QTL dissection and mining of candidate genes for Ascochyta fabae and Orobanche crenata resistance in faba bean (Vicia faba L.)

Background Ascochyta blight caused by Ascochyta fabae Speg. and broomrape (Orobanche crenata) are among the economically most significant pathogens of faba bean. Several QTLs conferring resistance against the two pathogens have been identified and validated in different genetic backgrounds. The aim of this study was to saturate the most stable QTLs for ascochyta and broomrape resistance in two Recombinant Inbred Line (RIL) populations, 29H x Vf136 and Vf6 x Vf136, to identify candidate genes conferring resistance against these two pathogens. Results We exploited the synteny between faba bean and the model species Medicago truncatula by selecting a set of 219 genes encoding putative WRKY transcription factors and defense related proteins falling within the target QTL intervals, for genotyping and marker saturation in the two RIL populations. Seventy and 50 of the candidate genes could be mapped in 29H x Vf136 and Vf6 x Vf136, respectively. Besides the strong reduction of the QTL intervals, the mapping process allowed replacing previous dominant and pedigree-specific RAPD flanking markers with robust and transferrable SNP markers, revealing promising candidates for resistance against the two pathogens. Conclusions Although further efforts in association mapping and expression studies will be required to corroborate the candidate genes for resistance, the fine-mapping approach proposed here increases the genetic resolution of relevant QTL regions and paves the way for an efficient deployment of useful alleles for faba bean ascochyta and broomrape resistance through marker-assisted breeding.

Conventional and Molecular Breeding Tools for Accelerating Genetic Gain in Faba Bean (Vicia Faba L.)

Faba bean is a cool-season grain legume crop, which is grown worldwide for food and feed. Despite a decrease in area under faba bean in the past, the interest in growing faba bean is increasing globally due to its high seed protein content and its excellent ecological service. The crop is, however, exposed to diverse biotic and abiotic stresses causing unstable, low grain yield. Although, sources of resistance to main diseases, such as ascochyta blight (Ascochyta fabae Speg.), rust (Uromyces viciae-fabae (Pers.) Schroet.), chocolate spot (Botrytis fabae Sard.) and gall disease (Physioderma viciae), have been identified, their resistance is only partial and cannot prevent grain yield losses without agronomical practices. Tightly associated DNA markers for host plant resistance genes are needed to enhance the level of resistance. Less progress has been made for abiotic stresses. Different breeding methods are proposed, but until now line breeding, based on the pedigree method, is the dominant practice in breeding programs. Nonetheless, the low seed multiplication coefficient and the requirement for growing under insect-proof enclosures to avoid outcrossing hampers breeding, along with the lack of tools such as double haploid system and cytoplasmic male sterility. This reduces breeding population size and speed of breeding hence the chances of capturing rare combinations of favorable alleles. Availability and use of the DNA markers such as vicine-convicine (vc−) and herbicide tolerance in breeding programs have encouraged breeders and given confidence in marker assisted selection. Closely linked QTL for several biotic and abiotic stress tolerance are available and their verification and conversion in breeder friendly platform will enhance the selection process. Recently, genomic selection and speed breeding techniques together with genomics have come within reach to accelerate the genetic gains in faba bean. Advancements in genomic resources with other breeding tools, methods and platforms will enable to accelerate the breeding process for enhancing genetic gain in this species.

Food legumes breeding program in eastern Mediterranean region and Turkey

Breeding is aimed to breed for varieties that are tolerant against disease, suitable for mechanized cultivation and harvest, and also offer them to the farmers as promising varieties. Since the purpose of legumes production is to obtain grain products of high yield and quality, developing suitable varieties for target regions where they will be grown is an important factor that needs to be considered. This breeding program aimed to develop new variety of recommended legumes varieties for different regions and will stimulate an increase in cultivation area. In Turkey chickpea is traditionally sown in spring and subjected to drought and heat stresses. Chickpea can be sown in autumn with new cultivars but winter-sown chickpea cultivars are not available for highlands. Some abiotic stresses (drought, heat, freezing etc.) and some biotic stresses (ascochyta blight, Fusarium wilt, and weeds) are common and important stresses, whereas nutrient imbalance includ-ing salinity are localized challenges. Lentil is usually traditionally sown in autumn and Central Anatolia green lentil, South Eastern Anatolia red lentil regions in Turkey. As a result of Turkish food legume Program, 48 chickpea, 41lentil, 49 beans, 3 faba beans, 3 pea and 4 cowpea varieties were registered.

Genetic Diversity and Population Structure of Didymella rabiei Affecting Chickpea in Ethiopia

Ascochyta blight, also known as chickpea blight, which is caused by the fungal pathogen, Didymella rabiei, is an important disease affecting chickpea (Cicer arietinum L.) in many countries. We studied the genetic diversity and population structure of 96 D. rabiei isolates collected from three geographic populations in Ethiopia using simple sequence repeat (SSR) markers. We confirmed the genetic identity of 89 of the D. rabiei isolates by sequencing their rRNA internal transcribed spacer region genes. The chickpea blight pathogen isolates were genetically diverse, with a total of 51 alleles identified across 6 polymorphic SSR loci, which varied from 3 to 18 (average 8.5) alleles per SSR marker. The observed heterozygosity and expected heterozygosity ranged from 0.01 to 0.92 and 0.19 to 0.86, respectively. The mean polymorphic information content value of the D. rabiei populations was 0.58, with a mean gene diversity of 0.61 among loci. Gene flow (Nm = number of migrants) for the three populations of D. rabiei isolates ranged from 1.51 to 24.10 (average 6.2) migrants/cluster. However, the genetic variation between the D. rabiei populations was small (8%), with most of the variation occurring within populations (92%). Principal component analysis to visualize genetic variation showed that the D. rabiei isolates obtained from most of the chickpea samples formed roughly three groups on a two-dimensional coordinate plane. Similarly, the clustering of individuals into populations based on multi-locus genotypes (using Clumpak) grouped isolates into three clusters but with individual isolate admixtures. Hence, no clear geographic origin-based structuring of populations could be identified. To our knowledge, this is the first report of D. rabiei diversity in Ethiopia. Virulence studies should be conducted to develop chickpea varieties that are resistant to more aggressive pathogen populations.

Application of Genomics Approaches for the Improvement in Ascochyta Blight Resistance in Chickpea

Advancements in high-throughput genotyping and sequencing technologies are enabling the development of a vast range of genomic tools and resources for a new revolution in plant breeding. Several genotyping-by-sequencing (GBS) methods including capture-based, genome complexity reduction and sequencing of cDNA (GBS-t) are available for application in trait dissection, association mapping, and genomic selection (GS) in crop plants. The aims of this study were to identify genomic regions conferring resistance to Ascochyta blight (AB) introgressed from the wild Cicer echinospernum into the domesticated C. arietinum, through a conventional recombinant inbred population genotyped using a variety of GBS methods. Evaluation of GBS methods revealed that capture-based approaches are robust and reproducible while GBS-t is rapid and flexible. A genetic linkage map consisting of 5886 polymorphic loci spanning 717.26 cM was generated. Using field phenotyping data from two years, a single genomic region on LG4 was identified with quantitative trait loci (QTL) mapping. Both GBS methods reported in this study are well suited for applications in genomics assisted plant breeding. Linked markers for AB resistance, identified in the current study, provide an important resource for the deployment into chickpea breeding programs for marker-assisted selection (MAS).

Effects of host plant resistance and fungicide applications on Ascochyta blight symptomology and yield of chickpea (Cicer arietinum L.).

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 to a no fungicide application control on AB score and yield. The mean grain yields across locations and years were 1753, 1283 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.

Effect of Some Agronomic Practices on Ascochyta Blight Severity and Yield of Faba Bean (Vicia faba L.) in Tunisia

Background: In Tunisia, faba bean (Vicia faba L.) is the first major food legume. The development of faba bean production is facing several biotic constraints. Faba bean Ascochyta blight caused by Ascochyta fabae is one of the most destructive diseases of faba bean and can cause significant yield loss under favorable conditions. As only incomplete resistance ABL varieties are available, some agronomic practices should be applied to control and reduce Ascochyta blight incidence wherever possible. Therefore, this work was undertaken to evaluate the effect of spacing row and seed rate on ABL severity, growth and yield of faba bean. Methods: A split-plot design with three replications was adopted to carry out this study during 2018 and 2019 cropping seasons. ‘Bachaar’ faba bean variety was sown at 40 and 60 cm row spacing and at three seed rates (100, 140 and 200 kg ha-1). ABL severity was assessed visually on a 0-9 scale and agro-morphological traits were measured. Analysis of variance was used to analyze the data. Correlations between agronomic traits, row spacing, seed rate and ABL severity were investigated. Result: Results showed that seed rate has a larger effect on yield than row spacing. In both cropping seasons, the highest grain yield was recorded in 60 cm row spacing and 140 kg ha-1 seed rate treatment. So, this treatment is recommended for obtaining high yield of faba bean. Most of the variation in disease severity was associated with seed rate (r=0.62). The highest ABL score severity was noted at 200 kg ha-1 rate. Over both years, wide row spacing and low seed rate reduced ABL severity. In this study, the small amounts of ABL disease (which reached a score of 5.3 and 4.7 in 2018 and 2019, respectively) had little or no effect on yield.

Effect of Row Spacing and Seed Rate on Ascochyta Blight Severity and Yield of Chickpea (Cicer arietinum L.) in Tunisia

Background: In Tunisia, chickpea (Cicer arietinum L.) is the second major food legume. The development of chickpea production is facing several biotic constraints. Ascochyta blight (ABL) caused by Ascochyta rabiei (Pass.) Labr. is the most devastating disease and can cause complete yield losses under favorable conditions. In absence of chickpea variety totally resistance to ABL, some methods should be used to control and reduce this disease effects and help for its management. Therefore, this work was undertaken to evaluate the effect of row spacing and seed rate on ABL severity, growth and yield of chickpea. Methods: A split-plot design with three replicates was adopted to carry out this study during 2018 and 2019 cropping seasons. ‘Beja1’ chickpea variety was sown at 40 and 60 cm row spacing and at three seed rates (80, 110 and 140 kg ha-1). ABL severity was assessed visually on a 0-9 scale and agro morphological traits were measured. Analysis of variance was used to analyze the data. Correlations between agronomic traits, row spacing, seed rate and ABL severity were investigated. Result: Results showed that most of the variation in disease severity was associated with seed rate (r=0.61). The highest ABL score severity was noted at 140 kg ha-1 rate. Over both years, wide row spacing and low seed rate reduced ABL severity. Chickpea sown under narrow row spacing (40 cm) produced higher grain yield (1014 and 1099.7 kg ha-1 for 2018 and 2019 cropping seasons, respectively). Grain yield was tending to decrease with increasing sowing rates but at a density higher than optimal, grain yields decrease. In this study, ABL disease severity reached a score of 3.7 and 4.3 in 2018 and 2019, respectively. These disease severities levels had little effect on yield.

The nuclear effector ArPEC25 from the necrotrophic fungus Ascochyta rabiei targets the chickpea transcription factor CaβLIM1a and negatively modulates lignin biosynthesis for host susceptibility

Fungal pathogens deploy a barrage of secreted effectors to subvert host immunity, often by evading, disrupting, or altering key components of transcription, defense signaling, and metabolic pathways. However, the underlying mechanisms of effectors and their host targets are largely unexplored in necrotrophic fungal pathogens. Here, we describe the effector protein ArPEC25, which is secreted by the necrotroph Ascochyta rabiei, the causal agent of Ascochyta blight disease in chickpea (Cicer arietinum), and is indispensable for virulence. After entering host cells, ArPEC25 localizes to the nucleus and targets the host LIM transcription factor CaβLIM1a. CaβLIM1a is a transcriptional regulator of CaPAL1, which encodes phenylalanine ammonia lyase, the regulatory, gatekeeping enzyme of the phenylpropanoid pathway. ArPEC25 inhibits the transactivation of Ca?LIM1a by interfering with its DNA binding ability. This results in negative regulation of the phenylpropanoid pathway and decreased levels of intermediates of lignin biosynthesis, thereby suppressing lignin production. Our findings illustrate the role of fungal effectors in enhancing virulence by targeting a key defense pathway that leads to the biosynthesis of various secondary metabolites and antifungal compounds. This study provides a template for the study of less explored necrotrophic effectors and their host target functions.