Cicer Species Research Articles

Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea.

Chickpea (Cicer arietinum L.)-an important legume crop cultivated in arid and semiarid regions-has limited genetic diversity. Efforts are being undertaken to broaden its diversity by utilizing its wild relatives, which remain largely unexplored. Here, we present the Cicer super-pangenome based on the de novo genome assemblies of eight annual Cicer wild species. We identified 24,827 gene families, including 14,748 core, 2,958 softcore, 6,212 dispensable and 909 species-specific gene families. The dispensable genome was enriched for genes related to key agronomic traits. Structural variations between cultivated and wild genomes were used to construct a graph-based genome, revealing variations in genes affecting traits such as flowering time, vernalization and disease resistance. These variations will facilitate the transfer of valuable traits from wild Cicer species into elite chickpea varieties through marker-assisted selection or gene-editing. This study offers valuable insights into the genetic diversity and potential avenues for crop improvement in chickpea.

Determination of the Bacterial Community in Soils Associated with Rare Wild Leguminous Species Cicer Montbretii Jaub. & Spach and Lupinus albus L. in Strandzha Natural Park

Determination of the Bacterial Community in Soils Associated with Rare Wild Leguminous Species Cicer Montbretii Jaub. & Spach and Lupinus albus L. in Strandzha Natural Park

First report of Ascochyta rabiei infections on endemic Turkish populations of Cicer bijugum and C. turcicum.

Ascochyta rabiei causes Ascochyta blight disease on C. arietinum as well as on annual C. reticulatum, C. pinnatifidum and C. judaicum and perennial C. montbretii, C. isauricum, C. ervoides species (Can et al. 2007; Frenkel et al. 2007; Ozkilinc et al. 2019; Peever et al. 2007; Tekin et al. 2018). During field survey studies carried out on annual Cicer spp. in June 2022, concentric ring-shaped lesions were observed on the stems and leaves of C. bijugum in Mardin province and C. turcicum in Elazig province. Cicer reticulatum and C. arietinum plants were also found in the location where C. bijugum was found. No disease symptoms were observed in other Cicer species, while C. bijugum had 32% disease incidence. The disease incidence among the C. turcicum population was 37.3 %, and no chickpea cultivation area was found near it. Diseased plant parts were surface sterilized, placed on ½ potato dextrose agar (PDA) and incubated at 24±2 oC in 12 hours light/dark photoperiod. Each symptomatic plant was considered as one isolate. Monosporic isolates were obtained and the same colony morphology developed from all plant parts of C. turcicum and C. bijugum. Spores were oblong and spore sizes were 10.73±0.62 µm (n=15) in length and 3.60±0.25 (n=15) µm in width, 10.64±0.98 (n=15) µm in length and 3.00±0.26 (n=15) µm in width for isolates obtained from C. turcicum and C. bijugum, respectively. Amplicons for all 40 isolates were generated with mating type (MAT) primers, and the ITS region was amplified and sequenced by using the ITS4 and ITS5 primers (Peever et al. 2007). For the MAT primers, a 700 bp amplicon was observed for all the 20 isolates obtained from C. bijugum conferring to MAT1.1 idiomorph. In contrast, for the isolates obtained from C. turcicum 14 isolates had a 700 bp amplicon for MAT1.1 and 6 isolates had a 500 bp amplicon for MAT1.2, thus representing both idiomorphs in a ~2:1 ratio. BLAST analysis of the ITS sequences showed 100% homology with the reference ITS sequences for A. rabiei except for 23 SVRC CT 09/22 and 23 SVRC CT 22/22 isolates showing 99.81 % similarity. All sequences were submitted to GenBank (OP967923, OP967924, OP967925, OP967926 and OP967927 for A. rabiei isolates from C. turcicum; OP981072, OP981073 and OP981074 for A. rabiei isolates from C. bijugum). A phylogenetic tree was constructed using MEGAX software and the Neighbor-Joining method, using the ITS sequences of A. rabiei, other Ascochyta spp. and Colletotrichum gloeosporioides. The A. rabiei isolates from C. turcicum and C. bijugum clustered together with A. rabiei sequences from the NCBI (Kumar et al. 2018). Twelve-day-old C. bijugum and C. turcicum seedlings were inoculated with 5 x 105 spore/mL concentration of spores from 5 C. turcicum and 3 C. bijugum isolates and put in plastic bags for 24 hours (Can et al. 2007). Pathogenicity tests were carried out in triplicate pots with four plants each for each isolate in a controlled climate chamber at 24±2 oC, 70% humidity under 12 hours light/dark conditions. The first symptoms were observed within 7 days after inoculation (dai) and severe Ascochyta blight symptoms developed on all plants by 21 dai. Cicer bijugum and C. turcicum are endemic Cicer species exhibiting narrow distribution in the Southeastern region of Republic of Türkiye. As a major biotic stress source, A. rabiei could be an important threat to Cicer spp (Abbo et al. 2003). To our knowledge, this is the first report of A. rabiei from C. bijugum and C. turcicum species.

Development of trait-specific genetic stocks derived from wild Cicer species as novel sources of resistance to important diseases for chickpea improvement

AbstractLow level of resistance to major diseases such as ascochyta blight (AB), botrytis grey mould (BGM) and dry root rot (DRR) in the cultivated chickpea genepool necessitates harnessing wild Cicer species. Sixty-eight accessions belonging to eight annual wild Cicer species and seven chickpea cultivars were screened for AB, BGM and DRR under controlled environmental conditions over the years. Intra-accession variability was observed among wild Cicer accessions for each disease. Hence, progenies of single resistant plants were selected for further evaluations and the trait-specific genetic stocks (TGS) were developed for each disease after re-screening following the single seed descent method. For AB, a high level of resistance was identified in four accessions belonging to tertiary genepool species, ICC 17334 (Cicer judaicum), ICC 17302, ICC 17308 and ICC 20177 (C. bijugum). Nine accessions, ICC 17160, ICC 17264, ICC 17270, ICC 20170, ICC 20186, ICC 20225, ICC 20247, ICC 20251 and IG 72941 of primary (C. reticulatum) and one accession, ICC 20190 of secondary (C. echinospermum) genepool species were resistant to BGM whereas, four accessions, ICC 20187 (C. reticulatum) and ICC 20218, ICC 20244 and ICC 20257 (C. echinospermum) were resistant to DRR. Development and utilization of these TGS in chickpea pre-breeding will assist in developing disease-resistant chickpea cultivars with broad genetic base.

Exploring the molecular basis of resistance to Botrytis cinerea in chickpea genotypes through biochemical and morphological markers.

Chickpea (Cicer arietinum L.) is an important pulse crop around the globe and a valuable source of protein in the human diet. However, it is highly susceptible to various plant pathogens such as fungi, bacteria, and viruses, which can cause significant damage from the seedling phase until harvest, leading to reduced yields and affecting its production. Botrytis cinerea can cause significant damage to chickpea crops, especially under high humidity and moisture conditions. This fungus can cause grey mould disease, which can lead to wilting, stem and pod rot, and reduced yields. Chickpea plants have developed specific barriers to counteract the harmful effects of this fungus. These barriers include biochemical and structural defences. In this study, the defence responses against B. cinerea were measured by the quantification of biochemical metabolites such as antioxidant enzymes, malondialdehyde (MDA), proline, glutathione (GSH), H2O2, ascorbic acid (AA) and total phenol in the leaf samples of chickpea genotypes (one accession of wild Cicer species, viz. Cicer pinnatifidum188 identified with high level of resistance to Botrytis grey mould (BGM) and a cultivar, Cicer arietinumPBG5 susceptible to BGM grown in the greenhouse). Seedlings of both the genotypes were inoculated with (1 × 104 spore mL-1) inoculum of isolate 24, race 510 of B. cinerea and samples were collected after 1, 3, 5, and 7 days post-inoculation (dpi). The enhanced enzymatic activity was observed in the pathogen-inoculated leaf samples as compared to uninoculated (healthy control). Among inoculated genotypes, the resistant one exhibited a significant change in enzymatic activity, total phenolic content, MDA, proline, GSH, H2O2, and AA, compared to the susceptible genotype. The study also examined the isozyme pattern of antioxidant enzymes at various stages of B. cinerea inoculation. Results from scanning electron microscopy (SEM) and Fourier transform infrared (FTIR) spectroscopy revealed that BGM had a more significant impact on susceptible genotypes compared to resistant ones when compared to the control (un-inoculated). In addition, SEM and FTIR spectroscopy analyses confirmed the greater severity of BGM on susceptible genotypes compared to their resistant counterparts. Our results suggest the role of antioxidant enzymes and other metabolites as defence tools and biochemical markers to understand compatible and non-compatible plant-pathogen interactions better. The present investigation will assist future plant breeding programs aimed at developing resistant varieties.

Estimation of genetic diversity using seed storage protein (SSP) profiling in wild and cultivated species of Cicer L

The narrow genetic diversity of chickpea is a serious impediment to modern cultivar creation. Seed storage proteins (SSPs) are stable and have minimal or no degradation when subjected to isolation and SDS-PAGE. We have characterized SSPs of 436 chickpea genotypes, belonging to nine annual Cicer species, originated from 47 countries by SDS-PAGE and determined the extent of genetic diversity in chickpea through clustering. Based on scoring, a total of 44 bands (10 to 170kDa) were identified, which were all polymorphic. The least appeared protein bands were 11, 160 and 170kDa where band of 11 and 160kDa was present exclusively in wild type. Five bands were present in < 10% of genotypes. Bands appeared in 200-300 genotypes were suggested less polymorphic, on contrary bands present in 10-150 genotypes were suggested more polymorphic. Polymorphism of protein bands in context to their potential functions reported in literature were explored and suggested that the glubulins were most and glutelins were least abundant, whereas albumins with their known role in stress tolerance can be used as marker in chickpea breeding. Cluster analysis produced 14 clusters, interestingly three clusters contained only Pakistani genotypes and thus Pakistani genotypes appeared as a separate entity from the rest of the genotypes. Our results indicate that SDS-PAGE of SSPs is a powerful technique in determining the genetic diversity plus it is easily adaptable, due to its cost effectiveness in comparison to other genomics tools.

Characterization in F1 generation of Kabuli, Desi and wild Cicer genotypes for plant traits

It is important to understand the magnitude of the changes in variation created by the crossbreeding of cultivated chickpea varieties with a narrow genetic base, desi and kabuli types, and C. reticulatum and C. echinospermum, which are closely related species to cultivated chickpeas. The study was conducted at Dicle University, Agriculture of Faculty, Diyarbakir, Turkiye, in 2023. The experiment laid out in randomized complete block design with three replications. Desi ? kabuli, kabuli ? kabuli and kabuli ? wild Cicer F1 crosses and their parents were evaluated to estimate the heterosis, heterobeltiosis, potence ratios and heritability for the days to first flowering, leave traits, plant height, number of nodes per plant, flower and foliage color, anthocyanin pigmentation and plant growth habit. The differences among genotypes were significant for all these traits. The magnitude of heterosis was differed between traits and crosses. For days to first flowering, heterosis for early crosses ranged from -2.56% to -7.13%. Azkan (lately) ? C. reticulatum (medium early) (-14.06%) had the highest negative heterobeltiosis for days to first flowering. The high heritability was estimated for days to first flowering, days from emergence to podded, and days from flowering to podded. The estimated values of potence ratios in most F1 crosses were negative for the number of days to first flowering. In crosses between the white-flowered parents Azkan, Gokce, ILC 533, ILC 1929 and ILC 482 and the pink-flowered parents JG 11, ICCV 96029, ICCV 03107, Black and wild Cicer species the F1s were pink. When the white-flowered the kabuli parents to the pink-flowered the desi parents were crossed, the F1s showed the anthocyanin pigmentation on various plant parts.

CicerSpTEdb2.0: An Upgrade of Cicer Species Transposable Elements Database.

To meet the critical demand of LTR-RTs data-driven research, we updated the CicerSpTEdb database to version 2.0, which includes more accurate intact LTR-RT elements with annotation of internal domains. We also added the ability to BLAST against TEs of Cicer species. As a result, 3701 intact LTR-RTs were detected in the studied genomes, including 2840 Copia and 861 Gypsy elements. Of the 3701 intact LTR-RTs, 588 were in C. arietinum, including 475 Copia and 113 Gypsy. While 1373 were detected in C. reticulatum, including 1041 Copia and 332 Gypsy. Furthermore, 1740 were found in C. echinospermum, including 1324 Copia and 416 Gypsy. Based on LTR-RT clades, the analysis classified the 3701 identified intact LTR-RTs in the studied genomes as Ale (850), SIRE (740), unknown (455), Ikeros (323), Reina (290), Tork (290), Ivana (282), Tekay (197), Athila (128), TAR (99), CRM (31), and Ogre (16) elements. The newly updated CicerSpTEdb2.0 will be a valuable resource for TEs of Cicer species and their comparative genomics.Database URL: http://cicersptedb.easyomics.org/index.php.

Molecular assessment of wild and cultivated Cicer species using ISSR markers

Characterization of germplasm is one of the prerequisites for utilizing it in crop improvement programs and this requires understanding of genetic relationship between the wild and the cultivar genotypes. For this purpose, we investigated genetic relationships between 12 wild and cultivated accessions of chickpea using ISSR markers. ISSR amplification result shows 123 band out of the 250 bands i.e, (49.2%) bands were polymorphic. The dendrogram classified all twelve accessions into two distinct major clusters A and B, with about 21% of the similarity coefficient value. Based on 20 ISSR primers, Jaccard's similarity indices between pairs of accessions ranged from 0.119 to 1.00. UPGMA dendrogram revealed that the cultivar genotype ICC2210 (Kabuli) from Algeria and the wild genotype ICC17156 (Desi) from Turkey had the lowest similarity indices. According to Principal Component Analysis (PCA), the top three principal components, with Eigen values of 5.40, 3.35, and 2.61, are the most informative, accounting for 61.33% of overall genetic variation. All the accessions were divided into three groups, which covered seven (58.33%) of the total, although five (41.66%) were scattered on the plot. The PCA results resemble to the cluster and similarity coefficient analysis although some deviations have been observed. This information could be useful in breeding strategies for the improvement of chickpea accessions.

Intraspecific versus interspecific crosses for superior progeny in Cicer species

AbstractBoth intraspecific and interspecific crosses are a well‐known breeding strategies to generate variations or assemble desirable traits in economically important plants. Interspecific crosses have been mined to improve resistance to (a)biotic stresses in chickpea (Cicer arietinum L.) in a limited number of research studies but have never been crosschecked for yield and yield criteria in intraspecific versus interspecific crosses. Comparison of superior progeny or superior recombinant inbred lines (RILs) and better progeny than their best parent for yield, yield criteria, and resistance to (a)biotic stresses in intraspecific versus interspecific crosses was the objectives of this study. Also, associations between superior progeny and genetic distance based on simple sequence repeat (SSR) markers were assessed among annual Cicer species including cultivated chickpea, C. reticulatum Ladiz. and C. echinospermum P.H. Davis. Each two genotypes of C. reticulatum and C. echinospermum were crossed with three genotypes of cultivated chickpea. Not only superior progeny for yield and yield criteria, but also superior RILs that were cold tolerant were detected higher in interspecific crosses than in intraspecific crosses. On the other hand, plant height, first pod height, and seed size were higher in intraspecific crosses than in interspecific crosses, indicating that seed size and traits suitable for combine harvest can be increased via intraspecific crosses. A significant association was found between superior progeny and genetic distance among Cicer species. It was concluded that interspecific crosses in Cicer species may increase yield and resistance to (a)biotic stresses, whereas intraspecific crosses may increase plant height and seed size.

Identification of promising chickpea interspecific derivatives for agro-morphological and major biotic traits

The wild Cicer species is well-known for having climate-resilient and productivity-enhancing traits of interest. Therefore, wide hybridization could be used as a realistic strategy for introgressing prospective traits from wild species into the cultivated gene pool. The present study was, thus, undertaken to evaluate F7 chickpea interspecific derivatives derived from Cicer reticulatum Ladiz. and C. echinospermum P. H. Davis wild annual Cicer species. As a result, a set of six interspecific crosses were advanced using the single seed descent (SSD) method of breeding. The F7 generation of these crosses was assessed in two diverse agro-ecological regions of India. The data revealed a wide range of variation with respect to seed yield and its important component traits, which resulted in the identification of the most promising derivatives carrying desirable characters as indicated by range, mean, and coefficient of variation. Further, fruitful heterosis was also estimated as promising selection criteria for identifying superior lines for earliness and high seed yield, including resistance against prevailing stresses (ascochyta blight, botrytis gray mold, dry root rot, and fusarium wilt). The superior derivatives carrying putative characters could be recommended for further breeding and selection of genetic materials for developing suitable genotypes.

Exploring Chickpea Germplasm Diversity for Broadening the Genetic Base Utilizing Genomic Resourses

Legume crops provide significant nutrition to humans as a source of protein, omega-3 fatty acids as well as specific macro and micronutrients. Additionally, legumes improve the cropping environment by replenishing the soil nitrogen content. Chickpeas are the second most significant staple legume food crop worldwide behind dry bean which contains 17%–24% protein, 41%–51% carbohydrate, and other important essential minerals, vitamins, dietary fiber, folate, β-carotene, anti-oxidants, micronutrients (phosphorus, calcium, magnesium, iron, and zinc) as well as linoleic and oleic unsaturated fatty acids. Despite these advantages, legumes are far behind cereals in terms of genetic improvement mainly due to far less effort, the bottlenecks of the narrow genetic base, and several biotic and abiotic factors in the scenario of changing climatic conditions. Measures are now called for beyond conventional breeding practices to strategically broadening of narrow genetic base utilizing chickpea wild relatives and improvement of cultivars through advanced breeding approaches with a focus on high yield productivity, biotic and abiotic stresses including climate resilience, and enhanced nutritional values. Desirable donors having such multiple traits have been identified using core and mini core collections from the cultivated gene pool and wild relatives of Chickpea. Several methods have been developed to address cross-species fertilization obstacles and to aid in inter-specific hybridization and introgression of the target gene sequences from wild Cicer species. Additionally, recent advances in “Omics” sciences along with high-throughput and precise phenotyping tools have made it easier to identify genes that regulate traits of interest. Next-generation sequencing technologies, whole-genome sequencing, transcriptomics, and differential genes expression profiling along with a plethora of novel techniques like single nucleotide polymorphism exploiting high-density genotyping by sequencing assays, simple sequence repeat markers, diversity array technology platform, and whole-genome re-sequencing technique led to the identification and development of QTLs and high-density trait mapping of the global chickpea germplasm. These altogether have helped in broadening the narrow genetic base of chickpeas.

Kök lezyon nematodlarının (Pratylenchus thornei) nohut bitkisinin rhizobium bakterileri üzerinde etkisi

Chickpea (Cicer arietinum) is one of the most significant legume crops and supply high-quality protein for human nutrition. legume crops such as chickpea are important agriculturally because of their symbiotic ability to nitrogen fixation with specific soil bacteria. Legumes like chickpea depend on nitrogen provided by the activity to grow, but these rhizobium bacteria are affected by plant-parasitic nematodes that cause less activity and decrease the number of nodules in the chickpea plant. The root-lesion nematodes (Pratylenchus thornei) are common and economically important pests described as one of the major limiting factors in agriculture and the growing chickpea field in the world. In this study, the effects of this nematode on the number of rhizobia (nodules) and rhizobium bacteria activity were assessed in both wild and domesticated accession of Cicer species under laboratory conditions. We inoculated all Cicer accession with the Mesorhizobium bacteria and with one species of the genus Pratylenchus (P. thornei). The result showed that P. thornei has a negative impact on the number of nodules and the activity of rhizobium bacteria. Nematode infection on chickpea caused decreased nodulation. Where, nematode infected plant formed 4-8 nodules/root and less nodule number than an uninfected plant.

Kök Lezyon Nematodlarının (Pratylenchus thornei (Sher et Allen) Pratylenchus neglectus (Rensch) Filipjev &amp; Schuurmans Stekhoven (Tylenchida: Pratylenchidae) ve Soğan-sak Nematodu Ditylenchus dipsaci (Kühn, 1857) (Tyleneida) 'nın Nohut Yetiştirme Alanlarında Dikey Dağılımı

Investigation of the vertical distribution of three plant-parasitic nematodes was conducted in two southeastern (Şanlıurfa) and central Anatolia (Ankara) Turkey chickpea fields during 2015/2016 and 2016/2017 growing season. Twelve accessions of wild Cicer species representing three Cicer species (Cicer reticulatum L. and C. echinospermum L.) were used in the experiments for it. Soil samples were collected around the plant roots at a 10-20 cm and 20-30 cm depth by using an auger at each site. Maximum population densities of the root-lesion nematodes (Pratylenchus thornei (Sher et Allen) and (Pratylenchus neglectus (Rensch) Filipjev &amp;amp; Schuurmans) were observed at the depth of 20-30 cm, pod filling stage, and harvest time on most sampling. Also, the population density of root-lesion nematodes at the depths of 20-30 cm was observed as higher than Ditylenchus dipsaci (Kühn, 1857) (Tylenchida: Anguinidae) in the chickpea field. Population density of root-lesion nematodes was positively correlated with the contents of depth, site, time sampling, species chickpea, and there was determined significant difference between soil depth and population density of nematodes in both sites statistically.

Minerals, vitamins, protein and amino acids in wild Cicer species and pure line chickpea genotypes selected from a local population

Minerals, vitamins, protein and amino acids in wild Cicer species and pure line chickpea genotypes selected from a local population

The complete chloroplast genome sequence of Cicer echinospermum, genome organization and comparison with related species

The Cicer genus, which has high agronomical importance, belongs to the Leguminosae family, and it comprises of 9 annual and 35 perennial species. Chloroplast (cp) DNA provides a detailed information for evolutionary and agronomic improvement studies. Due to high evolutionary conservation in its gene content and genomic organization, cpDNA is extremely useful for identification of taxonomic and phylogenetic relationships. In this study, we have constructed the complete chloroplast genome sequence of Cicer echinospermum, compared it with the cultivated type (Cicer arietinum), and re-examined the Cicers’ phylogenetic structure based on their cpDNAs among other legume species. We determined the chloroplast genome of Cicer echinospermum to be 126,713 bp in length with 83,129 bp of LSC, 13,288 bp of SSC and 30,296 bp of an IR region. This genome encodes 116 genes, 79 of which are protein coding, 33 tRNAs, and 4 rRNAs. Furthermore, our bioinformatic analysis revealed that this chloroplast genome has experienced an IR-loss in the evolutionary process like other IRLC family members and had undergone ∼21 kb inversion with respect to the Cicer arietinum. The result of the comparative analysis indicate that some regions showed certain nucleotide diversity, as in ycf1 and ycf2, which might be useful as potential markers for identification of Cicer genus. In the phylogenetic tree, C. arietinum and C. echinospermum clustered together among other legumes and confirmed the topology of Cicer species. These new genomic data are not only beneficial to elucidate phylogenetic relationships, but also provide information to develop and improve economically important crops through genetic engineering.

The Complete Chloroplast Genome Sequence of Cicer bijugum, Genome Organization, and Comparison with Related Species

BackgroundChickpea is one of Turkey's most significant legumes, and because of its high nutritional value, it is frequently preferred in human nourishment.Chloroplasts, which have their own genetic material, are organelles responsible for photosynthesis in plant cells and their genome contains non-trivial information about the molecular features and evolutionary process of plants.ObjectiveCurrent study aimed at revealing complete chloroplast genome sequence of one of the wild type Cicer species, Cicer bijugum, and comparing its genome with cultivated Cicer species, Cicer arietinum, by using bioinformatics analysis tools. Except for Cicer arietinum, there has been no study on the chloroplast genome sequence of Cicer species.Therefore, we targeted to reveal the complete chloroplast genome sequence of wild type Cicer species, Cicer bijugum, and compare the chloroplast genome of Cicer bijugum with the cultivated one Cicer arietinum.MethodsIn this study, we sequenced the whole chloroplast genome of Cicer bijugum, one of the wild types of chickpea species, with the help Next Generation Sequencing platform and compared it with the chloroplast genome of the cultivated chickpea species, Cicer arietinum, by using online bioinformatics analysis tools.ResultsWe determined the size of the chloroplast genome of C. bijugum as 124,804 bp and found that C. bijugum did not contain an inverted repeat region in its chloroplast genome. Comparative analysis of the C. bijugum chloroplast genome uncovered thirteen hotspot regions (psbA, matK, rpoB, rpoC1, rpoC2, psbI, psbK, accD, rps19, ycf2, ycf1, rps15, and ndhF) and seven of them (matK, accD, rps19, ycf1, ycf2, rps15 and ndhF) could potentially be used as strong molecular markers for species identification. It has been determined that C. bijugum was phylogenetically closer to cultivated chickpea as compared to the other species.ConclusionIt is aimed that the data obtained from this study, which is the first study in which whole chloroplast genomes of wild chickpea species were sequenced, will guide researchers in future molecular, evolutionary, and genetic engineering studies with chickpea species.

Molecular Assessment of Wild and Cultivated Cicer Species Using Issr Markers

Molecular Assessment of Wild and Cultivated Cicer Species Using Issr Markers

CicerSpTEdb: A web-based database for high-resolution genome-wide identification of transposable elements in Cicer species.

Recently, Cicer species have experienced increased research interest due to their economic importance, especially in genetics, genomics, and crop improvement. The Cicer arietinum, Cicer reticulatum, and Cicer echinospermum genomes have been sequenced and provide valuable resources for trait improvement. Since the publication of the chickpea draft genome, progress has been made in genome assembly, functional annotation, and identification of polymorphic markers. However, work is still needed to identify transposable elements (TEs) and make them available for researchers. In this paper, we present CicerSpTEdb, a comprehensive TE database for Cicer species that aims to improve our understanding of the organization and structural variations of the chickpea genome. Using structure and homology-based methods, 3942 C. echinospermum, 3579 C. reticulatum, and 2240 C. arietinum TEs were identified. Comparisons between Cicer species indicate that C. echinospermum has the highest number of LTR-RT and hAT TEs. C. reticulatum has more Mutator, PIF Harbinger, Tc1 Mariner, and CACTA TEs, while C. arietinum has the highest number of Helitron. CicerSpTEdb enables users to search and visualize TEs by location and download their results. The database will provide a powerful resource that can assist in developing TE target markers for molecular breeding and answer related biological questions.Database URL: http://cicersptedb.easyomics.org/index.php

Novel Sources of Tolerance to Aluminium Toxicity in Wild Cicer (Cicer reticulatum and Cicer echinospermum) Collections.

In acid soils, the toxic form of aluminium, Al3+, significantly inhibits root growth and elongation, leading to less water and nutrient uptake. Previous research had shown differential Al toxicity tolerance among cultivated Cicer arietinum L. (chickpea); however, the potential for developing tolerant cultivars is limited by the narrow genetic diversity of cultivated chickpeas. Recent collections from Turkey of wild Cicer species, Cicer reticulatum, and Cicer echinospermum, have increased the available gene pool significantly, but there has been no large-scale screening of wild Cicer for acid tolerance or Al3+ toxicity tolerance. This study evaluated 167 wild Cicer and 17 Australian chickpea cultivars in a series of screenings under controlled growth conditions. The pH of 4.2 and Al concentrations of 15 and 60 μM Al were selected for large-scale screening based on dose response experiments in a low ionic strength nutrient solution. The change in root length showed better discrimination between tolerant and sensitive lines when compared with shoot and root dry weights and was used as a selection criterion. In a large-scale screening, 13 wild Cicer reticulatum accessions had a higher root tolerance index (≥50%), and eight had higher relative change in root length (≥40%) compared with PBA Monarch, which showed greater tolerance among the Australian domestic cultivars screened. In general, C. reticulatum species were found to be more tolerant than C. echinospermum, while genetic population groups Ret_5, Ret_6, and Ret_7 from Diyarbakir and Mardin Province were more tolerant than other groups. Among C. echinospermum, Ech_6 from the Siv-Diyar collection site of the Urfa Province showed better tolerance than other groups. In this first detailed screening of aluminium toxicity tolerance in the new wild Cicer collections, we identified accessions that were more tolerant than current domestic cultivars, providing promising germplasm for breeding programs to expand chickpea adaptation to acid soils.