SNP genotypes of the international institute of tropical agriculture Cowpea Core

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.