Reproductive traits in Pura Raza Española mares manifest inbreeding depression from low levels of homozygosity.

Laseca, N
·
Ziadi, C
·
Perdomo-Gonzalez, DI
·
Valera, M
·
Demyda-Peyras, S
·
Molina, A

Abstract: Inbreeding depression is a genetic phenomenon associated with the loss of fitness and mean phenotypic performance due to mating between relatives. Historically, inbreeding coefficients have been estimated from pedigree information. However, the onset of genomic selection programs provides large datasets of individuals genotyped using SNP arrays, enabling more precise assessment of an individual's genomic-level inbreeding using genomic data. One of the traits most sensitive to issues stemming from increased inbreeding is reproduction. This is particularly important in equine, in which fertility is only moderate compared to other livestock species. To explore this further, we evaluated the effect of inbreeding on five reproductive traits (age at first foaling (AFF), average interval between foalings (AIF), total number of foalings (NF), productive life (PL) and reproductive efficiency (RE)) in Pura Raza Español mares using genomic data. Residual predicted phenotypes were obtained by purging these traits through the REML (wg ) and ssGREML (g ) approaches in reproductive data of 29,847 PRE mares using the BLUPF90+ program. Next, we used pedigree-based (F ) and ROH-based genomic (F ) inbreeding coefficients derived from 1018 animals genotyped with 61,271 SNPs to estimate the inbreeding depression (linear regression). Our results indicated significant levels of inbreeding depression for all reproductive traits, with the exception of the AIF trait when F was used. However, all traits were negatively affected by the increase in genomic inbreeding, and F was found to capture more inbreeding depression than F . Likewise, REML models (ssGREML) using genomic data for estimated predicted residual phenotypes resulted in higher variance explained by the model compared with the models not using genomics (REML). Finally, a segmented regression analysis was conducted to evaluate the effect of inbreeding depression, revealing that the levels of genealogical and genomic homozygosity do not manifest uniformly in reproductive traits. In contrast, the levels of inbreeding depression ranged from low to high as homozygosity increased. This analysis also showed that reproductive traits are very sensitive to inbreeding depression, even with relatively low levels of homozygosity.

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Publication Date: 2024-02-01 PubMed ID: 38299872DOI: 10.1111/jbg.12856Google 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.

The researchers found that inbreeding in Pura Raza Española mares or Spanish horses causes depression in several reproductive traits, with an increase in homozygosity leading to more severe effects, even with low levels of homozygosity.

Objective of the Study

The study aimed to investigate the effect of inbreeding on five reproductive traits in Pura Raza Española (PRE) mares (Spanish horses). Inbreeding is the mating between relatives which can lead to a decrease in the fitness and performance of offspring because of the increased homozygosity (similarity) of genes.

Methodology

The research team evaluated the effect of inbreeding on five reproductive traits namely, age at first foaling (AFF), average interval between foalings (AIF), total number of foalings (NF), productive life (PL), and reproductive efficiency (RE). They used genomic data collected from the horses, including their pedigree.
The researchers used modern genomic selection methods, which deliver large datasets of the horses’ genotypes, offering a more precise gauge of an individual’s inbreeding at the genomic level.
The statistical approaches REML and ssGREML were used to treat the reproductive data of 29,847 PRE mares using the BLUPF90+ program. Predicted phenotypes, or the expected physical traits of the horses, were established based on this data.

Results and Interpretation

The study found significant levels of inbreeding depression for all reproductive traits, except for the AIF trait when considering the pedigree-based inbreeding coefficient.
All traits were negatively affected by the increase in genomic inbreeding. The study concluded that the ROH-based genomic inbreeding coefficient captured more inbreeding depression than the pedigree-based coefficient.
The genomic models (ssGREML) used for estimating the predicted residual phenotypes, the remaining variations in traits after accounting for known factors, accounted for more variance than the models not using genomics (REML).
A segmented regression analysis showed inbreeding depression did not evenly influence reproductive traits across different homozygosity levels. The levels of inbreeding depression varied from low to high as homozygosity increased, indicating reproductive traits are very sensitive to inbreeding depression, even at relatively low levels of homozygosity.

Implications

This research provides valuable insights into the serious consequences of inbreeding within the breed of Spanish horses. It is a compelling argument for genetic diversity and careful breeding practices in order to maintain the health and reproductive vigor of this equine population.

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APA

Laseca N, Ziadi C, Perdomo-Gonzalez DI, Valera M, Demyda-Peyras S, Molina A. (2024). Reproductive traits in Pura Raza Española mares manifest inbreeding depression from low levels of homozygosity. J Anim Breed Genet. https://doi.org/10.1111/jbg.12856

Publication

Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie

ISSN: 1439-0388

NlmUniqueID: 100955807

Country: Germany

Language: English

Researcher Affiliations

Laseca, Nora

Department of Genetics, University of Cordoba, Cu00f3rdoba, Spain.

Ziadi, Chiraz

Department of Genetics, University of Cordoba, Cu00f3rdoba, Spain.

Perdomo-Gonzalez, Davinia I

Department of Agronomy, ETSIA, University of Seville, Seville, Spain.

Valera, Mercedes

Department of Agronomy, ETSIA, University of Seville, Seville, Spain.

Demyda-Peyras, Sebastiu00e1n

Department of Genetics, University of Cordoba, Cu00f3rdoba, Spain.

Molina, Antonio

Department of Genetics, University of Cordoba, Cu00f3rdoba, Spain.

Grant Funding

AGL-2017-84217-P Research project from the Ministry of Economy, Industry and Competitiveness of the Spanish Government
FPI fellowship (PRE2018-083492) from the Ministry of Science, Innovation, and Universities of the Spanish Government

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