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Genomic variation across European cattle: contribution of gene flow

Upadhyay, Maulik (2019). Genomic variation across European cattle: contribution of gene flow. Diss. (sammanfattning/summary) Uppsala : Sveriges lantbruksuniv., Acta Universitatis agriculturae Sueciae, 1652-6880 ; 2019:16
ISBN 978-91-7760-350-4
eISBN 978-91-7760-351-1
[Doctoral thesis]

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Abstract

European cattle display vast phenotypic diversity which can be attributed to genomic variation such as single nucleotide polymorphisms (SNPs) and structural variations (SVs).The distribution of these genomic variations in a population is heavily in uenced by different population genomic forces. In this thesis,I used genome-wide SNPs to characterize genomic variation and admixture across different European cattle populations. Broadly,I show the difference in the domestication histories for north-western and southern European cattle.I argue that this difference can be attributed to a differential pattern of genomic admixture involving wild local aurochs and zebu cattle. Genomic admixture analysis revealed share ancestry between Balkan and Italian cattle (BAI) breeds, and zebu cattle. Moreover,I also show that southern European cattle breeds displayed shared ancestry with African taurine cattle.Using linked SNP based approaches, I inferred a common origin of the African taurine and zebu cattle ancestry in BAI cattle breeds. Furthermore,I also characterized the genomic diversity and structure in European cattle populations. I show that, on average, nucleotide diversity is higher in southern European cattle than western European (British and commercial) cattle. However, some of these southern European cattle breeds such as Romagnola and Maltese appeared to have undergone a recent bottleneck. On the other hand, Swedish native cattle breeds like Swedish Mountain cattle, despite recorded bottleneck in the past, still display signifcant genomic diversity. However, southern Swedish cattle breeds like Väneko and Ringamåalako requires attention for conservation management as these breeds display lowest genetic diversity among all the Swedish cattle breeds. To understand the patterns of genomic variations comprehensively, I also characterized the structural variations (SVs) in the genome of European cattle. I inferred the in uence of demographic changes in the distribution of SVs in the cattle genome. In addition, I also identifed an SV CNV overlapping the KIT gene in English Longhorn cattle which has previously been associated with color-sidedness. Finally, using whole genome sequencing data, I identifed various protein-coding genes and regulatory elements encompassing SVs which represents valuable resources for future studies aimed at finding the association between physiological processes and SVs in cattle.

Authors/Creators:Upadhyay, Maulik
Title:Genomic variation across European cattle: contribution of gene flow
Series/Journal:Acta Universitatis agriculturae Sueciae (1652-6880)
Year of publishing :2019
Volume:2019:16
Number:2019:16
Number of Pages:53
Papers/manuscripts:
NumberReferences
IM. R. Upadhyay, W. Chen, J.A. Lenstra, C.R. Goderie, D.E. MacHugh, S.D. Park, D.A. Magee, D. Matassino, F. Ciani, H.J. Megens, J.A.M. van Arendonk, P. Ajmone-Marsan, V.A. B^alteanu, S. Dunner, J.F. Garcia, C. Ginja, J. Kantanen, M.A.M. Groenen and R.P.M.A. Crooijmans, Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle (2017), Heredity, 118(2), 169{176.
IIM. R. Upadhyay,C. Bortoluzzi, M. Barbato , P. Ajmone-Marsan, L. Colli,J.A. Lenstra, C. Ginja, T. Sonstegard, M. Bosse , M.A.M. Groenen and R.P.M.A. Crooijmans, Deciphering the pattern of genetic diversity and admixture using Genome-wide SNPs in Southern European cattle (2019), Evolutionary Applications. doi:10.1111/eva.12770.
IIIM. R. Upadhyay, S. Eriksson, S. Mikko, E. Strandberg, M.A.M. Groenen and R.P.M.A. Crooijmans, G. Andersson and A.M. Johansson, Genomic relatedness and diversity of Swedish native cattle breeds. Under review.
IVM. R. Upadhyay, V.H. da Silva, H.J. Megens, M.H.P.W. Visker, P. Ajmone-Marsan, V.A. B^alteanu, S. Dunner, J.F. Garcia, C. Ginja, J. Kantanen, M.A.M. Groenen and R.P.M.A. Crooijmans, Distribution and Functionality of Copy Number Variation across European Cattle Populations (2017), Frontiers in Genetics, 8. doi: 10.3389/fgene.2017.00108.
VM. R. Upadhyay, M.F.L. Derks, G. Andersson, M.A.M. Groenen and R.P.M.A. Crooijmans, Comparative evaluation of structural variations in taurine and indicine cattle using individual whole genome sequences.Under review.
Place of Publication:Uppsala
Publisher:Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences
ISBN for printed version:978-91-7760-350-4
ISBN for electronic version:978-91-7760-351-1
ISSN:1652-6880
Language:English
Additional Information:The research presented in this doctoral thesis was conducted under the joint auspices of the Swedish University of Agricultural Sciences and the Graduate School Wageningen Institute of Animal Sciences of Wageningen University and is part of the Erasmus Mundus Joint Doctorate program “EGS-ABG”.
Publication Type:Doctoral thesis
Article category:Other scientific
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 > 404 Agricultural Biotechnology > Genetics and Breeding
Keywords:cattle, genomic variation, Europe, animal breeds, gene pool, alleles
URN:NBN:urn:nbn:se:slu:epsilon-e-5228
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-e-5228
ID Code:15922
Faculty:V - Veterinärmedicinsk fakultet (t.o.m. 2003)
Department:(VH) > Dept. of Animal Breeding and Genetics
Deposited By: SLUpub Connector
Deposited On:19 Feb 2019 14:05
Metadata Last Modified:08 Mar 2019 14:41

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