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Genomewide association for a dominant pigmentation gene in sheep
Author(s) -
Kijas J.W.,
Serrano M.,
McCulloch R.,
Li Y.,
Salces Ortiz J.,
Calvo J.H.,
PérezGuzmán M.D.
Publication year - 2013
Publication title -
journal of animal breeding and genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.689
H-Index - 51
eISSN - 1439-0388
pISSN - 0931-2668
DOI - 10.1111/jbg.12048
Subject(s) - genome wide association study , biology , genetic association , genetics , snp , population , population stratification , trait , allele , quantitative trait locus , single nucleotide polymorphism , gene , genotype , medicine , computer science , environmental health , programming language
Summary 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 M anchega and R asa A ragonesa sheep that segregate solid black or white coat pigmentation were genotyped using the SNP 50 B ead C hip. Previous analysis in Manchegas demonstrated a complete association between the pigmentation trait and alleles of the MC 1R 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 SNP s. Following correction for substructure, GWAS identified the most strongly associated SNP ( s26449 ) was also the closest to the MC 1 R 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.