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

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 (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 Population Structure of Ethiopian Sheep Populations Revealed by High-Density SNP Markers

“…For all genotyped animals, the mean MAF ranged from 0.21 for OAR 11, 12, 14, 2, and 24 to 0.23 for OAR 23. These were lower than the reported average value (0.255 ± 0.136) for New Zealand sheep breeds based on an analysis of 517,902 SNPs and those reported for Corriedale and Merino sheep (0.27), but were higher than the value observed in Creole sheep ( Grasso et al, 2014 ).…”

Genetic characterization of four dog breeds with Illumina CanineHD BeadChip

“…Moderate and large differentiations had Fst values ranging from 0.05 to 0.15 and 0.15 to 0. 25, respectively [14].…”

“…Moreover, the quantity of "private SNPs" would be minimized when more samples were further tested. Grasso et al [14] found 99, 99, and 11 190 fixed SNPs for Corriedale, Merino and Creole sheep, respectively. Wiggans et al [15] reported that a set of 622 SNPs can be used to determine breed identity as part of the quality control process for dairy cattle.…”

Detection and evaluation of selection signatures in sheep

“…Data generated with different platforms from different labs can be easily and accurately combined, which was very difficult to achieve with earlier technologies, such as microsatellites, and resulted in high error rates. Therefore, SNPs are currently the preferred markers for the majority of genomic studies (Grasso et al, 2014). There are many commercial platforms available, which have been optimized for high efficiency, robustness, and speed of data generation, achieving excellent costbenefits, as, for example, the 777K SNP chip for cattle (BovineHD Genotyping BeadChip, Illumina, Inc., San Diego, CA, USA) and the 600K SNP chip for sheep (Ovine Infinium HD SNP BeadChip, Illumina, Inc., San Diego, CA, USA).…”

“…The domestication and selection processes of domestic animals occurred during a relative short period (last ~10.000 years), leading to a wide phenotypic diversity in traits related to production and type, with great differences observed between breeds (Grasso et al, 2014). According to Andersson (2012), animal and plant domestication is the most extensive genetic experiment that has been carried out by humans, resulting in huge shifts in the frequency of mutations that affect phenotypic traits.…”