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Home / Equine Research Bank / Front Vet Sci / Fine-Scale Analysis of Runs of Homozygosity Islands Affectin...
Frontiers in veterinary science2022; 9; 754028; doi: 10.3389/fvets.2022.754028

Fine-Scale Analysis of Runs of Homozygosity Islands Affecting Fertility in Mares.

Abstract: The loss of genetic variability in livestock populations bred under strict selection processes is a growing concern, as it may lead to increased inbreeding values and lower fertility, as a consequence of the "inbreeding depression" effect. This is particularly important in horses, where inbreeding levels tend to rise as individuals become more and more closely related. In this study, we evaluated the effect of increased inbreeding levels on mare fertility by combining an SNP-based genomic approach using runs of homozygosity and the estimation of genetic breeding values for reproductive traits in a large population of Pura Raza Española mares. Our results showed a negative correlation between whole-genome homozygosity and fertility estimated breeding values (EBVs) at the genome level ( = -0.144). However, the analysis at chromosome level revealed a wide variability, with some chromosomes showing higher correlations than others. Interestingly, the correlation was stronger (-0.241) when we repeated the analysis in a reduced dataset including the 10% most and least fertile individuals, where the latter showed an increase in average inbreeding values (F) of around 30%. We also found 41 genomic regions (ROHi, runs of homozygosity islands) where homozygosity increased 100-fold, 13 of which were significantly associated with fertility after cross-validation. These regions encompassed 17 candidate genes previously related to oocyte and embryo development in several species. Overall, we demonstrated the relationship between increased homozygosis at the genomic level and fertility in mares. Our findings may help to deal with the occurrence of inbreeding depression, as well as further our understanding of the mechanisms underlying fertility in mares.
Copyright © 2022 Laseca, Molina, Ramón, Valera, Azcona, Encina and Demyda-Peyrás.
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Publication Date: 2022-02-17 PubMed ID: 35252415PubMed Central: PMC8891756DOI: 10.3389/fvets.2022.754028Google Scholar: Lookup
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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.

This research explores the impact of inbreeding on fertility in the Pura Raza Española breed of mares based on runs of homozygosity (ROH). The study found that there’s a negative correlation between whole-genome ROH and fertility, with increased homozygosity linked to reduced fertility, especially in the least fertile subset of the population. Certain areas of the genome, known as ROH islands, exhibit a more pronounced impact on fertility.

Study Design and Analysis

  • The researchers evaluated the influence of increased inbreeding levels by integrating a technique examining runs of homozygosity, with the estimation of genetic breeding values for reproductive traits. The study group comprised a substantial population of Pura Raza Española mares.
  • They analyzed connections between fertility and whole-genome homozygosity, as well as correlations on a chromosomal level. This dual approach revealed that particular chromosomes held stronger correlations than others.
  • The team also assessed the data focusing on the top 10% most and least fertile mares. In this group, the correlation was more significant and the least fertile individuals demonstrated a 30% rise in average inbreeding values.

Identification of ROH Islands

  • The study identified 41 genomic regions, referred to as “runs of homozygosity islands” (ROHi), where homozygosity amplified 100-fold. These areas could potentially have a more profound impact on fertility.
  • Thirteen of the detected ROHi were notably associated with fertility after further cross-validation. This process provided more robust findings by reducing the risk of false associations.
  • These islands encompassed 17 genes previously linked with oocyte and embryo development across various species, supporting their potential role in impacting fertility.

Conclusions and Implications

  • Ultimately, the findings underscored the association between increased genomic level homozygosity and diminished fertility in mares. By understanding the regions of the genome most implicated in fertility, breeding programs could potentially be adjusted to mitigate the effects of inbreeding depression.
  • The 17 identified candidate genes and their correlation with fertility are also significant and may be subject to further exploration to grasp the underlying mechanisms of fertility in mares and other species.

Cite This Article

APA
Laseca N, Molina A, Ramón M, Valera M, Azcona F, Encina A, Demyda-Peyrás S. (2022). Fine-Scale Analysis of Runs of Homozygosity Islands Affecting Fertility in Mares. Front Vet Sci, 9, 754028. https://doi.org/10.3389/fvets.2022.754028

Publication

Frontiers in veterinary science
ISSN: 2297-1769
NlmUniqueID: 101666658
Country: Switzerland
Language: English
Volume: 9
Pages: 754028
PII: 754028

Researcher Affiliations

Laseca, Nora
  • Laboratorio de Diagnóstico Genético Veterinario, Departamento de Genética, Universidad de Córdoba, Córdoba, Spain.
Molina, Antonio
  • Laboratorio de Diagnóstico Genético Veterinario, Departamento de Genética, Universidad de Córdoba, Córdoba, Spain.
Ramón, Manuel
  • Cersyra de Valdepeñas, Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal Castilla La Mancha, Tomelloso, Spain.
Valera, Mercedes
  • Departamento de Agronomía, Escuela Técnica Superior de Ingeniería Agronómica, Universidad de Sevilla, Sevilla, Spain.
Azcona, Florencia
  • IGEVET (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina.
Encina, Ana
  • Departamento de Agronomía, Escuela Técnica Superior de Ingeniería Agronómica, Universidad de Sevilla, Sevilla, Spain.
  • Asociación Nacional de Criadores de Caballos de Pura Raza Española, Sevilla, Spain.
Demyda-Peyrás, Sebastián
  • Departamento de Producción Animal, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, Buenos Aires, Argentina.
  • Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET LA PLATA), La Plata, Argentina.

Conflict of Interest Statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

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Citations

This article has been cited 2 times.
  1. Jiménez JM, Morales RM, Menéndez-Buxadera A, Demyda-Peyrás S, Laseca N, Molina A. Estimation of the Genetic Components of (Co)variance and Preliminary Genome-Wide Association Study for Reproductive Efficiency in Retinta Beef Cattle.. Animals (Basel) 2023 Jan 31;13(3).
    doi: 10.3390/ani13030501pubmed: 36766391google scholar: lookup
  2. Perdomo-González DI, Laseca N, Demyda-Peyrás S, Valera M, Cervantes I, Molina A. Fine-tuning genomic and pedigree inbreeding rates in equine population with a deep and reliable stud book: the case of the Pura Raza Española horse.. J Anim Sci Biotechnol 2022 Nov 7;13(1):127.
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