Exome sequencing in genomic regions related to racing performance of Quarter Horses.
Abstract: Among horses selected for speed, the racing line of Quarter Horses is characterized by high performance in sprint races, with these animals being considered the fastest horses in the world. However, few studies have investigated in more detail the polymorphisms and genes that act on this trait. The objective of this study was to analyze exomes and UTRs in regions previously associated with this trait by GWAS in Quarter Horse racehorses with contrasting maximum speed index (SImax), prospecting causal gene polymorphisms that are related to or are in strong linkage disequilibrium with racing performance. Genotypic and phenotypic records from 360 animals of the racing line of Quarter Horses, previously genotyped with an SNP chip to obtain individual genomic estimated breeding values for performance, were used for the formation and sequencing of two groups of animals with contrasting racing performance (20 animals with superior SImax and 20 with inferior SImax). Two rapid runs were performed using two pools of libraries containing 20 and 19 samples randomly chosen among the 40 samples with contrasting SIs. A total of 1203 variants (1105 SNPs and 93 InDels) were identified in 33 regions of interest obtained previously by GWAS. Twenty-nine of the polymorphisms (24 SNPs and 5 InDels) were considered to be important based on three different and independent approaches: SIFT scores classified as deleterious (< 0.05), degree of impact on the consensus region of each polymorphism, and different allele frequencies identified by Fisher's exact test (p < 0.01) between the groups of horses with contrasting SImax. Thus, eight genes described as functional and positional candidates in previous studies (ABCG5, COL11A1, GEN1, SOCS3, MICAL1, SPTBN1, EPB41L3, and SHQ1) and nine new candidate genes (AKNA, ARMC2, FKBP15, LHX1, NOL10, TMEM192, ZFP37, FIG4, and HNRNPU), some of them with known function, were related to racing performance in Quarter Horses.
Publication Date: 2019-01-21 PubMed ID: 30666567DOI: 10.1007/s13353-019-00483-1Google Scholar: Lookup
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- Journal Article
Summary
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The research article focuses on identifying the specific genes and polymorphisms that influence the high-speed racing performance of Quarter Horses by analyzing exomes and UTRs in regions previously associated with this trait.
Objectives and Methodology
- The primary aim of this study was to analyze exomes, portions of the horse’s genome formed by exons and UTRs. The researchers sought to discover the polymorphisms that affect the trait of speed in Quarter Horses, a breed known for its exceptional racing performance.
- The team analyzed the genotypic and phenotypic records of 360 Quarter Horses drawn from the racing line. These horses were previously genotyped using an SNP chip that helped determine the individual genomic estimated breeding values for performance.
- A set of two groups, each consisting of 20 horses with contrasting maximum speed indexes (SImax), were created to observe the significant differences between them.
- The researchers performed two rapid runs using two pools of libraries containing 19 and 20 samples from the 40 horses with varying SIs.
Findings
- The team identified a total of 1203 variants (which included 1105 SNPs and 93 InDels) in 33 regions that were of interest due to previous GWAS.
- From these, 29 polymorphisms (which included 24 SNPs and 5 InDels) were interpreted as significant. This determination takes into account three approaches: SIFT scores classified as harmful, the degree of impact on the consensus region of each polymorphism, and varying allele frequencies discerned by Fisher’s exact test. All of these were found between the groups of horses with contrasting SImax.
- Eight genes that were highlighted as functional and positional candidates in previous studies (ABCG5, COL11A1, GEN1, SOCS3, MICAL1, SPTBN1, EPB41L3, and SHQ1) and nine new candidate genes (AKNA, ARMC2, FKBP15, LHX1, NOL10, TMEM192, ZFP37, FIG4, and HNRNPU) were related to racing performance in Quarter Horses.
Conclusion
- Though studies on the link between genes and racing performance in Quarter Horses have been limited, this research deepened the understanding of polymorphisms and genes acting on such traits.
- The findings could serve as essential information in future studies and genomic selection programs aimed at enhancing the racing performance of Quarter Horses.
Cite This Article
APA
Pereira GL, Malheiros JM, Ospina AMT, Chardulo LAL, Curi RA.
(2019).
Exome sequencing in genomic regions related to racing performance of Quarter Horses.
J Appl Genet, 60(1), 79-86.
https://doi.org/10.1007/s13353-019-00483-1 Publication
Researcher Affiliations
- Department of Animal Breeding and Nutrition, College of Veterinary and Animal Science, São Paulo State University (UNESP), Rubião Junior District, Botucatu, São Paulo, 18618-970, Brazil. guilherme.luis@unesp.br.
- Department of Animal Science, College of Agriculture and Veterinary Science, São Paulo State University (UNESP), Jaboticabal, São Paulo, Brazil.
- Department of Animal Science, College of Agriculture and Veterinary Science, São Paulo State University (UNESP), Jaboticabal, São Paulo, Brazil.
- Department of Animal Breeding and Nutrition, College of Veterinary and Animal Science, São Paulo State University (UNESP), Rubião Junior District, Botucatu, São Paulo, 18618-970, Brazil.
- Department of Animal Breeding and Nutrition, College of Veterinary and Animal Science, São Paulo State University (UNESP), Rubião Junior District, Botucatu, São Paulo, 18618-970, Brazil.
MeSH Terms
- Animals
- Genes
- Genome
- Horses / genetics
- Polymorphism, Single Nucleotide
- Running
- Sports
- Exome Sequencing / methods
Grant Funding
- 2014/20207-1 / Funda??o de Amparo ? Pesquisa do Estado de S?o Paulo
References
This article includes 18 references
- Hum Reprod. 2012 Sep;27(9):2872-5
- Equine Vet J Suppl. 2006 Aug;(36):128-32
- Bioinformatics. 2011 Aug 1;27(15):2156-8
- Curr Protoc Hum Genet. 2016 Jan 01;88:6.15.1-6.15.17
- Animal. 2014 Nov;8(11):1754-64
- Am J Hum Genet. 2007 Sep;81(3):559-75
- Cell Res. 2011 Nov;21(11):1528-30
- J Biomed Biotechnol. 2012;2012:251364
- PLoS One. 2016 Mar 22;11(3):e0151664
- Mol Biol Evol. 2009 Feb;26(2):473-80
- Asian-Australas J Anim Sci. 2015 Jun;28(6):771-81
- PLoS One. 2013;8(1):e54997
- Anim Genet. 2015 Apr;46(2):158-63
- Mol Carcinog. 2015 Jul;54(7):513-22
- Genome Res. 2011 Jun;21(6):936-9
- Bioinformatics. 2009 Aug 15;25(16):2078-9
- J Physiol. 1966 Jan;182(2):268-96
- Nucleic Acids Res. 2016 Jan 4;44(D1):D336-42
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