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]
This is the latest version of this item.
![]() |
PDF
10MB |
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 Name/Journal: | Acta Universitatis Agriculturae Sueciae | ||||||||||
Year of publishing : | 30 May 2016 | ||||||||||
Depositing date: | 2016 | ||||||||||
Number: | 2016:39 | ||||||||||
Number of Pages: | 49 | ||||||||||
Papers/manuscripts: |
| ||||||||||
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: | 10 Sep 2020 13:41 |
Available Versions of this Item
- Mapping and fine-mapping of genetic factors affecting bovine milk composition. (deposited 26 Apr 2016 06:21) [Currently Displayed]
Repository Staff Only: item control page