Genomic variation and population structure detected by single nucleotide polymorphism arrays in Corriedale, Merino and Creole sheep

Genetics and Molecular Biology

Andrés N Grasso²  Virginia Goldberg²  Elly A Navajas¹  Wanda Iriarte¹  Diego Gimeno¹  Ignacio Aguilar²  Juan F Medrano¹  Gonzalo Rincón¹  Gabriel Ciappesoni² 

[1] ,Instituto Nacional de Investigación Agropecuaria Meat and Wool National Program Las Brujas Canelones ,Uruguay

关键词: allele frequencies breed composition;    fixation index;    Ovine SNP50;    population stratification;    principal component analysis;   

DOI  :  10.1590/S1415-47572014000300011

来源: SciELO

【 摘 要 】

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.

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