Data Sources and their Data Sets

Cowpea Crop Ontology
Cowpea Crop Ontology
A controlled vocabulary to describe crop traits in cowpea.
The Gene Ontology (GO) knowledgebase is the world's largest source of information on the functions of genes. This knowledge is both human-readable and machine-readable, and is a foundation for computational analysis of large-scale molecular biology and genetics experiments in biomedical research.
InterMine post-processor
InterMine gene-flanking regions
Gene-flanking regions created by the core InterMine post-processor
InterMine intergenic regions
Intergenic regions created by the InterMine core post-processor
InterPro data set
InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites.
InterPro domain GO annotations
Mapping of GO terms to InterPro entries.
LIS Datastore
LIS gene family phylogenetic tree files
Three cowpea RIL populations which segregate for Fot race 4 resistance were used for QTL mapping studies. The CB27 (resistant) × IT82E-18/Big Buff (susceptible) population consisted of 162 RILs and was advanced to the F8 generation by single seed descent. IT82E-18 is an advanced breeding line developed at IITA which was released as cultivar Big Buff in Australia (Imrie 1995). IT82E-18 is highly susceptible to Fot race 4. A/a=CB27 genotype; B/b=IT82E-18 genotype; U=uncalled; X=heterozygous.
Cowpea aphid (Aphis craccivora, CPA) resistance was studied using F8 RILs derived from a cross between susceptible California Blackeye 27 (CB27), which was bred by University of California–Riverside (UCR), and a resistant breeding line IT97K-556-6 from the International Institute of Tropical Agriculture (IITA) breeding nursery in Nigeria.
Three cowpea RIL populations which segregate for Fot race 4 resistance were used for QTL mapping studies. The IT93K-503-1 (resistant) × CB46 (susceptible) population consisted of 113 lines advanced to the F10 generation using single seed descent. IT93K-503-1 is an advanced breeding line developed by the International Institute for Tropical Agriculture (IITA) with strong resistance to Fot race 4. CB46 was bred for resistance to Fot race 3 but is highly susceptible to Fot race 4.
CB5-2.gnm1.ann1 genome annotation
Genome assembly (scaffolds, pseudomolecules, and information about scaffold placement in pseudomolecules)
Gene annotations, on genome assembly
Synteny between Vigna angularis Gyeongwon.gnm3 and other species and strains.
In this study, we identified three QTLs: Hbs-1, Hbs-2, and Hbs-3, associated with heat-induced browning of seed coats using the cowpea RIL populations IT93K-503-1 x CB46 and IT84S-2246 x TVu14676. SNP markers were identified which co-segregated with the heat-induced browning of seed coats phenotype in the Hbs-1 and Hbs-3 loci, and could be used for indirect selection in breeding a higher quality cowpea grain. Additionally, ethylene forming enzymes were identified as a cowpea candidate gene for the Hbs-1 locus and an ACC synthase 1 gene was identified as a cowpea candidate gene for the Hbs-3 locus.
Cowpea, Vigna unguiculata L. Walp, is a diploid warm-season legume, also known as black-eyed pea among other common names. Cowpea is relevant as a grain legume in the USA and Europe, and as a fresh vegetable in China and elsewhere, and is of major importance as food and fodder in sub-Saharan Africa. This release of the annotated genome (v1.0) of elite African variety IT97K-499-35 was derived from Pacific Biosciences long reads, two Bionano Genomics optical maps and ten genetic linkage maps. This work was conducted mainly under the NSF BREAD project "Advancing the Cowpea Genome for Food Security" with partial support from the Feed the Future Innovation Lab for Climate Resilient Cowpea.
The black-eyed pea reference genotype has been used to generate a gene expression atlas of the major plant tissues (i.e. leaf, root, stem, flower, pod and seed), with a developmental time series for pods and seeds. From these various organs, 27 cDNA libraries were generated and sequenced, resulting in more than one billion reads. Following filtering, these reads were de novo assembled into 36 529 transcript sequences that were annotated and quantified across the different tissues. A set of 24,866 unique transcript sequences, called Unigenes, was identified. All the information related to transcript identification, annotation and quantification were stored into a gene expression atlas webserver (, providing a user-friendly interface and necessary tools to analyse transcript expression in black-eyed pea organs and to compare data with other legume species. Using this gene expression atlas, we inferred details of molecular processes that are active during seed development, and identified key putative regulators of seed maturation. Additionally, we found evidence for conservation of regulatory mechanisms involving miRNA in plant tissues subjected to drought and seeds undergoing desiccation.
Synteny between cowpea IT97K-499-35.gnm1 and other species and strains.
This gene set (v1.1) release represents a joined effort of UC, Riverside on assembly and JGI on gene annotation.
A MAGIC (Multi-parent Advanced Generation Inter-Cross) population for cowpea from eight founder parents which are genetically diverse and carry many abiotic and biotic stress resistance, seed quality and agronomic traits relevant to cowpea improvement in the USA and sub-Saharan Africa. The eight parents were inter-crossed using structured matings to ensure the population would have balanced representation from each parent, followed by single-seed descent, resulting in 305 F8 recombinant inbred lines (RILs) each carrying a mosaic of genome blocks contributed from all founders. These lines were on average 99.74% homozygous while also diverse in agronomic traits across environments.
Cowpea Illumina GoldenGate marker positions on the vigun.IT97K-499-35.gnm1 genome
Cowpea domestication-related traits (DRTs) were studied with a biparental mapping population of F8 RILs derived from a cross between IT99K-573-1-1 and TVNu-1158, cultivated and wild cowpea accessions, respectively. IT99K-573-1-1 is an early-maturing, white-seeded, high-yielding and Striga-resistant variety that was released in Nigeria under the name SAMPEA 14. TVNu-1158 is small seeded and has a perennial growth habit.
We developed a MAGIC population for cowpea 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. 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. A total of 305 MAGIC F8 RILs were generated from unique eight‐way crosses derived from six pedigree funnels. Genotyping with the 51,128 single nucleotide polymorphism (SNP) Illumina iSelect BeadArray resulted in 36,346 SNPs that were polymorphic between the eight parents (68.26%).
Sanzi.gnm1.ann1 genome annotation
In this study, we analyzed the genetics of leaf morphology in a segregating cowpea RIL population, Sanzi (sub-globose) x Vita 7 (hastate). A QTL was identified for the “hastate leaf shape” locus, Hls, which was positioned on the cowpea consensus genetic map and cowpea physical map. A candidate gene was identified using syntenic relationships between cowpea, soybean and Medicago. In addition, a SNP marker was found which co-segregated with the leaf morphology genotypes and phenotype, which could be used as a molecular marker for breeding purposes.
Genome assembly for the Vigna angularis, accession Shumari
Gene models for Vigna angularis, accession Shumari
Suvita2.gnm1.ann1 genome annotation
TZ30.gnm1.ann2 genome annotation
UCR779.gnm1.ann1 genome annotation
Genome assembly (scaffolds and pseudomolecules) for Vigna radiata
Genome annotations
Microsatellite marker positions on the VC1973A.gnm6 genome
ZN016.gnm1.ann2 genome annotation
The population used in genetic mapping included 132 recombinant inbred lines (F6:8, ‘ZZ’ population) developed by single‐seed descent from the cross ZN016 x Zhijiang282. ZN016 is a landrace vegetable cowpea accession originating from southern China with medium‐long pods (~38 cm) while Zhijiang282 is a typical asparagus bean cultivar with long pods.
The Illumina Cowpea iSelect Consortium Array was built from 37 cowpea accessions relevant to Africa, China, and the USA aligned to the WGS assembly of IT97K‐499‐35 to discover SNPs. The design also included 1163 SNPs from the prior GoldenGate assay and 60 presumed organelle SNPs. 51,128 SNPs are represented in the final product, which is available from Illumina.
LIS gene families
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. A diversity panel of 189 entries including traditional cultivars (landraces) and elite breeding lines representing worldwide cowpea genetic diversity was assembled and seed-multiplied by University of California—Riverside (UCR).
This study of black seed coat and pod tip color in cowpea used: (1) 94 F6-8 RILs derived from California Blackeye 27 (CB27), which has a medium-sized black eye seed coat and purple pod tips, and IT82E-18, which has a solid brown coat and green pod tips; (2) a RIL population provided by the IITA with 121 F6-8 RILs derived from a cross between Sanzi, a landrace with a speckled black and purple seed coat and purple pod tips, and Vita 7, which has a solid tan coat and green pod tips; (3) the UC-Riverside MAGIC population of 305 F8 RILs; (4) the UC-Riverside minicore population of 367. Accessions within the minicore population show great phenotypic diversity, including in seed coat color traits.
Cowpea is a susceptible host of root-knot nematodes (RKN), major plant-parasitic pests in global agriculture. To facilitate marker-based selection, we aimed to identify and map quantitative trait loci (QTL) conferring the resistance trait. Three cowpea segregating populations used in genetic mapping included (1) 87 recombinant inbred lines (RILs) from the cross CB27 × 24-125-B-1, (2) 170 F2:3 families from the cross IT84S-2049 × UCR779 and (3) 132 F2:3 families from the cross IT93K-503-1 × UCR779.
To better decipher the genetic basis of seed size, a genome-wide association study (GWAS) and meta-analysis were conducted on a panel of 368 cowpea diverse accessions from 51 countries. Four traits, including seed weight, length, width and density were evaluated across three locations. Using 51,128 single nucleotide polymorphisms covering the cowpea genome, 17 loci were identifed for these traits. One locus was common to weight, width and length, suggesting pleiotropy.
Plant Ontology
Plant Ontology
The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies.
Plant Trait Ontology
Plant Trait Ontology
A controlled vocabulary of describe phenotypic traits in plants.
Sequence Ontology
Sequence Ontology
The Sequence Ontology is a set of terms and relationships used to describe the features and attributes of biological sequence.
Legume Federation
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The Legume Information System (LIS) is a research project of the USDA-ARS:Corn Insects and Crop Genetics Research in Ames, IA.
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