Context and Relevance of Cowpea Genome Resources.

My trek as a research scientist began with a desire as a graduate student to gain a solid background in genetics for the purpose of applying my skills to contemporary problems in agriculture, the environment and human health. More specifically, I envisioned my future to be tightly associated with agriculture. I joined a research team at the University of California in Davis, which included my professor as the lead investigator, several other faculty members, at least 10 post-docs and numerous graduate students. It was an exciting time shortly after recombinant DNA methods were first developed, when one could imagine endless possibilities. The group was unified by a goal of extending symbiotic nitrogen fixation to cereal plants, which encompassed basic research on nitrogen fixation in bacteria, nitrogen metabolism in legumes, and interactions between soil components, bacteria and plants. I studied the genetics of nitrogen metabolism in the nitrogen fixing enteric bacterium Klebsiella pneumoniae, which is closely related to Escherichia coli and was chosen as a model organism for Rhizobium species since genetic methods had not yet been developed for Rhizobia. I became masterful with methods of bacterial genetics and began to work with recombinant DNA. I had not intended to become a bacterial geneticist, but I continued along that path for several years as a graduate student and then a post-doc during a period when recombinant DNA methods and plasmid biology revolutionized research on plant-pathogen interactions. This included my own work on the virulence genes of Agrobacterium tumefaciensduring a tremendously exciting period of discovery. Yet, despite having success as a bacterial geneticist – publishing papers, participating in conferences, having some success writing grants – I still yearned to apply knowledge to solve problems. As a consequence, I changed direction to join a plant physiology group at the Commonwealth Scientific and Industrial Research Organization (CSIRO) in Australia, where my skills in molecular biology were useful for advancement of knowledge about hormonal control of gene expression during cereal seed germination and response to water stress. I was fortunate to come into a project at the early stages of discovery of a group of stress-related proteins, the “dehydrins”, which then propelled me into my current faculty position. These proteins and the gene family encoding them were the primary focus of my research at UC Riverside (UCR) for about 10 years, a period that included advancement to tenure. But, still I yearned to apply knowledge more directly. In the late 1990’s the NSF Plant Genome Research Program began. As an active member of the barley genetics community my skills as a bacterial geneticist suddenly became quite valuable for the development of basic genome resources, initially production of genomic and cDNA libraries. One thing led to another, progressing through library construction, sequencing, assembly, design of microarrays, design of SNP genotyping assays, genetic map development, and on into mapping several traits and gene-trait associations. This was a satisfying progression toward application, as the genomic tools gradually became integrated into breeding and germplasm management, as well as supporting a surge in basic research and elegant publications by numerous colleagues using resources that I helped to create. It was a period of great collegiality, and along with it endless communication.

Opportunities in genome resource development expanded from barley to wheat, citrus, rice, soybean, a few other plants, and eventually to cowpea in 2006 when major funding became available to begin to develop cowpea genome resources. I had dabbled with cowpea in the context of dehydrins in the decade prior to 2006, but in 2006 I realized that at last I had an opportunity to focus my efforts more exclusively on application. Research on cowpea at UCR began in the mid-1970’s by now-retired professor Anthony Hall. I made a promise to Dr. Hall on his retirement in 2003 that I would do my best to continue UCR’s cowpea legacy. I was fortunately welcomed to join the cowpea team in earnest by two of Dr. Hall’s very close colleagues at UCR, Dr. Jeffrey Ehlers and Professor Philip Roberts. The three of us charged forward with genome resource development, always with a goal of applying the new knowledge to address issues related to cowpea breeding.

Cowpea (Vigna unguiculata [L.] Walp.) is the number one source of protein in the human diet in sub-Saharan Africa, and an important climate-resilient legume crop the USA and elsewhere. The present cowpea team at UC Riverside operates a breeding program for California and is partnered with leading cowpea breeders in West Africa (Burkina Faso, Ghana, Nigeria, Senegal) and Mozambique, supported by funding from USAID (Feed the Future), NSF BREAD, CGIAR, the California Dry Beans Advisory Board and USDA Hatch Projects in the University of California. Now that we have excellent SNP genotyping capabilities, an advanced reference genome sequence, an ever-expanding list of marker-trait associations, and web-based tools to access existing and new genetic information, we are able to address a range of needs in the breeding programs including pedigree validation, germplasm management and marker-assisted breeding. I will provide a summary of current genome resources, including new genetic populations in addition to sequences and genotyping tools, and present several examples to illustrate how these resources are being used to generate new knowledge relevant to cowpea as crop plant.