Abstract
BackgroundCowpea [Vigna unguiculata (L.) Walp.] is one of the most important legumes in tropical and semi-arid regions. However, there is relatively little genomic information available for genetic research on and breeding of cowpea. The objectives of this study were to analyse the cowpea transcriptome and develop genic molecular markers for future genetic studies of this genus.ResultsApproximately 54 million high-quality cDNA sequence reads were obtained from cowpea based on Illumina paired-end sequencing technology and were de novo assembled to generate 47,899 unigenes with an N50 length of 1534 bp. Sequence similarity analysis revealed 36,289 unigenes (75.8%) with significant similarity to known proteins in the non-redundant (Nr) protein database, 23,471 unigenes (49.0%) with BLAST hits in the Swiss-Prot database, and 20,654 unigenes (43.1%) with high similarity in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Further analysis identified 5560 simple sequence repeats (SSRs) as potential genic molecular markers. Validating a random set of 500 SSR markers yielded 54 polymorphic markers among 32 cowpea accessions.ConclusionsThis transcriptomic analysis of cowpea provided a valuable set of genomic data for characterizing genes with important agronomic traits in Vigna unguiculata and a new set of genic SSR markers for further genetic studies and breeding in cowpea and related Vigna species.
Highlights
Cowpea [Vigna unguiculata (L.) Walp.] is one of the most important legumes in tropical and semi-arid regions
A relatively small number of expressed sequence tags (ESTs) and genome sequences of cowpea are available in public databases [1], even though its genome size is relatively small among legume species
Sequencing and de novo assembly A total of 57,214,890 paired-end raw reads were generated by Illumina next-generation sequencing for the cowpea cultivar Zhongjiang No 1
Summary
Cowpea [Vigna unguiculata (L.) Walp.] is one of the most important legumes in tropical and semi-arid regions. There is relatively little genomic information available for genetic research on and breeding of cowpea. Cowpea [Vigna unguiculata (L.) Walp.] is a diploid Vigna crop (2n = 2× = 22), and its genome size is estimated to be 620 Mb [1]. It is the most important legume and semi-arid crop in sub-Saharan Africa and other parts of the world [2, 3] and is widely cultivated in Africa, Latin America, Southeast Asia, and southwestern regions of North America. Genetic mapping and molecular breeding has lagged behind those of other pulse crop species, including common bean (Phaseolus vulgaris) and soybean
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