Abstract
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 (FST). 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 (FST = 0.08) between them. In contrast, Creole had only 69% polymorphic SNPs and showed greater genetic differentiation from the other two breeds (FST = 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.
Highlights
Natural and artificial selection processes in domestic animals occurred over a relatively short period of time (10,000 years) (Zeder, 2008), leading to a wide range of phenotypes with large genetic differences between breeds (Kijas et al, 2009)
Despite the differences among the three breeds, our results showed that OvineSNP50 had a coverage similar to that expected in the design of the beadchip, as well as a good genotyping quality as shown by the high sample and marker call rates (Table 1)
Neither Corriedale nor Creole were included among the genotyped breeds in the original beadchip validation (OvineSNP50 Datasheet - Illumina, 2010), the results obtained here were promising
Summary
Natural and artificial selection processes in domestic animals occurred over a relatively short period of time (10,000 years) (Zeder, 2008), leading to a wide range of phenotypes with large genetic differences between breeds (Kijas et al, 2009). Genomic information and the vast databases of polymorphisms that are currently available provide a unique opportunity to study loci that were under selection between breeds in this recent history (Hayes et al, 2008; Flori et al, 2009). Several genomes have been sequenced and provide the information needed to identify single nucleotide polymorphisms (SNPs) (Ding and Jin, 2009), the most common variations in DNA sequences. The abundance of SNPs, their genome-wide distribution and the availability of a large number of commercial platforms for high-throughput genotyping make SNPs ideal markers for a variety of genomic studies (Ding and Jin, 2009).
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