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Home / Equine Research Bank / Sci Rep / Genetic diversity and selection in Puerto Rican horses.
Scientific reports2022; 12(1); 515; doi: 10.1038/s41598-021-04537-5

Genetic diversity and selection in Puerto Rican horses.

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.
© 2022. The Author(s).
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Publication Date: 2022-01-11 PubMed ID: 35017609PubMed Central: PMC8752667DOI: 10.1038/s41598-021-04537-5Google Scholar: Lookup
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  • Journal Article

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research is about the genetic study of two horse breeds from Puerto Rico, the Puerto Rican Non-Purebred (PRNPB) and the Puerto Rican Paso Fino (PRPF), to understand the ancestral connection between these breeds and how genetic selection has impacted their characteristics.

Overview of the Research

  • The researchers undertook a comprehensive genetic study of two horse breeds from Puerto Rico – the PRNPB, also referred to as the “Criollo” horses, and the PRPF. The key objective was to evaluate whether these two breeds share a common ancestry and to determine the genetic factors that contributed to their varied characteristics.
  • Previous studies suggested these two breeds might share a common ancestral lineage since they were both established on the Caribbean Island of Puerto Rico. However, this had yet to be proven scientifically.

Research Methodology

  • A total of 200 horses from 27 locations around Puerto Rico were selected for the research. These included both PRNPB and PRPF breeds.
  • Firstly, the research projected to assess the genetic lineage and diversity of these horses by performing a DNA analysis, specifically looking at a 668 base pair fragment of the mitochondrial DNA D-loop (HVR1).
  • The researchers also examined the samples for the presence of a specific mutant allele, “gait-keeper” DMRT3, known to be responsible for the paso gait, a trait highly valued in these breeds.
  • In addition, a subset of 24 samples were genotyped using the Illumina Neogen Equine Community genome-wide array with 65,000 SNPs. This data was amalgamated with existing PRPF genomes from prior studies to enhance the comprehensive understanding.

Research Findings

  • The study found a significant genetic connection between the two horse breeds, corroborating the theory that PRNPB horses represent descendants of the original genetic pool, primarily constituted of horses imported from the Iberian Peninsula and elsewhere in Europe.
  • It was inferred that the “gait-keeper” DMRT3 allele existed in the original founders of the PRNRB population, implying that these traits were preferentially selected over centuries by local persons. This pre-dates the establishment of the PRPF breed, suggesting the paso gait already had been a dominant feature in the local breeds even before the PRPF breed emerged.
  • The researchers found a signature of selection in the genomic region of PRNPB horses encompassing the DMRT3 locus. Conversely, in the purebred PRPF, there was no detectable signature of selection associated with the DMRT3.
  • This implied that the PRPF breed originated from the genetic pool of the previously established PRNPB horses, focusing selection on alleles in other genes that have not been associated with the paso gait phenotype. This has resulted in these other genes setting the PRPF apart from its PRNPB counterparts.

Cite This Article

APA
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. (2022). Genetic diversity and selection in Puerto Rican horses. Sci Rep, 12(1), 515. https://doi.org/10.1038/s41598-021-04537-5

Publication

Scientific reports
ISSN: 2045-2322
NlmUniqueID: 101563288
Country: England
Language: English
Volume: 12
Issue: 1
Pages: 515
PII: 515

Researcher Affiliations

Wolfsberger, Walter W
  • 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.
Ayala, Nikole M
  • Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico.
Castro-Marquez, Stephanie O
  • Department of Biological Sciences, Oakland University, Rochester, MI, USA.
  • Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico.
Irizarry-Negron, Valerie M
  • Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico.
Potapchuk, Antoliy
  • Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico.
Shchubelka, Khrystyna
  • 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.
Potish, Ludvig
  • Department of Forestry, Uzhhorod National University, Uzhhorod, Ukraine.
Majeske, Audrey J
  • Department of Biological Sciences, Oakland University, Rochester, MI, USA.
  • Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico.
Oliver, Luis Figueroa
  • Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico.
Lameiro, Alondra Diaz
  • Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico.
Martínez-Cruzado, Juan Carlos
  • Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico.
Lindgren, Gabriella
  • Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.
  • Livestock Genetics, Department of Biosystems, KU Leuven, Leuven, Belgium.
Oleksyk, Taras K
  • Department of Biological Sciences, Oakland University, Rochester, MI, USA. oleksyk@oakland.edu.
  • Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico. oleksyk@oakland.edu.
  • Biology Department, Uzhhorod National University, Uzhhorod, Ukraine. oleksyk@oakland.edu.

MeSH Terms

  • Animals
  • Horses

Grant Funding

  • DUE 1044714 / National Science Foundation
  • Startup Fund / Oakland University

Conflict of Interest Statement

The authors declare no competing interests.

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Citations

This article has been cited 2 times.
  1. Vincelette A. The Characteristics, Distribution, Function, and Origin of Alternative Lateral Horse Gaits.. Animals (Basel) 2023 Aug 8;13(16).
    doi: 10.3390/ani13162557pubmed: 37627349google scholar: lookup
  2. Li Q, Li L, Zhang T, Xiang P, Wu Q, Tu W, Bao Z, Zou L, Chen C. The first two mitochondrial genomes for the genus Ramaria reveal mitochondrial genome evolution of Ramaria and phylogeny of Basidiomycota.. IMA Fungus 2022 Sep 13;13(1):16.
    doi: 10.1186/s43008-022-00100-7pubmed: 36100951google scholar: lookup
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