Genome wide association study on milk production traits in a nucleus flock of Sarda breed sheep using a novel method combining linkage and linkage disequilibrium mapping

Abstract Text: We present the results of a genome wide association analysis on milk traits performed in a nucleus flock of Sarda breed sheep. Data were available on 2,373 ewes and their 43 sires. Genomic information consisted of genotypes for 44,859 SNP from OvineSNP50Beadchip. Phenotypes were the individual average performance deviations of milk, fat and protein yields and fat and protein contents. A combined Linkage and Linkage Disequilibrium mapping with a principal component analysis to synthesize identity-by-descent matrix information was performed. Chromosome-wide and genome-wide significance thresholds were determined by 10,000 permutations. The number of principal components explaining more than 99% of the 76 Sarda base haplotypes variance was on average 18.7. Fifty-one positions were chromosome-wide significant. Most positions (39) were also genome-wide significant. The most significant result was obtained for protein content on OAR6 with the peak close to the caseins genes cluster.

Keywords:

GWA

LDLA

Principal Component