Cowpea mid-density genotyping services

Genotyping panel containing 2,602 high minor allele frequency (MAF) SNP markers distributed evenly throughout 11 cowpea chromosomes. Suitable for marker-assisted breeding, diversity analyses and germplasm management applications.

This mid-density marker platform for cowpea (Vigna unguiculata [L.] Walp.) genotyping contains 2,602 SNP markers with an average density of about 3 SNPs per cM (or 4 per Mbp) throughout the 11 cowpea chromosomes. Marker density is higher by physical distance in high recombination regions and lower in low recombination regions.

These markers are a subset from the 51,128-SNP Cowpea iSelect Consortium Array (Muñoz-Amatriaín et al, 2017), and were selected based on iSelect data from 2,714 diverse cultivated cowpea accessions, with extra weight given to 184 accessions most commonly used in African breeding programs.

The criteria used for marker selection (with some exceptions to fill gaps) were: 1) iSelect missing data rate less than 5%, 2) iSelect data MAF > 0.2 (all but 21 SNPs), 3) even spacing along the genetic linkage map (by cM) weighted slightly by Mbp/cM (as calculated in Data S1 of Lonardi et al. 2019) to improve coverage of low recombination regions. A total of 2,753 SNPs matching these criteria were included in a DArTag test set against 376 cowpea DNA samples. Data were obtained from 362 of these samples, including 307 that were previously genotyped using the iSelect array. These samples included 191 RILs, 31 F1s and 140 diverse accessions. When considering the DArTag data from only 107 diverse accessions that were previously genotyped using the iSelect array, a total of 2,073 SNPs had no missing data, 2,435 SNPs had less than 10% missing data, and 2,602 SNPs had less than 50% missing data.

This transfer of marker knowledge to enable development of a cowpea SNP panel for the Excellence in Breeding Program represents an output from the Feed the Future Innovation Lab for Climate Resilient Cowpea (AID-OAA-A-13-00070), the 2014 Illumina Agricultural Greater Good Award, and the National Science Foundation Basic Research to Enable Agricultural Development project “Advancing the Cowpea Genome for Food Security” (IOS-1543963).

Further information on SNP markers and other aspects of the cowpea genome can be retrieved from CowpeaPan (, the Legume Information System (, the National Center for Biotechnology Information (, EnsemblPlants ( and Lonardi et al. (2019).

This panel is suitable for marker-assisted breeding, diversity analyses and germplasm management applications.



  1. Lonardi S, Muñoz-Amatriaín M, Liang Q, Shu S, Wanamaker SI, Lo S, Tanskanen J, Schulman AH, Zhu T, Luo MC, Alhakami H, Ounit R, Hasan AM, Verdier J, Roberts PA, Santos JRP, Ndeve A, Doležel J, Vrána J, Hokin SA, Farmer AD, Cannon SB, Close TJ (2019) The genome of cowpea (Vigna unguiculata [L.] Walp.). The Plant Journal 98:767-782.
  2. Muñoz-Amatriaín M, Mirebrahim H, Xu P, Wanamaker SI, Luo M, Alhakami H, Alpert M, Atokple I, Batieno BJ, Boukar O, Bozdag S, Cisse N, Drabo I, Ehlers JD, Farmer A, Fatokun C, Gu YQ, Guo Y, Huynh B, Jackson SA, Kusi F, Lawley CT, Lucas MR, Ma Y, Timko MP, Wu J, You F, Barkley NA, Roberts PA, Lonardi S, Close TJ (2017) Genome resources for climate-resilient cowpea, an essential crop for food security. The Plant Journal 89: 1042-1054.