The UCR Minicore: a resource for cowpea research and breeding

Abstract

Incorporation of new sources of genetic diversity into plant breeding programs is crucial for continuing to improve yield and quality, as well as tolerance to abiotic and biotic stresses. A minicore (the “University of California, Riverside (UCR) Minicore”) composed of 368 worldwide accessions of cultivated cowpea has been assembled, having been derived from the UCR cowpea collection. High‐density genotyping with 51,128 SNPs followed by principal component and genetic assignment analyses identified six subpopulations in the UCR Minicore, mainly differentiated by cultivar group and geographic origin. All six subpopulations were present to some extent in West African material, suggesting that West Africa is a center of diversity for cultivated cowpea. Additionally, population structure analyses supported two routes of introduction of cowpea into the U.S.: (1) from Spain to the southwest U.S. through Northern Mexico and (2) from Africa to the southeast U.S. via the Caribbean. Genome‐wide association studies (GWAS) narrowed several traits to regions containing strong candidate genes. For example, orthologs of the Arabidopsis FLOWERING LOCUS T lie within a major QTL for flowering time. In summary, this diverse, yet compact cowpea collection constitutes a suitable resource to identify loci controlling complex traits, consequently providing markers to assist with breeding to improve this crop of high relevance to global food and nutritional security.

Genome-Wide Association Study Reveals Candidate Genes for Flowering Time in Cowpea (Vigna unguiculata [L.] Walp.)

“…A total of 368 accessions from the cowpea UCR Minicore (Muñoz-Amatriaín et al, 2021) were planted in Ft. Collins, CO (40.6553 • N, −104.9966 • W) on June 17, 2019. This collection includes landraces and breeding materials from 50 countries.…”

“…A diverse set of 768 cultivated cowpea genotypes from 58 countries were also studied using SNP markers from genotyping by sequencing (GBS) that divided the population into three gene pools (America, Africa, and Central West Asia) (Xiong et al, 2016). Lastly, a set of 368 cultivated cowpeas genotyped with 51,128 SNPs revealed six major subpopulations (Muñoz-Amatriaín et al, 2021). Large collections of diverse cowpea accessions are conserved in the International Institute of Tropical Agriculture (IITA) (∼15,000 accessions), United States Department of Agriculture-Genetic Resources Information Network (USDA-GRIN) (7,737 accessions), and University of California, Riverside, CA, United States (∼6,000 accessions).…”

“…Therefore, a mini-core collection consisting 298 lines from the IITA collection were genotyped based on GBS using 2,276 SNP markers in order to make the characterization and utilization of the germplasm more practical (Fatokun et al, 2018). Similarly, another mini-core collection, the University of California-Riverside Minicore (UCR Minicore), consisting of 368 accessions that included landraces and breeding materials from 50 countries was also developed (Muñoz-Amatriaín et al, 2021) and genotyped using a publicly available Cowpea iSelect Consortium Array (Muñoz-Amatriaín et al, 2017). This array consists of 51,128 assays developed from sequencing 36 diverse accessions and was released to facilitate easy high-throughput genotyping in cowpea (Muñoz-Amatriaín et al, 2017).…”

“…Recent advances in genomic technologies has enabled a better understanding of the genetic basis of variation using genome-wide association studies (GWAS), as it can be used for identification and high resolution mapping of useful genetic variability from germplasm sets that have resulted from many rounds of historical recombination (Yu and Buckler, 2006). GWAS studies have been reported in cowpea for pod length (Xu et al, 2017), root architecture (Burridge et al, 2017), black seed coat color (Herniter et al, 2018), seed weight, length, width, and density , and plant productivity traits and flowering time (Muñoz-Amatriaín et al, 2021). The study of Muñoz-Amatriaín et al (2021) evaluated flowering time in five different environments in Nigeria and California, most of which were short-day environments.…”

“…GWAS studies have been reported in cowpea for pod length (Xu et al, 2017), root architecture (Burridge et al, 2017), black seed coat color (Herniter et al, 2018), seed weight, length, width, and density , and plant productivity traits and flowering time (Muñoz-Amatriaín et al, 2021). The study of Muñoz-Amatriaín et al (2021) evaluated flowering time in five different environments in Nigeria and California, most of which were short-day environments.…”