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Population level genome-wide association studies in dairy cattle

Mao, Xiaowei (2016). Population level genome-wide association studies in dairy cattle. Diss. (sammanfattning/summary) Uppsala : Sveriges lantbruksuniv., Acta Universitatis agriculturae Sueciae, 1652-6880 ; 2016:120
ISBN 978-91-576-8743-2
eISBN 978-91-576-8744-9
[Doctoral thesis]

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Abstract

In recent years, genome-wide association studies (GWAS) has become a dominant tool for detecting genetic architectures for complex traits. Thousands of associated genetic variants have been reported. However, the resolution of these studies was limited by the available marker density for the quantitative trait loci (QTL) region. Moreover, the X chromosome and non-additive genetic effects has often been excluded from GWAS, despite of their potentially important biological functions.

In chapter 2, we carried out the fine-mapping of a previously reported QTL in Holstein cattle on Bos taurus autosome 18 (BTA18) for calving traits, using imputed high-density SNP chip (HD) genotypes followed by imputed whole-genome sequence (WGS) variants. Genes SIGLEC12, CD33 and CEACAM18 were proposed as candidate genes. In addition, pleiotropic effects of this QTL region were observed on direct calving traits and conformation traits.

In chapter 3, we performed a GWAS for growth traits in Nordic Holstein, Jersey, and Red Dairy Cattle. First, GWAS was performed within breeds using WGS variants. Then a meta-analysis was performed to combine information across the three breeds. Several QTL were identified to have large effects on growth traits in Holstein and Red Dairy Cattle, but only one QTL located nearby gene CYP19A1 on chromosome 10 was shared between Holstein and Red Dairy Cattle. Meta-analysis of these three breeds enhanced the power to detect QTL.

In chapter 4, we performed the imputation of markers on the X chromosome in Holstein cattle for non-genotyped animals and animals genotyped with low density (Illumina BovineLD) chips, using animals genotyped with medium density (Illumina BovineSNP50) chips. We found that the imputation accuracy of markers on the X chromosome was improved by treating the pseudoautosomal region as autosomal and by increasing the proportion of females in the reference group.

In chapter 5, we aimed to detect dominance effects on female fertility traits in Danish Holstein cattle using Illumina BovineSNP50 data, and evaluate the power, precision, and type 1 error of detecting dominance effects through simulations. Four QTL were detected for IFL in heifers, while one QTL was detected for cows. All these five QTL were detected with significant additive and dominance effects. Simulations showed that the current sample size had limited power to detect dominance effects for female fertility in cattle.

Authors/Creators:Mao, Xiaowei
Title:Population level genome-wide association studies in dairy cattle
Series/Journal:Acta Universitatis agriculturae Sueciae (1652-6880)
Year of publishing :2016
Volume:2016:120
Number of Pages:66
Papers/manuscripts:
NumberReferences
IMao, X., N. K. Kadri, J. R. Thomasen, D.J. De Koning, G. Sahana, and B. Guldbrandtsen. 2015. Fine mapping of a calving QTL on Bos taurus autosome 18 in Holstein cattle. J. Anim. Breed. Genet. 133:207–218.
IIMao, X., G. Sahana, D.J. De Koning, and B. Guldbrandtsen. 2016. Genome-wide association studies of growth traits in three dairy cattle breeds using whole-genome sequence data. J. Anim. Sci. 94:1426.
IIIMao, X., A. M. Johansson, G. Sahana, B. Guldbrandtsen, and D.J. de Koning. 2016. Imputation of markers on the Bovine X chromosome. J. Dairy Sci. 833:1–6.
IVMao, X., G. Sahana, A. M. Johansson, A. Ismael, P. Løvendahl, D.J. de Koning, and B. Guldbrandtsen. 2016. Genome-wide association mapping for dominance effects in female fertility using real and simulated data from Danish Holstein cattle. (Manuscript)
Place of Publication:Uppsala
Publisher:Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences
ISBN for printed version:978-91-576-8743-2
ISBN for electronic version:978-91-576-8744-9
ISSN:1652-6880
Language:English
Additional Information:The research presented in this thesis was conducted under the joint auspices of Aarhus University and the Swedish University of Agricultural Sciences and is part of the Erasmus Mundus Joint Doctorate Program “EGS-ABG”.
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 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Genetics (medical genetics to be 30107 and agricultural genetics to be 40402)
(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 403 Veterinary Science > Other Veterinary Science
Agrovoc terms:dairy cattle, breeds (animals), genomes, chromosomes, quantitative trait loci, genetic markers, genetic correlation, calving, growth, fertility
Keywords:genome-wide association studies, dairy cattle, whole-genome sequence, meta-analysis, X chromosome, quantitative trait loci, dominance effects
URN:NBN:urn:nbn:se:slu:epsilon-e-3772
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-e-3772
ID Code:13822
Faculty:VH - Faculty of Veterinary Medicine and Animal Science
Department:(VH) > Dept. of Animal Breeding and Genetics
Deposited By: Xiaowei Mao
Deposited On:10 Nov 2016 09:52
Metadata Last Modified:10 Nov 2016 09:52

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