Advances in the Integration of Genomic and Phenomic Tools in Cowpea Breeding for Improving Stress Resilience and Grain Yield and Quality

Abstract

Cowpea (Vigna unguiculata L. Walp) is a multi-use crop highly valued as a food crop, high-protein fodder, and sustainable cover crop. Yet, it remains underused, and yields in most growing regions are below the crop's potential due to multiple biotic and abiotic stresses. Recent advances in genomics and phenomics present new opportunities to speed up genetic gain for trait improvement in this species. A high-quality reference genome, a pangenome, and high-density genotyping platforms have aided genome-wide association studies, marker-assisted selection, and genomic selection, allowing for the dissection of genetic mechanisms controlling important traits and for the development of prediction models. Complementing these approaches, phenomic selection uses spectral data from near-infrared spectroscopy as a cost-effective, high-throughput option to molecular markers in predicting complex traits. This review puts together current knowledge on the genetic diversity of cowpea germplasm and information on target traits in cowpea breeding that include grain yield, protein content, nematode resistance, and drought and heat tolerance. We also detail successful applications of genomic tools, examine the emerging role of phenomic approaches, and explain the importance of synchronizing these methods with conventional breeding and participatory approaches to ensure adoption of technologies. Challenges remain, including reduced use of wild relatives, socioeconomic hiccups, and unequal access to advanced technologies, especially in low-income demographics. Nevertheless, the joint use of genomic and phenomic innovations into cowpea breeding pipelines offers great potential to deliver high-yielding, resilient and nutritionally improved varieties that can meet global food security requirements.