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The aim of this study was to investigate the genetic diversity within and among three breeds of sheep: Corriedale, Merino and Creole. Sheep from the three breeds (Merino n = 110, Corriedale n = 108 and Creole n = 10) were genotyped using the Illumina Ovine SNP50 beadchip ® . Genetic diversity was evaluated by comparing the minor allele frequency (MAF) among breeds. Population structure and genetic differentiation were assessed using STRUCTURE software, principal component analysis (PCA) and fixation index (F ST ). Fixed markers (MAF = 0) that were different among breeds were identified as specific breed markers. Using a subset of 18,181 single nucleotide polymorphisms (SNPs), PCA and STUCTURE analysis were able to explain population stratification within breeds. Merino and Corriedale divergent lines showed high levels of polymorphism (89.4% and 86% of polymorphic SNPs, respectively) and moderate genetic differentiation (F ST = 0.08) between them. In contrast, Creole had only 69% polymorphic SNPs and showed greater genetic differentiation from the other two breeds (F ST = 0.17 for both breeds). Hence, a subset of molecular markers present in the OvineSNP50 is informative enough for breed assignment and population structure analysis of commercial and Creole breeds.

Genetic diversity and structure of plant germplasm collections, frequently determined by molecular markers, can be used to assist breeding programs, to validate core collections determined by other methodologies, to identify priority accessions for conservation, and to confirm genetic integrity after regeneration. This research aimed to study the genetic diversity and structure of the Uruguayan white dent maize collection, to evaluate the genetic representativeness of its core collection (previously defined by phenotypic traits), and to confirm the genetic integrity of seven regenerations made in Mexico and Uruguay in comparison with the original accessions. Ninety accessions were fingerprinted using 26 simple sequence repeat (SSR) markers. Genetic structure was analyzed by Ward clustering, canonical analysis, and a Bayesian approach based on allelic frequencies. All SSR markers were polymorphic with a mean number of alleles (A) of 7.43, an effective allele number (Ae) of 3.04, and expected heterozygosity of 0.579. The genetic variation between accessions was 0.251, and variation within accessions was 0.749. Four genetic groups were obtained using the three approaches. The core collection represented the structure of the whole collection because the four genetic groups were proportionally represented. The genetic diversity in the core collection did not differ from the entire collection in A, Ae, expected heterozygosity (He) percentage of polymorphic loci (%P), and expected heterozygosity within accessions (Hs). Most regenerations (9 out of 14) preserved the genetic integrity of original accessions, whereas in other cases, either new or lost alleles caused genetic differences. The analysis of genetic structure and diversity of germplasm collections, in combination with morphological characterizations, helps to define ex situ conservation strategies and usage in breeding programs.

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