A major QTL corresponding to the Rk locus for resistance to root-knot nematodes in cowpea (Vigna unguiculata L. Walp.)

Combating Root-Knot Nematodes (Meloidogyne spp.): From Molecular Mechanisms to Resistant Crops

Root-knot nematodes (RKNs; Meloidogyne spp.) are significant plant-parasitic nematodes that cause major yield losses worldwide. With growing awareness of the harmful effects of chemical pesticides on human health and the environment, there is an urgent need to develop alternative strategies for controlling RKN in agricultural fields. In recent years, implementing multiple approaches based on transcriptomics, genomics, and genome engineering, including modern platforms like CRISPR/Cas9, along with traditional genetic mapping, has led to great advances in understanding the plant-RKN interactions and the underlying molecular mechanisms of plant RKN resistance. In this literature review, we synthesize the contributions of relevant studies in this field and discuss key findings. This includes, for instance, transcriptomics studies that helped expand our understanding of plant RKN-resistance mechanisms, the overexpression of plant hormone-related genes, and the silencing of susceptibility genes that lead to plant RKN resistance. This review was conducted by searching scientific sources, including PubMed and Google Scholar, for relevant publications and filtering them using keywords such as RKN-plant defense mechanisms, host-plant resistance against RKN, and genetic mapping for RKN. This knowledge can be leveraged to accelerate the development of RKN-resistant plants and substantially improve RKN management in economically important crops.

Quantitative Trait Loci Mapping for Yield and Related Traits in Cowpea

Background/Objectives: Cowpea is a major source of dietary protein and plays a key role in sustainable agriculture across sub-Saharan Africa (SSA), Asia, and Latin America. Research efforts have focused mainly on enhancing productivity through higher yield and resistance to biotic and abiotic stresses in cowpea. Understanding the genetic basis of yield and associated agronomic traits is crucial for improving crop productivity. This study aims to identify quantitative trait loci (QTL) associated with grain yield and related traits in cowpea under regular rainfed conditions. Methods: We developed a set of 316 F6:7 recombinant inbred lines (RILs) mapping populations derived from a cross between RP270 and CB27 using a single-seed descent breeding method. The RILs and their two parental lines were evaluated in the field for two years, 2022 and 2023, at the International Institute of Tropical Agriculture (IITA) in Ibadan, Nigeria. The cowpea mid-density genotyping panel consisting of 2602 quality DArTag single nucleotide polymorphisms (SNPs) was used to genotype the RIL population. Results: Seven major QTLs, each explaining ≥10% of phenotypic variance, were detected for 100-seed weight, number of days to flower, number of pods per plant, number of branches per plant, and number of peduncles per plant. Putative genes associated with yield and related traits were identified within significant flanking markers. Further efforts to validate these loci will help to better understand their roles in yield and associated traits in cowpea.

Harnessing Walnut-Based Zinc Oxide Nanoparticles: A Sustainable Approach to Combat the Disease Complex of Meloidogyne arenaria and Macrophomina phaseolina in Cowpea

Zinc oxide nanoparticles (ZnO NPs) exhibit diverse applications, including antimicrobial, UV-blocking, and catalytic properties, due to their unique structure and properties. This study focused on the characterization of zinc oxide nanoparticles (ZnO NPs) synthesized from Juglans regia leaves and their application in mitigating the impact of simultaneous infection by Meloidogyne arenaria (root-knot nematode) and Macrophomina phaseolina (root-rot fungus) in cowpea plants. The characterization of ZnO NPs was carried out through various analytical techniques, including UV-visible spectrophotometry, Powder-XRD analysis, FT-IR spectroscopy, and SEM-EDX analysis. The study confirmed the successful synthesis of ZnO NPs with a hexagonal wurtzite structure and exceptional purity. Under in vitro conditions, ZnO NPs exhibited significant nematicidal and antifungal activities. The mortality of M. arenaria juveniles increased with rising ZnO NP concentrations, and a similar trend was observed in the inhibition of M. phaseolina mycelial growth. SEM studies revealed physical damage to nematodes and structural distortions in fungal hyphae due to ZnO NP treatment. In infected cowpea plants, ZnO NPs significantly improved plant growth parameters, including plant length, fresh mass, and dry mass, especially at higher concentrations. Leghemoglobin content and the number of root nodules also increased after ZnO NP treatment. Additionally, ZnO NPs reduced gall formation and egg mass production by M. arenaria nematodes and effectively inhibited the growth of M. phaseolina in the roots. Furthermore, histochemical analyses demonstrated a reduction in oxidative stress, as indicated by decreased levels of reactive oxygen species (ROS) and lipid peroxidation in ZnO NP-treated plants. These findings highlight the potential of green-synthesized ZnO NPs as an eco-friendly and effective solution to manage disease complex in cowpea caused by simultaneous nematode and fungal infections.

The pattern of genetic variability in a core collection of 2,021 cowpea accessions

Cowpea is a highly drought-adapted leguminous crop with great promise for improving agricultural sustainability and food security. Here, we report analyses derived from array-based genotyping of 2,021 accessions constituting a core subset of the world's largest cowpea collection, held at the International Institute of Tropical Agriculture (IITA) in Ibadan, Nigeria. We used this dataset to examine genetic variation and population structure in worldwide cowpea. We confirm that the primary pattern of population structure is two geographically defined subpopulations originating in West and East Africa, respectively, and that population structure is associated with shifts in phenotypic distribution. Furthermore, we establish the cowpea core collection as a resource for genome-wide association studies by mapping the genetic basis of several phenotypes, with a focus on seed coat pigmentation patterning and color. We anticipate that the genotyped IITA Cowpea Core Collection will serve as a powerful tool for mapping complex traits, facilitating the acceleration of breeding programs to enhance the resilience of this crop in the face of rapid global climate change.

Differential selection of yield and quality traits has shaped genomic signatures of cowpea domestication and improvement

Cowpeas (tropical legumes) are important in ensuring food and nutritional security in developing countries, especially in sub-Saharan Africa. Herein, we report two high-quality genome assemblies of grain and vegetable cowpeas and we re-sequenced 344 accessions to characterize the genomic variations landscape. We identified 39 loci for ten important agronomic traits and more than 541 potential loci that underwent selection during cowpea domestication and improvement. In particular, the synchronous selections of the pod-shattering loci and their neighboring stress-relevant loci probably led to the enhancement of pod-shattering resistance and the compromise of stress resistance during the domestication from grain to vegetable cowpeas. Moreover, differential selections on multiple loci associated with pod length, grain number per pod, seed weight, pod and seed soluble sugars, and seed crude proteins shaped the yield and quality diversity in cowpeas. Our findings provide genomic insights into cowpea domestication and improvement footprints, enabling further genome-informed cultivar improvement of cowpeas.

Proteomic Insights of Cowpea Response to Combined Biotic and Abiotic Stresses

The co-occurrence of biotic and abiotic stresses in agricultural areas severely affects crop performance and productivity. Drought is one of the most adverse environmental stresses, and its association with root-knot nematodes further limits the development of several economically important crops, such as cowpea. Plant responses to combined stresses are complex and require novel adaptive mechanisms through the induction of specific biotic and abiotic signaling pathways. Therefore, the present work aimed to identify proteins involved in the resistance of cowpea to nematode and drought stresses individually and combined. We used the genotype CE 31, which is resistant to the root-knot nematode Meloidogyne spp. And tolerant to drought. Three biological replicates of roots and shoots were submitted to protein extraction, and the peptides were evaluated by LC-MS/MS. Shotgun proteomics revealed 2345 proteins, of which 1040 were differentially abundant. Proteins involved in essential biological processes, such as transcriptional regulation, cell signaling, oxidative processes, and photosynthesis, were identified. However, the main defense strategies in cowpea against cross-stress are focused on the regulation of hormonal signaling, the intense production of pathogenesis-related proteins, and the downregulation of photosynthetic activity. These are key processes that can culminate in the adaptation of cowpea challenged by multiple stresses. Furthermore, the candidate proteins identified in this study will strongly contribute to cowpea genetic improvement programs.

Cowpea Constraints and Breeding in Europe

Cowpea (Vigna unguiculata (L.) Walp.) is a legume with a constant rate of cultivation in Southern European countries. Consumer demand for cowpea worldwide is rising due to its nutritional content, while Europe is constantly attempting to reduce the deficit in the production of pulses and invest in new, healthy food market products. Although the climatic conditions that prevail in Europe are not so harsh in terms of heat and drought as in the tropical climates where cowpea is mainly cultivated, cowpea confronts with a plethora of abiotic and biotic stresses and yield-limiting factors in Southern European countries. In this paper, we summarize the main constraints for cowpea cultivation in Europe and the breeding methods that have been or can be used. A special mention is made of the availability plant genetic resources (PGRs) and their potential for breeding purposes, aiming to promote more sustainable cropping systems as climatic shifts become more frequent and fiercer, and environmental degradation expands worldwide.

Tomato Mi-gene Resistance-Breaking Populations of Meloidogyne Show Variable Reproduction on Susceptible and Resistant Crop Cultivars

Sixteen Meloidogyne isolates from tomato fields in California grown with resistant cultivars were multiplied on resistant tomato in a greenhouse. Of these resistance-breaking isolates, one was identified as M. javanica, and all others as M. incognita. The reproduction of the M. javanica isolate and four M. incognita isolates on six resistant tomato cultivars and on susceptible and resistant cultivars of pepper, sweetpotato, green bean, cotton, and cowpea was evaluated and compared to an avirulent M. incognita population in greenhouse pot trials. On resistant tomato cultivars, there were minor but significant differences between the resistance-breaking Meloidogyne isolates and between the different tomato cultivars. Of the other resistant crop cultivars, pepper was resistant to all isolates and green bean to all M. incognita isolates, while cotton and cowpea allowed reproduction of one of the resistance-breaking M. incognita isolates. The resistant sweetpotato cv. Bonita behaved like resistant tomato, allowing reproduction of all five resistance-breaking isolates but not of the avirulent M. incognita. Our results showed that variability exists among resistance-breaking Meloidogyne isolates, and that isolates overcoming resistance in tomato may also be virulent on resistant sweetpotato.

Breeding of Vegetable Cowpea for Nutrition and Climate Resilience in Sub-Saharan Africa: Progress, Opportunities, and Challenges

Currently, the world population is increasing, and humanity is facing food and nutritional scarcity. Climate change and variability are a major threat to global food and nutritional security, reducing crop productivity in the tropical and subtropical regions of the globe. Cowpea has the potential to make a significant contribution to global food and nutritional security. In addition, it can be part of a sustainable food system, being a genetic resource for future crop improvement, contributing to resilience and improving agricultural sustainability under climate change conditions. In malnutrition prone regions of sub-Saharan Africa (SSA) countries, cowpea has become a strategic dryland legume crop for addressing food insecurity and malnutrition. Therefore, this review aims to assess the contribution of cowpea to SSA countries as a climate-resilient crop and the existing production challenges and perspectives. Cowpea leaves and immature pods are rich in diverse nutrients, with high levels of protein, vitamins, macro and micronutrients, minerals, fiber, and carbohydrates compared to its grain. In addition, cowpea is truly a multifunctional crop for maintaining good health and for reducing non-communicable human diseases. However, as a leafy vegetable, cowpea has not been researched and promoted sufficiently because it has not been promoted as a food security crop due to its low yield potential, susceptibility to biotic and abiotic stresses, quality assurance issues, policy regulation, and cultural beliefs (it is considered a livestock feed). The development of superior cowpea as a leafy vegetable can be approached in different ways, such as conventional breeding and gene stacking, speed breeding, mutation breeding, space breeding, demand-led breeding, a pan-omics approach, and local government policies. The successful breeding of cowpea genotypes that are high-yielding with a good nutritional value as well as having resistance to biotics and tolerant to abiotic stress could also be used to address food security and malnutrition-related challenges in sub-Saharan Africa.

Genetic mapping reveals complex architecture and candidate genes involved in common bean response to Meloidogyne incognita infection

Root-knot nematodes (RKNs), particularly Meloidogyne incognita, are among the most damaging and prevalent agricultural pathogens due to their ability to infect roots of almost all crops. The best strategy for their control is through the use of resistant cultivars. However, laborious phenotyping procedures make it difficult to assess nematode resistance in breeding programs. For common bean, this task is especially challenging because little has been done to discover resistance genes or markers to assist selection. We performed genome-wide association studies and quantitative trait loci mapping to explore the genetic architecture and genomic regions underlying the resistance to M. incognita and to identify candidate resistance genes. Phenotypic data were collected by a high-throughput assay, and the number of egg masses and the root-galling index were evaluated. Complex genetic architecture and independent genomic regions were associated with each trait. Single nucleotide polymorphisms on chromosomes Pv06, Pv07, Pv08, and Pv11 were associated with the number of egg masses, and SNPs on Pv01, Pv02, Pv05, and Pv10 were associated with root-galling. A total of 216 candidate genes were identified, including 14 resistance gene analogs and five differentially expressed in a previous RNA sequencing analysis. Histochemical analysis indicated that reactive oxygen species might play a role in the resistance response. Our findings open new perspectives to improve selection efficiency for RKN resistance, and the candidate genes are valuable targets for functional investigation and gene editing approaches.

Genetic architecture of salt tolerance in a Multi-Parent Advanced Generation Inter-Cross (MAGIC) cowpea population

Background

Previous reports have shown that soil salinity is a growing threat to cowpea production, and thus the need for breeding salt-tolerant cowpea cultivars. A total of 234 Multi-Parent Advanced Generation Inter-Cross (MAGIC) lines along with their 8 founders were evaluated for salt tolerance under greenhouse conditions. The objectives of this study were to evaluate salt tolerance in a multi-parent advanced generation inter-cross (MAGIC) cowpea population, to identify single nucleotide polymorphism (SNP) markers associated with salt tolerance, and to assess the accuracy of genomic selection (GS) in predicting salt tolerance, and to explore possible epistatic interactions affecting salt tolerance in cowpea. Phenotyping was validated through the use of salt-tolerant and salt-susceptible controls that were previously reported. Genome-wide association study (GWAS) was conducted using a total of 32,047 filtered SNPs. The epistatic interaction analysis was conducted using the PLINK platform.

Results

Results indicated that: (1) large variation in traits evaluated for salt tolerance was identified among the MAGIC lines, (2) a total of 7, 2, 18, 18, 3, 2, 5, 1, and 23 were associated with number of dead plants, salt injury score, leaf SPAD chlorophyll under salt treatment, relative tolerance index for leaf SPAD chlorophyll, fresh leaf biomass under salt treatment, relative tolerance index for fresh leaf biomass, relative tolerance index for fresh stem biomass, relative tolerance index for the total above-ground fresh biomass, and relative tolerance index for plant height, respectively, with overlapping SNP markers between traits, (3) candidate genes encoding for proteins involved in ion transport such as Na+/Ca2+ K+ independent exchanger and H+/oligopeptide symporter were identified, and (4) epistatic interactions were identified.

Conclusions

These results will have direct applications in breeding programs aiming at improving salt tolerance in cowpea through marker-assisted selection. To the best of our knowledge, this study was one of the earliest reports using a MAGIC population to investigate the genetic architecture of salt tolerance in cowpea.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08332-y.

Disparate genetic variants associated with distinct components of cowpea resistance to the seed beetle Callosobruchus maculatus

Polygenic genome-wide association mapping identified two regions of the cowpea genome associated with different components of resistance to its major post-harvest pest, the seed beetle Callosobruchus maculatus. Cowpea (Vigna unguiculata) is an important grain and fodder crop in arid and semi-arid regions of Africa, Asia, and South America, where the cowpea seed beetle, Callosobruchus maculatus, is a serious post-harvest pest. Development of cultivars resistant to C. maculatus population growth in storage could increase grain yield and quality and reduce reliance on insecticides. Here, we use a MAGIC (multi-parent, advanced-generation intercross) population of cowpea consisting of 305 recombinant inbred lines (RILs) to identify genetic variants associated with resistance to seed beetles. Because inferences regarding the genetic basis of resistance may depend on the source of the pest or the assay protocol, we used two divergent geographic populations of C. maculatus and two complementary assays to measure several aspects of resistance. Using polygenic genome-wide association mapping models, we found that the cowpea RILs harbor substantial additive-genetic variation for most resistance measures. Variation in several components of resistance, including larval development time and survival, was largely explained by one or several linked loci on chromosome 5. A second region on chromosome 8 explained increased seed resistance via the induction of early-exiting larvae. Neither of these regions contained genes previously associated with resistance to insects that infest grain legumes. We found some evidence of gene-gene interactions affecting resistance, but epistasis did not contribute substantially to resistance variation in this mapping population. The combination of mostly high heritabilities and a relatively consistent and simple genetic architecture increases the feasibility of breeding for enhanced resistance to C. maculatus.

The witchweed Striga gesnerioides and the cultivated cowpea: A geographical and historical analysis of their West African distribution points to the prevalence of agro-ecological factors and the parasite's multilocal evolution potential

The increasing severity of Striga gesnerioides attacks on cowpea across West Africa has been related to its prolificity, seed mobility and longevity, and adaptation to aridity, in a context of agricultural intensification. To understand this fast extension, we analyzed (1) the distributions of the crop and the witchweed with ecological niche modeling and multivariate climate analysis, and (2) the chronological information available from collections and the literature. The ecoclimatic envelope of S. gesnerioides attacks on cowpea is the same as on wild hosts. Consistently, the modeled distribution of cowpea infestations is closely similar to the simple superposition of the parasite model (involving all hosts) and the crop model. Striga gesnerioides infestations are restricted to the driest component of the cultivated cowpea ecoclimatic niche, corresponding to the Sahelian and Sudano-Sahelian belts and the Dahomey gap. Thus, the parasite distribution, determined by its own requirements, does not constrain cowpea cultivation under Guinean climates. The spatial and temporal distributions of S. gesnerioides field infestations are consistent with an earlier impact on cowpea production in eastern West Africa, related itself to a similar trend in cowpea cultivation intensification from Niger, Nigeria and Benin to Burkina Faso and Ghana. Mali and Senegal were affected later, and literature reports of Senegalese strains of S. gesnerioides from the wild developing virulence on cowpea offer a model for the diffusion of witchweed parasitism by multilocal evolution, through host-driven selection, instead of epidemic diffusion. A contrario, in Côte d’Ivoire, cowpea is much less widespread, so the parasite has remained confined to the wild compartment. Thus, both historical and ecogeographic analyses refute the vision of S. gesnerioides as an invader. Instead, they point to the increasing importance and intensification of the crop, and the consequent loss of biodiversity, as the main drivers of the extension and diversification of its crop-specific strains.

Genome-wide association study for resistance to the Meloidogyne javanica causing root-knot nematode in soybean

KEY MESSAGE

A locus on chromosome 13, containing multiple TIR-NB-LRR genes and SNPs associated with M. javanica resistance, was identified using a combination of GWAS, resequencing, genetic mapping and expression profiling. Meloidogyne javanica, a root-knot nematode, is an important problem in soybean-growing areas, leading to severe yield losses. Some accessions have been identified carrying resistance loci to this nematode. In this study, a set of 317 soybean accessions was characterized for resistance to M. javanica. A genome-wide association study was performed using SNPs from genotyping-by-sequencing, and a region of 29.2 kb on chromosome 13 was identified. An analysis of haplotypes showed that SNPs were able to discriminate between susceptible and resistant accessions, with 25 accessions sharing the haplotype associated with resistance. Furthermore, five accessions that exhibited resistance without carrying this haplotype may carry different loci conferring resistance to M. javanica. We also conducted the screening of the SNPs in the USDA soybean germplasm, revealing that several soybean accessions previously reported as resistant to other nematodes also shared the resistance haplotype on chromosome 13. Two SNP-based TaqMan® assays were developed and validated in two panels of soybean cultivars and in biparental populations. In silico analysis of the region associated with resistance identified the occurrence of genes with structural similarity with classical major resistance genes (NBS-LRR genes). Specifically, several nonsynonymous SNPs were observed in Glyma.13g194800 and Glyma.13g194900. The expression profile of these candidate genes demonstrated that the two gene models were up-regulated in the resistance source PI 505,099 after nematode infection. Overall, the SNPs associated with resistance and the genes identified constitute an important tool for introgression of resistance to the root-knot nematode by marker-assisted selection in soybean breeding programs.

Loci discovery, network-guided approach, and genomic prediction for drought tolerance index in a multi-parent advanced generation intercross (MAGIC) cowpea population

Cowpea is a nutrient-dense legume that significantly contributes to the population's diet in sub-Saharan Africa and other regions of the world. Improving cowpea cultivars to be more resilient to abiotic stress such as drought would be of great importance. The use of a multi-parent advanced generation intercross (MAGIC) population has been shown to be efficient in increasing the frequency of rare alleles that could be associated with important agricultural traits. In addition, drought tolerance index has been reported to be a reliable parameter for assessing crop tolerance to water-deficit conditions. Therefore, the objectives of this study were to evaluate the drought tolerance index for plant growth habit, plant maturity, flowering time, 100-seed weight, and grain yield in a MAGIC cowpea population, to conduct genome-wide association study (GWAS) and identify single nucleotide polymorphism (SNP) markers associated with the drought tolerance indices, to investigate the potential relationship existing between the significant loci associated with the drought tolerance indices, and to conduct genomic selection (GS). These analyses were performed using the existing phenotypic and genotypic data published for the MAGIC population which consisted of 305 F8 recombinant inbred lines (RILs) developed at University of California, Riverside. The results indicated that: (1) large variation in drought tolerance indices existed among the cowpea genotypes, (2) a total of 14, 18, 5, 5, and 35 SNPs were associated with plant growth habit change due to drought stress, and drought tolerance indices for maturity, flowering time, 100-seed weight, and grain yield, respectively, (3) the network-guided approach revealed clear interactions between the loci associated with the drought tolerance traits, and (4) the GS accuracy varied from low to moderate. These results could be applied to improve drought tolerance in cowpea through marker-assisted selection (MAS) and genomic selection (GS). To the best of our knowledge, this is the first report on marker loci associated with drought tolerance indices in cowpea.

Developing the role of legumes in West Africa under climate change

West Africa is faced with significant challenges from climate change, including parts of the region becoming hotter with more variable rainfall. The Sahelian region in particular is already subject to severe droughts. To address this better adapted crop varieties (such as for cowpea) are clearly a central element, a complementary one is a greater use of resilient alternative crops especially underutilized legumes particularly Bambara groundnut, African yam bean, winged bean and Kersting's groundnut. Genetic diversity of these crops conserved in genebanks and farmer's field provides an opportunity to exploit climate resilient traits using cutting-edge genomic tools and to use genomics-assisted breeding to accelerate genetic gains in combination of rapid cycle breeding strategy to develop climate-resilient cultivars for sub-Saharan Africa.

Construction, characteristics and high throughput molecular screening methodologies in some special breeding populations: a horticultural perspective

Advanced marker technologies are widely used for evaluation of genetic diversity in cultivated crops, wild ancestors, landraces or any special plant genotypes. Developing agricultural cultivars requires the following steps: (i) determining desired characteristics to be improved, (ii) screening genetic resources to help find a superior cultivar, (iii) intercrossing selected individuals, (iv) generating genetically hybrid populations and screening them for agro-morphological or molecular traits, (v) evaluating the superior cultivar candidates, (vi) testing field performance at different locations, and (vii) certifying. In the cultivar development process valuable genes can be identified by creating special biparental or multiparental populations and analysing their association using suitable markers in given populations. These special populations and advanced marker technologies give us a deeper knowledge about the inherited agronomic characteristics. Unaffected by the changing environmental conditions, these provide a higher understanding of genome dynamics in plants. The last decade witnessed new applications for advanced molecular techniques in the area of breeding,with low costs per sample. These, especially, include next-generation sequencing technologies like reduced representation genome sequencing (genotyping by sequencing, restriction site-associated DNA). These enabled researchers to develop new markers, such as simple sequence repeat and single- nucleotide polymorphism, for expanding the qualitative and quantitative information onpopulation dynamics. Thus, the knowledge acquired from novel technologies is a valuable asset for the breeding process and to better understand the population dynamics, their properties, and analysis methods.

Towards Exploitation of Adaptive Traits for Climate-Resilient Smart Pulses

Pulses are the main source of protein and minerals in the vegetarian diet. These are primarily cultivated on marginal lands with few inputs in several resource-poor countries of the world, including several in South Asia. Their cultivation in resource-scarce conditions exposes them to various abiotic and biotic stresses, leading to significant yield losses. Furthermore, climate change due to global warming has increased their vulnerability to emerging new insect pests and abiotic stresses that can become even more serious in the coming years. The changing climate scenario has made it more challenging to breed and develop climate-resilient smart pulses. Although pulses are climate smart, as they simultaneously adapt to and mitigate the effects of climate change, their narrow genetic diversity has always been a major constraint to their improvement for adaptability. However, existing genetic diversity still provides opportunities to exploit novel attributes for developing climate-resilient cultivars. The mining and exploitation of adaptive traits imparting tolerance/resistance to climate-smart pulses can be accelerated further by using cutting-edge approaches of biotechnology such as transgenics, genome editing, and epigenetics. This review discusses various classical and molecular approaches and strategies to exploit adaptive traits for breeding climate-smart pulses.

A Novel QTL for Root-Knot Nematode Resistance is Identified from a South African Sweet Sorghum Line

Southern root-knot nematodes, Meloidogyne incognita, feed on the underground portions of hundreds of plant species and affect nutrient partitioning and water uptake of the host plants. Sorghum (Sorghum bicolor) is often not significantly damaged by southern root-knot nematodes (RKN) but some sorghum genotypes support greater population densities of RKN than other genotypes. These higher nematode populations increase the risk of damage to subsequently planted susceptible crops. A previous study identified a major quantitative trait locus (QTL) for RKN resistance on sorghum chromosome (chr.) 3. To maintain long-term resistance, multiple resistance genes should be pyramided in a cultivar. In this study, we identified a new source of RKN resistance, created a mapping population, and identified single-nucleotide polymorphism markers using genotyping-by-sequencing of the segregating population. Use of single-marker analysis and composite interval mapping identified a single QTL on chr. 5 that was associated with egg number and egg number per gram of root from the resistant sweet sorghum line PI 144134. This region on chr. 5 and the prior QTL on chr. 3 can be potentially moved from PI 144134 and Honey Drip, respectively, into elite sorghum germplasm via marker-assisted selection for more durable resistance.

A Novel Root-Knot Nematode Resistance QTL on Chromosome Vu01 in Cowpea

The root-knot nematode (RKN) species Meloidogyne incognita and M. javanica cause substantial root system damage and suppress yield of susceptible cowpea cultivars. The narrow-based genetic resistance conferred by the Rk gene, present in some commercial cultivars, is not effective against Rk-virulent populations found in several cowpea production areas. The dynamics of virulence within RKN populations require a broadening of the genetic base of resistance in elite cowpea cultivars. As part of this goal, F1 and F2 populations from the cross CB46-Null (susceptible) x FN-2-9-04 (resistant) were phenotyped for M. javanica induced root-galling (RG) and egg-mass production (EM) in controlled growth chamber and greenhouse infection assays. In addition, F[Formula: see text] families of the same cross were phenotyped for RG on field sites infested with Rk-avirulent M. incognita and M. javanica The response of F1 to RG and EM indicated that resistance to RKN in FN-2-9-04 is partially dominant, as supported by the degree of dominance in the F2 and F[Formula: see text] populations. Two QTL associated with both RG and EM resistance were detected on chromosomes Vu01 and Vu04. The QTL on Vu01 was most effective against aggressive M. javanica, whereas both QTL were effective against avirulent M. incognita Allelism tests with CB46 x FN-2-9-04 progeny indicated that these parents share the same RKN resistance locus on Vu04, but the strong, broad-based resistance in FN-2-9-04 is conferred by the additive effect of the novel resistance QTL on Vu01. This novel resistance in FN-2-9-04 is an important resource for broadening RKN resistance in elite cowpea cultivars.

Genome-wide identification and functional prediction of tobacco lncRNAs responsive to root-knot nematode stress

Root-knot nematodes (RKNs, Meloidogyne spp.) are destructive plant parasites with a wide host range. They severely reduce crop quality and yield worldwide. Tobacco is a versatile model plant organism for studying RKNs-host interactions and a key plant material for molecular research. Long noncoding RNAs (lncRNAs) play critical roles in post transcriptional and transcriptional regulation in a wide range of biological pathways, especially plant development and stress response. In the present study, we obtained 5,206 high-confidence lncRNAs based on RNA sequencing data. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed that the target genes of these lncRNAs are mainly involved in plant biotic and abiotic stresses, plant hormone signal transduction, induced systemic resistance, plant-type hypersensitive response, plant-type cell wall organization or biogenesis. The 565 differentially expressed lncRNAs found to be involved in nematode stress response were validated by quantitative PCR using 15 randomly-selected lncRNA genes. Our study provides insights into the molecular mechanisms of RKNs-plant interactions that might help preventing nematode damages to crops.

Quantitative trait loci analysis of brown blotch resistance in cowpea variety KN1

Cowpea is one of the most important crops in West Africa and is essential for the region's food and nutrition security and economic development. Consequently, improving its agronomic performance and yield is a desirable goal. Brown blotch disease, caused by the fungal pathogen Colletotrichum capsici, is an important constraint of cowpea productivity, and at present, only limited genetic resources are available for breeding improved brown blotch-resistant varieties. The current study has characterized the genetic basis for brown blotch resistance conferred by the cowpea cultivar KN1 and identified a major dominant quantitative trait locus (QTL) for resistance on chromosome Vu02. A segregating F₂ population (n = 200), derived from a cross between KN1 and brown blotch-susceptible Tiligre (KVx775-33-2G), was developed and scored for disease severity following controlled inoculation. A subset of the population (n = 94) was genotyped with 99 newly developed allele-specific polymerase chain reaction (AS-PCR) markers, and multiple interval mapping was performed. One major and three minor QTL were identified. This is the first reported mapping of QTL conferring resistance to C. capsici in cowpea, and it is expected that the markers identified here will be a valuable resource for developing elite cowpea cultivars with resistance to brown blotch.

A multi-parent advanced generation inter-cross (MAGIC) population for genetic analysis and improvement of cowpea (Vigna unguiculata L. Walp.)

Multi-parent advanced generation inter-cross (MAGIC) populations are an emerging type of resource for dissecting the genetic structure of traits and improving breeding populations. We developed a MAGIC population for cowpea (Vigna unguiculata L. Walp.) from eight founder parents. These founders were genetically diverse and carried many abiotic and biotic stress resistance, seed quality and agronomic traits relevant to cowpea improvement in the United States and sub-Saharan Africa, where cowpea is vitally important in the human diet and local economies. The eight parents were inter-crossed using structured matings to ensure that the population would have balanced representation from each parent, followed by single-seed descent, resulting in 305 F₈ recombinant inbred lines each carrying a mosaic of genome blocks contributed by all founders. This was confirmed by single nucleotide polymorphism genotyping with the Illumina Cowpea Consortium Array. These lines were on average 99.74% homozygous but also diverse in agronomic traits across environments. Quantitative trait loci (QTLs) were identified for several parental traits. Loci with major effects on photoperiod sensitivity and seed size were also verified by biparental genetic mapping. The recombination events were concentrated in telomeric regions. Due to its broad genetic base, this cowpea MAGIC population promises breakthroughs in genetic gain, QTL and gene discovery, enhancement of breeding populations and, for some lines, direct releases as new varieties.

QTL mapping and transcriptome analysis of cowpea reveals candidate genes for root-knot nematode resistance

Cowpea is one of the most important food and forage legumes in drier regions of the tropics and subtropics. However, cowpea yield worldwide is markedly below the known potential due to abiotic and biotic stresses, including parasitism by root-knot nematodes (Meloidogyne spp., RKN). Two resistance genes with dominant effect, Rk and Rk2, have been reported to provide resistance against RKN in cowpea. Despite their description and use in breeding for resistance to RKN and particularly genetic mapping of the Rk locus, the exact genes conferring resistance to RKN remain unknown. In the present work, QTL mapping using recombinant inbred line (RIL) population 524B x IT84S-2049 segregating for a newly mapped locus and analysis of the transcriptome changes in two cowpea near-isogenic lines (NIL) were used to identify candidate genes for Rk and the newly mapped locus. A major QTL, designated QRk-vu9.1, associated with resistance to Meloidogyne javanica reproduction, was detected and mapped on linkage group LG9 at position 13.37 cM using egg production data. Transcriptome analysis on resistant and susceptible NILs 3 and 9 days after inoculation revealed up-regulation of 109 and 98 genes and down-regulation of 110 and 89 genes, respectively, out of 19,922 unique genes mapped to the common bean reference genome. Among the differentially expressed genes, four and nine genes were found within the QRk-vu9.1 and QRk-vu11.1 QTL intervals, respectively. Six of these genes belong to the TIR-NBS-LRR family of resistance genes and three were upregulated at one or more time-points. Quantitative RT-PCR validated gene expression to be positively correlated with RNA-seq expression pattern for eight genes. Future functional analysis of these cowpea genes will enhance our understanding of Rk-mediated resistance and identify the specific gene responsible for the resistance.

Broad-based root-knot nematode resistance identified in cowpea gene-pool two

Cowpea (Vigna unguiculata L. Walp) is an affordable source of protein and strategic legume crop for food security in Africa and other developing regions; however, damage from infection by root-knot nematodes (RKN) suppresses cowpea yield. The deployment through breeding of resistance gene Rk in cowpea cultivars has provided protection to cowpea growers worldwide for many years. However, occurrence of more aggressive nematode isolates threatens the effectiveness of this monogenic resistance. A cowpea germplasm collection of 48 genotypes representing the cowpea gene-pool from Eastern and Southern Africa (cowpea has two major pools of genetic resources - Western Africa and Eastern/Southern Africa) was screened in replicated experiments under field, greenhouse and controlled-growth conditions to identify resistance to RKN, to determine the spectrum of resistance to RKN, the relative virulence (VI) among RKN species and isolates, and the relationship between root-galling (RG) and egg-mass production (EM). Analysis of variance of data for RG and EM per root system identified seven genotypes with broad-based resistance to Meloidogyne javanica (Mj), avirulent (Avr-Mi), and virulent (Mi) M. incognita isolates. Two of the 48 genotypes exhibited specific resistance to both Mi isolates. Most of the genotypes were resistant to Avr-Mi indicating predominance of Rk gene in the collection. Based on RG data, both Mj (VI = 50%) and Mi (VI = 42%) were fourfold more virulent than Avr-Mi (VI = 12%). Resistant genotypes had more effective resistance than the Rk-based resistance in cowpea genotype CB46 against Mj and Mi. Root-galling was correlated across isolates (Avr-Mi/Mj: r = 0.72; Mi/Mj: r = 0.98), and RG was correlated with EM (r = 0.60), indicating resistance to RG and EM is under control by the same genetic factors. These new sources of resistance identified in cowpea gene-pool two provide valuable target traits for breeders to improve cowpea production on RKN-infested fields.

Cowpea (Vigna unguiculata L. Walp) is an affordable source of protein and strategic legume crop for food security in Africa and other developing regions; however, damage from infection by root-knot nematodes (RKN) suppresses cowpea yield. The deployment through breeding of resistance gene Rk in cowpea cultivars has provided protection to cowpea growers worldwide for many years. However, occurrence of more aggressive nematode isolates threatens the effectiveness of this monogenic resistance. A cowpea germplasm collection of 48 genotypes representing the cowpea gene-pool from Eastern and Southern Africa (cowpea has two major pools of genetic resources – Western Africa and Eastern/Southern Africa) was screened in replicated experiments under field, greenhouse and controlled-growth conditions to identify resistance to RKN, to determine the spectrum of resistance to RKN, the relative virulence (VI) among RKN species and isolates, and the relationship between root-galling (RG) and egg-mass production (EM). Analysis of variance of data for RG and EM per root system identified seven genotypes with broad-based resistance to Meloidogyne javanica (Mj), avirulent (Avr-Mi), and virulent (Mi) M. incognita isolates. Two of the 48 genotypes exhibited specific resistance to both Mi isolates. Most of the genotypes were resistant to Avr-Mi indicating predominance of Rk gene in the collection. Based on RG data, both Mj (VI = 50%) and Mi (VI = 42%) were fourfold more virulent than Avr-Mi (VI = 12%). Resistant genotypes had more effective resistance than the Rk-based resistance in cowpea genotype CB46 against Mj and Mi. Root-galling was correlated across isolates (Avr-Mi/Mj: r = 0.72; Mi/Mj: r = 0.98), and RG was correlated with EM (r = 0.60), indicating resistance to RG and EM is under control by the same genetic factors. These new sources of resistance identified in cowpea gene-pool two provide valuable target traits for breeders to improve cowpea production on RKN-infested fields.

Application of seed germination pouch for culture and initial resistance screening of the soybean cyst nematode Heterodera glycines

Seed germination pouches or seedling growth pouches have been utilised previously for high throughput resistance screening of root-knot nematodes, Meloidogyne spp., on legume plants. In this study we demonstrated that soybean cyst nematode (SCN) Heterodera glycines, with a different reproduction mode from root-knot nematode, is also able to invade, complete its life cycle and reproduce in soybean roots in seedling pouches similar to the pot system with soil, indicating seedling pouches can be utilised as an alternate SCN culture method when glasshouse/growth chamber space is limited. Moreover, seedling pouches provide an easy approach to collect large numbers of clean male nematodes, which could accelerate SCN biological study such as SCN mating behaviour and molecular signals associated with mating. The results of SCN resistance screening indicate that seedling pouches could be utilised for initial resistance screening with SCN.

Variation in relative water content, proline accumulation and stress gene expression in two cowpea landraces under drought

Many landraces of cowpea [Vigna unguiculata (L.) Walp.] are adapted to particular geographical and climatic conditions. Here we describe two landraces grown respectively in arid and temperate areas of Algeria and assess their physiological and molecular responses to drought stress. As expected, when deprived of water cowpea plants lose water over time with a gradual reduction in transpiration rate. The landraces differed in their relative water content (RWC) and whole plant transpiration rate. The landrace from Menia, an arid area, retained more water in adult leaves. Both landraces responded to drought stress at the molecular level by increasing expression of stress-related genes in aerial parts, including proline metabolism genes. Expression of gene(s) encoding proline synthesis enzyme P5CS was up regulated and gene expression of ProDH, a proline catabolism enzyme, was down regulated. Relatively low amounts of proline accumulated in adult leaves with slight differences between the two landraces. During drought stress the most apical part of plants stayed relatively turgid with a high RWC compared to distal parts that wilted. Expression of key stress genes was higher and more proline accumulated at the apex than in distal leaves indicating that cowpea has a non-uniform stress response at the whole plant level. Our study reveals a developmental control of water stress through preferential proline accumulation in the upper tier of the cowpea plant. We also conclude that cowpea landraces display physiological adaptations to water stress suited to the arid and temperate climates in which they are cultivated.

Molecular, Genetic and Agronomic Approaches to Utilizing Pulses as Cover Crops and Green Manure into Cropping Systems

Cover crops constitute one of the most promising agronomic practices towards a more sustainable agriculture. Their beneficial effects on main crops, soil and environment are many and various, while risks and disadvantages may also appear. Several legumes show a high potential but further research is required in order to suggest the optimal legume cover crops for each case in terms of their productivity and ability to suppress weeds. The additional cost associated with cover crops should also be addressed and in this context the use of grain legumes such as cowpea, faba bean and pea could be of high interest. Some of the aspects of these grain legumes as far as their use as cover crops, their genetic diversity and their breeding using conventional and molecular approaches are discussed in the present review. The specific species seem to have a high potential for use as cover crops, especially if their noticeable genetic diversity is exploited and their breeding focuses on several desirable traits.

Genome-wide association mapping and agronomic impact of cowpea root architecture

Genetic analysis of data produced by novel root phenotyping tools was used to establish relationships between cowpea root traits and performance indicators as well between root traits and Striga tolerance. Selection and breeding for better root phenotypes can improve acquisition of soil resources and hence crop production in marginal environments. We hypothesized that biologically relevant variation is measurable in cowpea root architecture. This study implemented manual phenotyping (shovelomics) and automated image phenotyping (DIRT) on a 189-entry diversity panel of cowpea to reveal biologically important variation and genome regions affecting root architecture phenes. Significant variation in root phenes was found and relatively high heritabilities were detected for root traits assessed manually (0.4 for nodulation and 0.8 for number of larger laterals) as well as repeatability traits phenotyped via DIRT (0.5 for a measure of root width and 0.3 for a measure of root tips). Genome-wide association study identified 11 significant quantitative trait loci (QTL) from manually scored root architecture traits and 21 QTL from root architecture traits phenotyped by DIRT image analysis. Subsequent comparisons of results from this root study with other field studies revealed QTL co-localizations between root traits and performance indicators including seed weight per plant, pod number, and Striga (Striga gesnerioides) tolerance. The data suggest selection for root phenotypes could be employed by breeding programs to improve production in multiple constraint environments.

Genomic Tools in Cowpea Breeding Programs: Status and Perspectives

Cowpea is one of the most important grain legumes in sub-Saharan Africa (SSA). It provides strong support to the livelihood of small-scale farmers through its contributions to their nutritional security, income generation and soil fertility enhancement. Worldwide about 6.5 million metric tons of cowpea are produced annually on about 14.5 million hectares. The low productivity of cowpea is attributable to numerous abiotic and biotic constraints. The abiotic stress factors comprise drought, low soil fertility, and heat while biotic constraints include insects, diseases, parasitic weeds, and nematodes. Cowpea farmers also have limited access to quality seeds of improved varieties for planting. Some progress has been made through conventional breeding at international and national research institutions in the last three decades. Cowpea improvement could also benefit from modern breeding methods based on molecular genetic tools. A number of advances in cowpea genetic linkage maps, and quantitative trait loci associated with some desirable traits such as resistance to Striga, Macrophomina, Fusarium wilt, bacterial blight, root-knot nematodes, aphids, and foliar thrips have been reported. An improved consensus genetic linkage map has been developed and used to identify QTLs of additional traits. In order to take advantage of these developments single nucleotide polymorphism (SNP) genotyping is being streamlined to establish an efficient workflow supported by genotyping support service (GSS)-client interactions. About 1100 SNPs mapped on the cowpea genome were converted by LGC Genomics to KASP assays. Several cowpea breeding programs have been exploiting these resources to implement molecular breeding, especially for MARS and MABC, to accelerate cowpea variety improvement. The combination of conventional breeding and molecular breeding strategies, with workflow managed through the CGIAR breeding management system (BMS), promises an increase in the number of improved varieties available to farmers, thereby boosting cowpea production and productivity in SSA.