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Skeletal variation in Tennessee Walking Horses maps to the LCORL/NCAPG gene region.
Abstract: Conformation has long been a driving force in horse selection and breed creation as a predictor for performance. The Tennessee Walking Horse (TWH) ranges in size from 1.5 to 1.7 m and is often used as a trail, show, and pleasure horse. To investigate the contribution of genetics to body conformation in the TWH, we collected DNA samples, body measurements, and gait/training information from 282 individuals. We analyzed the 32 body measures with a principal component analysis. Principal component (PC)1 captured 28.5% of the trait variance, while PC2 comprised just 9.5% and PC3 6.4% of trait variance. All 32 measures correlated positively with PC1, indicating that PC1 describes overall body size. We genotyped 109 horses using the EquineSNP70 bead chip and marker association assessed the data using PC1 scores as a phenotype. Mixed-model linear analysis (EMMAX) revealed a well-documented candidate locus on ECA3 (raw P = 3.86 × 10(-9)) near the LCORL gene. A custom genotyping panel enabled fine-mapping of the PC1 body-size trait to the 3'-end of the LCORL gene (P = 7.09 × 10(-10)). This position differs from other reports suggesting single nucleotide polymorphisms (SNPs) upstream of the LCORL coding sequence regulate expression of the gene and, therefore, body size in horses. Fluorescent in situ hybridization analysis defined the position of a highly homologous 5 kb retrogene copy of LCORL (assigned to unplaced contigs of the EquCab 2.0 assembly) at ECA9 q12-q13. This is the first study to identify putative causative SNPs within the LCORL transcript itself, which are associated with skeletal size variation in horses.
Copyright © 2016 the American Physiological Society.
Publication Date: 2016-03-01 PubMed ID: 26931356DOI: 10.1152/physiolgenomics.00100.2015Google 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
- Research Support
- Non-U.S. Gov't
- Research Support
- U.S. Gov't
- Non-P.H.S.
Summary
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The research article focuses on studying the correlation between genetic markers and body size variation in Tennessee Walking Horses. The study finds a connection between the LCORL/NCAPG gene region and size variation and suggests the existence of causative single nucleotide polymorphisms (SNPs) within the LCORL transcript itself. It is a breakthrough research in the field of equine genetics, providing the first known evidence for such SNPs influencing body size in horses.
Analysis on Horse DNA
- The research was conducted on Tennessee Walking Horses (TWH), a breed commonly used as trail, show, and pleasure horses. This breed exhibits significant variation in size from 1.5 to 1.7 metres.
- DNA samples, body measurements, and information about gait and training were collected from 282 individual horses.
- The gathered data was analyzed using principal component analysis on 32 body measures. Principal component 1 (PC1) accounted for 28.5% of the trait variance, while the remaining measures accounted for lesser variances.
- All 32 measures correlated positively with PC1, leading to the conclusion that PC1 describes the overall body size of these horses.
Genetic Relationships
- Genotypic data was collected from 109 horses using the EquineSNP70 bead chip—a method for profiling many genetic variations at once.
- This genotypic data was assessed using mixed-model linear analysis (EMMAX), and a strong candidate locus was found on ECA3 (third equine chromosome), right near the LCORL gene, which is known to be involved in animal body size.
- A finer analysis by custom genotyping assigned the PC1 body-size trait to the 3′-end of the LCORL gene itself.
- This particular position contradicts other reports that previously suggested SNPs upstream of the LCORL coding sequence being responsible for regulating gene expression and hence, body size in horses.
Fluorescent in situ Hybridization Analysis and Results
- Fluorescent in situ hybridization analysis was used to define the position of a highly homologous 5kb retrogene copy of LCORL. This was assigned to unplaced contigs of the EquCab 2.0 assembly at ECA9 q12-q13.
- The research marks the first study to identify plausible causative SNPs within the LCORL transcript itself that are associated with skeletal size variation in horses.
Cite This Article
APA
Staiger EA, Al Abri MA, Pflug KM, Kalla SE, Ainsworth DM, Miller D, Raudsepp T, Sutter NB, Brooks SA.
(2016).
Skeletal variation in Tennessee Walking Horses maps to the LCORL/NCAPG gene region.
Physiol Genomics, 48(5), 325-335.
https://doi.org/10.1152/physiolgenomics.00100.2015 Publication
Researcher Affiliations
- Department of Animal Science, Cornell University, Ithaca, New York;
- Department of Animal and Veterinary Sciences, College of Agriculture and Marine Sciences, Sultan Qaboos University, Muscat, Oman;
- Department of Animal Science, University of Florida, Gainesville, Florida;
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York;
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York;
- Baker Institute for Animal Health, Cornell University, Ithaca, New York;
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas; and.
- Department of Biology, La Sierra University, Riverside, California.
- Department of Animal Science, University of Florida, Gainesville, Florida; samantha.brooks@ufl.edu.
MeSH Terms
- Animals
- Body Size / genetics
- Breeding / methods
- Chromosome Mapping / methods
- Female
- Genome-Wide Association Study / methods
- Genotype
- Horses / genetics
- Male
- Phenotype
- Polymorphism, Single Nucleotide / genetics
- Quantitative Trait Loci / genetics
- Tennessee
- Walking
Citations
This article has been cited 16 times.- Batcher K, Varney S, Raudsepp T, Jevit M, Dickinson P, Jagannathan V, Leeb T, Bannasch D. Ancient segmentally duplicated LCORL retrocopies in equids. PLoS One 2023;18(6):e0286861.
- Finno CJ. Science-in-brief: Genomic and transcriptomic approaches to the investigation of equine diseases. Equine Vet J 2022 Mar;54(2):444-448.
- Lyu G, Feng C, Zhu S, Ren S, Dang W, Irwin DM, Wang Z, Zhang S. Whole Genome Sequencing Reveals Signatures for Artificial Selection for Different Sizes in Japanese Primitive Dog Breeds. Front Genet 2021;12:671686.
- Asadollahpour Nanaei H, Esmailizadeh A, Ayatollahi Mehrgardi A, Han J, Wu DD, Li Y, Zhang YP. Comparative population genomic analysis uncovers novel genomic footprints and genes associated with small body size in Chinese pony. BMC Genomics 2020 Jul 20;21(1):496.
- Mendoza MN, Raudsepp T, More MJ, Gutiérrez GA, Ponce de León FA. Cytogenetic Mapping of 35 New Markers in the Alpaca (Vicugna pacos). Genes (Basel) 2020 May 8;11(5).
- Al Abri MA, Holl HM, Kalla SE, Sutter NB, Brooks SA. Whole genome detection of sequence and structural polymorphism in six diverse horses. PLoS One 2020;15(4):e0230899.
- Raudsepp T, Finno CJ, Bellone RR, Petersen JL. Ten years of the horse reference genome: insights into equine biology, domestication and population dynamics in the post-genome era. Anim Genet 2019 Dec;50(6):569-597.
- Gmel AI, Druml T, von Niederhäusern R, Leeb T, Neuditschko M. Genome-Wide Association Studies Based on Equine Joint Angle Measurements Reveal New QTL Affecting the Conformation of Horses. Genes (Basel) 2019 May 14;10(5).
- Alkhilaiwi F, Wang L, Zhou D, Raudsepp T, Ghosh S, Paul S, Palechor-Ceron N, Brandt S, Luff J, Liu X, Schlegel R, Yuan H. Long-term expansion of primary equine keratinocytes that maintain the ability to differentiate into stratified epidermis. Stem Cell Res Ther 2018 Jul 4;9(1):181.
- Moore LG. Human Genetic Adaptation to High Altitudes: Current Status and Future Prospects. Quat Int 2017 Dec 15;461:4-13.
- Lewczuk D, Wypchło M, Hecold M, Buczkowska R, Korwin-Kossakowska A. Connections Between Gene Polymorphism and Fetlock and Hock Measurements in Polish Sport Horses. Int J Mol Sci 2025 Oct 2;26(19).
- Nazari-Ghadikolaei A, Fikse WF, Viklund ÅG, Mikko S, Eriksson S. Single-Step Genome-Wide Association Study of Factors for Evaluated and Linearly Scored Traits in Swedish Warmblood Horses. J Anim Breed Genet 2025 Sep;142(5):499-512.
- Reich P, Möller S, Stock KF, Nolte W, von Depka Prondzinski M, Reents R, Kalm E, Kühn C, Thaller G, Falker-Gieske C, Tetens J. Genomic analyses of withers height and linear conformation traits in German Warmblood horses using imputed sequence-level genotypes. Genet Sel Evol 2024 Jun 13;56(1):45.
- Majeres LE, Dilger AC, Shike DW, McCann JC, Beever JE. Defining a Haplotype Encompassing the LCORL-NCAPG Locus Associated with Increased Lean Growth in Beef Cattle. Genes (Basel) 2024 Apr 30;15(5).
- Zhang WW, Weng ZY, Wang X, Yang Y, Li D, Wang L, Liu XC, Meng ZN. Genetic mechanism of body size variation in groupers: Insights from phylotranscriptomics. Zool Res 2024 Mar 18;45(2):314-328.
- Li C, Li J, Wang H, Zhang R, An X, Yuan C, Guo T, Yue Y. Genomic Selection for Live Weight in the 14th Month in Alpine Merino Sheep Combining GWAS Information. Animals (Basel) 2023 Nov 14;13(22).
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