Resistance to Plant-Parasitic Nematodes in Chickpea: Current Status and Future Perspectives

Genome-wide association mapping reveals novel genes and genomic regions controlling root-lesion nematode resistance in chickpea mini core collection

Root-lesion nematodes (RLN) pose a significant threat to chickpea (Cicer arietinum L.) by damaging the root system and causing up to 25% economic losses due to reduced yield. Worldwide commercially grown chickpea varieties lack significant genetic resistance to RLN, necessitating the identification of genetic variants contributing to natural resistance. This study identifies genomic loci responsible for resistance to the RLN, Pratylenchus thornei Sher & Allen, in chickpea by utilizing high-quality single nucleotide polymorphisms from whole-genome sequencing data of 202 chickpea accessions. Phenotypic evaluations of the genetically diverse set of chickpea accessions in India and Australia revealed a wide range of responses from resistant to susceptible. Genome-wide association studies (GWAS) employing Fixed and Random Model Circulating Probability Unification (FarmCPU) and Bayesian-Information and Linkage-Disequilibrium Iteratively Nested Keyway (BLINK) models identified 44 marker-trait associations distributed across all chromosomes except Ca1. Crucially, genomic regions on Ca2 and Ca5 consistently display significant associations across locations. Of 25 candidate genes identified, five genes were putatively involved in RLN resistance response (glucose-6-phosphate dehydrogenase, heat shock proteins, MYB-like DNA-binding protein, zinc finger FYVE protein and pathogenesis-related thaumatin-like protein). One notably identified gene (Ca_10016) presents four haplotypes, where haplotypes 1-3 confer moderate susceptibility, and haplotype 4 contributes to high susceptibility to RLN. This information provides potential targets for marker development to enhance breeding for RLN resistance in chickpea. Additionally, five potential resistant genotypes (ICC3512, ICC8855, ICC5337, ICC8950, and ICC6537) to P. thornei were identified based on their performance at a specific location. The study's significance lies in its comprehensive approach, integrating multiple-location phenotypic evaluations, advanced GWAS models, and functional genomics to unravel the genetic basis of P. thornei resistance. The identified genomic regions, candidate genes, and haplotypes offer valuable insights for breeding strategies, paving the way for developing chickpea varieties resilient to P. thornei attack.

Auxin-Mediated Lateral Root Development in Root Galls of Cucumber under Meloidogyne incognita Stress

Root-knot nematodes induce the formation of feeding sites within the host roots and the relocation of auxin into galls results in abnormal lateral root growth. Here, we analyzed the changes in cucumber root architecture under Meloidogyne incognita stress and the distribution of auxin in these morphological and molecular root changes. The number of root tips significantly decreased, and regression analysis showed a positive relationship between the size of root galls and the numbers of nematodes in galls compared with the lateral roots on galls, emphasizing the effect of nematode parasitism on root development. Data generated via a promoter-reporter system using the transgenic hairy root system first characterized the auxin distribution during nematode parasitism in cucumber. Using DR5:GUS staining of root galls, we further detected the expression of CsPIN1 and CsAUX1, which regulate polar auxin transport. The results showed that both CsPIN1 and CsAUX1 were induced in galls, and the relative expression of the two genes significantly increased at 21 DAI. The TIBA treatment, which can disrupt polar auxin transport inhibited the numbers of cucumber root tips and total length following increasing concentration gradients. Moreover, the numbers of galls were significantly affected by TIBA treatment, which showed the vital role of auxin during nematode parasitism. Our findings suggest that the transportation of auxin plays an important role during gall formation and induces cucumber lateral root development within nematode feeding sites.

Optimization and utilization of emerging waste (fly ash) for growth performance of chickpea (Cicer arietinum L.) plant and mitigation of root-knot nematode (Meloidogyne incognita) stress

The sustainable management of large amounts of fly ash (FA) is a concern for researchers, and we aim to determine the FA application in plant development and nematicidal activity in the current study. A pot study is therefore performed to assess the effects of adding different, FA-concentrations to soil (w/w) on the infection of chickpea plants with the root-knot nematode Meloidogyne incognita. Sequence characteristic amplified region (SCAR) and internal transcribed spacer (ITS) region-based-markers were used to molecularly confirm M. incognita. With better plant growth and chickpea yield performance, FA enhanced the nutritious components of the soil. When compared with untreated, uninoculated control (UUC) plants, the inoculation of M. incognita dramatically reduced chickpea plant growth, yield biomass, and metabolism. The findings showed that the potential of FA to lessen the root-knot nematode illness in respect of galls, egg-masses, and reproductive attributes may be used to explain the mitigating effect of FA. Fascinatingly, compared with the untreated, inoculated control (UIC) plants, the FA treatment, primarily at 20%, considerably (p ≤ 0.05) boosted plant growth, yield biomass, and pigment content. Additionally, when the amounts of FA rose, the activity of antioxidants like superoxide dismutase-SOD, catalase-CAT, and peroxidase-POX as well as osmo-protectants like proline gradually increased. Therefore, our findings imply that 20% FA can be successfully applied as a potential strategy to increase biomass yield and plant growth while simultaneously reducing M. incognita infection in chickpea plants.

A Quantitative Trait Locus with a Major Effect on Root-Lesion Nematode Resistance in Barley

Although the root-lesion nematode Pratylenchus thornei is known to affect barley (Hordeum vulgare L.), there have been no reports on the genetic control of P. thornei resistance in barley. In this research, P. thornei resistance was assessed for a panel of 46 barley mapping parents and for two mapping populations (Arapiles/Franklin and Denar/Baudin). With both populations, a highly significant quantitative trait locus (QTL) was mapped at the same position on the long arm of chromosome 7H. Single-nucleotide polymorphisms (SNPs) in this region were anchored to an RGT Planet pan-genome assembly and assayed on the mapping parents and other barley varieties. The results indicate that Arapiles, Denar, RGT Planet and several other varieties likely have the same resistance gene on chromosome 7H. Marker assays reported here could be used to select for P. thornei resistance in barley breeding. Analysis of existing barley pan-genomic and pan-transcriptomic data provided a list of candidate genes along with information on the expression and differential expression of some of those genes in barley root tissue. Further research is required to identify a specific barley gene that affects root-lesion nematode resistance.

Recent Advances and Outlook of Benzopyran Derivatives in the Discovery of Agricultural Chemicals

Scaffold structures, new mechanisms of action, and targets present enormous challenges in the discovery of novel pesticides. The discovery of new scaffolds is the basis for the continuous development of modern agrochemicals. Identification of a good scaffold such as triazole, carbamate, methoxy acrylate, pyrazolamide, pyrido-pyrimidinone mesoionic, and bisamide often leads to the development of a new series of pesticides. In addition, pesticides with the same target, including the inhibitors of succinate dehydrogenase (SDH), oxysterol-binding-protein, and p-hydroxyphenyl pyruvate dioxygenase (HPPD), may have the same or similar scaffold structure. Recent years have witnessed significant progress in the discovery of new pesticides using natural products as scaffolds or bridges. In recent years, there have been increasing reports on the application of natural benzopyran compounds in the discovery of new pesticides, especially osthole and coumarin. A systematic and comprehensive review of benzopyran active compounds in the discovery of new agricultural chemicals is helpful to promote the discussion and development of benzopyran active compounds. Therefore, this work systematically reviewed the research and application of benzopyran derivatives in the discovery of agricultural chemicals, summarized the antiviral, herbicidal, antibacterial, fungicidal, insecticidal, nematicidal and acaricidal activities of benzopyran active compounds, and discussed the structural-activity relationship and mechanism of action. In addition, some active fragments were recommended to further optimize the chemical structure of benzopyran active compounds based on reference information.

Photorhabdus-Derived Secondary Metabolites Reduce Root Infection by Meloidogyne incognita in Cowpea

Root-knot nematodes (RKNs) cause significant economic damage to crop plants, spurring demand for safe, affordable, and sustainable nematicides. A previous study by our research team showed that the combination of two nematicidal secondary metabolites (SMs) derived from Photorhabdus bacteria, trans-cinnamic acid (t-CA), and (4E)-5-phenylpent-4-enoic acid (PPA) have a synergistic effect against RKNs in vitro. In this study, we considered in planta assays to assess the effects of this SM mixture on the virulence and reproductive fitness of the RKN Meloidogyne incognita in a cowpea. Factorial combinations of five t-CA + PPA concentrations (0, 9.0, 22.9, 57.8, and 91.0 μg/ml) and two nematode inoculation conditions (presence or absence) were evaluated in 6-week growth chamber experiments. Results from this study showed that a single root application of the t-CA + PPA mixture significantly reduced the penetration of M. incognita infective juveniles (J2s) into the cowpea roots. The potential toxicity of t-CA + PPA on RKN-susceptible cowpea seedlings was also investigated. The effect of t-CA + PPA × nematode inoculation interactions and the t-CA + PPA mixture did not show significant phytotoxic effects, nor did it adversely affect plant growth parameters or alter leaf chlorophyll content. Total leaf chlorophyll and chlorophyll b content were significantly reduced (by 15 and 22%, respectively) only by the nematode inoculum and not by any of the SM treatments. Our results suggest that a single root application of a mixture of t-CA and PPA reduces M. incognita J2's ability to infect the roots without impairing plant growth or chlorophyll content.

Multi-locus genome-wide association study of chickpea reference set identifies genetic determinants of Pratylenchus thornei resistance

Pratylenchus thornei is an economically important species of root-lesion nematode adversely affecting chickpea (Cicer arietinum) yields globally. Integration of resistant crops in farming systems is recognised as the most effective and sustainable management strategy for plant-parasitic nematodes. However, breeding for P. thornei resistance in chickpea is limited by the lack of genetic diversity. We deployed a genome-wide association approach to identify genomic regions and candidate genes associated with P. thornei resistance in 285 genetically diverse chickpea accessions. Chickpea accessions were phenotyped for P. thornei resistance in replicated glasshouse experiments performed for two years (2018 and 2020). Whole genome sequencing data comprising 492,849 SNPs were used to implement six multi-locus GWAS models. Fourteen chickpea genotypes were found to be resistant to P. thornei. Of the six multi-locus GWAS methods deployed, FASTmrMLM was found to be the best performing model. In all, 24 significant quantitative trait nucleotides (QTNs) were identified, of which 13 QTNs were associated with lower nematode population density and 11 QTNs with higher nematode population density. These QTNs were distributed across all of the chickpea chromosomes, except chromosome 8. We identified, receptor-linked kinases (RLKs) on chromosomes 1, 4 and 6, GDSL-like Lipase/Acylhydrolase on chromosome 3, Aspartic proteinase-like and Thaumatin-like protein on chromosome 4, AT-hook DNA-binding and HSPRO2 on chromosome 6 as candidate genes for P. thornei resistance in the chickpea reference set. New sources of P. thornei resistant genotypes were identified that can be harnessed into breeding programs and putative candidate P. thornei resistant genes were identified that can be explored further to develop molecular markers and accelerate the incorporation of improved P. thornei resistance into elite chickpea cultivars.

First Reports and Morphological and Molecular Characterization of Pratylenchus delattrei and Quinisulcius capitatus Associated with Chickpea in Ethiopia

Chickpea (Cicer arietinum L.) is classed among the most important leguminous crops of high economic value in Ethiopia. Two plant-parasitic nematode species, Pratylenchus delattrei and Quinisulcius capitatus, were recovered from chickpea-growing areas in Ethiopia and characterized using molecular and morphological data, including the first scanning electron microscopy data for P. delattrei. New sequences of D2-D3 of 28S, ITS rDNA and mtDNA COI genes have been obtained from these species, providing the first COI sequences for P. delattrei and Q. capitatus, with both species being found for the first time on chickpea in Ethiopia. Furthermore, Pratylenchus delattrei was recovered in Ethiopia for the first time. The information obtained about these nematodes will be crucial to developing effective nematode management plans for future chickpea production.

Grass-Shaped Zinc Oxide Nanoparticles Synthesized by the Sol-Gel Process and Their Antagonistic Properties towards the Biotrophic Parasite, Meloidogyne incognita

The presence of Meloidogyne spp., also known as root-knot nematodes, presents a significant danger to global agricultural progress. Since chemical nematicides have high levels of toxicity, it is imperative to develop environmentally friendly methods to manage root-knot nematodes. Nanotechnology is now the most progressive way to attract researchers due to its innovative quality in combating plant diseases. Our study focused on the sol-gel process to synthesize grass-shaped zinc oxide nanoparticles (G-ZnO NPs) and assess its nematicidal behavior against Meloidogyne incognita. Various concentrations (250, 500, 750, and 1000 ppm) of G-ZnO NPs were utilized to expose both the infectious stage (J2s) and egg masses of M. incognita. Laboratory results revealed that G-ZnO NPs showed toxicity to J2s with LC50 values of 1352.96, 969.64, and 621.53 ppm at 12, 24, and 36 hours, respectively, and the result was the inhibition of egg hatching in M. incognita. All three exposure periods were reported linked with the concentration strength of G-ZnO NPs. The pot experiment results exhibited that G-ZnO NPs significantly reduced the root-gall infection of chickpea plants under M. incognita attack. Compared with the untreated control, there was a significant improvement in plant growth attributes and physiological parameters as well, when distinct G-ZnO NP doses (250, 500, 750, and 1000 ppm) were applied. In the pot study, we noticed a reduction in the root-gall index with an increase in the concentration of G-ZnO NPs. The results confirmed that G-ZnO NPs have enormous potential in sustainable agriculture for controlling the root-knot nematode, M. incognita, in chickpea production.

Pea Breeding for Resistance to Rhizospheric Pathogens

Pea (Pisum sativum L.) is a grain legume widely cultivated in temperate climates. It is important in the race for food security owing to its multipurpose low-input requirement and environmental promoting traits. Pea is key in nitrogen fixation, biodiversity preservation, and nutritional functions as food and feed. Unfortunately, like most crops, pea production is constrained by several pests and diseases, of which rhizosphere disease dwellers are the most critical due to their long-term persistence in the soil and difficulty to manage. Understanding the rhizosphere environment can improve host plant root microbial association to increase yield stability and facilitate improved crop performance through breeding. Thus, the use of various germplasm and genomic resources combined with scientific collaborative efforts has contributed to improving pea resistance/cultivation against rhizospheric diseases. This improvement has been achieved through robust phenotyping, genotyping, agronomic practices, and resistance breeding. Nonetheless, resistance to rhizospheric diseases is still limited, while biological and chemical-based control strategies are unrealistic and unfavourable to the environment, respectively. Hence, there is a need to consistently scout for host plant resistance to resolve these bottlenecks. Herein, in view of these challenges, we reflect on pea breeding for resistance to diseases caused by rhizospheric pathogens, including fusarium wilt, root rots, nematode complex, and parasitic broomrape. Here, we will attempt to appraise and harmonise historical and contemporary knowledge that contributes to pea resistance breeding for soilborne disease management and discuss the way forward.

Recent advancement in OMICS approaches to enhance abiotic stress tolerance in legumes

The world is facing rapid climate change and a fast-growing global population. It is believed that the world population will be 9.7 billion in 2050. However, recent agriculture production is not enough to feed the current population of 7.9 billion people, which is causing a huge hunger problem. Therefore, feeding the 9.7 billion population in 2050 will be a huge target. Climate change is becoming a huge threat to global agricultural production, and it is expected to become the worst threat to it in the upcoming years. Keeping this in view, it is very important to breed climate-resilient plants. Legumes are considered an important pillar of the agriculture production system and a great source of high-quality protein, minerals, and vitamins. During the last two decades, advancements in OMICs technology revolutionized plant breeding and emerged as a crop-saving tool in wake of the climate change. Various OMICs approaches like Next-Generation sequencing (NGS), Transcriptomics, Proteomics, and Metabolomics have been used in legumes under abiotic stresses. The scientific community successfully utilized these platforms and investigated the Quantitative Trait Loci (QTL), linked markers through genome-wide association studies, and developed KASP markers that can be helpful for the marker-assisted breeding of legumes. Gene-editing techniques have been successfully proven for soybean, cowpea, chickpea, and model legumes such as Medicago truncatula and Lotus japonicus. A number of efforts have been made to perform gene editing in legumes. Moreover, the scientific community did a great job of identifying various genes involved in the metabolic pathways and utilizing the resulted information in the development of climate-resilient legume cultivars at a rapid pace. Keeping in view, this review highlights the contribution of OMICs approaches to abiotic stresses in legumes. We envisage that the presented information will be helpful for the scientific community to develop climate-resilient legume cultivars.

A QTL on the Ca7 chromosome of chickpea affects resistance to the root-lesion nematode Pratylenchus thornei

The root-lesion nematode Pratylenchus thornei Sher & Allen, 1953 is a damaging parasite of many crop plants, including the grain legume chickpea (Cicer arietinum L.). Within cultivated chickpea, there are no known sources of strong resistance to P. thornei, but some cultivars have partial resistance. In the research reported here, the genetic basis for differences in P. thornei resistance was analysed using a population derived by accelerated single seed descent from a cross between a partially resistant cultivar, PBA HatTrick, and a very susceptible cultivar, Kyabra. A genetic linkage map was constructed from genotyping-by-sequencing data. Two quantitative trait loci were mapped, one on the Ca4 chromosome and one on the Ca7 chromosome. The Ca7 locus had a greater and more consistent effect than the Ca4 locus. Marker assays designed for single nucleotide polymorphisms on Ca7 were applied to a panel of chickpea accessions. Some of these markers should be useful for marker-assisted selection in chickpea breeding. Haplotype analysis confirmed the Iranian landrace ICC14903 to be the source of the resistance allele in PBA HatTrick and indicated that other Australian cultivars inherited the same allele from other Iranian landraces. A candidate region was defined on the Ca7 pseudomolecule. Within that region, 69 genes have been predicted with high confidence. Among these, two have annotations related to biotic stress response. Three others have previously been reported to be expressed in roots of PBA HatTrick and Kyabra, including one that is more highly expressed in PBA HatTrick than in Kyabra.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-021-01271-8.

Optimizing Safe Approaches to Manage Plant-Parasitic Nematodes

Plant-parasitic nematodes (PPNs) infect and cause substantial yield losses of many foods, feed, and fiber crops. Increasing concern over chemical nematicides has increased interest in safe alternative methods to minimize these losses. This review focuses on the use and potential of current methods such as biologicals, botanicals, non-host crops, and related rotations, as well as modern techniques against PPNs in sustainable agroecosystems. To evaluate their potential for control, this review offers overviews of their interactions with other biotic and abiotic factors from the standpoint of PPN management. The positive or negative roles of specific production practices are assessed in the context of integrated pest management. Examples are given to reinforce PPN control and increase crop yields via dual-purpose, sequential, and co-application of agricultural inputs. The involved PPN control mechanisms were reviewed with suggestions to optimize their gains. Using the biologicals would preferably be backed by agricultural conservation practices to face issues related to their reliability, inconsistency, and slow activity against PPNs. These practices may comprise offering supplementary resources, such as adequate organic matter, enhancing their habitat quality via specific soil amendments, and reducing or avoiding negative influences of pesticides. Soil microbiome and planted genotypes should be manipulated in specific nematode-suppressive soils to conserve native biologicals that serve to control PPNs. Culture-dependent techniques may be expanded to use promising microbial groups of the suppressive soils to recycle in their host populations. Other modern techniques for PPN control are discussed to maximize their efficient use.

Transcriptome analysis reveals key genes associated with root-lesion nematode Pratylenchus thornei resistance in chickpea

The root-lesion nematode, Pratylenchus thornei, is one of the major plant-parasitic nematode species causing significant yield losses in chickpea (Cicer arietinum). In order to identify the underlying mechanisms of resistance to P. thornei, the transcriptomes of control and inoculated roots of three chickpea genotypes viz. D05253 > F3TMWR2AB001 (resistant advanced breeding line), PBA HatTrick (moderately resistant cultivar), and Kyabra (susceptible cultivar) were studied at 20 and 50 days post inoculation using the RNA-seq approach. On analyzing the 633.3 million reads generated, 962 differentially expressed genes (DEGs) were identified. Comparative analysis revealed that the majority of DEGs upregulated in the resistant genotype were downregulated in the moderately resistant and susceptible genotypes. Transcription factor families WRKY and bZIP were uniquely expressed in the resistant genotype. The genes Cysteine-rich receptor-like protein kinase 10, Protein lifeguard-like, Protein detoxification, Bidirectional sugar transporter Sugars Will Eventually be Exported Transporters1 (SWEET1), and Subtilisin-like protease were found to play cross-functional roles in the resistant chickpea genotype against P. thornei. The identified candidate genes for resistance to P. thornei in chickpea can be explored further to develop markers and accelerate the introgression of P. thornei resistance into elite chickpea cultivars.

Fusarium spp. Associated With Root Rot of Pulse Crops and Their Cross-Pathogenicity to Cereal Crops in Montana

Root rot caused by Fusarium species is a major problem in the pulse growing regions of Montana. Fusarium isolates (n = 112) were obtained from seeds and roots of chickpea, dry pea, and lentil. Isolates were identified by comparing the sequences of the internal transcribed spacer region and the translation elongation factor 1-α in Fusarium-ID database. Fusarium avenaceum was the most abundant species (28%), followed by F. acuminatum (21%), F. poae (13%), F. oxysporum (8%), F. culmorum (6%), F. redolens (6%), F. sporotrichioides (6%), F. solani (4%), F. graminearum (2%), F. torulosum (2%), and F. tricinctum (0.9%). The aggressiveness of a subset of 50 isolates that represent various sources of isolation was tested on three pulse crops and two cereal crops. Nonparametric analysis of variance conducted on ranks of disease severity indicated that F. avenaceum and F. solani isolates were highly aggressive on pea and chickpea. In lentil, F. avenaceum and F. culmorum were highly aggressive. In barley, F. avenaceum, F. solani, F. culmorum, and F. graminearum were highly aggressive. In wheat, F. avenaceum, F. graminearum, and F. culmorum were highly aggressive. Two F. avenaceum isolates were highly aggressive across all the crops tested and found to be cross-pathogenic. One isolate of F. culmorum and an isolate of F. graminearum obtained from chickpea and lentil seed were highly aggressive on barley and wheat. The results indicate that multiple Fusarium spp. from seeds and roots can cause root rot on both pulse and cereal crops. Rotating these crops may still lead to an increase in inoculum levels, making crop rotation limited in efficacy as a disease management strategy.