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Cowpea [Vigna unguiculata (L.) Walp.] is a major tropical legume crop grown in warm to hot areas throughout the world and especially important to the people of sub-Saharan Africa where the crop was domesticated. To date, relatively little is understood about its domestication origins and patterns of genetic variation. In this study, a worldwide collection of cowpea landraces and African ancestral wild cowpea was genotyped with more than 1200 single nucleotide polymorphism markers. Bayesian inference revealed the presence of two major gene pools in cultivated cowpea in Africa. Landraces from gene pool 1 are mostly distributed in western Africa while the majority of gene pool 2 are located in eastern Africa. Each gene pool is most closely related to wild cowpea in the same geographic region, indicating divergent domestication processes leading to the formation of two gene pools. The total genetic variation within landraces from countries outside Africa was slightly greater than within African landraces. Accessions from Asia and Europe were more related to those from western Africa while accessions from the Americas appeared more closely related to those from eastern Africa. This delineation of cowpea germplasm into groups of genetic relatedness will be valuable for guiding introgression efforts in breeding programs and for improving the efficiency of germplasm management.

Linkage mapping is relevant to modern plant biology and provides a framework for downstream analyses including quantitative trait loci identifi cation, map-based cloning, assessment of diversity, association mapping, and molecular breeding. Here, we report a consensus genetic map of cowpea [Vigna unguiculata (L.) Walp.] and synteny to other legumes based on expressed sequence tag (EST)-derived single nucleotide polymorphisms (SNPs). In total, 1293 individuals representing 13 mapping populations were genotyped using an Illumina 1536 GoldenGate Assay. A consensus map containing 1107 ESTderived SNP markers (856 bins) on 11 linkage groups (680 cM) was constructed from 13 population-specifi c maps. This effort combined six new population-specifi c maps and seven revised population-specifi c maps to construct an improved consensus map with 33% more bins, 19% more markers, and improved marker order when compared to the previous cowpea SNP consensus map. Comparative and whole genome visualizations are presented as a framework for discussing map quality and synteny with soybean [Glycine max (L.) Merr.].is a leguminous crop cultivated for fresh and dry grains, leaves, and fodder. Th e crop is a valuable component of rotations and intercrops due to symbiotic N fi xation (Quaye et al., 2009). Important cowpea producing regions span the globe; however, it is an especially valuable component of low-input farming systems in sub-Saharan Africa, South America, and Asia. Cowpea is popular in resource-poor farming because of its consistent production under abiotic stresses (drought, heat, or low soil fertility) and in many regions it is a protein-rich component of an otherwise protein-poor diet (Ehlers and Hall, 1997;Hall, 2004).Research and development of improved crop varieties encompasses advances in genomics and biotechnology. Consensus genetic maps are available for many model and important crop and animal species including soybean [Glycine max (L.) Merr.] (Song et al., 2004), wheat (Triticum aestivum L.) (Somers et al., 2004), barley (Hordeum vulgare L.) (Wenzl et al., 2006), and chicken (Gallus-gallus domesticus L.) (Groenen et al., 2000) and are central to breeding and diversity initiatives. Recently, technological advances that have substantially reduced costs of sequencing and genotyping promoted the development of genome resources for many non-model species (Varshney et al., 2009). Linkage mapping in cowpea has progressed with marker technology to yield informative and increasingly dense genetic maps (Menendez et al., 1997;Ouedraego et al., 2002;Muchero et al., 2009). Abbreviations: AFLP, amplifi ed fragment length polymorphism; EST, expressed sequence tag; LOD, logarithm of the odds; QTL, quantitative trait loci; RAPD, random amplifi ed polymorphic DNA; RIL, recombinant inbred line; RFLP, restriction fragment length polymorphism; SNP, single nucleotide polymorphism; SSR, simple sequence repeat; VuLG, Vigna unguiculata linkage group.

BackgroundCowpea (Vigna unguiculata) is an important crop in arid and semi-arid regions and is a good model for studying drought tolerance. MicroRNAs (miRNAs) are known to play critical roles in plant stress responses, but drought-associated miRNAs have not been identified in cowpea. In addition, it is not understood how miRNAs might contribute to different capacities of drought tolerance in different cowpea genotypes.ResultsWe generated deep sequencing small RNA reads from two cowpea genotypes (CB46, drought-sensitive, and IT93K503-1, drought-tolerant) that grew under well-watered and drought stress conditions. We mapped small RNA reads to cowpea genomic sequences and identified 157 miRNA genes that belong to 89 families. Among 44 drought-associated miRNAs, 30 were upregulated in drought condition and 14 were downregulated. Although miRNA expression was in general consistent in two genotypes, we found that nine miRNAs were predominantly or exclusively expressed in one of the two genotypes and that 11 miRNAs were drought-regulated in only one genotype, but not the other.ConclusionsThese results suggest that miRNAs may play important roles in drought tolerance in cowpea and may be a key factor in determining the level of drought tolerance in different cowpea genotypes.

The stay-green phenomenon is a key plant trait with wide usage in managing crop production under limited water conditions. This trait enhances delayed senescence, biomass, and grain yield under drought stress. In this study we sought to identify QTLs in cowpea (Vigna unguiculata) consistent across experiments conducted in Burkina Faso, Nigeria, Senegal, and the United States of America under limited water conditions. A panel of 383 diverse cowpea accessions and a recombinant inbred line population (RIL) were SNP genotyped using an Illumina 1536 GoldenGate assay. Phenotypic data from thirteen experiments conducted across the four countries were used to identify SNP-trait associations based on linkage disequilibrium association mapping, with bi-parental QTL mapping as a complementary strategy. We identified seven loci, five of which exhibited evidence suggesting pleiotropic effects (stay-green) between delayed senescence, biomass, and grain yield. Further, we provide evidence suggesting the existence of positive pleiotropy in cowpea based on positively correlated mean phenotypic values (0.34< r <0.87) and allele effects (0.07< r <0.86) for delayed senescence and grain yield across three African environments. Three of the five putative stay-green QTLs, Dro-1, 3, and 7 were identified in both RILs and diverse germplasm with resolutions of 3.2 cM or less for each of the three loci, suggesting that these may be valuable targets for marker-assisted breeding in cowpea. Also, the co-location of early vegetative delayed senescence with biomass and grain yield QTLs suggests the possibility of using delayed senescence at the seedling stage as a rapid screening tool for post-flowering drought tolerance in cowpea breeding. BLAST analysis using EST sequences harboring SNPs with the highest associations provided a genomic context for loci identified in this study in closely related common bean (Phaseolus vulgaris) and soybean (Glycine max) reference genomes.