Structure and genetic variability of the Costa Rican Paso horse.
Abstract: The Costa Rican Paso Horse (CPC) is a breed developed in Costa Rica. The objectives were to estimate the genetic structure and evaluate the levels of genetic variability of the population. The genotypes of 14 microsatellites in 3654 records (2052 females and 1602 males) were analyzed. Expected (He) and observed (Ho) heterozygosity, polymorphic information content (CIP), fixation index (FIS), Shannon index, as well as Hardy-Weinberg disequilibrium (DHW) were evaluated. Kinship relationships (Rij) were estimated throughout the entire population. The effective population size (Ne) was calculated, alternating allele frequencies less than 0.05, 0.02 and 0.01. The Bayesian clustering study was carried out to infer how many lines are appropriate from the analysis of genotypes using multiple loci. The number of alleles per locus ranged from 7 to 17, with an average value of 9.6; nine loci presented DHW (P < 0.05); two loci presented negative FIS values, the same as Ho > He; the average of CIP, Ho and He was 0.254, 0.756 and 0.785, respectively. At the 12 loci where He > Ho, the differences ranged from 0.002 to 0.341 (0.036 on average). For Ne, the estimates were 201.9, 230.1, and 241.5. In the Rij, 54.86% of the estimates were in the interval of 0.01 to 77.7%. The number of lines that define the population corresponds to three, with an approximate composition of 33.1%, 32.4% and 34.5%, respectively. The CPC, as a subdivided population with DHW and a reduction in heterozygotes may be associated with possible Wahlund effects. Keywords: Wahlund effect, equines, genetic markers, synthetic breed, Hardy Weinberg.
Copyright © 2023. Published by Elsevier Inc.
Publication Date: 2023-12-12 PubMed ID: 38096926DOI: 10.1016/j.jevs.2023.104985Google Scholar: Lookup
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Summary
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This research is about investigating the genetic structure of the Costa Rican Paso horse breed by analyzing the genotypes of several microsatellite markers and calculating several parameters including heterozygosity, fixation index, and effective population size.
Genotype Analysis
- The Costa Rican Paso Horse (CPC) breed was examined by analyzing the genotypes of 14 different microsatellite markers in a group of 3654 horses, including both males and females.
- Heterozygosity, the genetic variability in a population, was evaluated in two ways – expected (He) and observed (Ho).
- The Polymorphic Information Content (CIP), which measures the expected heterozygosity of a certain marker, was also calculated.
- The Fixation Index (FIS), which indicates the level of inbreeding in the studied breed, was evaluated. The Shannon index, which is a measure of species diversity, was assessed as well.
Hardy-Weinberg Disequilibrium
- Nine out of fourteen loci were found to deviate from Hardy-Weinberg equilibrium (DHW), hinting at possible influences of non-random mating, selection, or genetic drift.
- The differences in heterozygosity (He > Ho) at 12 loci ranged between 0.002 and 0.341.
- Negative FIS values in two loci along with a higher observed heterozygosity (Ho) than expected (He) suggests the possible occurrence of outbreeding or the presence of a subpopulation with excess heterozygotes.
Effective Population Size and Kinship Relationships
- Researchers estimated the effective population size (Ne) considering different allele frequencies. The estimates ranged between 201.9 and 241.5.
- Kinship relationships were identified throughout the entire population, with a majority (54.86%) of the estimates falling within an interval of 0.01 to 77.7%.
- According to Bayesian clustering study, the population of CPC can be divided into three distinct lines, with proportions of 33.1%, 32.4% and 34.5% respectively.
Conclusion
- The observation of a subdivided population structure, Hardy-Weinberg disequilibrium and a decrease in heterozygotes in the CPC breed suggests the presence of the Wahlund effect, a reduction in heterozygosity caused by the subdivision of the population.
- Possible causes of this outcome may include inbreeding or genetic drift, and they pose a risk for the loss of genetic diversity in the breed.
Cite This Article
APA
Domínguez-Viveros J, Molina-Villalobos JR, Camacho-Sandoval J, Cruz-Méndez A, Martínez-Rocha R, Jahuey-Martínez F.
(2023).
Structure and genetic variability of the Costa Rican Paso horse.
J Equine Vet Sci, 104985.
https://doi.org/10.1016/j.jevs.2023.104985 Publication
Researcher Affiliations
- Facultad de Zootecnia y Ecología, Universidad Autónoma de Chihuahua, Chihuahua, México. Electronic address: jodominguez@uach.mx.
- Asociación de Criadores del Caballo Costarricense de Paso, San José, Costa Rica.
- Asociación de Criadores del Caballo Costarricense de Paso, San José, Costa Rica.
- Instituto Nacional de Innovación y Transferencia en Tecnología Agropecuaria, San José, Costa Rica.
- Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Ciudad de México, México.
- Facultad de Zootecnia y Ecología, Universidad Autónoma de Chihuahua, Chihuahua, México.
Conflict of Interest Statement
Declaration of Competing Interest The authors do not have any conflict of interest to declare.
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