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Wolfsberger WW, Ayala NM, Castro-Marquez SO, Irizarry-Negron VM, Potapchuk A, Shchubelka K, Potish L, Majeske AJ, Oliver LF, Lameiro AD, Martínez-Cruzado JC, Lindgren G, Oleksyk TK. Genetic diversity and selection in Puerto Rican horses. Sci Rep 2022; 12:515. [PMID: 35017609 PMCID: PMC8752667 DOI: 10.1038/s41598-021-04537-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 12/23/2021] [Indexed: 11/21/2022] Open
Abstract
Since the first Spanish settlers brought horses to America centuries ago, several local varieties and breeds have been established in the New World. These were generally a consequence of the admixture of the different breeds arriving from Europe. In some instances, local horses have been selectively bred for specific traits, such as appearance, endurance, strength, and gait. We looked at the genetics of two breeds, the Puerto Rican Non-Purebred (PRNPB) (also known as the "Criollo") horses and the Puerto Rican Paso Fino (PRPF), from the Caribbean Island of Puerto Rico. While it is reasonable to assume that there was a historic connection between the two, the genetic link between them has never been established. In our study, we started by looking at the genetic ancestry and diversity of current Puerto Rican horse populations using a 668 bp fragment of the mitochondrial DNA D-loop (HVR1) in 200 horses from 27 locations on the island. We then genotyped all 200 horses in our sample for the "gait-keeper" DMRT3 mutant allele previously associated with the paso gait especially cherished in this island breed. We also genotyped a subset of 24 samples with the Illumina Neogen Equine Community genome-wide array (65,000 SNPs). This data was further combined with the publicly available PRPF genomes from other studies. Our analysis show an undeniable genetic connection between the two varieties in Puerto Rico, consistent with the hypothesis that PRNPB horses represent the descendants of the original genetic pool, a mix of horses imported from the Iberian Peninsula and elsewhere in Europe. Some of the original founders of PRNRB population must have carried the "gait-keeper" DMRT3 allele upon arrival to the island. From this admixture, the desired traits were selected by the local people over the span of centuries. We propose that the frequency of the mutant "gait-keeper" allele originally increased in the local horses due to the selection for the smooth ride and other characters, long before the PRPF breed was established. To support this hypothesis, we demonstrate that PRNPB horses, and not the purebred PRPF, carry a signature of selection in the genomic region containing the DMRT3 locus to this day. The lack of the detectable signature of selection associated with the DMRT3 in the PRPF would be expected if this native breed was originally derived from the genetic pool of PRNPB horses established earlier and most of the founders already had the mutant allele. Consequently, selection specific to PRPF later focused on allels in other genes (including CHRM5, CYP2E1, MYH7, SRSF1, PAM, PRN and others) that have not been previously associated with the prized paso gait phenotype in Puerto Rico or anywhere else.
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Affiliation(s)
- Walter W Wolfsberger
- Department of Biological Sciences, Oakland University, Rochester, MI, USA
- Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico
- Biology Department, Uzhhorod National University, Uzhhorod, Ukraine
| | - Nikole M Ayala
- Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico
| | - Stephanie O Castro-Marquez
- Department of Biological Sciences, Oakland University, Rochester, MI, USA
- Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico
| | | | - Antoliy Potapchuk
- Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico
| | - Khrystyna Shchubelka
- Department of Biological Sciences, Oakland University, Rochester, MI, USA
- Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico
- Biology Department, Uzhhorod National University, Uzhhorod, Ukraine
| | - Ludvig Potish
- Department of Forestry, Uzhhorod National University, Uzhhorod, Ukraine
| | - Audrey J Majeske
- Department of Biological Sciences, Oakland University, Rochester, MI, USA
- Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico
| | - Luis Figueroa Oliver
- Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico
| | - Alondra Diaz Lameiro
- Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico
| | | | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Livestock Genetics, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Taras K Oleksyk
- Department of Biological Sciences, Oakland University, Rochester, MI, USA.
- Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico.
- Biology Department, Uzhhorod National University, Uzhhorod, Ukraine.
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Oleksyk TK, Wolfsberger WW, Weber AM, Shchubelka K, Oleksyk OT, Levchuk O, Patrus A, Lazar N, Castro-Marquez SO, Hasynets Y, Boldyzhar P, Neymet M, Urbanovych A, Stakhovska V, Malyar K, Chervyakova S, Podoroha O, Kovalchuk N, Rodriguez-Flores JL, Zhou W, Medley S, Battistuzzi F, Liu R, Hou Y, Chen S, Yang H, Yeager M, Dean M, Mills RE, Smolanka V. Genome diversity in Ukraine. Gigascience 2021; 10:6079618. [PMID: 33438729 PMCID: PMC7804371 DOI: 10.1093/gigascience/giaa159] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 08/21/2020] [Accepted: 12/15/2020] [Indexed: 01/21/2023] Open
Abstract
Background The main goal of this collaborative effort is to provide genome-wide data for the previously underrepresented population in Eastern Europe, and to provide cross-validation of the data from genome sequences and genotypes of the same individuals acquired by different technologies. We collected 97 genome-grade DNA samples from consented individuals representing major regions of Ukraine that were consented for public data release. BGISEQ-500 sequence data and genotypes by an Illumina GWAS chip were cross-validated on multiple samples and additionally referenced to 1 sample that has been resequenced by Illumina NovaSeq6000 S4 at high coverage. Results The genome data have been searched for genomic variation represented in this population, and a number of variants have been reported: large structural variants, indels, copy number variations, single-nucletide polymorphisms, and microsatellites. To our knowledge, this study provides the largest to-date survey of genetic variation in Ukraine, creating a public reference resource aiming to provide data for medical research in a large understudied population. Conclusions Our results indicate that the genetic diversity of the Ukrainian population is uniquely shaped by evolutionary and demographic forces and cannot be ignored in future genetic and biomedical studies. These data will contribute a wealth of new information bringing forth a wealth of novel, endemic and medically related alleles.
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Affiliation(s)
- Taras K Oleksyk
- Department of Biological Sciences, Uzhhorod National University, 32 Voloshyna Str., Uzhhorod 88000, Ukraine.,Department of Biological Sciences,Oakland University, Dodge Hall, 118 Library Dr., Rochester, MI 48309, USA.,Departamento de Biología, Universidad de Puerto Rico, Mayagüez, PR 00682, USA
| | - Walter W Wolfsberger
- Department of Biological Sciences, Uzhhorod National University, 32 Voloshyna Str., Uzhhorod 88000, Ukraine.,Department of Biological Sciences,Oakland University, Dodge Hall, 118 Library Dr., Rochester, MI 48309, USA.,Departamento de Biología, Universidad de Puerto Rico, Mayagüez, PR 00682, USA
| | - Alexandra M Weber
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Khrystyna Shchubelka
- Department of Biological Sciences,Oakland University, Dodge Hall, 118 Library Dr., Rochester, MI 48309, USA.,Departamento de Biología, Universidad de Puerto Rico, Mayagüez, PR 00682, USA.,Department of Medicine, Uzhhorod National University, Uzhhorod 88000, Ukraine
| | - Olga T Oleksyk
- A. Novak Transcarpathian Regional Clinical Hospital, Uzhhorod 88000, Ukraine
| | | | | | | | - Stephanie O Castro-Marquez
- Department of Biological Sciences,Oakland University, Dodge Hall, 118 Library Dr., Rochester, MI 48309, USA.,Departamento de Biología, Universidad de Puerto Rico, Mayagüez, PR 00682, USA
| | - Yaroslava Hasynets
- Department of Biological Sciences, Uzhhorod National University, 32 Voloshyna Str., Uzhhorod 88000, Ukraine
| | - Patricia Boldyzhar
- Department of Medicine, Uzhhorod National University, Uzhhorod 88000, Ukraine
| | - Mikhailo Neymet
- Velyka Kopanya Family Hospital, Transcarpatia 90330, Ukraine
| | | | | | - Kateryna Malyar
- I.I.Mechnikov Dnipro Regional Clinical Hospital, Dnipro 49000, Ukraine
| | | | | | - Natalia Kovalchuk
- Rivne Regional Specialized Hospital of Radiation Protection, Rivne 33028, Ukraine
| | | | - Weichen Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sarah Medley
- Department of Biological Sciences,Oakland University, Dodge Hall, 118 Library Dr., Rochester, MI 48309, USA
| | - Fabia Battistuzzi
- Department of Biological Sciences,Oakland University, Dodge Hall, 118 Library Dr., Rochester, MI 48309, USA
| | - Ryan Liu
- BGI Shenzhen, Shenzhen, 518083, China
| | - Yong Hou
- BGI Shenzhen, Shenzhen, 518083, China
| | - Siru Chen
- BGI Shenzhen, Shenzhen, 518083, China
| | | | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ryan E Mills
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Volodymyr Smolanka
- Department of Medicine, Uzhhorod National University, Uzhhorod 88000, Ukraine
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