Marker-assisted selection is important to facilitate the process of genetic improvement in vegetable breeding programs. A set of 192 trait-associated single nucleotide polymorphism (SNP) markers identified from previous genome-wide mapping studies has been developed at the New Mexico State University (NMSU) Chile Pepper Breeding and Genetics Program (NMSU-192) through the PlexSeq Genotyping Technology of AgriPlex Genomics (https://www.agriplexgenomics.com/plexseq-technology). The NMSU-192 SNP array consists of SNPs associated with easy destemming (14 SNPs), plant architecture and morphology (76), yield and yield components (78), and Phytophthora capsici resistance (24). Genetic diversity analysis using the NMSU-192 demonstrated the feasibility of the SNP array to characterize 188 Capsicum spp. genotypes based on fruit architecture and morphology. Together with parental and reference genotypes, F2:3, F3:4, and F4:5 segregating families of chile pepper breeding lines will be genotyped using the NMSU-192 for marker-assisted breeding and selection at the NMSU Chile Pepper Breeding and Genetics Program. The NMSU-192 will be a valuable component of the breeding toolbox for the genetic improvement of traits relevant to the chile pepper industry in New Mexico and in the pepper genetics community.
