Soil-borne fungi of the Fusarium oxysporum species complex cause devastating wilt disease on many crops including legumes that supply human dietary protein needs across many parts of the globe. We present and compare draft genome assemblies for three legume-infecting formae speciales (ff. spp.): F. oxysporum f. sp. ciceris (Foc-38-1) and f. sp. pisi (Fop-37622), significant pathogens of chickpea and pea respectively, the world’s second and third most important grain legumes, and lastly f. sp. medicaginis (Fom-5190a) for which we developed a model legume pathosystem utilising Medicago truncatula. Focusing on the identification of pathogenicity gene content, we leveraged the reference genomes of Fusarium pathogens F. oxysporum f. sp. lycopersici (tomato-infecting) and F. solani (pea-infecting) and their well-characterised core and dispensable chromosomes to predict genomic organisation in the newly sequenced legume-infecting isolates. Dispensable chromosomes are not essential for growth and in Fusarium species are known to be enriched in host-specificity and pathogenicity-associated genes. Comparative genomics of the publicly available Fusarium species revealed differential patterns of sequence conservation across F. oxysporum formae speciales, with legume-pathogenic formae speciales not exhibiting greater sequence conservation between them relative to non-legume-infecting formae speciales, possibly indicating the lack of a common ancestral source for legume pathogenicity. Combining predicted dispensable gene content with in planta expression in the model legume-infecting isolate, we identified small conserved regions and candidate effectors, four of which shared greatest similarity to proteins from another legume-infecting ff. spp. We demonstrate that distinction of core and potential dispensable genomic regions of novel F. oxysporum genomes is an effective tool to facilitate effector discovery and the identification of gene content possibly linked to host specificity. While the legume-infecting isolates didn’t share large genomic regions of pathogenicity-related content, smaller regions and candidate effector proteins were highly conserved, suggesting that they may play specific roles in inducing disease on legume hosts.

Ascochyta blight (AB) caused by Ascochyta rabiei (Pass.) Labr. is an important and widespread disease of chickpea (Cicer arietinum L.) worldwide. The disease is particularly severe under cool and humid weather conditions. Breeding for host resistance is an efficient means to combat this disease. In this paper, attempts have been made to summarize the progress made in identifying resistance sources, genetics and breeding for resistance, and genetic variation among the pathogen population. The search for resistance to AB in chickpea germplasm, breeding lines and land races using various screening methods has been updated. Importance of the genotype × environment (GE) interaction in elucidating the aggressiveness among isolates from different locations and the identification of pathotypes and stable sources of resistance have also been discussed. Current and modern breeding programs for AB resistance based on crossing resistant/multiple resistant and high-yielding cultivars, stability of the breeding lines through multi-location testing and molecular marker-assisted selection method have been discussed. Gene pyramiding and the use of resistant genes present in wild relatives can be useful methods in the future. Identification of additional sources of resistance genes, good characterization of the host–pathogen system, and identification of molecular markers linked to resistance genes are suggested as the key areas for future study.

Fusarium oxysporum f. sp. ciceris (Foc), the causal agent of Fusarium wilt is a devastating pathogen of chickpea. In chickpea, various soil borne pathogens produce (s) similar symptoms, therefore cannot be distinguished easily at field level. There is real need for a rapid, inexpensive, and easy to operate and maintain genotyping tool to facilitate accurate disease diagnosis and surveillance for better management of Fusarium wilt outbreaks. In this study, we developed a loop-mediated isothermal amplification (LAMP) assay targeting the elongation factor 1 alpha gene sequence for visual detection of Foc. The LAMP reaction was optimal at 63°C for 60 min. When hydroxynaphthol blue (HNB) was added before amplification, samples with Foc DNA developed a characteristic sky blue colour but those without DNA or with the DNA of six other plant pathogenic fungi did not. Results obtained with LAMP and HNB were confirmed when LAMP products were subjected to gel electrophoresis. The detection limit of this LAMP assay for Foc was 10 fg of genomic DNA per reaction, while that of conventional PCR was 100 pg. In conclusion, it was found that a LAMP assay combined with HNB is simple, rapid, sensitive, and specific. The LAMP assay does not require specialized equipment, hence can be used in the field for the rapid detection of Foc. This is the first report of the use of LAMP assay for the detection of Foc. The presented LAMP method provides a specific, sensitive and rapid diagnostic tool for the distinction of Foc, with the potential to be standardized as a detection method for Foc in endemic areas and will be very useful for monitoring the disease complex in the field further suggesting the management strategies.

Fusarium wilt (Fusarium udum Butler) is an important biotic constraint to pigeonpea (Cajanus cajan L.) production worldwide. Breeding for fusarium wilt resistance continues to be an integral part of genetic improvement of pigeonpea. Therefore, the study was aimed to identify and validate resistant genotypes to fusarium wilt and determine the magnitude of genotype × environment (G × E) interactions through multi-environment and multi-year screening. Total 976 genotypes including germplasm and breeding lines were screened against wilt in wilt sick plot at Patancheru, India. Ninety two genotypes found resistant to wilt were tested further for two more years in wilt sick plot at Patancheru and Pigeonpea Wilt Nursery (PWN) comprising of 29 genotypes was constituted. PWN was evaluated at nine locations representing different agro-climatic zones of India for wilt resistance during two crop seasons 2007/08 and 2008/09. Genotypes (G), environment (E) and G × E interactions biplot partitioned main effect into G, E and G × E interactions and significant effects (p≤0.001) were obtained for wilt incidence. Genotype contributed 36.51% of resistance variation followed by environment (29.32%). GGE biplot in integration with boxplot and multiple comparison tests enabled us to identify seven stable genotypes (ICPL 20109, ICPL 20096, ICPL 20115, ICPL 20116, ICPL 20102, ICPL 20106 and ICPL 20094) based on their performance across diverse environments. These genotypes have broad based resistance and can be exploited in pigeonpea breeding program.

This paper reports an evaluation of eleven oat genotypes in four environments for two consecutive years to identify high-biomass-yielding, stable, and broadly adapted genotypes in selected parts of Ethiopia. Genotypes were planted and evaluated with a randomized complete block design, which was repeated three times. The additive main effect and multiplicative interaction analysis of variances revealed that the environment, genotype, and genotype–environment interaction had a significant (p ≤ 0.001) influence on the biomass yield in the dry matter base (t ha⁻¹). The interaction of the first and second principal component analysis accounted for 73.43% and 14.97% of the genotype according to the environment interaction sum of squares, respectively. G6 and G5 were the most stable and widely adapted genotypes and were selected as superior genotypes. The genotype-by-environment interaction showed a 49.46% contribution to the total treatment of sum-of-squares variation, while genotype and environment effects explained 34.94% and 15.60%, respectively. The highest mean yield was obtained from G6 (12.52 kg/ha), and the lowest mean yield was obtained from G7 (8.65 kg/ha). According to the additive main effect and multiplicative interaction biplot, G6 and G5 were high-yielding genotypes, whereas G7 was a low-yielding genotype. Furthermore, according to the genotype and genotype–environment interaction biplot, G6 was the winning genotype in all environments. However, G7 was a low-yielding genotype in all environments. Finally, G6 was an ideal genotype with a higher mean yield and relatively good stability. However, G7 was a poor-yielding and unstable genotype. The genotype, environment, and genotype x environment interaction had extremely important effects on the biomass yield of oats. The findings of the graphic stability methods (additive main effect and multiplicative interaction and the genotype and genotype–environment interaction) for identifying high-yielding and stable oat genotypes were very similar.

Plants being sessile are under constant threat of multiple abiotic and biotic stresses within its natural habitat. A combined stress involving an abiotic and a biotic factor reportedly increases susceptibility of the plants to pathogens. The emerging threat, collar rot disease of chickpea (caused by Sclerotium rolfsii Sacc.) is reported to be influenced by soil moisture condition (SMC). Hence, we studied the influence of differential SMC viz. upper optimum (100%), optimum (80%), lower optimum (60%), and limiting (40%) soil moisture conditions on colonization and collar rot development over the course of infection in two chickpea cultivars, Annigeri (susceptible to collar rot) and ICCV 05530 (moderately resistant to collar rot). Disease incidence was found to be directly proportional to increase in soil moisture (R² = 0.794). Maximum incidence was observed at 80% SMC, followed by 100 and 60% SMC. Expression of genes (qPCR analysis) associated with host cell wall binding (lectin) and degradation viz. endopolygalacturonase-2, endoglucosidase, and cellobiohydrolase during collar rot development in chickpea were relatively less at limiting soil moisture condition (40%) as compared to optimum soil moisture condition (80%). As compared to individual stress, the expression of defense response genes in chickpea seedlings were highly up-regulated in seedlings challenged with combined stress. Our qPCR results indicated that the expression of defense-related genes in chickpea during interaction with S. rolfsii at low SMC was primarily responsible for delayed disease reaction. Involvement of moisture and biotic stress-related genes in combined stress showed a tailored defense mechanism.