Genomic data of two chickpea populations sharing a potential Ascochyta blight resistance region

Chickpea (Cicer arietinum L.) is one of the most important crops worldwide and a valuable nutritional source. The availability of data from different genotypes and populations is important for the comprehension of the biology and trait control of chickpea. Tissue from young leaves was collected from adult plants and sequenced using an Illumina HiSeq X platform, which provided sequencing data for a total of 169 individuals from two different populations. Furthermore, functional annotation was performed with BLAST2GO software in a candidate region for resistance to Ascochyta blight, a devastating disease that produces huge yield reductions if the growth conditions are optimal for the fungus. A total of 273 different genes in a region spanning ∼4.67 Mb in chromosome 4 were fully annotated. The raw DNA sequences and functional annotation data can be reused by the scientific community for the analysis of different agronomic traits of interest in chickpea.

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.

Genomics-assisted genetics of complex region from chickpea chromosome 4 reveals two candidate genes for Ascochyta blight resistance

Ascochyta blight (AB) disease caused by the fungus Ascochyta rabiei is a major threat to global chickpea production. Molecular breeding for improved AB resistance requires the identification of robust fine-mapped QTLs/candidate genes and associated markers. Earlier, we identified three QTLs (qABR4.1, qABR4.2, and qABR4.3) for AB resistance on chickpea chromosome 4 by employing multiple quantitative trait loci sequencing strategy on an intra-specific (FLIP84-92C x PI359075) and an inter-specific (FLIP84-92C x PI599072) crosses derived recombinant inbred lines. Here, we report the identification of AB resistance providing candidate genes under the fine mapped qABR4.2 and qABR4.3 genomic region by combining genetic mapping, haplotype block inheritance, and expression analysis. The qABR4.2 region was narrowed down from 5.94Mb to ~800kb. Among 34 predicted gene models, a secreted class III peroxidase encoding gene showed higher expression in AB resistant parent after A. rabiei conidia inoculation. Under qABR4.3, we identified a frame-shift mutation in a cyclic nucleotide-gated channel CaCNGC1 gene leading to the truncated N-terminal domain in resistant accession of chickpea. This N-terminal domain of CaCNGC1 interacts with chickpea calmodulin. Thus, our analysis has revealed narrowed genomic regions and their associated polymorphic markers, CaNIP43 and CaCNGCPD1. These co-dominant markers significantly associate with AB resistance on qABR4.2 and qABR4.3 regions. Our genetic analysis revealed that the presence of resistant alleles for two major QTLs (qABR4.1 and qABR4.2) together provide AB resistance in the field while minor QTL qABR4.3 determines the degree of resistance. The identified candidate genes and their diagnostic markers will help in biotechnological and AB resistance introgression into farmers adapted local chickpea varieties.

Ascochyta Blight in Chickpea: An Update

Chickpea (Cicer arietinum L.), one of the most cultivated legumes worldwide, is crucial for the economy of several countries and a valuable source of nutrients. Yields may be severely affected by Ascochyta blight, a disease caused by the fungus Ascochyta rabiei. Molecular and pathological studies have not yet managed to establish its pathogenesis, since it is highly variable. Similarly, much remains to be elucidated about plant defense mechanisms against the pathogen. Further knowledge of these two aspects is fundamental for the development of tools and strategies to protect the crop. This review summarizes up-to-date information on the disease's pathogenesis, symptomatology, and geographical distribution, as well as on the environmental factors that favor infection, host defense mechanisms, and resistant chickpea genotypes. It also outlines existing practices for integrated blight management.

The relationship between natural rain intensity and Ascochyta blight in chickpea development

Ascochyta blight management strategy in chickpea standing crops in Australia is solely based on applying protective fungicides before a forecast rainfall event. Despite this, studies on the likely interaction between natural rain (as well as simulated rain) amount, duration and Ascochyta blight development are rare. This study was conducted to investigate the relationship between natural rain intensity (mm/h) and Ascochyta blight development. Infested chickpea residue were placed at the soil surface, and three pots of a susceptible chickpea cultivar were randomly placed on each side of the plot (total 12 pots and 36 plants), preceding a forecast rainfall event. Trap plants were transferred to a controlled temperature room after rain events. After a 48 h incubation period, trap plants were transferred to a glasshouse to allow lesion development. The number of lesions on all plant parts were counted after two weeks. Lesions developed in rain amounts as low as 1.4 mm and rain durations as short as 0.7 h. The number of lesions significantly increased with increasing rain amount. There was a positive effect of increasing rain duration and a negative effect of increasing wind speed. This study suggests that small rain amounts, shorter duration rains or a limited amount of primary inoculum are not barriers to conidial dispersal or host infection, and that the current value of a rainfallthreshold (2 mm) for conidial spread and host infection is not accurate for susceptible cultivars.

Effects of Host Plant Resistance and Fungicide Applications on Ascochyta Blight Symptomology and Yield of Chickpea

Ascochyta blight (AB), caused by the pathogen Ascochyta rabiei, is a major threat to chickpea production worldwide, causing major yield losses and decreasing quality. Control of AB requires integrating pest management options including resistant cultivars and fungicide applications. To address this, fungicides with different modes of action were evaluated on three chickpea cultivars with differing levels of susceptibility to AB under irrigated and dryland conditions in 2015 to 2017. The fungicides were applied once or twice and compared with a no-fungicide application control on AB score and yield. The mean grain yields across locations and years were 1,753, 1,283, and 981 kg/ha, with a corresponding AB mean score of 2.6, 3.2, and 3.3 on 0 to 7 scale (where 0 is no disease and 7 is completely dead) for the moderately resistant, moderately susceptible, and susceptible chickpea cultivars, respectively. Fungicide application was not enough to control disease throughout the season. The use of AB-resistant cultivars had the most significant impact on minimizing the disease and maximizing yield, irrespective of year and location. This study supports previous research indicating that planting AB-resistant chickpea cultivars is essential for disease control, regardless of the fungicides applied.

A Mechanistic Weather-Driven Model for Ascochyta rabiei Infection and Disease Development in Chickpea

Ascochyta blight caused by Ascochyta rabiei is an important disease of chickpea. By using systems analysis, we retrieved and analyzed the published information on A. rabiei to develop a mechanistic, weather-driven model for the prediction of Ascochyta blight epidemics. The ability of the model to predict primary infections was evaluated using published data obtained from trials conducted in Washington (USA) in 2004 and 2005, Israel in 1996 and 1998, and Spain from 1988 to 1992. The model showed good accuracy and specificity in predicting primary infections. The probability of correctly predicting infections was 0.838 and the probability that there was no infection when not predicted was 0.776. The model's ability to predict disease progress during the growing season was also evaluated by using data collected in Australia from 1996 to 1998 and in Southern Italy in 2019; a high concordance correlation coefficient (CCC = 0.947) between predicted and observed data was obtained, with an average distance between real and fitted data of root mean square error (RMSE) = 0.103, indicating that the model was reliable, accurate, and robust in predicting seasonal dynamics of Ascochyta blight epidemics. The model could help growers schedule fungicide treatments to control Ascochyta blight on chickpea.

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). 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 C. echinospermum harbor predominantly resistant accessions, knowledge that can inform future collection missions. Furthermore, a genome-wide association study identified regions of the C. reticulatum genome associated with AB resistance and investigation of these regions identified candidate resistance genes. Taken together, these results can be utilized to enhance the resistance of chickpea cultivars to this globally yield-limiting disease.

Fungal endophytes in Peperomia obtusifolia and their potential as inhibitors of chickpea fungal pathogens

Chickpea (Cicer arietinum L., Fabaceae) is the second most important legume after common bean (Phaseolus vulgaris L., Fabaceae) and third in production among the legumes grains worldwide. Ascochyta blight and Fusarium wilt are among the main fungal infections which cause the major losses of chickpea crop. In this work we report the phyto-pathogen controlling properties of 24 endophyte Phomopsis/Diaporthe isolates on the chickpea fungal pathogens Ascochyta rabiei, Fusarium oxysporum and Fusarium solani. The Phomopsis/Diaporthe strains were isolated amongst a total of 62 endophytic fungi from the aerial parts of the herbaceous perennial American plant Peperomia obtusifolia (Piperaceae) along with Fusarium, Septoria, Colletotrichum, Alternaria and Roussoella genera among others. Phomopsis/Diaporthe isolates were identified as Diaporthe infecunda (12 isolates), Diaporthe sackstoni (1 isolate), Diaporthe cf. brasiliensis (4 isolates) and Phomopsis cf. tuberivora (7 isolates). All the Phomopsis/Diaporthe strains antagonized A. rabiei strain AR2 with a mean of inhibition (% I) of 86.59 ± 1.49% in dual cultures. The metabolic characterization of the Phomopsis/Diaporthe strains showed groups in three clusters which were in agreement with the taxonomic identification. Bioautographic evaluation of organic extracts showed that those of D. cf. brasiliensis and D. infecunda were better as inhibitors. Strain Po 45 was one of the most active (cluster 1, 96.87% I), and its ethyl acetate extract inhibited A. rabiei growth in a bioautographic assay until at least 10 μg/mm applied showing a specific chromatographic band as the responsible of the A. rabiei inhibition.

Development of a sequence-characterized amplified region marker for detection of Ascochyta rabiei causing Ascochyta blight in chickpea

Ascochyta blight of chickpea is caused by Ascochyta rabiei (Pass.) Labr. which is primarily seedborne. For rapid detection and precise identification of A. rabiei, a sequence-characterized amplified region (SCAR) marker was developed for detection of genomic DNA and infected plant DNA. An SSR primer amplified monomorphic band was cloned in pGEM®-T easy vector and sequenced. The best primer pair was selected and validated on A. rabiei. The specificity and sensitivity of the SCAR-based marker designated as MBAR was evaluated using conventional PCR and real-time PCR. The marker produced consistently an amplicon size of 196 bp in all A. rabiei isolates tested. The sensitivity of the marker was 0.1 ng of genomic fungal DNA and 0.5 ng of plant DNA by conventional PCR and 0.5 pg of A. rabiei DNA and 1.0 pg of plant DNA by real-time PCR. This is the first SCAR marker having high specificity and sensitivity towards A. rabiei. The marker may be useful in detecting the pathogen before the disease appearance and in plant quarantine program to detect the pathogen in seed lots.

mQTL-seq and classical mapping implicates the role of an AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL) family gene in Ascochyta blight resistance of chickpea

Ascochyta blight (AB) caused by the fungal pathogen Ascochyta rabiei is a serious foliar disease of chickpea (Cicer arietinum L.). Despite many genetic studies on chickpea-Ascochyta interaction, genome-wide scan of chickpea for the identification of AB-associated quantitative trait loci (QTLs) and their gene(s) has not been accomplished. To elucidate narrow QTLs for AB resistance, here, we report the use of multiple QTL-sequencing approach on 2 sets of extreme AB phenotype bulks derived from Cicer intraspecific and interspecific crosses. Two major QTLs, qABR4.1 and qABR4.2, and a minor QTL, qABR4.3, were identified on assembled chickpea pseudomolecule 4. We narrowed qABR4.1 to a "robust region" at 4.568-4.618 Mb through mapping on a larger intraspecific cross-derived population and comparative analysis. Among 4 genes, the CaAHL18 gene showed higher expression under Ascochyta stress in AB resistant parent suggesting that it is the candidate gene under "robust qABR4.1." Dual-luciferase assay with CaAHL18 polymorphic cis-regulatory sequences showed that allelic variation is associated with higher expression. Thus, our findings on chickpea-Ascochyta interaction have narrowed down AB resistance associated QTLs on chickpea physical map. The narrowed QTLs and gene-associated markers will help in biotechnological and breeding programs for chickpea improvement.

Evidence and Consequence of a Highly Adapted Clonal Haplotype within the Australian Ascochyta rabiei Population

The Australian Ascochyta rabiei (Pass.) Labr. (syn. Phoma rabiei) population has low genotypic diversity with only one mating type detected to date, potentially precluding substantial evolution through recombination. However, a large diversity in aggressiveness exists. In an effort to better understand the risk from selective adaptation to currently used resistance sources and chemical control strategies, the population was examined in detail. For this, a total of 598 isolates were quasi-hierarchically sampled between 2013 and 2015 across all major Australian chickpea growing regions and commonly grown host genotypes. Although a large number of haplotypes were identified (66) through short sequence repeat (SSR) genotyping, overall low gene diversity (Hexp = 0.066) and genotypic diversity (D = 0.57) was detected. Almost 70% of the isolates assessed were of a single dominant haplotype (ARH01). Disease screening on a differential host set, including three commonly deployed resistance sources, revealed distinct aggressiveness among the isolates, with 17% of all isolates identified as highly aggressive. Almost 75% of these were of the ARH01 haplotype. A similar pattern was observed at the host level, with 46% of all isolates collected from the commonly grown host genotype Genesis090 (classified as "resistant" during the term of collection) identified as highly aggressive. Of these, 63% belonged to the ARH01 haplotype. In conclusion, the ARH01 haplotype represents a significant risk to the Australian chickpea industry, being not only widely adapted to the diverse agro-geographical environments of the Australian chickpea growing regions, but also containing a disproportionately large number of aggressive isolates, indicating fitness to survive and replicate on the best resistance sources in the Australian germplasm.

Transcription Factor Repertoire of Necrotrophic Fungal Phytopathogen Ascochyta rabiei: Predominance of MYB Transcription Factors As Potential Regulators of Secretome

Transcription factors (TFs) are the key players in gene expression and their study is highly significant for shedding light on the molecular mechanisms and evolutionary history of organisms. During host-pathogen interaction, extensive reprogramming of gene expression facilitated by TFs is likely to occur in both host and pathogen. To date, the knowledge about TF repertoire in filamentous fungi is in infancy. The necrotrophic fungus Ascochyta rabiei, that causes destructive Ascochyta blight (AB) disease of chickpea (Cicer arietinum), demands more comprehensive study for better understanding of Ascochyta-legume pathosystem. In the present study, we performed the genome-wide identification and analysis of TFs in A. rabiei. Taking advantage of A. rabiei genome sequence, we used a bioinformatic approach to predict the TF repertoire of A. rabiei. For identification and classification of A. rabiei TFs, we designed a comprehensive pipeline using a combination of BLAST and InterProScan software. A total of 381 A. rabiei TFs were predicted and divided into 32 fungal specific families of TFs. The gene structure, domain organization and phylogenetic analysis of abundant families of A. rabiei TFs were also carried out. Comparative study of A. rabiei TFs with that of other necrotrophic, biotrophic, hemibiotrophic, symbiotic, and saprotrophic fungi was performed. It suggested presence of both conserved as well as unique features among them. Moreover, cis-acting elements on promoter sequences of earlier predicted A. rabiei secretome were also identified. With the help of published A. rabiei transcriptome data, the differential expression of TF and secretory protein coding genes was analyzed. Furthermore, comprehensive expression analysis of few selected A. rabiei TFs using quantitative real-time polymerase chain reaction revealed variety of expression patterns during host colonization. These genes were expressed in at least one of the time points tested post infection. Overall, this study illustrates the first genome-wide identification and analysis of TF repertoire of A. rabiei. This work would provide the basis for further studies to dissect role of TFs in the molecular mechanisms during A. rabiei-chickpea interactions.

QTL mapping of early flowering and resistance to ascochyta blight in chickpea

In western Canada, chickpea (Cicer arietinum L.) production is challenged by short growing seasons and infestations with ascochyta blight. Research was conducted to determine the genetic basis of the association between flowering time and reaction to ascochyta blight in chickpea. Ninety-two chickpea recombinant inbred lines (RILs) developed from a cross between ICCV 96029 and CDC Frontier were evaluated for flowering responses and ascochyta blight reactions in growth chambers and fields at multiple locations and during several years. A wide range of variation was exhibited by the RILs for days to flower, days to maturity, node of first flowering, plant height, and ascochyta blight resistance. Moderate to high broad sense heritability was estimated for ascochyta blight reaction (H(2) = 0.14-0.34) and for days to flowering (H(2) = 0.45-0.87) depending on the environments. Negative correlations were observed among the RILs for days to flowering and ascochyta blight resistance, ranging from r = -0.21 (P < 0.05) to -0.58 (P < 0.0001). A genetic linkage map consisting of eight linkage groups was developed using 349 SNP markers. Seven QTLs for days to flowering were identified that individually explained 9%-44% of the phenotypic variation. Eight QTLs were identified for ascochyta blight resistance that explained phenotypic variation ranging from 10% to 19%. Clusters of QTLs for days to flowering and ascochyta blight resistances were found on chromosome 3 at the interval of 8.6-23.11 cM and on chromosome 8 at the interval of 53.88-62.33 cM.

WRKY domain-encoding genes of a crop legume chickpea (Cicer arietinum): comparative analysis with Medicago truncatula WRKY family and characterization of group-III gene(s)

The WRKY genes have been identified as important transcriptional modulators predominantly during the environmental stresses, but they also play critical role at various stages of plant life cycle. We report the identification of WRKY domain (WD)-encoding genes from galegoid clade legumes chickpea (Cicer arietinum L.) and barrel medic (Medicago truncatula). In total, 78 and 98 WD-encoding genes were found in chickpea and barrel medic, respectively. Comparative analysis suggests the presence of both conserved and unique WRKYs, and expansion of WRKY family in M. truncatula primarily by tandem duplication. Exclusively found in galegoid legumes, CaWRKY16 and its orthologues encode for a novel protein having a transmembrane and partial Exo70 domains flanking a group-III WD. Genomic region of galegoids, having CaWRKY16, is more dynamic when compared with millettioids. In onion cells, fused CaWRKY16-EYFP showed punctate fluorescent signals in cytoplasm. The chickpea WRKY group-III genes were further characterized for their transcript level modulation during pathogenic stress and treatments of abscisic acid, jasmonic acid, and salicylic acid (SA) by real-time PCR. Differential regulation of genes was observed during Ascochyta rabiei infection and SA treatment. Characterization of A. rabiei and SA inducible gene CaWRKY50 showed that it localizes to plant nucleus, binds to W-box, and have a C-terminal transactivation domain. Overexpression of CaWRKY50 in tobacco plants resulted in early flowering and senescence. The in-depth comparative account presented here for two legume WRKY genes will be of great utility in hastening functional characterization of crop legume WRKYs and will also help in characterization of Exo70Js.

In planta Identification of Putative Pathogenicity Factors from the Chickpea Pathogen Ascochyta rabiei by De novo Transcriptome Sequencing Using RNA-Seq and Massive Analysis of cDNA Ends

The most important foliar diseases in legumes worldwide are ascochyta blights. Up to now, in the Ascochyta-legume pathosystem most studies focused on the identification of resistance genes in the host, while very little is known about the pathogenicity factors of the fungal pathogen. Moreover, available data were often obtained from fungi growing under artificial conditions. Therefore, in this study we aimed at the identification of the pathogenicity factors of Ascochyta rabiei, causing ascochyta blight in chickpea. To identify potential fungal pathogenicity factors, we employed RNA-seq and Massive Analysis of cDNA Ends (MACE) to produce comprehensive expression profiles of A. rabiei genes isolated either from the fungus growing in absence of its host or from fungi infecting chickpea leaves. We further provide a comprehensive de novo assembly of the A. rabiei transcriptome comprising 22,725 contigs with an average length of 1178 bp. Since pathogenicity factors are usually secreted, we predicted the A. rabiei secretome, yielding 550 putatively secreted proteins. MACE identified 596 transcripts that were up-regulated during infection. An analysis of these genes identified a collection of candidate pathogenicity factors and unraveled the pathogen's strategy for infecting its host.

Accumulation and Biosynthesis of Solanapyrone Phytotoxins by Ascochyta rabiei

The biosynthesis of the phytotoxins solanapyrone A , B and C produced by the phytopathogenic fungus Ascochyta rabiei has been investigated. To optimize feeding conditons for the tracer experiments the growth of the fungus and the accumulation of the toxins in submers culture were determined. The accumulation kinetics revealed that formation of the toxins occurs in the stationary phase of the growth indicating that synthesis of solanapyrones follows a typical pattern of secondary metabolism. Incorporation experiments with sodium [1-14C]- and [2-13C]acetate were performed and the NMR-spectroscopically determined labelling pattern of the 13C-enriched solanapyrone A compound confirmed that the carbon skeleton of this compound is formed via the polyketide pathway. The biosynthetic route to solanapyrone B is discussed.