SNP Genotyping

Single nucleotide polymorphism (SNP) genotyping is previously described (Muñoz-Amatriaín et al., 2017). Briefly, total genomic DNA from single plants was extracted from dried leaves using Plant DNeasy (Qiagen, Germany) and genotyped using the Cowpea iSelect Consortium Array that contained 51,128 SNPs. SNPs were called using GenomeStudio software V.2011.1 (Illumina, Inc., San Diego, CA, United States) and the physical positions of the SNPs were determined by using the IT97K-499-35 reference genome v1.0 (Lonardi et al., 2019). Linkage disequilibrium (LD) estimates between marker pairs were obtained using GAPIT (Lipka et al., 2012) with 41,902 SNPs after filtering for minor allele frequency (MAF) threshold of 5%. The pairwise LD values (r²) were plotted against genetic distance using R statistical package (R Core Team, 2020) and a LOESS regression curve was fitted. The pattern of LD decay was determined where the LOESS regression of mean r² between pairs of SNPs intercepted the threshold of 0.2.