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Santos WB, Pereira CB, Maiorano AM, Arce CDS, Baldassini WA, Pereira GL, Chardulo LAL, Neto ORM, Oliveira HN, Curi RA. Genomic inbreeding estimation, runs of homozygosity, and heterozygosity-enriched regions uncover signals of selection in the Quarter Horse racing line. J Anim Breed Genet 2023; 140:583-595. [PMID: 37282810 DOI: 10.1111/jbg.12812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 03/30/2023] [Accepted: 05/28/2023] [Indexed: 06/08/2023]
Abstract
With the advent of genomics, significant progress has been made in the genetic improvement of livestock species, particularly through increased accuracy in predicting breeding values for selecting superior animals and the possibility of performing a high-resolution genetic scan throughout the genome of an individual. The main objectives of this study were to estimate the individual genomic inbreeding coefficient based on runs of homozygosity (FROH ), to identify and characterize runs of homozygosity and heterozygosity (ROH and ROHet, respectively; length and distribution) throughout the genome, and to map selection signatures in relevant chromosomal regions in the Quarter Horse racing line. A total of 336 animals registered with the Brazilian Association of Quarter Horse Breeders (ABQM) were genotyped. One hundred and twelve animals were genotyped using the Equine SNP50 BeadChip (Illumina, USA), with 54,602 single nucleotide polymorphisms (SNPs; 54K). The remaining 224 samples were genotyped using the Equine SNP70 BeadChip (Illumina, USA) with 65,157 SNPs (65K). To ensure data quality, we excluded animals with a call rate below 0.9. We also excluded SNPs located on non-autosomal chromosomes, as well as those with a call rate below 0.9 or a p-value below 1 × 10-5 for Hardy-Weinberg equilibrium. The results indicate moderate to high genomic inbreeding, with 46,594 ROH and 16,101 ROHet detected. In total, 30 and 14 candidate genes overlap with ROH and ROHet regions, respectively. The ROH islands showed genes linked to crucial biological processes, such as cell differentiation (CTBP1, WNT5B, and TMEM120B), regulation of glucose metabolic process (MAEA and NKX1-1), heme transport (PGRMC2), and negative regulation of calcium ion import (VDAC1). In ROHet, the islands showed genes related to respiratory capacity (OR7D19, OR7D4G, OR7D4E, and OR7D4J) and muscle repair (EGFR and BCL9). These findings could aid in selecting animals with greater regenerative capacity and developing treatments for muscle disorders in the QH breed. This study serves as a foundation for future research on equine breeds. It can contribute to developing reproductive strategies in animal breeding programs to improve and preserve the Quarter Horse breed.
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Affiliation(s)
- Wellington B Santos
- Department of Animal Science, São Paulo State University, Jaboticabal, Brazil
| | - Camila B Pereira
- Department of Breeding and Animal Nutrition, São Paulo State University, Botucatu, Brazil
| | - Amanda M Maiorano
- Department of Animal Science, Federal University of Uberlândia, Uberlândia, Brazil
| | | | - Welder A Baldassini
- Department of Breeding and Animal Nutrition, São Paulo State University, Botucatu, Brazil
| | - Guilherme L Pereira
- Department of Breeding and Animal Nutrition, São Paulo State University, Botucatu, Brazil
| | - Luis Artur L Chardulo
- Department of Breeding and Animal Nutrition, São Paulo State University, Botucatu, Brazil
| | - Otávio R M Neto
- Department of Breeding and Animal Nutrition, São Paulo State University, Botucatu, Brazil
| | - Henrique N Oliveira
- Department of Animal Science, São Paulo State University, Jaboticabal, Brazil
| | - Rogério A Curi
- Department of Breeding and Animal Nutrition, São Paulo State University, Botucatu, Brazil
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Pan J, Purev C, Zhao H, Zhang Z, Wang F, Wendoule N, Qi G, Liu Y, Zhou H. Discovery of exercise-related genes and pathway analysis based on comparative genomes of Mongolian originated Abaga and Wushen horse. Open Life Sci 2022; 17:1269-1281. [PMID: 36249530 PMCID: PMC9518662 DOI: 10.1515/biol-2022-0487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 07/21/2022] [Accepted: 07/28/2022] [Indexed: 11/17/2022] Open
Abstract
The Mongolian horses have excellent endurance and stress resistance to adapt to the cold and harsh plateau conditions. Intraspecific genetic diversity is mainly embodied in various genetic advantages of different branches of the Mongolian horse. Since people pay progressive attention to the athletic performance of horse, we expect to guide the exercise-oriented breeding of horses through genomics research. We obtained the clean data of 630,535,376,400 bp through the entire genome second-generation sequencing for the whole blood of four Abaga horses and ten Wushen horses. Based on the data analysis of single nucleotide polymorphism, we severally detected that 479 and 943 positively selected genes, particularly exercise related, were mainly enriched on equine chromosome 4 in Abaga horses and Wushen horses, which implied that chromosome 4 may be associated with the evolution of the Mongolian horse and athletic performance. Four hundred and forty genes of positive selection were enriched in 12 exercise-related pathways and narrowed in 21 exercise-related genes in Abaga horse, which were distinguished from Wushen horse. So, we speculated that the Abaga horse may have oriented genes for the motorial mechanism and 21 exercise-related genes also provided a molecular genetic basis for exercise-directed breeding of the Mongolian horse.
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Affiliation(s)
- Jing Pan
- Faculty of Life Sciences, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia Autonomous Region, People’s Republic of China
- Department of Reproductive Medicine, Inner Mongolia Maternal and Child Health Care Hospitaly, Hohhot, Inner Mongolia Autonomous Region, People’s Republic of China
| | - Chimge Purev
- Mongolia-China Joint Laboratory of Applied Molecular Biology, “Administration of the Science Park” CSTI, Ulaanbaatar, Mongolia
| | - Hongwei Zhao
- Beijing 8omics Gene Technology Co. Ltd, Beijing, People’s Republic of China
| | - Zhipeng Zhang
- Faculty of Life Sciences, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia Autonomous Region, People’s Republic of China
| | - Feng Wang
- Faculty of Life Sciences, Nankai University, Tianjin, People’s Republic of China
| | - Nashun Wendoule
- Animal Husbandry Workstation of Ewenki Autonomous County, Hulun Buir, Inner Mongolia Autonomous Region, People’s Republic of China
| | - Guichun Qi
- Bayanta Village of Animal Husbandry and Veterinary Station of Ewenki Autonomous County, Hulun Buir, Inner Mongolia Autonomous Region, People’s Republic of China
| | - Yongbin Liu
- Sheep Collaboration and Innovation Center, Inner Mongolia Universityy, Hohhot, Inner Mongolia Autonomous Region, People’s Republic of China
| | - Huanmin Zhou
- Faculty of Life Sciences, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia Autonomous Region, People’s Republic of China
- Sheep Collaboration and Innovation Center, Inner Mongolia Universityy, Hohhot, Inner Mongolia Autonomous Region, People’s Republic of China
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Roth IT, Schielke B, Rensing M, Bernau M. Comparison of American Quarter Horses Competing in Western Pleasure, Hunter under Saddle, and Reining Using Linear Traits. Animals (Basel) 2021; 11:2861. [PMID: 34679888 PMCID: PMC8532615 DOI: 10.3390/ani11102861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 12/04/2022] Open
Abstract
To investigate differences in American Quarter Horses conformation suggesting specialization and subpopulations within the breed, a total of 45 horses were studied. These horses were classified according to their specific sport discipline: Western Pleasure (WPL, n = 15), Hunter under Saddle (HUS, n = 15), and Reining (RN, n = 15). Fifteen linear traits (comprising lengths, angles, and circumferences) were measured analogically and photometrically. Afterwards, 9 ratios and differences were calculated, so that a total of 24 traits were examined. The results showed significant differences between horses depending on their sport discipline. HUS horses were significant taller and were characterized by higher values in (nearly) all length traits; they were followed by WPL and RN horses. RN horses displayed the lowest values in length traits but the largest difference between height at withers and height at croup. Nine parameters were analyzed through correlations to the height at withers; all differences were significant, with high to moderate correlation coefficients. The detected differences between the groups support recent studies on the conformation and genotype of subpopulations within a breed and reveal new findings in relation to the selected disciplines. Image analysis worked well and provided reliable data; therefore, this method can be used to examine horses in a time-efficient manner, reducing the stress caused to the animal. Further studies are required to gain more information and to associate the features of AQH anatomic structures with successful performance.
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Affiliation(s)
- Isabel Thea Roth
- Fakultät Agrarwirtschaft, Volkswirtschaft und Management, Hochschule für Wirtschaft und Umwelt Nürtingen-Geislingen, Neckarsteige 6-10, 72622 Nürtingen, Germany;
| | - Britta Schielke
- Independent Researcher (former: Deutsche Quarter Horse Association Breeding Management), Wickengartenstraße 3, 35428 Langgöns, Germany;
| | - Markus Rensing
- Independent Researcher (former: Deutsche Quarter Horse Association Breeding Management), Astenstraße 13, 57392 Schmallenberg, Germany;
| | - Maren Bernau
- Fakultät Agrarwirtschaft, Volkswirtschaft und Management, Hochschule für Wirtschaft und Umwelt Nürtingen-Geislingen, Neckarsteige 6-10, 72622 Nürtingen, Germany;
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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; 50:569-597. [PMID: 31568563 PMCID: PMC6825885 DOI: 10.1111/age.12857] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2019] [Indexed: 12/14/2022]
Abstract
The horse reference genome from the Thoroughbred mare Twilight has been available for a decade and, together with advances in genomics technologies, has led to unparalleled developments in equine genomics. At the core of this progress is the continuing improvement of the quality, contiguity and completeness of the reference genome, and its functional annotation. Recent achievements include the release of the next version of the reference genome (EquCab3.0) and generation of a reference sequence for the Y chromosome. Horse satellite‐free centromeres provide unique models for mammalian centromere research. Despite extremely low genetic diversity of the Y chromosome, it has been possible to trace patrilines of breeds and pedigrees and show that Y variation was lost in the past approximately 2300 years owing to selective breeding. The high‐quality reference genome has led to the development of three different SNP arrays and WGSs of almost 2000 modern individual horses. The collection of WGS of hundreds of ancient horses is unique and not available for any other domestic species. These tools and resources have led to global population studies dissecting the natural history of the species and genetic makeup and ancestry of modern breeds. Most importantly, the available tools and resources, together with the discovery of functional elements, are dissecting molecular causes of a growing number of Mendelian and complex traits. The improved understanding of molecular underpinnings of various traits continues to benefit the health and performance of the horse whereas also serving as a model for complex disease across species.
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Affiliation(s)
- T Raudsepp
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Research, Texas A&M University, College Station, TX, 77843, USA
| | - C J Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - R R Bellone
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA.,School of Veterinary Medicine, Veterinary Genetics Laboratory, University of California-Davis, Davis, CA, 95616, USA
| | - J L Petersen
- Department of Animal Science, University of Nebraska, Lincoln, NE, 68583-0908, USA
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Exome sequencing in genomic regions related to racing performance of Quarter Horses. J Appl Genet 2019; 60:79-86. [DOI: 10.1007/s13353-019-00483-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 12/04/2018] [Accepted: 01/10/2019] [Indexed: 12/26/2022]
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Marchiori CM, Pereira GL, Maiorano AM, Rogatto GM, Assoni AD, Augusto II V. Silva J, Chardulo LAL, Curi RA. Linkage disequilibrium and population structure characterization in the cutting and racing lines of Quarter Horses bred in Brazil. Livest Sci 2019. [DOI: 10.1016/j.livsci.2018.11.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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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. [PMID: 30105047 PMCID: PMC6060370 DOI: 10.3389/fgene.2018.00249] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 06/22/2018] [Indexed: 11/13/2022] Open
Abstract
Selective breeding for athletic performance in various disciplines has resulted in population stratification within the American Quarter Horse (QH) breed. The goals of this study were to utilize high density genotype data to: (1) identify genomic regions undergoing positive selection within and among QH subpopulations; (2) investigate haplotype structure within each QH subpopulation; and (3) identify candidate genes within genomic regions of interest (ROI), as well as biological pathways, predicted to play a role in elite performance in each group. For that, 65K SNP genotyping data on 143 elite individuals from 6 QH subpopulations (cutting, halter, racing, reining, western pleasure, and working cow) were imputed to 2M SNPs. Signatures of selection were identified using FST-based (di ) and haplotype-based (hapFLK) analyses, accompanied by identification of local haplotype structure and sharing within subpopulations (hapQTL). Regions undergoing positive selection were identified on all 31 autosomes, and ROI on 2 chromosomes were identified by all 3 methods combined. Genes within each ROI were retrieved and used to identify pathways and genes that might contribute to performance in each subpopulation. These included, among others, candidate genes associated with skeletal muscle development, metabolism, and central nervous system development. This work improves our understanding of equine breed development, and provides breeders with a better understanding of how selective breeding impacts the performance of QH populations.
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Affiliation(s)
- Felipe Avila
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States
| | - James R Mickelson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States
| | - Robert J Schaefer
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States
| | - Molly E McCue
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States
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Weigand H, Leese F. Detecting signatures of positive selection in non-model species using genomic data. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly007] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Hannah Weigand
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße, Essen, Germany
| | - Florian Leese
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße, Essen, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße, Essen, Germany
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Meira CT, Fortes MR, Farah MM, Porto-Neto LR, Kelly M, Moore SS, Pereira GL, Chardulo LAL, Curi RA. Speed Index in the Racing Quarter Horse: A Genome-wide Association Study. J Equine Vet Sci 2014. [DOI: 10.1016/j.jevs.2014.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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