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SNP genotypes of the international institute of tropical agriculture Cowpea Core

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Sep 26, 2023 version files 717.98 MB

Abstract

Cowpea (Vigna unguiculata [L.], Walp.) is a member of the family Fabaceae, subfamily Faboideae (a.k.a. Papilionoideae) and tribe Phaseoleae, along with other “warm season” legumes such as soybean, common bean, mung bean, adzuki bean, Bambara groundnut and others. The International Institute of Tropical Agriculture (IITA) in Ibadan, Nigeria maintains the world’s largest collection of cowpea germplasm with a collection size of 16,460 accessions as of September 2023. Information on these accessions is available online (https://my.iita.org/accession2/collection.jspx?id=1), including passport data, characterization descriptors and images. A subset known as the “IITA Cowpea Core” is comprised of nearly 2,100 accessions (Mahalakshmi et al. 2007; doi: 10.1017/S1479262107837166). Here we present single nucleotide polymorphism (SNP) data for most of the accessions in the IITA Cowpea Core, along with a few simple observations resulting from analyses of the SNP data.

The SNP data were generated using the Illumina iSelect Cowpea Consortium Array, described in Muñoz-Amatriaín et al. 2017 (doi: 10.1111/tpj.13404). A characteristic of this platform is that missing data (a.k.a. “nocall”) is nearly always either attributable to a SNP assay that failed technically and is excluded from all samples (“zeroed”) or a result of either the absence of a DNA segment in the genome or a sequence difference near the SNP position that precludes a successful assay. As a consequence, the frequency of “nocall” provides a broad indicator of whether or not a given accession is in the same species as cowpea. A few accessions in the IITA Cowpea Core are outliers, as follows. Three accessions (TVu-14726, TVu-16409, TVu-8383) had more than 31,000 nocalls (after excluding 1,863 zeroed SNPs) and fairly low (181 or 246) or moderate (1,337) heterozygous calls, indicating that these are not in the same species as cowpea. The passport data from IITA notes TVu-8383 as “wild” and TVu-14726 as “landrace”. There is no additional passport information on TVu-16409, but based on its SNP characteristics TVu-16409 clearly also is not in the same species as cowpea. Three other accessions (TVu-5540, TVu-6968, TVu-14935) have from 8,985 to 10,025 nocalls (after excluding 1,863 zeroed SNPs), which indicates that these accessions are more closely related to cowpea, but also are from a different species. Among these three accessions, TVu-14935 also had 18,134 heterozygous SNPs, which indicates that the plant representing this accession was not highly inbred. Residual heterozygosity is a common characteristic among single plant representatives of germplasm accessions, which begin as one or more seeds collected from their original open-pollenating location and then proceed through a variable number of selfed generations to become more inbred in germplasm collections.

Five accessions that are stated in the passport data to be from three V. unguiculata subspecies other than subspecies unguiculata had the same range of nocalls (708 to 943) as accessions reported to be subspecies unguiculata, consistent with the expectation that the cultivated subspecies all are closely related to each other. Two of these (TVu-3661 and TVu-3662) are stated in the passport data to be subspecies dekindtiana, which is generally considered to be the reservoir of variation for subspecies unguiculata, and one (TVu-3657) is stated to be subspecies cylindrica. The other two (TVu-3652, TVu-3656) of these five accessions are stated to be subspecies sesquipedalis, which has been well documented to be readily crossable with subspecies unguiculata. It should be noted also that there are several other accessions from Asia that are not specifically marked as sesquipedalis. Analysis of the overall population structure of the IITA Cowpea Core places these Asian accessions within the same sub-population as the accessions stated to be sub-species sesquipedalis. Based on principle component analysis, five sub-populations are evident among the IITA Cowpea Core, one from West Africa represented by Sanzi, another from West Africa represented by Suvita-2, one from Asia represented by TZ30 and ZN016, one from Northeast Africa, Europe and California represented by CB5-2, and one from South and East Africa represented by UCR779.

It is anticipated that the IITA Cowpea Core SNP dataset can provide a useful resource for a number of genome-wide association studies (GWAS) and decisions related to germplasm management.