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Molecular markers are increasingly being deployed to accelerate genetic gain in crop plants. The objective of this study was to assess the potential of a mid-density genotyping panel for molecular applications in cowpea breeding. A core set of 2,602 targeted diversity array technology (DArTag) single-nucleotide polymorphisms (SNPs) was designed from an existing 51,128 Cowpea iSelect Consortium Array. The panels usefulness was assessed using 376 genotypes from different populations of known genetic backgrounds. The panel was informative, with over 78% of SNPs exceeding a minor allele frequency of 0.20. The panel decoded three stratifications in the constituted population, as was expected. Linkage disequilibrium (LD) decay was correctly depicted as slower in a biparental subset than in other populations. A known flower and seed coat color gene region was located on chromosome Vu07, suggesting that the mid-density panel may be used to hypothesize genomic regions underlying target traits in cowpea. Unexpected heterozygosity was detected in some lines and highly among F1 progenies, divulging the panels potential application in germplasm purity and hybridity verification. The study unveils the potential of an excellent genomic resource that can be tapped to enhance the development of improved cowpea cultivars.

Perennial habit and floral scent are major traits that distinguish domesticated cowpeas from their wild relatives. However, the genetic basis of these two important traits remains largely unknown in cowpea. Plant longevity, a perenniality-related trait, and floral scent, an outcrossing trait, were investigated using a RIL population derived from a cross between a domesticated and a wild cowpea. QTL analysis revealed three significant loci, one on chromosome 8 associated with plant longevity and two, on chromosomes 1 and 11, for floral scent. Genes within the QTL regions were identified. Genes encoding an F-box protein (Vigun08g215300) and two kinases (Vigun08g217000, Vigun08g217800), and involved in physiological processes including regulation of flowering time and plant longevity, were identified within the perenniality QTL region. A cluster of O-methyltransferase genes (Vigun11g096800, Vigun11g096900, Vigun11g097000, Vigun11g097600, and Vigun11g097800) was identified within the floral scent QTL region. These O-methyltransferase cowpea genes are orthologs of the Arabidopsis N-acetylserotonin O-methyltransferase (ASMT) gene, which is involved in the biosynthesis of melatonin. Melatonin is an indole derivative, which is an essential molecule for plant interactions with pollinators. These findings lay the foundation for further exploration of the genetic mechanisms of perenniality and floral scent in cowpea. Knowledge from this study can help in the development of new extended-growth cycle lines with increased yield or lines with increased outcrossing for population breeding.

Assessment of the genetic variability is an important step in improving nitrogen (N2) fixation potential of faba bean (Vicia faba L.) genotypes. The study was conducted to evaluate the genotypic variation for symbiotic N2 fixation traits of faba bean under contrasting phosphorus (P) fertilizer regimes. Twenty and 12 genotypes in the field and greenhouse, respectively, were planted under two P fertilizer regimes (P− and P+ corresponding to 0 and 46 kg/ha) using a randomized complete block design with three replications. Analysis of variance indicated highly significant (p < 0.01) variation among genotypes for all N2 fixation traits under both P regimes, indicating the availability of genotypic variation. Genotypes Obse, Dosha, Didea, Gebelcho, Gora, Moti, and Hachalu had better performance for N2 fixation traits and higher grain yield (GY) across all study conditions. Performances of all N2 fixation traits, except nitrogen harvest index, were better under P+ than under P−. P fertilizer application in the field resulted in 12.3, 12.9%, 18.9%, and 24.2% increase in the number of nodules per plant, nodule dry weight per plant (NDWP), N2 yield (NY), and the amount of N2 fixed (NF), respectively. In the greenhouse, 18.9%, 22.5%, and 27.2% increment was obtained for NDWP, NY, and NF, respectively, due to fertilizer application. Biplot analysis revealed that NF, NY, percentage of nitrogen derived from atmosphere (%Ndfa), shoot nitrogen concentration (ShN), and GY were the traits responsible for large genetic variation for N2 fixation. NF had higher heritability and formed a significant positive correlation with most nitrogen fixation traits, suggesting the potential of the trait to be improved through breeding. Core Ideas: The performance of all nitrogen fixation traits was significantly reduced under phosphorus‐unfertilized treatments.The faba bean genotypes were significantly different for all N2 fixation traits under both soil phosphorus regimes.Genotypes that had higher N2 fixation performance had higher grain yield. [ABSTRACT FROM AUTHOR]

Cowpea is one of the most important leguminous crops in Sub-Saharan Africa (SSA), and moisture stress is among the constraints affecting its productivity. This study was conducted to understand the response of cowpea accessions to moisture stress. A total of 255 cowpea accessions from Togo and four checks from the International Institute of Tropical Agriculture (IITA), were assessed. The trials were conducted in the glasshouse and an open field (which was divided into moisture-stressed (MS) and non-moisture-stressed fields (NMS)). In the non-moisture-stressed environment compared to the moisture-stressed environment, there was a greater heritability for agronomic traits such as biomass, seed weight, and pod weight. The accessions with the highest seed weights (yield-related traits), surpassing the checks under both moisture-stressed and non-moisture-stressed conditions in the field, were six viz.: RK173 (49.8 g (MS); 90.4 g (NMS)), RP225 (34.6 g (MS); 119.9 g (NMS)), RP232 (33.4 g (MS); 51.9 g (NMS)), RM357 (27.9 g (MS); 62.9 g (NMS)), RK148 (23.9 g (MS); 63.4 g (NMS)), and Vu081_2_2 (21.8 g (MS); 46.7 g (NMS)). The most promising accession was RK173; this was ranked first under the moisture-stressed condition and ranked second under the non-moisture-stressed condition with a loss in weight of 44.9% due to drought stress. Of the top 20 accessions that recovered after watering resumed in the glasshouse screening, only the following 9 had a recovery percentage higher than 5% viz.: RS029 (34.5%), RK014 (14.2%), RS114 (9.6%), RK121 (8.3%), RS007 (7.6%), RK123 (7.3%), RS037 (7.3%), RS101 (5.6%), and RS108 (5.1%). The best line and those with a higher recovery percentage could be exploited further in order to improve them in future drought breeding programs by crossing them with lines susceptible to drought or using other drought breeding techniques. [ABSTRACT FROM AUTHOR]

Cowpea (Vigna unguiculata L. Walp) is a warm-season legume with a genetically diverse gene-pool composed of wild and cultivated forms. Cowpea domestication involved considerable phenotypic changes from the wild progenitor, including reduction of pod shattering, increased organ size, and changes in flowering time. Little is known about the genetic basis underlying these changes. In this study, 215 recombinant inbred lines derived from a cross between a cultivated and a wild cowpea accession were used to evaluate nine domestication-related traits (pod shattering, peduncle length, flower color, days to flowering, 100-seed weight, pod length, leaf length, leaf width and seed number per pod). A high-density genetic map containing 17,739 single nucleotide polymorphisms was constructed and used to identify 16 quantitative trait loci (QTL) for these nine traits. Based on annotations of the cowpea reference genome, genes within these regions are reported. Four regions with clusters of QTL were identified, including one on chromosome 8 related to increased organ size. This study provides new knowledge of the genomic regions controlling domestication-related traits in cowpea as well as candidate genes underlying those QTL. This information can help to exploit wild relatives in cowpea breeding programs.

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.

Cowpea (Vigna unguiculata L. Walp.) is a legume crop that is resilient to hot and drought-prone climates, and a primary source of protein in sub-Saharan Africa and other parts of the developing world. However, genome resources for cowpea have lagged behind most other major crops. Here we describe foundational genome resources and their application to the analysis of germplasm currently in use in West African breeding programs. Resources developed from the African cultivar IT97K-499-35 include a whole-genome shotgun (WGS) assembly, a bacterial artificial chromosome (BAC) physical map, and assembled sequences from 4355 BACs. These resources and WGS sequences of an additional 36 diverse cowpea accessions supported the development of a genotyping assay for 51 128 SNPs, which was then applied to five bi-parental RIL populations to produce a consensus genetic map containing 37 372 SNPs. This genetic map enabled the anchoring of 100 Mb of WGS and 420 Mb of BAC sequences, an exploration of genetic diversity along each linkage group, and clarification of macrosynteny between cowpea and common bean. The SNP assay enabled a diversity analysis of materials from West African breeding programs. Two major subpopulations exist within those materials, one of which has significant parentage from South and East Africa and more diversity. There are genomic regions of high differentiation between subpopulations, one of which coincides with a cluster of nodulin genes. The new resources and knowledge help to define goals and accelerate the breeding of improved varieties to address food security issues related to limited-input small-holder farming and climate stress.

Background/Objectives: Hybridity authentication is an important component of quality assurance and control (QA/QC) in breeding programs. Here, we introduce HybridQC v1.0, a QA/QC software program specially designed for parental purity and hybridity determination. HybridQC rapidly detects molecular marker polymorphism between parents of a cross and utilizes only the informative markers for hybridity authentication. Methods: HybridQC is written in Python and designed with a graphical user interface (GUI) compatible with Windows operating systems. We demonstrated the QA/QC analysis workflow and functionality of HybridQC using Kompetitive allele-specific PCR (KASP) SNP genotype data for cowpea (Vigna unguiculata). Its performance was validated in other crop data, including sorghum (Sorghum bicolor) and maize (Zea mays). Results: The application efficiently analyzed low-density SNP data from multiple cowpea bi-parental crosses embedded in a single Microsoft Excel file. HybridQC is optimized for the auto-generation of key summary statistics and visualization patterns for marker polymorphism, parental heterozygosity, non-parental alleles, missing data, and F1 hybridity. An added graphical interface correctly depicted marker efficiency and the proportions of true F1 versus self-fertilized progenies in the data sets used. The output of HybridQC was consistent with the results of manual hybridity discernment in sorghum and maize data sets. Conclusions: This application uses QA/QC SNP markers to rapidly verify true F1 progeny. It eliminates the extensive time often required to manually curate and process QA/QC data. This tool will enhance the optimization efforts in breeding programs, contributing to increased genetic gain. [ABSTRACT FROM AUTHOR]

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.

Abstract Background Cowpea [Vigna unguiculata (L.) Walp] exhibits a considerable variation in leaf shape. Although cowpea is mostly utilized as a dry grain and animal fodder crop, cowpea leaves are also used as a high-protein pot herb in many countries of Africa. Results Leaf morphology was studied in the cowpea RIL population, Sanzi (sub-globose leaf shape) x Vita 7 (hastate leaf shape). A QTL for leaf shape, Hls (hastate leaf shape), was identified on the Sanzi x Vita 7 genetic map spanning from 56.54 cM to 67.54 cM distance on linkage group 15. SNP marker 1_0910 was the most significant over the two experiments, accounting for 74.7% phenotypic variance (LOD 33.82) in a greenhouse experiment and 71.5% phenotypic variance (LOD 30.89) in a field experiment. The corresponding Hls locus was positioned on the cowpea consensus genetic map on linkage group 4, spanning from 25.57 to 35.96 cM. A marker-trait association of the Hls region identified SNP marker 1_0349 alleles co-segregating with either the hastate or sub-globose leaf phenotype. High co-linearity was observed for the syntenic Hls region in Medicago truncatula and Glycine max. One syntenic locus for Hls was identified on Medicago chromosome 7 while syntenic regions for Hls were identified on two soybean chromosomes, 3 and 19. In all three syntenic loci, an ortholog for the EZA1/SWINGER (AT4G02020.1) gene was observed and is the candidate gene for the Hls locus. The Hls locus was identified on the cowpea physical map via SNP markers 1_0910, 1_1013 and 1_0992 which were identified in three BAC contigs; contig926, contig821 and contig25. Conclusions This study has demonstrated how integrated genomic resources can be utilized for a candidate gene approach. Identification of genes which control leaf morphology may be utilized to improve the quality of cowpea leaves for vegetable and or forage markets as well as contribute to more fundamental research understanding the control of leaf shape in legumes.

Three hundred and ninety accessions comprising 260 cultivated and 130 wild cowpea accessions were evaluated phenotypically using 27 cowpea descriptors. Morphological evaluation of some qualitative traits revealed 11.92% and 29.23% presence of pigmentation on the stem, 1.53% and 20.76% presence of stripes on the pod, and 0% and 20% presence of hairiness on the plant of cultivated and wild cowpeas respectively. As for the molecular analysis, sixteen SSR primers were employed for genotyping 48 accessions from both wild and cultivated cowpeas. The data generated a dendrogram with three clusters, two of which consisted of wild cowpea while the third cluster comprised all the cultivated cowpeas, including the yard-long-bean (Vigna unguiculata subsp. sesquipedalis) and Vigna unguiculata subsp. cylindrica accessions. Two wild accessions of subsp. dekindtiana, and one each of subsp. kgalagadensis and protracta clustered with cultivated cowpea indicating their relationships with cultivated cowpea, but not with other wild cowpeas. The numbers of polymorphic SSR bands in cultivated and wild cowpeas were 38 and 54, respectively, while the PIC values were 4.47 and 6.14, respectively, showing a greater genetic diversity in wild than in cultivated cowpeas. The subsp. dekindtiana had the highest number (80%) of shared SSR bands with cultivated cowpea followed by subsp. protracta with 54% of shared bands. Five species of wild cowpea have hairs and so could be used in breeding for resistance to insects.

The yield of cowpea varieties is affected by environmental variability. Hence, candidate varieties must be tested for yield stability before release. This study assessed the impacts of genotypes, environments, and their interaction on the performance of elite cowpea lines for key adaptive, grain yield, and associated traits across different locations. A total of 42 elite genotypes were evaluated in five Nigerian environments, representing various savanna ecologies, during the 2021 growing season. The experimental design employed was an alpha lattice arrangement, with each genotype replicated three times. The results revealed significant differences among genotypes, environments, and genotype-by-environment interaction (G × E) for most traits, including days to maturity, 100-seed weight, and grain yield. The genotype and genotype-by-environment interaction (GGE) biplot showed G21 (IT14K-2111-2) and G25 (IT15K-2386-1) as the most stable genotypes across the five environments, G41 (IT11K-61-82) was best adapted to Ibadan and Shika, G5 (245-1) was best adapted to Bagauda and Gumel, and G30 (IT16K-2365-1) was best adapted to Bauchi. G21 (IT14K-2111-2) and G25 (IT15K-2386-1) could be recommended across the five test environments, whereas G41 (IT11K-61-82), G30 (IT16K-2365-1), and G5 (245-1) were specific to the adapted environments. [ABSTRACT FROM AUTHOR]

Consensus genetic linkage maps provide a genomic framework for quantitative trait loci identification, map-based cloning, assessment of genetic diversity, association mapping, and applied breeding in marker-assisted selection schemes. Among 'orphan crops' with limited genomic resources such as cowpea [Vigna unguiculata (L.) Walp.] (2n = 2x = 22), the use of transcript-derived SNPs in genetic maps provides opportunities for automated genotyping and estimation of genome structure based on synteny analysis. Here, we report the development and validation of a high-throughput EST-derived SNP assay for cowpea, its application in consensus map building, and determination of synteny to reference genomes. SNP mining from 183,118 ESTs sequenced from 17 cDNA libraries yielded [approximately equal to] 10,000 high-confidence SNPs from which an Illumina 1,536-SNP GoldenGate genotyping array was developed and applied to 741 recombinant inbred lines from six mapping populations. Approximately 90% of the SNPs were technically successful, providing 1,375 dependable markers. Of these, 928 were incorporated into a consensus genetic map spanning 680 cM with 11 linkage groups and an average marker distance of 0.73 cM. Comparison of this cowpea genetic map to reference legumes, soybean (Glycine max) and Medicago truncatula, revealed extensive macrosynteny encompassing 85 and 82%, respectively, of the cowpea map. Regions of soybean genome duplication were evident relative to the simpler diploid cowpea. Comparison with Arabidopsis revealed extensive genomic rearrangement with some conserved microsynteny. These results support evolutionary closeness between cowpea and soybean and identify regions for synteny-based functional genomics studies in legumes. legume | diploid | recombinant inbred lines | segregating traits | 1536-plex genotyping doi/10.1073/pnas.0905886106

Field experiments were conducted for 2 yr (2014 and 2015) in Fashola, southwestern Nigeria, a low‐phosphorus (P) environment (approx. 1 mg kg−1), to determine the effect of P application on nutrient uptake, growth parameters, and yield in four cowpea [Vigna unguiculata (L.) Walp.] genotypes (two low‐P tolerant and two low‐P sensitive). Applications were 0 and 30 kg P ha−1 using single super phosphate broadcast on the soil surface just before planting. Phosphorus is very important for leaf and stem development in cowpea at the vegetative stage (i.e., 5 or 6 wk after seeding). This effect appeared more strongly on the genotype with a high amount of biomass ('Iron bean') than on genotypes with low biomass ('IT97K‐499‐38', 'Sanzi', and 'TVu 7778'). However, in all tested genotypes, P application resulted in taller plants, more leaf area, and heavier shoot dry weight. Uptake of P was increased at flowering stage and at the beginning of pod formation, suggesting that P is necessary for pod formation. As proof, the seed weight per pod in both years (with the exception of 'Iron bean' in 2015) was significantly higher under P application. An adequate amount of P uptake can lead to high‐quality seeds. Core Ideas: P application leads to the development of leaves and stem at vegetative stage.P uptake was increased at flowering and at the beginning of pod formation.Seed weight per pod was increased with P application.An adequate amount of P uptake leads to high‐quality seed. [ABSTRACT FROM AUTHOR]

Genomic maps for cowpea and mung bean based on restriction fragment length polymorphisms (RFLPs) are studied and developed. The maps provide information regarding quantitative trait loci (QTLs) describing seed weight in both species. Analysis shows that genomic regions for both which exhibited much impact on seed weight covered similar RFLP markers in the same linkage. The results support findings that QTLs in the region have not varied much in evolution.