TY - JOUR
T1 - A quantitative trait locus on Bos taurus autosome 17 explains a large proportion of the genetic variation in de novo synthesized milk fatty acids
AU - Duchemin, S.I.
AU - Visker, M.H.P.W.
AU - van Arendonk, J.A.M.
AU - Bovenhuis, H.
PY - 2014
Y1 - 2014
N2 - A genomic region associated with milk fatty acid (FA) composition has been detected on Bos taurus autosome (BTA)17 based on 50,000 (50K) single nucleotide polymorphism (SNP) genotypes. The aim of our study was to fine-map BTA17 with imputed 777,000 (777K) SNP genotypes to identify candidate genes associated with milk FA composition. Phenotypes consisted of gas chromatography measurements of 14 FA based on winter and summer milk samples. Phenotypes and genotypes were available on 1,640 animals in winter milk, and on 1,581 animals in summer milk samples. Single-SNP analyses showed that several SNP in a region located between 29.0 and 34.0 Mbp were in strong association with C6:0, C8:0, and C10:0. This region was further characterized based on haplotypes. In summer milk samples, for example, these haplotypes explained almost 10% of the genetic variance in C6:0, 9% in C8:0, 3.5% in C10:0, 1.8% in C12:0, and 0.9% in C14:0. Two groups of haplotypes with distinct predicted effects could be defined, suggesting the presence of one causal variant. Predicted haplotype effects tended to increase from C6:0 to C14:0; however, the proportion of genetic variance explained by the haplotypes tended to decrease from C6:0 to C14:0. This is an indication that the quantitative trait locus (QTL) region is involved either in the elongation process or in early termination of de novo synthesized FA. Although many genes are present in this QTL region, most of these genes on BTA17 have not been characterized yet. The strongest association was found close to the progesterone receptor membrane component 2 (PGRMC2) gene, which has not yet been associated with milk FA composition. Therefore, no clear candidate gene associated with milk FA composition could be identified for this QTL.
AB - A genomic region associated with milk fatty acid (FA) composition has been detected on Bos taurus autosome (BTA)17 based on 50,000 (50K) single nucleotide polymorphism (SNP) genotypes. The aim of our study was to fine-map BTA17 with imputed 777,000 (777K) SNP genotypes to identify candidate genes associated with milk FA composition. Phenotypes consisted of gas chromatography measurements of 14 FA based on winter and summer milk samples. Phenotypes and genotypes were available on 1,640 animals in winter milk, and on 1,581 animals in summer milk samples. Single-SNP analyses showed that several SNP in a region located between 29.0 and 34.0 Mbp were in strong association with C6:0, C8:0, and C10:0. This region was further characterized based on haplotypes. In summer milk samples, for example, these haplotypes explained almost 10% of the genetic variance in C6:0, 9% in C8:0, 3.5% in C10:0, 1.8% in C12:0, and 0.9% in C14:0. Two groups of haplotypes with distinct predicted effects could be defined, suggesting the presence of one causal variant. Predicted haplotype effects tended to increase from C6:0 to C14:0; however, the proportion of genetic variance explained by the haplotypes tended to decrease from C6:0 to C14:0. This is an indication that the quantitative trait locus (QTL) region is involved either in the elongation process or in early termination of de novo synthesized FA. Although many genes are present in this QTL region, most of these genes on BTA17 have not been characterized yet. The strongest association was found close to the progesterone receptor membrane component 2 (PGRMC2) gene, which has not yet been associated with milk FA composition. Therefore, no clear candidate gene associated with milk FA composition could be identified for this QTL.
KW - selection signatures
KW - genotype imputation
KW - dairy-cattle
KW - protein
KW - dgat1
KW - association
KW - population
KW - parameters
KW - lactation
KW - summer
U2 - 10.3168/jds.2014-8178
DO - 10.3168/jds.2014-8178
M3 - Article
SN - 0022-0302
VL - 97
SP - 7276
EP - 7285
JO - Journal of Dairy Science
JF - Journal of Dairy Science
IS - 11
ER -