Abstract
AbstractIncorporation 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.
Highlights
Breeding for increased heat and drought tolerance as well as for key agronomic traits and pest and disease-resistance is crucial as climate changes associated with global warming increase, and given that cowpea is primarily grown in regions that are quite vulnerable to climate change (Knox et al, 2012; Müller & Robertson, 2014)
A total of 668 accessions representing a core subset from the University of California Riverside (UCR) cowpea germplasm collection were genotyped with an Illumina GoldenGate assay (Muchero et al, 2009) (1536-SNPs) in previous studies (Huynh et al, 2013; Muchero et al, 2013)
Vigun09g059700, which encodes a MADS-box protein and is orthologous to the Arabidopsis AGAMOUS-LIKE 8 (AGL8) gene known as FRUITFULL (FUL), was identified 140 kb from this SNP. Another of these five QTLs was associated with flowering under long days. This locus was detected at position 37,711,373 on Vu11 for the Riverside 2017 environment (Table 1 and Figure 3), which is contained within a flowering time QTL previously identified in the same environment using the cowpea MAGIC population (Huynh et al, 2018)
Summary
Carvalho et al (2017) genotyped a smaller set of 96 worldwide cowpea accessions emphasizing Iberian Peninsula germplasm, but at a much higher SNP density using the Illumina Cowpea iSelect Consortium Array containing 51,128 SNPs (Muñoz-Amatriaín et al, 2017) In this latter work, logical relationships were noted between the genetic composition of accessions and colonial-era movement of germplasm from the Iberian Peninsula to the Caribbean, and from Africa to South America. We report the development of a minicore ( referred as the “UCR Minicore”) composed of 368 domesticated cowpeas selected from a larger set of $5000 accessions comprising the UC Riverside cowpea collection This minicore was genotyped using the 51,128-SNPs Cowpea iSelect Consortium Array (MuñozAmatriaín et al, 2017) and the genotypic information was used to gain a better understanding of the genetic diversity of domesticated cowpea. Genome-wide association studies (GWAS) were conducted, identifying significant SNPs and candidate genes associated with each of these traits
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