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

Nohut (Cicer arietinum L.) Genetik Kaynaklarının IMI Grubu Herbisitlere Dayanıklılık ve Morfolojik Özelliklerinin Belirlenmesi

Bu çalışma, nohut genetik kaynaklarında imidazolinone grubu herbisitlere dayanıklılık için genetik varyasyonun belirlenmesi amacıyla, 2019-2020 yıllarında GAP Tarımsal Araştırma Enstitüsü Müdürlüğü’ne ait Koruklu-Talat Demirören Araştırma İstasyonu’nda yürütülmüştür. Araştırmada bitki materyali olarak kültürü yapılan nohut türünün tek yıllık yabani formlarına ait, Güneydoğu Anadolu Bölgesi’nden toplanan 238 adet nohut genotipi (165 Cicer reticulatum, 72 adet Cicer echinospermum, 1 adet Cicer arietinum L.) kullanılmıştır. Araştırma sonucunda seçilen 15 genotip kendi aralarında değerlendirildiğinde bütün parametreler (100 tohum ağırlığı hariç) istatistiki olarak önemli (p<0.01) bulunmuştur. IMI uygulaması genotiplerde çiçeklenme ve olgunlaşma sürelerini uzatmıştır. IMI uygulanan genotiplerde bitki taç genişliği ortalama 8.01 cm2 olurken kontrolde 19.78 cm2 olmuştur. Uygulama yapılan genotiplerde verim ortalaması 71.60 kg/da iken kontrollerde ortalama 287.34 kg/da olmuştur.

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.

Identification of sources of Sclerotinia sclerotiorum resistance in a collection of wild Cicer germplasm

Sclerotinia sclerotiorum is an important fungal pathogen of chickpea (Cicer arietinum L.) and it can cause yield losses up to 100%. The wild progenitors are much more diverse than domesticated chickpea and this study describes how this relates to S. sclerotiorum resistance. Initially, the pathogenicity of nine Australian S. sclerotiorum isolates was examined on three Cicer lines to develop a robust phenotyping assay and significant differences in isolate aggressiveness were identified with 6 isolates being classed as highly aggressive and 3 as moderately aggressive. We identified two S. sclerotiorum isolates, CU8.20 and CU10.12, to be highly aggressive and moderately aggressive, respectively. A subsequent phenotyping assay was conducted using the two isolates to evaluate 86 wild Cicer accessions (Cicer reticulatum and Cicer echinospermum) and two C. arietinum varieties for resistance to S. sclerotiorum. A subset of 12 genotypes was further evaluated, and subsequently, two wild Cicer accessions with consistently high levels of resistance to S. sclerotiorum were examined using the initially characterised nine isolates. Wild Cicer accessions Karab_084 and Deste_063 demonstrated consistent partial resistance to S. sclerotiorum. There were significant differences in responses to S. sclerotiorum across wild Cicer collection sites. The Cermik, Karabahce and Destek sites’ responses to the aggressive isolate CU8.20 ranged from resistant to susceptible, highlighting an interaction between isolate genotype and chickpea collection site for sclerotinia stem rot resistance. This is the first evidence of partial stem resistance identified in wild Cicer germplasm, which can be adopted in chickpea breeding programs to enhance S. sclerotiorum resistance in future chickpea varieties.

Variation of Cicer Germplasm to Manganese Toxicity Tolerance

After aluminum, manganese toxicity is the most limiting factor for crops grown in acidic soils worldwide. But overall, research on Mn toxicity is still limited. The poor acid tolerance of chickpea may be related to Mn toxicity, but there has been no previous screening of chickpea germplasm (nor in its wild Cicer relatives, Cicer reticulatum and Cicer echinospermum) for tolerance to Mn toxicity. A screening technique was developed for tolerance to Mn toxicity using three released cultivars of chickpea (Cicer arietinum L), Ambar, PBA HatTrick, and PBA Striker; one accession each of C. reticulatum and C. echinospermum; and lupin (Lupinus angustifolius) as a Mn-tolerant check, with eight Mn concentrations of 2, 25, 50, 100, 150, 200, 250, and 500 μM Mn as MnSO4 in a low-ionic-strength nutrient solution. The plants were harvested at 14 and 28 days after Mn treatments. The nutrient uptake in shoots (young, old leaves, and the rest of the shoot) and roots was investigated. The best discrimination between tolerant and intolerant Cicer genotypes based on relative shoot dry weight, root dry weight, total root length, and scoring of toxicity symptoms was achieved at 150 μM Mn after 14 days of growth in Mn solution. Among the chickpea cultivars, the greater relative plant growth (both shoot and root) of Ambar and PBA Striker at 100–200 μM Mn contrasted with that of PBA HatTrick, while the C. echinospermum accession was more tolerant to Mn toxicity than C. reticulatum. Manganese tolerance in both domestic cultivars and wild accessions was associated with internal tolerance to excess Mn following greater uptake of Mn and translocation of Mn from roots to shoots.

Identification of novel sources of resistance to ascochyta blight in a collection of wild Cicer accessions

Chickpea production is constrained worldwide by the necrotrophic fungal pathogen Ascochyta rabiei, the causal agent of ascochyta blight (AB). In order to reduce the impact of this disease, novel sources of resistance are required in chickpea cultivars. Here, we screened a new collection of wild Cicer accessions for AB resistance and identified accessions resistant to multiple, highly pathogenic isolates. In addition to this, analyses demonstrated that some collection sites of Cicer echinospermum harbour predominantly resistant accessions, knowledge that can inform future collection missions. Furthermore, a genome-wide association study identified regions of the Cicer reticulatum genome associated with AB resistance and investigation of these regions identified candidate resistance genes. Taken together, these results can be utilised to enhance the resistance of chickpea cultivars to this globally yield-limiting disease.

Characterization of chickpea gene pools for nutrient concentrations under agro-climatic conditions of North-Western Himalayas

Chickpea is one of the most important nutritious grain legume crops in the world. There is limited information available on micro- and macro-nutrients in chickpea. Therefore, an effort was made to evaluate a set of 40 chickpea genotypes belonging to all the gene pools including cultivated (Cicer arietinum) as well as wild, Cicer reticulatum from the primary gene pool, Cicer echinospermum from the secondary gene pool and Cicer microphyllum from the tertiary gene pools. Concentration in the seed of the micro- (Zn, Fe, Cu and Mn) and macro-nutrients (Ca, Mg and K) was studied. Substantial variation was observed among different gene pools for the concentration of all the nutrients. The cultivated chickpea exhibited higher seed Cu, Mn, Mg and Ca than wilds indicating positive domestication effect, whereas wild crop relatives were found to have higher levels than cultivated chickpeas for seed Zn, Fe and K concentrations. While comparing desi-type chickpeas with Kabulis, it was revealed that desi types possessed more Zn, Cu, Ca and Mg than Kabulis but reverse was true for seed Fe, Mn and K. Among different desi types (desi brown, desi green and desi black), desi brown types were generally associated with higher mineral nutrient levels. The present study led to the identification of most promising genotypes for different seed micro- and macro-nutrients. These promising lines may serve as genetic resources useful in gene discovery programmes and for alleviating malnutrition or hidden hunger in the developing world.