Genomewide association for a dominant pigmentation gene in sheep
Publisher DOI
PubMed ID
24236609
Abstract
Most published genomewide association studies (GWAS) in sheep have investigated recessively inherited monogenic traits. The objective here was to assess the feasibility of performing GWAS for a dominant trait for which the genetic basis was already known. A total of 42 Manchega and Rasa Aragonesa sheep that segregate solid black or white coat pigmentation were genotyped using the SNP50 BeadChip. Previous analysis in Manchegas demonstrated a complete association between the pigmentation trait and alleles of the MC1R gene, setting an a priori expectation for GWAS. Multiple methods were used to identify and quantify the strength of population substructure between black and white animals, before allelic association testing was performed for 49 034 SNPs. Following correction for substructure, GWAS identified the most strongly associated SNP (s26449) was also the closest to the MC1R gene. The finding was strongly supported by the permutation tree-based random forest (RF) analysis. Importantly, GWAS identified unlinked SNP with only slightly lower p-values than for s26449. Random forest analysis indicated these were false positives, suggesting interpretation based on both approaches was beneficial. The results indicate that a combined analytical approach can be successful in studies where a modest number of animals are available and substantial population stratification exists.
Date Issued
2013-12
Publication Type
Article
Subject(s)
Subjects
SNP50 chip
•
Sheep genomewide association studies
•
pigmentation
Language(s)
en
Author(s)
Kijas, J. W. | |
Serrano, M. | |
McCulloch, R. | |
Li, Y. | |
Salces Ortiz, J. | |
Calvo, J. H. | |
Pérez-Guzmán, M. D. | |
The International Sheep Genomics Consortium, ISGC |
Additional Credits
Journal
Journal of animal breeding and genetics
Publisher
Wiley-Blackwell
ISSN
0931-2668
Access(Rights)
metadata.only