SNP data set of Peruvian highland maize races

Peruvian maize exhibits significant morphological diversity, with landraces cultivated from sea level up to 3,500 meters above sea level. Previous research based on morphological descriptors identified at least 52 Peruvian maize races, but their genetic diversity and population structure remain largely unknown. In this study, we used genotyping-by-sequencing (GBS) to infer the genetic structure and diversity of 423 maize accessions from the Genebank of La Molina National Agrarian University (UNALM). These accessions represent nine races and one sub-race, along with 15 open-pollinated lines (purple corn) and two yellow maize hybrids. We obtained 14,235 high-quality SNPs distributed along the 10 maize chromosomes. Gene diversity ranged from 0.33 (Pachia) to 0.362 (Ancashino), with Cusco showing the lowest inbreeding coefficient (0.205) and Ancashino the highest (0.274) among the landraces. Population divergence (FST) was very low (mean = 0.017), indicating extensive interbreeding among Peruvian maize varieties. Population structure analysis revealed that these 423 distinct genotypes could be grouped into 10 clusters, with some maize races clustering together. Peruvian maize races did not form monophyletic groups; instead, our phylogenetic tree identified two clades corresponding to the chronological classification of Peruvian maize races: Anciently Derived or Primary Races (ADPR) and Lately Derived or Secondary Races (LDSR). These clades also align with the geographic origins of the maize races, reflecting their mixed evolutionary backgrounds. Further investigation of Peruvian maize germplasm using modern technologies is essential to enhance their use in breeding programs, particularly in the Andean region of Peru.