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Mapping and fine-mapping of genetic factors affecting bovine milk composition

Duchemin, Sandrine Isolde (2016). Mapping and fine-mapping of genetic factors affecting bovine milk composition. Diss. (sammanfattning/summary) Uppsala : Sveriges lantbruksuniv., Acta Universitatis agriculturae Sueciae, 1652-6880 ; 2016:39
ISBN 978-91-576-8580-3
eISBN 978-91-576-8581-0
[Doctoral thesis]

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Abstract

Bovine milk is an important source of nutrients in Western diets. Unraveling the genetic background of bovine milk composition by finding genes associated with milk-fat composition and non-coagulation of milk were the main goals of this thesis. In Chapter 1, a brief description of phenotypes and genotypes used throughout the thesis is given. In Chapter 2, I calculated the genetic parameters for winter and summer milk-fat composition from ~2,000 Holstein-Friesian cows, and concluded that most of the fatty acids (FA) can be treated as genetically the same trait. The main differences between milk-fat composition between winter and summer milk samples are most likely due to differences in diets. In Chapter 3, I performed genome-wide association studies (GWAS) with imputed 777,000 single nucleotide polymorphism (SNP) genotypes. I targeted a quantitative trait locus (QTL) region on Bos taurus autosome (BTA) 17 previously identified with 50,000 SNP genotypes, and identified a region covering 5 mega-base pairs on BTA17 that explained a large proportion of the genetic variation in de novo synthesized milk FA. In Chapter 4, the availability of whole-genome sequences of keys ancestors of our population of cows allowed to fine-mapped BTA17 with imputed sequences. The resolution of the 5 mega base-pairs region substantially improved, which allowed the identification of the LA ribonucleoprotein domain family, member 1B (LARP1B) gene as the most likely candidate gene associated with de novo synthesized milk FA on BTA17. The LARP1B gene has not been associated with milk-fat composition before. In Chapter 5, I explored the genetic background of non-coagulation of bovine milk. I performed a GWAS with 777,000 SNP genotypes in 382 Swedish Red cows, and identified a region covering 7 mega base-pairs on BTA18 strongly associated with noncoagulation of milk. This region was further characterized by means of fine-mapping with imputed sequences. In addition, haplotypes were built, genetically differentiated by means of a phylogenetic tree, and tested in phenotype-genotype association studies. As a result, I identified the vacuolar protein sorting 35 homolog, mRNA (VPS35) gene, as candidate. The VPS35 gene has not been associated to milk composition before. In Chapter 6, the general discussion is presented. I start discussing the challenges with respect to high-density genotypes for gene discovery, and I continue discussing future possibilities to expand gene discovery studies, with which I propose some alternatives to identify causal variants underlying complex traits in cattle.

Authors/Creators:Duchemin, Sandrine Isolde
Title:Mapping and fine-mapping of genetic factors affecting bovine milk composition
Series/Journal:Acta Universitatis agriculturae Sueciae (1652-6880)
Year of publishing :30 May 2016
Depositing date:2016
Volume:2016:39
Number of Pages:49
Papers/manuscripts:
NumberReferences
IDuchemin, S. , H. Bovenhuis, W. M. Stoop, A. C. Bouwman, J. A. M. van Arendonk, and M. H. P. W. Visker. 2013. Genetic correlation between composition of bovine milk fat in winter and summer, and DGAT1 and SCD1 by season interactions. J Dairy Sci 96:592-604.
IIDuchemin, S. I., Visker, M.H.P.W., Van Arendonk, J.A.M., and Bovenhuis, H. 2014. A quantitative trait locus on Bos taurus autosome 17 explains a large proportion of the genetic variation in de novo synthesized milk fatty acids. J Dairy Sci 97: 7276-7285.
IIIDuchemin, S. I., Bovenhuis, H., Megens, H-J., Van Arendonk, J. A. M., and M. H. P. W. Visker. Fine-mapping of BTA17 using imputed sequences for associations with de novo synthesized fatty acids in bovine milk. (manuscript)
IVDuchemin, S. I., Glantz, M., de Koning, D-J., Paulsson, M., and W.F. Fikse. 2016. Identification of QTL on chromosome 18 associated with non-coagulating milk in Swedish Red cows. Front Genet 7:57. doi: 10.3389/fgene.2016.00057.
Place of Publication:Uppsala
Publisher:Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences
ISBN for printed version:978-91-576-8580-3
ISBN for electronic version:978-91-576-8581-0
ISSN:1652-6880
Language:English
Additional Information:Joint PhD thesis, Swedish University of Agricultural Sciences, Uppsala, Sweden and Wageningen University, the Netherlands (2016)
Publication Type:Doctoral thesis
Full Text Status:Public
Agris subject categories.:L Animal production > L10 Animal genetics and breeding
Subjects:(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 402 Animal and Dairy Science > Animal and Dairy Science.
Agrovoc terms:dairy cattle, breeds (animals), milk, proximate composition, milk fat, fatty acids, coagulation, genes, genetic correlation, genetic markers, genomes
Keywords:Milk composition, fatty acid composition, non-coagulating milk, GWAS, fine-mapping, genes, dairy cattle, Holstein cows, Swedish Reds cows, VPS35, LARP1B
URN:NBN:urn:nbn:se:slu:epsilon-e-3398
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-e-3398
ID Code:13303
Faculty:VH - Faculty of Veterinary Medicine and Animal Science
Department:(VH) > Dept. of Animal Breeding and Genetics
External funders:CRV and European Commission
Deposited By: Sandrine Duchemin
Deposited On:26 Apr 2016 06:21
Metadata Last Modified:26 Apr 2016 06:21

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