The Cowpea Genomics Initiative (CGI)

The Cowpea Genomics Initiative (CGI) aims to leverage modern molecular-based technologies, in combination with conventional breeding strategies, to increase the speed at which a greater number of superior-performing, well-adapted cowpea varieties containing pyramided agronomic productivity, disease and pest resistance traits can be delivered to local farmers. Initiation of the Cowpea Genome Initiative is supported by funding from the Kirkhouse Trust, a UK-based charity.

History of the Project

     Cowpea (Vigna unguiculata L.) is major crop worldwide, providing a source of economic livelihood and nutritional well-being for millions of farmers and urban consumers in the developed and developing world. Cowpea currently ranks 23^rd among important crop species, with approximately 21 million acres being grown over vast and diverse agro-ecosystems in tropical Africa, Asia, and Latin America. Current estimates place world cowpea production at 3 million tons annually, with 80% of its production taking place on small farms in the dry savannah of tropical West and Central Africa. It is an important food grain for over 200 million people in this region.
     Cowpea growth and yield are constrained by a variety of biotic and abiotic factors. Insects, fungi, bacteria, parasitic plants and nematodes are the major biotic stresses, and drought, salinity and heat are among the major environmental limitations to cowpea productivity. In most years, the combined effects of biotic and abiotic stress in the field and in storage limit cowpea seed yields, and in severe cases can lead to total crop loss. Conventional breeding efforts aimed at pyramiding disease and pest resistance traits with other important agronomic traits are ongoing at various national and government laboratories in international research stations. There has been some positive impact, but these efforts remains time-consuming and difficult. The CGI aims to leverage modern molecular-based technologies, in combination with conventional breeding strategies, to gain a more rapid genetic improvement of this important crop species. Such an initiative will increase the speed at which a greater number of superior-performing, well-adapted cowpea varieties containing pyramided agronomic productivity, disease and pest resistance traits can be delivered to local farmers.

     The genomes of most higher plants contain significant amounts of repetitive DNA surrounding the low-copy number expressed regions of the genome. Cowpea, with a genome size estimated at 620 Mbp, has one of the smaller genomes present in leguminous plants. A number of experimental approaches have been developed that focus on targeted sequencing of gene-rich regions as an alternative to whole-genome sequencing. In collaboration with Orion Genomics, LLC (St. Louis, MO), a pilot study was carried out at the University of Virginia to assess the efficacy of the GeneThresher® sequencing technology in cowpea genomics. GeneThresher® is a methylation filtering technique, in which hypomethylated regions of the plant nuclear genome are selectively cloned and their nucleotide sequences determined. In vascular plant genomes, repetitive elements are generally heavily methylated (hypermethylated) while expressed genes reside in islands of hypomethylated space. The results of the pilot study conducted in 2004 indicate that GeneThresher® technology is capable of generating a 4-fold enrichment, thus effectively reducing the estimated genome size of cowpea from 620 Mb genome to a hypomethylated, gene-rich space of 151 Mb.

Based on the success of the pilot project, The Kirkhouse Trust has contracted with Orion Genomics, LLC, to generate a 1X sequence of the cowpea gene space allowing for the predicted annotation of more than 95% of the open reading frames in the cowpea genome. It is hoped that the information derived from this analysis will serve as a catalyst for additional work in cowpea genomics by other groups interested in cowpea improvement and legume genomics.

The CGI web site and data curation are maintained by the Department of Biology at the University of Virginia (Charlottesville Virginia). CGI data available to academic researchers who have submitted a registration with CGI.

For further information about the CGI contact Dr. Michael P. Timko