Genome-Wide SNP Genotyping Reveals the Genetic Diversity and Population Structure of the Chilean National Maize Germplasm Collection

Chile marks the southern frontier of maize diversification in the Americas. Along its steep latitudinal and altitudinal gradients, centuries of farmer selection and seed exchange gave rise to a distinctive set of local races, now conserved in the national collection of the Instituto de Investigaciones Agropecuarias (INIA). Yet this collection had never been characterized at the genome-wide level. We genotyped 1157 accessions as DNA pools with 20,956 DArTseq single-nucleotide polymorphism (SNP) markers to describe their genetic diversity, population structure and linkage disequilibrium and to build a core collection. The main genetic division followed geography rather than race, separating a homogeneous group of floury maize from the northern Andean highlands from a more diverse and admixed central-southern complex. At a finer scale, groups associated with specific races emerged, whereas some traditionally distinct races, such as Capio Chileno Chico and Grande, were genetically indistinguishable. Landraces carried 459 alleles absent from breeding materials and greater within-accession variation. Genomic data also helped classify accessions lacking passport information. A core collection of 231 accessions retained all detected alleles, all 22 standard races and 96% of the gene diversity. These results provide the first genomic framework for conserving and using the maize diversity of Chile.