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Inter- and intra-br...
Inter- and intra-breed genome-wide copy number diversity in a large cohort of European equine breeds
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- Sole, Marina (författare)
- Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för husdjursgenetik (HGEN),Department of Animal Breeding and Genetics,Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden
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- Ablondi, Michela (författare)
- Univ Parma, Dept Vet Sci, Parma, Italy
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- Binzer, Amrei (författare)
- Uppsala universitet,Institutionen för medicinska vetenskaper
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- Velie, Brandon D. (författare)
- Univ Sydney, Fac Life & Environm Sci, Sydney, NSW, Australia
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- Hollfelder, Nina (författare)
- Uppsala universitet,Institutionen för medicinska vetenskaper,Science for Life Laboratory, SciLifeLab
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- Buys, Nadine (författare)
- Katholieke Univ Leuven, Dept Biosyst, Livestock Genet, B-3001 Leuven, Belgium
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- Ducro, Bart J. (författare)
- Wageningen Univ & Res, Anim Breeding & Genom, POB 338, NL-6700 AH Wageningen, Netherlands
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- Francois, Liesbeth (författare)
- Katholieke Univ Leuven, Dept Biosyst, Livestock Genet, B-3001 Leuven, Belgium
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- Janssens, Steven (författare)
- Katholieke Univ Leuven, Dept Biosyst, Livestock Genet, B-3001 Leuven, Belgium
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- Schurink, Anouk (författare)
- Wageningen Univ & Res, Anim Breeding & Genom, POB 338, NL-6700 AH Wageningen, Netherlands;Wageningen Univ & Res, Ctr Genet Resources, Netherlands CGN, POB 338, NL-6700 AH Wageningen, Netherlands
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- Viklund, Åsa (författare)
- Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för husdjursgenetik (HGEN),Department of Animal Breeding and Genetics,Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden
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- Eriksson, Susanne (författare)
- Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för husdjursgenetik (HGEN),Department of Animal Breeding and Genetics,Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden
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- Isaksson, Anders (författare)
- Uppsala universitet,Institutionen för medicinska vetenskaper,Science for Life Laboratory, SciLifeLab
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- Göransson, Hanna (författare)
- Uppsala universitet,Institutionen för medicinska vetenskaper,Science for Life Laboratory, SciLifeLab
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- Mikko, Sofia (författare)
- Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för husdjursgenetik (HGEN),Department of Animal Breeding and Genetics,Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden
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- Lindgren, Gabriella (författare)
- Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för husdjursgenetik (HGEN),Department of Animal Breeding and Genetics,Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden;Katholieke Univ Leuven, Dept Biosyst, Livestock Genet, B-3001 Leuven, Belgium
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(creator_code:org_t)
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- 2019-10-22
- 2019
- Engelska.
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Ingår i: BMC Genomics. - : BMC. - 1471-2164. ; 20:1
- Relaterad länk:
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https://doi.org/10.1...
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https://uu.diva-port... (primary) (Raw object)
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https://bmcgenomics....
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https://urn.kb.se/re...
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https://doi.org/10.1...
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https://res.slu.se/i...
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Abstract
Ämnesord
Stäng
- Background Copy Number Variation (CNV) is a common form of genetic variation underlying animal evolution and phenotypic diversity across a wide range of species. In the mammalian genome, high frequency of CNV differentiation between breeds may be candidates for population-specific selection. However, CNV differentiation, selection and its population genetics have been poorly explored in horses. Results We investigated the patterns, population variation and gene annotation of CNV using the Axiom (R) Equine Genotyping Array (670,796 SNPs) from a large cohort of individuals (N = 1755) belonging to eight European horse breeds, varying from draught horses to several warmblood populations. After quality control, 152,640 SNP CNVs (individual markers), 18,800 segment CNVs (consecutive SNP CNVs of same gain/loss state or both) and 939 CNV regions (CNVRs; overlapping segment CNVs by at least 1 bp) compared to the average signal of the reference (Belgian draught horse) were identified. Our analyses showed that Equus caballus chromosome 12 (ECA12) was the most enriched in segment CNV gains and losses (similar to 3% average proportion of the genome covered), but the highest number of segment CNVs were detected on ECA1 and ECA20 (regardless of size). The Friesian horses showed private SNP CNV gains (> 20% of the samples) on ECA1 and Exmoor ponies displayed private SNP CNV losses on ECA25 (> 20% of the samples). The Warmblood cluster showed private SNP CNV gains located in ECA9 and Draught cluster showed private SNP CNV losses located in ECA7. The length of the CNVRs ranged from 1 kb to 21.3 Mb. A total of 10,612 genes were annotated within the CNVRs. The PANTHER annotation of these genes showed significantly under- and overrepresented gene ontology biological terms related to cellular processes and immunity (Bonferroni P-value < 0.05). We identified 80 CNVRs overlapping with known QTL for fertility, coat colour, conformation and temperament. We also report 67 novel CNVRs. Conclusions This work revealed that CNV patterns, in the genome of some European horse breeds, occurred in specific genomic regions. The results provide support to the hypothesis that high frequency private CNVs residing in genes may potentially be responsible for the diverse phenotypes seen between horse breeds.
Ämnesord
- NATURVETENSKAP -- Biologi -- Genetik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Genetics (hsv//eng)
- LANTBRUKSVETENSKAPER -- Bioteknologi med applikationer på växter och djur -- Genetik och förädling inom lantbruksvetenskap (hsv//swe)
- AGRICULTURAL SCIENCES -- Agricultural Biotechnology -- Genetics and Breeding in Agricultural Sciences (hsv//eng)
Nyckelord
- Copy number variation
- Horse
- Structural variation
- SNP genotyping array
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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Till lärosätets databas
- Av författaren/redakt...
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Sole, Marina
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Ablondi, Michela
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Binzer, Amrei
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Velie, Brandon D ...
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Hollfelder, Nina
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Buys, Nadine
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visa fler...
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Ducro, Bart J.
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Francois, Liesbe ...
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Janssens, Steven
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Schurink, Anouk
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Viklund, Åsa
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Eriksson, Susann ...
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Isaksson, Anders
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Göransson, Hanna
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Mikko, Sofia
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Lindgren, Gabrie ...
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visa färre...
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- NATURVETENSKAP
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NATURVETENSKAP
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och Genetik
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BMC Genomics
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Uppsala universitet
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