa protein bands were unique in LC1 and LC4 respectively whereas 66 KDa protein band was common in all landraces. A Considerable variation in protein banding pattern was observed in four landraces which is localized from different villages of Yavatmal district of Maharashtra.

Correlation and path coefficient analysis among seed yield and yield related traits of Ethiopian chickpea (Cicer arietinum L.) landraces

The experiment was done on 202 new chickpea (Cicer arietinum L.) landraces with 2 checks to assess the association, direct and indirect effect of different characters on yield. The experiment was planted at Sirinka and Jari, Ethiopia, 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 among genotypes. The correlation of grain yield with biomass and with harvest index 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 mass was positive but insignificant both at genotypic and phenotypic levels. Path coefficient analysis at genotypic level showed that among the 15 causal (independent) traits; biomass, harvest index, pod length, days to pod setting, pod filing period, canopy width, primary branches, secondary branches, and number of pods per plant had positive and directly influence on grain yield. Although the days to flowering, plant height and hundred seed mass had positive genotypic correlation with grain yield. In general correlation coupled with path coefficient analysis revealed that biomass and harvest index had a direct relationship with seed yield.

Characterization and Assessment of Genetic Diversity for Agro-Morphological Traits of Ethiopian Chickpea (Cicer arietinum L.) landraces

This experiment was conducted in 2016 at Sirinka and Jari, under rainfed conditions to characterize and assess genetic diversity among the Ethiopian chickpea landraces. Two hundred two new germplasm accessions were grown in an alpha lattice design with three replications. Data on 16 traits were collected and analysed. Differences among the accessions were significant P<0.01). The genotypes were grouped into five clusters with different sizes. The genetic distances among the clusters were significant. The highest diversity indices pooled over characters within zones were recorded for accessions from South West Shewa (H= 2.03 ± 0.05) followed by Gurage (H=0.81 ± 0.08), West Shewa (H=0.73 ± 0.04) and North Gonder (H= 0.72 ± 0.05). The existence of wider morpho-agronomic diversity among the chickpea collections implies the potential to improve the crop and the need to conserve the diversity. Future collecting operations of chickpea accessions should strategically focus on areas with relatively large variation. From a genetic conservation point of view, it appears that South West Shewa, Gurage, West Shewa and North Gonder could be suitable as in situ conservation sites. Keywords: Accessions; diversity; clustering

Genetic Diversity, Population Structure, and Genetic Correlation with Climatic Variation in Chickpea (Cicer arietinum) Landraces from Pakistan.

Chickpea ( L.) production in arid regions, such as those predominant in Pakistan, faces immense challenges of drought and heat stress. Addressing these challenges is made more difficult by the lack of genetic and phenotypic characterization of available cultivated varieties and breeding materials. Genotyping-by-sequencing offers a rapid and cost-effective means to identify genome-wide nucleotide variation in crop germplasm. When combined with extended crop phenotypes deduced from climatic variation at sites of collection, the data can predict which portions of genetic variation might have roles in climate resilience. Here we use 8113 single nucleotide polymorphism markers to determine genetic variation and compare population structure within a previously uncharacterized collection of 77 landraces and 5 elite cultivars, currently grown in situ on farms throughout the chickpea growing regions of Pakistan. The compiled landraces span a striking aridity gradient into the Thal Desert of the Punjab. Despite low levels of variation across the collection and limited genetic structure, we found some differentiation between accessions from arid, semiarid, irrigated, and coastal areas. In a subset of 232 markers, we found evidence of differentiation along gradients of elevation and isothermality. Our results highlight the utility of exploring large germplasm collections for nucleotide variation associated with environmental extremes, and the use of such data to nominate germplasm accessions with the potential to improve crop drought tolerance and other environmental traits.

Molecular marker based diversity of chickpea landraces, wild derivatives and breeding lines using SSR and gene markers

Molecular marker based diversity of chickpea landraces, wild derivatives and breeding lines using SSR and gene markers