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

Cicer turcicum: A New Cicer Species and Its Potential to Improve Chickpea

Genetic resources of the genus Cicer L. are not only limited when compared to other important food legumes and major cereal crops but also, they include several endemic species with endangered status based on the criteria of the International Union for Conservation of Nature. The chief threats to endemic and endangered Cicer species are over-grazing and habitat change in their natural environments driven by climate changes. During a collection mission in east and south-east Anatolia (Turkey), a new Cicer species was discovered, proposed here as C. turcicum Toker, Berger & Gokturk. Here, we describe the morphological characteristics, images, and ecology of the species, and present preliminary evidence of its potential utility for chickpea improvement. C. turcicum is an annual species, endemic to southeast Anatolia and to date has only been located in a single population distant from any other known annual Cicer species. It belongs to section Cicer M. Pop. of the subgenus Pseudononis M. Pop. of the genus Cicer L. (Fabaceae) and on the basis of internal transcribed spacer (ITS) sequence similarity appears to be a sister species of C. reticulatum Ladiz. and C. echinospermum P.H. Davis, both of which are inter-fertile with domestic chickpea (C. arietinum L.). With the addition of C. turcicum, the genus Cicer now comprises 10 annual and 36 perennial species. As a preliminary evaluation of its potential for chickpea improvement two accessions of C. turcicum were field screened for reproductive heat tolerance and seeds were tested for bruchid resistance alongside a representative group of wild and domestic annual Cicer species. C. turcicum expressed the highest heat tolerance and similar bruchid resistance as C. judaicum Boiss. and C. pinnatifidum Juab. & Spach, neither of which are in the primary genepool of domestic chickpea. Given that C. arietinum and C. reticulatum returned the lowest and the second lowest tolerance and resistance scores, C. turcicum may hold much potential for chickpea improvement if its close relatedness supports interspecific hybridization with the cultigen. Crossing experiments are currently underway to explore this question.

Transferability of newly developed genomic lentil SSR markers to Cicer species

Development of microsatellite markers requires a great effort, expertise and research infrastructure. Therefore, cross genera or species transferability of already developed markers has constituted a significant alternative. In this study, transferability of newly developed 53 genomic lentil (Lens culinaris Medik.) SSR markers to 32 accessions of Cicer species including C. arietinum L., C. bijugum K.H. Rech., C. echinospermum P.H. Davis, C. reticulatum Ladiz., C. pinnatifidium Jaub. and Sp., C. anatolicum Alef. was investigated. Of these markers, 33.09% were found to be transferrable to C. arietinum, 37.7% to C. echinospermum, 35.8% to C.reticulatum, 39.6% to C. bijugum, 18.8% to C. pinnatifidium and finally 15.09% to C. anatolicum species. From these markers, 11.3% were found to be transferable to all Cicer species. Transferable 6 polymorphic SSR primers had 19 alleles in 32 accessions with a mean of 3.16 alleles per locus. Polymorphic information content (PIC) values varied between 0.375 (Lc_MCu21) and 0.587 (Lc_MCu53) with an average value of 0.528. Transferable SSR markers were thought to provide significant contributions to inter and intra-specific studies in Cicer species.

Unveiling of suppressed genes in interspecific and backcross populations derived from mutants of Cicer species

Although many interspecific crosses in Cicer species have successfully been carried out to improve the population in cultivated chickpea (Cicer arietinum L.), interspecific and backcross populations derived from mutants of Cicer species have not been studied for revealing suppressed genes responsible for heterotic effects and transgressive segregations. Therefore, the study aimed (i) to estimate heterosis (here, offspring superior to mid-parent value) and heterobeltiosis (offspring superior to better parent) for yield and yield components in the F1; (ii) to decipher transgressive segregation (extreme phenotypes) in F2 and backcross populations; and (iii) to reveal suppressed genes in interspecific and backcross populations (C. arietinum × F1 and C. reticulatum Ladiz.× F1) derived from interspecific crosses between a mutant of C. arietinum and a mutant of C. reticulatum. Heterobeltiosis was found for seed and biological yields, number of branches, and number of pods per plant in F1 progeny; heterosis was determined for the additional traits of 100-seed weight and harvest index. Heterobeltiosis and heterosis for yield and yield components in F1 progeny prompted transgressive segregation for these traits in F2 and backcross populations. In the backcrosses, C. arietinum × F1 crosses produced greater seed size and more pods per plant than C. reticulatum × F1, suggesting that C. arietinum × F1 backcrossing could improve yield components and lead to large seed size. Most of the high-yielding progeny in F2 and C. arietinum × F1 populations had double-podded nodes. It was concluded that the suppressed genes in a mutant of C. reticulatum or a mutant of C. arietinum played a crucial role in increasing transgressive segregations and allowing the cultivated chickpea to gain increased yield and yield components as well as large seed size.

Small-Seeded Legumes as a Novel Food Source. Variation of Nutritional, Mineral and Phytochemical Profiles in the Chain: Raw Seeds-Sprouted Seeds-Microgreens

Growing public concerns about health haves prompted the search for novel food sources. The study is focused on the seeds, sprouted seeds and microgreens of Trifolium pratense, T. medium, Medicago sativa, M. lupulina, Onobrychis viciifolia, Astragalus glycyphyllos and A. cicer species as a potential source of value-added food ingredientsr. The samples were analysed for nutritional (wet chemistry, standard methods) and mineral (atomic absorption spectroscopy, UV-Vis spectrophotometry) profiles, isoflavones (ultra-performance liquid with diode array detector –UPLC-DAD), coumestrol (UPLC-DAD), condensed tannins (CT) (vanillin-H2SO4 assay) and triterpene saponins (UPLC with triple-stage quadrupole MS). In our study, each species displayed high, but species-dependent nutritional, mineral and phytochemical value. All counterparts of legumes were mineral and protein rich. A. glycyphyllos samples, especially seeds, were abundant in iron. Trifolium spp. were found to be important sources of isoflavones, Medicago spp. of coumestrol and saponins, and O. viciifolia of CT. The protein and phytochemical contents increased and total carbohydrates decreased from seeds to microgreens.Our findings proved for the first time that seeds, sprouted seeds, and especially microgreens of small-seeded legumes are promising new sources of ingredients for fortification of staple foods with bioactive compounds, minerals and nutrients.

Morpho-molecular characterization of landraces/wild genotypes of Cicer for Biotic/ Abiotic stresses

Chickpea is one of the most important pulse crops in the world. However, chickpea productivity is not high enough to fulfill the requirements of an ever-increasing demand. One of the major constraints in the chickpea improvement is the narrow genetic base in the cultivated chickpea (Cicer arietinum L) and its sexual incompatibility with other Cicer species. Knowledge of molecular characterization, genetic diversity, and relatedness in the germplasm is a prerequisite for varietal registration, protection and overall crop improvement. The present study reports molecular characterization of 75 genotypes using 46 STMS markers. All the STMS loci were found to be highly polymorphic. A total of 132 alleles were found with an average of 2.87 per locus. The highest numbers of alleles were observed with marker TA-21. A cluster analysis arranged these 75 genotypes in 7 clusters. The genotypes ICRISAT 3073 and Pusa 212 showed remarkable genetic similarity (0.796) and the largest genetic distance was observed between C. reticulatum wild-1 and CSG 9505 (0.547). The present analysis provides an insight into the interrelationship among the genotypes and highlights the requirement for effective supplementation of morphological data with additional molecular markers to efficiently unearth the genetic inter-relationship among the genotypes.