1
|
Han H, McGivney BA, Allen L, Bai D, Corduff LR, Davaakhuu G, Davaasambuu J, Dorjgotov D, Hall TJ, Hemmings AJ, Holtby AR, Jambal T, Jargalsaikhan B, Jargalsaikhan U, Kadri NK, MacHugh DE, Pausch H, Readhead C, Warburton D, Dugarjaviin M, Hill EW. Common protein-coding variants influence the racing phenotype in galloping racehorse breeds. Commun Biol 2022; 5:1320. [PMID: 36513809 PMCID: PMC9748125 DOI: 10.1038/s42003-022-04206-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 11/01/2022] [Indexed: 12/14/2022] Open
Abstract
Selection for system-wide morphological, physiological, and metabolic adaptations has led to extreme athletic phenotypes among geographically diverse horse breeds. Here, we identify genes contributing to exercise adaptation in racehorses by applying genomics approaches for racing performance, an end-point athletic phenotype. Using an integrative genomics strategy to first combine population genomics results with skeletal muscle exercise and training transcriptomic data, followed by whole-genome resequencing of Asian horses, we identify protein-coding variants in genes of interest in galloping racehorse breeds (Arabian, Mongolian and Thoroughbred). A core set of genes, G6PC2, HDAC9, KTN1, MYLK2, NTM, SLC16A1 and SYNDIG1, with central roles in muscle, metabolism, and neurobiology, are key drivers of the racing phenotype. Although racing potential is a multifactorial trait, the genomic architecture shaping the common athletic phenotype in horse populations bred for racing provides evidence for the influence of protein-coding variants in fundamental exercise-relevant genes. Variation in these genes may therefore be exploited for genetic improvement of horse populations towards specific types of racing.
Collapse
Affiliation(s)
- Haige Han
- grid.411638.90000 0004 1756 9607Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018 China
| | - Beatrice A. McGivney
- grid.496984.ePlusvital Ltd, The Highline, Dun Laoghaire Business Park, Dublin, A96 W5T3 Ireland
| | - Lucy Allen
- grid.417905.e0000 0001 2186 5933Royal Agricultural University, Cirencester, Gloucestershire GL7 6JS UK
| | - Dongyi Bai
- grid.411638.90000 0004 1756 9607Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018 China
| | - Leanne R. Corduff
- grid.496984.ePlusvital Ltd, The Highline, Dun Laoghaire Business Park, Dublin, A96 W5T3 Ireland
| | - Gantulga Davaakhuu
- grid.425564.40000 0004 0587 3863Institute of Biology, Mongolian Academy of Sciences, Peace Avenue 54B, Ulaanbaatar, 13330 Mongolia
| | - Jargalsaikhan Davaasambuu
- Ajnai Sharga Horse Racing Team, Encanto Town 210-11, Ikh Mongol State Street, 26th Khoroo, Bayanzurkh district Ulaanbaatar, 13312 Mongolia
| | - Dulguun Dorjgotov
- grid.440461.30000 0001 2191 7895School of Industrial Technology, Mongolian University of Science and Technology, Ulaanbaatar, 661 Mongolia
| | - Thomas J. Hall
- grid.7886.10000 0001 0768 2743UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin D04 V1W8 Ireland
| | - Andrew J. Hemmings
- grid.417905.e0000 0001 2186 5933Royal Agricultural University, Cirencester, Gloucestershire GL7 6JS UK
| | - Amy R. Holtby
- grid.496984.ePlusvital Ltd, The Highline, Dun Laoghaire Business Park, Dublin, A96 W5T3 Ireland
| | - Tuyatsetseg Jambal
- grid.440461.30000 0001 2191 7895School of Industrial Technology, Mongolian University of Science and Technology, Ulaanbaatar, 661 Mongolia
| | - Badarch Jargalsaikhan
- grid.444534.60000 0000 8485 883XDepartment of Obstetrics and Gynecology, Mongolian National University of Medical Sciences, Ulaanbaatar, 14210 Mongolia
| | - Uyasakh Jargalsaikhan
- Ajnai Sharga Horse Racing Team, Encanto Town 210-11, Ikh Mongol State Street, 26th Khoroo, Bayanzurkh district Ulaanbaatar, 13312 Mongolia
| | - Naveen K. Kadri
- grid.5801.c0000 0001 2156 2780Animal Genomics, Institute of Agricultural Sciences, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - David E. MacHugh
- grid.7886.10000 0001 0768 2743UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin D04 V1W8 Ireland ,grid.7886.10000 0001 0768 2743UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin D04 V1W8 Ireland
| | - Hubert Pausch
- grid.5801.c0000 0001 2156 2780Animal Genomics, Institute of Agricultural Sciences, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - Carol Readhead
- grid.20861.3d0000000107068890Biology and Bioengineering, California Institute of Technology, Pasadena, CA 91125 USA
| | - David Warburton
- grid.42505.360000 0001 2156 6853The Saban Research Institute, Children’s Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA 90027 USA
| | - Manglai Dugarjaviin
- grid.411638.90000 0004 1756 9607Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018 China
| | - Emmeline W. Hill
- grid.496984.ePlusvital Ltd, The Highline, Dun Laoghaire Business Park, Dublin, A96 W5T3 Ireland ,grid.7886.10000 0001 0768 2743UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin D04 V1W8 Ireland
| |
Collapse
|
2
|
Abstract
Thoroughbred horses have been selected for racing performance for more than 400 years. Despite continued selection, race times have not improved significantly during the past 60 years, raising the question of whether genetic variation for racing performance still exists. Studies using phenotypes such as race time, money earned, and handicapping, however, demonstrate that there is extensive variation within these traits and that they are heritable. Even so, these are poor measures of racing success since Thoroughbreds race at different ages and distances and on different types of tracks, and some may not race at all. With the advent of genomic tools, DNA variants are being identified that contribute to racing success. Aside from strong associations for myostatin variants with best racing distance, weak to modest associations with racing phenotypes are reported for other genomic regions. These data suggest that diverse genetic strategies have contributed to producing a successful racehorse, and genetic variation contributing to athleticism remains important. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Ernest Bailey
- MH Gluck Equine Research Center, University of Kentucky, Lexington, Kentucky, USA; ,
| | - Jessica L Petersen
- Department of Animal Science, University of Nebraska, Lincoln, Nebraska, USA;
| | | |
Collapse
|
3
|
A highly prevalent SINE mutation in the myostatin (MSTN) gene promoter is associated with low circulating myostatin concentration in Thoroughbred racehorses. Sci Rep 2021; 11:7916. [PMID: 33846367 PMCID: PMC8041750 DOI: 10.1038/s41598-021-86783-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/19/2021] [Indexed: 02/07/2023] Open
Abstract
Horse racing is a popular and financially important industry worldwide and researchers and horse owners are interested in genetic and training influences that maximise athletic performance. An association has been found between the presence of a short interspersed nuclear element (SINE) mutation in the myostatin (MSTN) gene promoter and optimal race distance in Thoroughbred horses. There is previous laboratory evidence that this mutation reduces MSTN expression in a cell culture model and influences skeletal muscle fibre type proportions in horses. Manipulating MSTN expression has been proposed for illicit gene doping in human and equine athletes and already, researchers have generated homozygous and heterozygous MSTN-null horse embryos following CRISPR/Cas9 editing at the equine MSTN locus and nuclear transfer, aiming artificially to enhance performance. To date however, the role of the naturally-occurring equine MSTN SINE mutation in vivo has remained unclear; here we hypothesised that it reduces, but does not ablate circulating myostatin expression. Following validation of an ELISA for detection of myostatin in equine serum and using residual whole blood and serum samples from 176 Thoroughbred racehorses under identical management, horses were genotyped for the SINE mutation by PCR and their serum myostatin concentrations measured. In our population, the proportions of SINE homozygotes, heterozygotes and normal horses were 27%, 46% and 27% respectively. Results indicated that horses that are homozygous for the SINE mutation have detectable, but significantly lower (p < 0.0001) serum myostatin concentrations (226.8 pg/ml; 69.3–895.4 pg/ml; median; minimum–maximum) than heterozygous (766 pg/ml; 64.6–1182 pg/ml) and normal horses (1099 pg/ml; 187.8–1743 pg/ml). Heterozygotes have significantly lower (p < 0.0001) myostatin concentrations than normal horses. Variation in serum myostatin concentrations across horses was not influenced by age or sex. This is the first study to reveal the direct functional effect of a highly prevalent mutation in the equine MSTN gene associated with exercise performance. Determining the reason for variation in expression of myostatin within SINE-genotyped groups might identify additional performance-associated environmental or genetic influences in Thoroughbreds. Understanding the mechanism by which altered myostatin expression influences skeletal muscle fibre type remains to be determined.
Collapse
|
4
|
Pira E, Vacca GM, Dettori ML, Piras G, Moro M, Paschino P, Pazzola M. Polymorphisms at Myostatin Gene ( MSTN) and the Associations with Sport Performances in Anglo-Arabian Racehorses. Animals (Basel) 2021; 11:964. [PMID: 33808485 PMCID: PMC8065447 DOI: 10.3390/ani11040964] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/17/2021] [Accepted: 03/29/2021] [Indexed: 11/17/2022] Open
Abstract
One hundred and eighty Anglo-Arabian horses running 1239 races were sampled for the present study. DNA was extracted from the blood and myostatin gene, MSTN, was genotyped. Moreover, prizes won and places were achieved for the 1239 races to perform association analyses between the different genotypes and sport traits. Two SNPs already reported in previous studies regarding the Thoroughbred breed, rs69472472 and rs397152648, were revealed as polymorphic. The linkage disequilibrium analysis investigating the haplotype structure of MSTN did not evidence any association block. Polymorphism at SNP rs397152648, previously known as g.66493737 T>C, significantly influenced sport traits, with heterozygous horses TC showing better results than homozygotes TT. The portion of variance due to the random effect of the individual animal, and the other phenotypic effects of sex, percentage of Arabian blood and race distance, computed together with the genotype at MSTN in the statistical models, exerted a significant influence. Hence, this information is useful to improve knowledge of the genetic profile of Anglo-Arabian horses and a possible selection for better sport performance.
Collapse
Affiliation(s)
- Emanuela Pira
- Local Health Authority 7 Pedemontana, Via dei Lotti 40, 36061 Bassano del Grappa, Italy;
| | - Giuseppe Massimo Vacca
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100 Sassari, Italy; (G.M.V.); (M.L.D.); (P.P.)
| | - Maria Luisa Dettori
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100 Sassari, Italy; (G.M.V.); (M.L.D.); (P.P.)
| | - Gianpiera Piras
- Local Health Authority of Oristano, Via Carducci 35, 09170 Oristano, Italy;
| | - Massimiliano Moro
- Local Health Authority of Nuoro, Via Amerigo Demurtas 1, 08110 Nuoro, Italy;
| | - Pietro Paschino
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100 Sassari, Italy; (G.M.V.); (M.L.D.); (P.P.)
| | - Michele Pazzola
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100 Sassari, Italy; (G.M.V.); (M.L.D.); (P.P.)
| |
Collapse
|
5
|
Darbandi H, Serra Bragança F, van der Zwaag BJ, Voskamp J, Gmel AI, Haraldsdóttir EH, Havinga P. Using Different Combinations of Body-Mounted IMU Sensors to Estimate Speed of Horses-A Machine Learning Approach. SENSORS 2021; 21:s21030798. [PMID: 33530288 PMCID: PMC7865839 DOI: 10.3390/s21030798] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/08/2021] [Accepted: 01/20/2021] [Indexed: 12/13/2022]
Abstract
Speed is an essential parameter in biomechanical analysis and general locomotion research. It is possible to estimate the speed using global positioning systems (GPS) or inertial measurement units (IMUs). However, GPS requires a consistent signal connection to satellites, and errors accumulate during IMU signals integration. In an attempt to overcome these issues, we have investigated the possibility of estimating the horse speed by developing machine learning (ML) models using the signals from seven body-mounted IMUs. Since motion patterns extracted from IMU signals are different between breeds and gaits, we trained the models based on data from 40 Icelandic and Franches-Montagnes horses during walk, trot, tölt, pace, and canter. In addition, we studied the estimation accuracy between IMU locations on the body (sacrum, withers, head, and limbs). The models were evaluated per gait and were compared between ML algorithms and IMU location. The model yielded the highest estimation accuracy of speed (RMSE = 0.25 m/s) within equine and most of human speed estimation literature. In conclusion, highly accurate horse speed estimation models, independent of IMU(s) location on-body and gait, were developed using ML.
Collapse
Affiliation(s)
- Hamed Darbandi
- Pervasive Systems Group, Department of Computer Science, University of Twente, 7522 NB Enschede, The Netherlands; (B.J.v.d.Z.); (P.H.)
- Correspondence:
| | - Filipe Serra Bragança
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands;
| | - Berend Jan van der Zwaag
- Pervasive Systems Group, Department of Computer Science, University of Twente, 7522 NB Enschede, The Netherlands; (B.J.v.d.Z.); (P.H.)
- Inertia Technology B.V., 7521 AG Enschede, The Netherlands
| | - John Voskamp
- Rosmark Consultancy, 6733 AA Wekerom, The Netherlands;
| | - Annik Imogen Gmel
- Equine Department, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland; (A.I.G.); (E.H.H.)
- Agroscope—Swiss National Stud Farm, Les Longs-Prés, 1580 Avenches, Switzerland
| | - Eyrún Halla Haraldsdóttir
- Equine Department, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland; (A.I.G.); (E.H.H.)
| | - Paul Havinga
- Pervasive Systems Group, Department of Computer Science, University of Twente, 7522 NB Enschede, The Netherlands; (B.J.v.d.Z.); (P.H.)
| |
Collapse
|
6
|
Denham J, McCluskey M, Denham MM, Sellami M, Davie AJ. Epigenetic control of exercise adaptations in the equine athlete: Current evidence and future directions. Equine Vet J 2020; 53:431-450. [PMID: 32671871 DOI: 10.1111/evj.13320] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/04/2020] [Accepted: 06/25/2020] [Indexed: 12/11/2022]
Abstract
Horses (Equus ferus caballus) have evolved over the past 300 years in response to man-made selection for particular athletic traits. Some of the selected traits were selected based on the size and horses' muscular power (eg Clydesdales), whereas other breeds were bred for peak running performance (eg Thoroughbred and Arabian). Although the physiological changes and some of the cellular adaptations responsible for athletic potential of horses have been identified, the molecular mechanisms are only just beginning to be comprehensively investigated. The purpose of this review was to outline and discuss the current understanding of the molecular mechanisms underpinning the athletic performance and cardiorespiratory fitness in athletic breeds of horses. A brief review of the biology of epigenetics is provided, including discussion on DNA methylation, histone modifications and small RNAs, followed by a summary and critical review of the current work on the exercise-induced epigenetic and transcriptional changes in horses. Important unanswered questions and currently unexplored areas that deserve attention are highlighted. Finally, a rationale for the analysis of epigenetic modifications in the context with exercise-related traits and ailments associated with athletic breeds of horses is outlined in order to help guide future research.
Collapse
Affiliation(s)
- Joshua Denham
- RMIT University, School of Health and Biomedical Sciences, Melbourne, VIC, Australia
| | | | | | - Maha Sellami
- Qatar University, College of Arts and Sciences (CAS), Sport Science Program (SSP), Doha, Qatar
| | - Allan J Davie
- Australian Equine Racing and Research Centre (AERR), Ballina, NSW, Australia
| |
Collapse
|
7
|
Schaefer RJ, Cullen J, Manfredi J, McCue M. Functional contexts of adipose and gluteal muscle tissue gene co-expression networks in the domestic horse. Integr Comp Biol 2020; 63:icaa134. [PMID: 32970803 DOI: 10.1093/icb/icaa134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 08/14/2020] [Accepted: 08/27/2020] [Indexed: 11/13/2022] Open
Abstract
A gene's response to an environment is tightly bound to the underlying genetic variation present in an individual's genome and varies greatly depending on the tissue it is being expressed in. Gene co-expression networks provide a mechanism to understand and interpret the collective transcriptional responses of genes. Here, we use the Camoco co-expression network framework to characterize the transcriptional landscape of adipose and gluteal muscle tissue in 83 domestic horses (Equus caballus) representing 5 different breeds. In each tissue, gene expression profiles, capturing transcriptional response due to variation across individuals, were used to build two separate, tissue-focused, genotypically-diverse gene co-expression networks. The aim of our study was to identify significantly co-expressed clusters of genes in each tissue, then compare the clusters across networks to quantify the extent that clusters were found in both networks as well as to identify clusters found in a single network. The known and unknown functions for each network were quantified using complementary, supervised and unsupervised approaches. First, supervised ontological enrichment was utilized to quantify biological functions represented by each network. Curated ontologies (GO and KEGG) were used to measure the known biological functions present in each tissue. Overall, a large percentage of terms (40.3% of GO and 41% of KEGG) were co-expressed in at least one tissue. Many terms were co-expressed in both tissues, however a small proportion of terms exhibited single tissue co-expression suggesting functional differentiation based on curated, functional annotation. To complement this, an unsupervised approach not relying on ontologies was employed. Strongly co-expressed sets of genes defined by Markov clustering identified sets of unannotated genes showing similar patterns of co-expression within a tissue. We compared gene sets across tissues and identified clusters of genes the either segregate in co-expression by tissue or exhibit high levels of co-expression in both tissues. Clusters were also integrated with GO and KEGG ontologies to identify gene sets containing previously curated annotations versus unannotated gene sets indicating potentially novel biological function. Coupling together these transcriptional datasets, we mapped the transcriptional landscape of muscle and adipose setting up a generalizable framework for interpreting gene function for additional tissues in the horse and other species.
Collapse
Affiliation(s)
- Robert J Schaefer
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN
| | - Jonah Cullen
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN
| | - Jane Manfredi
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI
| | - Molly McCue
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN
| |
Collapse
|
8
|
Tian J, Hu J, He W, Zhou L, Huang Y. Parental exposure to cadmium chloride causes developmental toxicity and thyroid endocrine disruption in zebrafish offspring. Comp Biochem Physiol C Toxicol Pharmacol 2020; 234:108782. [PMID: 32339758 DOI: 10.1016/j.cbpc.2020.108782] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 04/20/2020] [Accepted: 04/22/2020] [Indexed: 12/11/2022]
Abstract
Cadmium is a common heavy metal pollutant. Previous studies have found that long-term cadmium exposure can cause damage to multiple organs/systems in humans and experimental animals; however, there are few studies that elucidate its effects on offspring development, discuss whether it can be transmitted to offspring from the parent, and debate whether it affects the functional development of the thyroid hormone system in offsprings. In this study, sexually mature zebrafish were exposed to different concentrations of cadmium chloride (0.01 μmol/L, 0.1 μmol/L, and 1 μmol/L) to study reproductive toxicity. It was found that parental zebrafish exposed to 1 μmol/L of cadmium chloride produced offsprings with different degrees of malformation. At 5 days post-fertilization (dpf), the levels of 3,5,3'-triiododenosine (T3) and thyroxine (T4) in the zebrafish were decreased. At 10 dpf, the T4 and T3 levels in the zebrafish of the offspring were significantly reduced. At the same time, the expression of thyroid receptor (trα and trβ) genes in five dpf larvae was significantly up-regulated in the 1 μmol/L treatment group relative to the control group. The mRNAs of thyroid hormone synthesis and metabolism-related genes (tshβ, dio1, dio2, ugt1ab, and ttr) were significantly up-regulated in the 0.1 μmol/L and 1 μmol/L treatment groups. This study demonstrates that parental cadmium chloride exposure produces reproductive toxicity in zebrafish and that the effects can be transferred from the parent to the offspring, resulting in developmental toxicity in the thyroid endocrine system.
Collapse
Affiliation(s)
- Jingjing Tian
- Academy for Engineering & Technology, Fudan University, Shanghai 200433, PR China; CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, PR China
| | - Jia Hu
- School of Biology & Basic Medical Sciences, Medical College, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Wei He
- Shaanxi Institute of Pediatric Diseases, Xi'an Key Laboratory of Children's Health and Diseases, Xi'an Children's Hospital, Xi'an, Shaanxi 710003, PR China
| | - Lianqun Zhou
- Academy for Engineering & Technology, Fudan University, Shanghai 200433, PR China; CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, PR China.
| | - Yinong Huang
- Shaanxi Institute of Pediatric Diseases, Xi'an Key Laboratory of Children's Health and Diseases, Xi'an Children's Hospital, Xi'an, Shaanxi 710003, PR China.
| |
Collapse
|
9
|
Curi RA, Pereira GL, Alvarez MVN, Baldassini WA, Machado Neto OR, Chardulo LAL. Exome analysis and functional classification of identified variants in racing Quarter Horses. Anim Genet 2020; 51:716-721. [PMID: 32696541 DOI: 10.1111/age.12976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/27/2020] [Accepted: 06/15/2020] [Indexed: 11/26/2022]
Abstract
The main objectives of this study were to identify and functionally classify SNPs and indels by exome sequencing of animals of the racing line of Quarter Horses. Based on the individual genomic estimated breeding values (GEBVs) for maximum speed index (SImax) obtained for 349 animals, two groups of 20 extreme animals were formed. Of these individuals, 20 animals with high GEBVs for SImax and 19 with low GEBVs for SImax had their exons and 5' and 3' UTRs sequenced. Considering SNPs and indels, 105 182 variants were identified in the expressed regions of the Quarter Horse genome. Of these, 72 166 variants were already known and 33 016 are new variants and were deposited in a database. The analysis of the set of gene variants significantly related (Padjusted < 0.05) to extreme animals in conjunction with the predicted impact of the changes and the physiological role of protein product pointed to two candidate genes potentially related to racing performance: SLC3A1 on ECA15 and CCN6 on ECA10.
Collapse
Affiliation(s)
- R A Curi
- Department of Animal Breeding and Nutrition, College of Veterinary and Animal Science, São Paulo State University, Rubião Junior District, Botucatu, São Paulo, 18618-970, Brazil
| | - G L Pereira
- Department of Animal Breeding and Nutrition, College of Veterinary and Animal Science, São Paulo State University, Rubião Junior District, Botucatu, São Paulo, 18618-970, Brazil
| | - M V N Alvarez
- Department of Parasitology, Institute of Biosciences, São Paulo State University, Rubião Junior District, Botucatu, São Paulo, 18618-970, Brazil
| | - W A Baldassini
- Department of Animal Breeding and Nutrition, College of Veterinary and Animal Science, São Paulo State University, Rubião Junior District, Botucatu, São Paulo, 18618-970, Brazil
| | - O R Machado Neto
- Department of Animal Breeding and Nutrition, College of Veterinary and Animal Science, São Paulo State University, Rubião Junior District, Botucatu, São Paulo, 18618-970, Brazil
| | - L A L Chardulo
- Department of Animal Breeding and Nutrition, College of Veterinary and Animal Science, São Paulo State University, Rubião Junior District, Botucatu, São Paulo, 18618-970, Brazil
| |
Collapse
|
10
|
Farries G, Bryan K, McGivney CL, McGettigan PA, Gough KF, Browne JA, MacHugh DE, Katz LM, Hill EW. Expression Quantitative Trait Loci in Equine Skeletal Muscle Reveals Heritable Variation in Metabolism and the Training Responsive Transcriptome. Front Genet 2019; 10:1215. [PMID: 31850069 PMCID: PMC6902038 DOI: 10.3389/fgene.2019.01215] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 11/04/2019] [Indexed: 01/10/2023] Open
Abstract
While over ten thousand genetic loci have been associated with phenotypic traits and inherited diseases in genome-wide association studies, in most cases only a relatively small proportion of the trait heritability is explained and biological mechanisms underpinning these traits have not been clearly identified. Expression quantitative trait loci (eQTL) are subsets of genomic loci shown experimentally to influence gene expression. Since gene expression is one of the primary determinants of phenotype, the identification of eQTL may reveal biologically relevant loci and provide functional links between genomic variants, gene expression and ultimately phenotype. Skeletal muscle (gluteus medius) gene expression was quantified by RNA-seq for 111 Thoroughbreds (47 male, 64 female) in race training at a single training establishment sampled at two time-points: at rest (n = 92) and four hours after high-intensity exercise (n = 77); n = 60 were sampled at both time points. Genotypes were generated from the Illumina Equine SNP70 BeadChip. Applying a False Discovery Rate (FDR) corrected P-value threshold (PFDR < 0.05), association tests identified 3,583 cis-eQTL associated with expression of 1,456 genes at rest; 4,992 cis-eQTL associated with the expression of 1,922 genes post-exercise; 1,703 trans-eQTL associated with 563 genes at rest; and 1,219 trans-eQTL associated with 425 genes post-exercise. The gene with the highest cis-eQTL association at both time-points was the endosome-associated-trafficking regulator 1 gene (ENTR1; Rest: PFDR = 3.81 × 10-27, Post-exercise: PFDR = 1.66 × 10-24), which has a potential role in the transcriptional regulation of the solute carrier family 2 member 1 glucose transporter protein (SLC2A1). Functional analysis of genes with significant eQTL revealed significant enrichment for cofactor metabolic processes. These results suggest heritable variation in genomic elements such as regulatory sequences (e.g. gene promoters, enhancers, silencers), microRNA and transcription factor genes, which are associated with metabolic function and may have roles in determining end-point muscle and athletic performance phenotypes in Thoroughbred horses. The incorporation of the eQTL identified with genome and transcriptome-wide association may reveal useful biological links between genetic variants and their impact on traits of interest, such as elite racing performance and adaptation to training.
Collapse
Affiliation(s)
- Gabriella Farries
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Kenneth Bryan
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | | | - Paul A McGettigan
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Katie F Gough
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - John A Browne
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - David E MacHugh
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Lisa Michelle Katz
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Emmeline W Hill
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland.,Research and Development, Plusvital Ltd., Dublin, Ireland
| |
Collapse
|