Cowpea is an important legume crop worldwide. However, the diversity and relationship of current accessions remain unclear due to a lack of robust genetic information. A set of 40,089 single nucleotide polymorphisms (SNPs) adapted to the Kompetitive Allele Specific PCR (KASP) SNP genotyping platform were developed from the existing Illumina Cowpea iSelect Consortium Array for cowpea germplasm genetic diversity assessment and variety identification. Using the genotypic data of 299 cowpea accessions obtained from this SNP assay, a precore pool of 434 SNPs and 50 informative core SNPs was selected and validated for use in future genetic diversity analyses of cowpea germplasm. By further genotyping 75 commercial cultivars using the set of 50 core SNPs, pairwise genotype alignment and dendrogram analysis both showed that each cultivar could be uniquely identified by this core set of markers. The KASP markers developed in this study provide a flexible marker resource for both basic and applied research of cowpea. The precore SNP pool and the core SNP set also provide valuable tools for genetic variation assessment and variety rights protection for cowpea breeders.

Faba bean is an important edible legume crop in China. Due to its huge genome size and no available reference genome, SNP marker is very limited in faba bean. To identify genome-wide SNP markers, we obtained 35.47 Gb data from eight landraces by RAD-sequencing, with an average of 4.77 Gb data for each accession. A total of 245443516 reads were generated, the single accession has an average of 30680439.5 reads, and the average length of the reads reaches to 144 bp. The Q20 and Q30 values were over 97.89% and 93.83%, respectively. The GC content between the reads varied from 38.05% to 40.09%. Using a special Bayesian method under the situation of no reference genome, we identified 3722 SNPs among the eight landraces. Regarding the single accession, the detected SNPs varied from 3278 to 3578, and the homozygous SNPs number was larger than that of heterozygous SNPs for most of accessions. For the SNP types, T:A->C:G type has the largest proportion (38.8%), followed by C:G->T:A (28.0%) and the smallest is T:A->A:T (7.5%). 31 SNPs were selected to convert into KASP markers, and they showed a success rate of 66.7% through amplifying on 46 accessions. The SNPs in this study provide a strong genetic tool for germplasm identification, gene mapping and molecular breeding in faba bean.