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Selection signatures in Shetland ponies.
Abstract: Shetland ponies were selected for numerous traits including small stature, strength, hardiness and longevity. Despite the different selection criteria, Shetland ponies are well known for their small stature. We performed a selection signature analysis including genome-wide SNPs of 75 Shetland ponies and 76 large-sized horses. Based upon this dataset, we identified a selection signature on equine chromosome (ECA) 1 between 103.8 Mb and 108.5 Mb. A total of 33 annotated genes are located within this interval including the IGF1R gene at 104.2 Mb and the ADAMTS17 gene at 105.4 Mb. These two genes are well known to have a major impact on body height in numerous species including humans. Homozygosity mapping in the Shetland ponies identified a region with increased homozygosity between 107.4 Mb and 108.5 Mb. None of the annotated genes in this region have so far been associated with height. Thus, we cannot exclude the possibility that the identified selection signature on ECA1 is associated with some trait other than height, for which Shetland ponies were selected.
© 2016 Stichting International Foundation for Animal Genetics.
Publication Date: 2016-02-09 PubMed ID: 26857482DOI: 10.1111/age.12416Google Scholar: Lookup The Equine Research Bank provides access to a large database of publicly available scientific literature. Inclusion in the Research Bank does not imply endorsement of study methods or findings by Mad Barn.
- Journal Article
Summary
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This research studies the selection signatures in Shetland ponies with a focus on their small size. it suggests that genes impacting body height in other species have also had a major impact on the height of the Shetland ponies studied.
Methodology:
- Genome-wide single nucleotide polymorphisms (SNPs) of 75 Shetland ponies and 76 large-sized horses were compared. SNPs are common variations in the DNA sequence of different individuals, which can be used to study genetic diversity and evolution.
- A selection signature analysis was performed to identify any regions of the genome that may have been affected by artificial or natural selection.
- This study focused on a specific region on equine chromosome 1 (ECA1), between 103.8 Mb and 108.5 Mb.
Findings:
- Within the studied interval, 33 annotated genes were identified, including the IGF1R gene at 104.2 Mb and the ADAMTS17 gene at 105.4 Mb.
- Both of these genes have been noted to be major contributors to body height in various species, suggesting they could be the key to the traits distinguishing Shetland ponies from larger horses.
- Researchers further conducted a homozygosity mapping in the Shetland ponies, which can help identify regions of the genome where the two copies of each gene are identical. A region with increased homozygosity was found between 107.4 Mb and 108.5 Mb. However, none of the genes within this region were previously associated with height.
Conclusions:
- The study suggests that the height of Shetland ponies could mainly come from the IGF1R and the ADAMTS17 genes.
- However, it is also possible that the identified selection signature on ECA1 could be associated with traits other than height. This implies that the smaller stature of Shetland ponies may not be the result of selection for height alone, but for other characteristics as well.
Cite This Article
APA
Frischknecht M, Flury C, Leeb T, Rieder S, Neuditschko M.
(2016).
Selection signatures in Shetland ponies.
Anim Genet, 47(3), 370-372.
https://doi.org/10.1111/age.12416 Publication
Researcher Affiliations
- Agroscope, Swiss National Stud Farm, Les Longs-Prés, 1580, Avenches, Switzerland.
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bremgartenstrasse 109a, 3012, Bern, Switzerland.
- Swiss Competence Center of Animal Breeding and Genetics, University of Bern, Bern University of Applied Sciences HAFL & Agroscope, Bremgartenstrasse 109a, 3001, Bern, Switzerland.
- Swiss Competence Center of Animal Breeding and Genetics, University of Bern, Bern University of Applied Sciences HAFL & Agroscope, Bremgartenstrasse 109a, 3001, Bern, Switzerland.
- School of Agricultural, Bern University of Applied Sciences, Forest and Food Sciences, Länggasse 85, 3052, Zollikofen, Switzerland.
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bremgartenstrasse 109a, 3012, Bern, Switzerland.
- Swiss Competence Center of Animal Breeding and Genetics, University of Bern, Bern University of Applied Sciences HAFL & Agroscope, Bremgartenstrasse 109a, 3001, Bern, Switzerland.
- Agroscope, Swiss National Stud Farm, Les Longs-Prés, 1580, Avenches, Switzerland.
- Swiss Competence Center of Animal Breeding and Genetics, University of Bern, Bern University of Applied Sciences HAFL & Agroscope, Bremgartenstrasse 109a, 3001, Bern, Switzerland.
- Agroscope, Swiss National Stud Farm, Les Longs-Prés, 1580, Avenches, Switzerland.
- Swiss Competence Center of Animal Breeding and Genetics, University of Bern, Bern University of Applied Sciences HAFL & Agroscope, Bremgartenstrasse 109a, 3001, Bern, Switzerland.
MeSH Terms
- ADAMTS Proteins / genetics
- Animals
- Body Height
- Breeding
- Genotype
- Homozygote
- Horses / genetics
- Humans
- Polymorphism, Single Nucleotide
- Receptors, Somatomedin / genetics
- Selection, Genetic
Citations
This article has been cited 13 times.- Peripolli E, Reimer C, Ha NT, Geibel J, Machado MA, Panetto JCDC, do Egito AA, Baldi F, Simianer H, da Silva MVGB. Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using whole-genome re-sequencing data. BMC Genomics 2020 Sep 11;21(1):624.
- Warburton CL, Engle BN, Ross EM, Costilla R, Moore SS, Corbet NJ, Allen JM, Laing AR, Fordyce G, Lyons RE, McGowan MR, Burns BM, Hayes BJ. Use of whole-genome sequence data and novel genomic selection strategies to improve selection for age at puberty in tropically-adapted beef heifers. Genet Sel Evol 2020 May 27;52(1):28.
- Han H, McGivney BA, Farries G, Katz LM, MacHugh DE, Randhawa IAS, Hill EW. Selection in Australian Thoroughbred horses acts on a locus associated with early two-year old speed. PLoS One 2020;15(2):e0227212.
- Lee YL, Bosse M, Mullaart E, Groenen MAM, Veerkamp RF, Bouwman AC. Functional and population genetic features of copy number variations in two dairy cattle populations. BMC Genomics 2020 Jan 28;21(1):89.
- Salek Ardestani S, Aminafshar M, Zandi Baghche Maryam MB, Banabazi MH, Sargolzaei M, Miar Y. Whole-Genome Signatures of Selection in Sport Horses Revealed Selection Footprints Related to Musculoskeletal System Development Processes. Animals (Basel) 2019 Dec 26;10(1).
- Ablondi M, Eriksson S, Tetu S, Sabbioni A, Viklund Å, Mikko S. Genomic Divergence in Swedish Warmblood Horses Selected for Equestrian Disciplines. Genes (Basel) 2019 Nov 27;10(12).
- Ablondi M, Viklund Å, Lindgren G, Eriksson S, Mikko S. Signatures of selection in the genome of Swedish warmblood horses selected for sport performance. BMC Genomics 2019 Sep 18;20(1):717.
- Nolte W, Thaller G, Kuehn C. Selection signatures in four German warmblood horse breeds: Tracing breeding history in the modern sport horse. PLoS One 2019;14(4):e0215913.
- Gurgul A, Jasielczuk I, Semik-Gurgul E, Pawlina-Tyszko K, Stefaniuk-Szmukier M, Szmatoła T, Polak G, Tomczyk-Wrona I, Bugno-Poniewierska M. A genome-wide scan for diversifying selection signatures in selected horse breeds. PLoS One 2019;14(1):e0210751.
- Avila F, Mickelson JR, Schaefer RJ, McCue ME. Genome-Wide Signatures of Selection Reveal Genes Associated With Performance in American Quarter Horse Subpopulations. Front Genet 2018;9:249.
- Metzger J, Rau J, Naccache F, Bas Conn L, Lindgren G, Distl O. Genome data uncover four synergistic key regulators for extremely small body size in horses. BMC Genomics 2018 Jun 25;19(1):492.
- Sevane N, Dunner S, Boado A, Cañon J. Polymorphisms in ten candidate genes are associated with conformational and locomotive traits in Spanish Purebred horses. J Appl Genet 2017 Aug;58(3):355-361.
- Davoudi P, Do DN, Rathgeber B, Colombo S, Sargolzaei M, Plastow G, Wang Z, Miar Y. Identification of consensus homozygous regions and their associations with growth and feed efficiency traits in American mink. BMC Genom Data 2024 Jul 10;25(1):68.
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