Fine-scale analysis of runs of homozygosity islands affecting fertility in mares

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 l...

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Detalles Bibliográficos
Autores principales: Laseca, Nora, Molina,Antonio, Ramón, Manuel, Valera, Mercedes, Azcona, Florencia, Encina, Ana, Demyda Peyrás, Sebastián
Formato: Articulo
Lenguaje:Inglés
Publicado: 2022
Materias:
Ciencias Veterinarias
runs of homozygosity
genomics
reproductive efficiency
mares
inbreeding
SNP
fertility
ROHi
Acceso en línea:http://sedici.unlp.edu.ar/handle/10915/156291
Aporte de:
SEDICI (UNLP) de Universidad Nacional de La Plata
id I19-R120-10915-156291
record_format dspace
spelling I19-R120-10915-1562912023-08-14T20:09:34Z http://sedici.unlp.edu.ar/handle/10915/156291 Fine-scale analysis of runs of homozygosity islands affecting fertility in mares Laseca, Nora Molina,Antonio Ramón, Manuel Valera, Mercedes Azcona, Florencia Encina, Ana Demyda Peyrás, Sebastián 2022 2023-08-14T14:45:29Z en Ciencias Veterinarias runs of homozygosity genomics reproductive efficiency mares inbreeding SNP fertility ROHi 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 (ρ = −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 (FROH) 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. Instituto de Genética Veterinaria Articulo Articulo http://creativecommons.org/licenses/by/4.0/ Creative Commons Attribution 4.0 International (CC BY 4.0) application/pdf
institution Universidad Nacional de La Plata
institution_str I-19
repository_str R-120
collection SEDICI (UNLP)
language Inglés
topic Ciencias Veterinarias
runs of homozygosity
genomics
reproductive efficiency
mares
inbreeding
SNP
fertility
ROHi
spellingShingle Ciencias Veterinarias
runs of homozygosity
genomics
reproductive efficiency
mares
inbreeding
SNP
fertility
ROHi
Laseca, Nora
Molina,Antonio
Ramón, Manuel
Valera, Mercedes
Azcona, Florencia
Encina, Ana
Demyda Peyrás, Sebastián
Fine-scale analysis of runs of homozygosity islands affecting fertility in mares
topic_facet Ciencias Veterinarias
runs of homozygosity
genomics
reproductive efficiency
mares
inbreeding
SNP
fertility
ROHi
description 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 (ρ = −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 (FROH) 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.
format Articulo
Articulo
author Laseca, Nora
Molina,Antonio
Ramón, Manuel
Valera, Mercedes
Azcona, Florencia
Encina, Ana
Demyda Peyrás, Sebastián
author_facet Laseca, Nora
Molina,Antonio
Ramón, Manuel
Valera, Mercedes
Azcona, Florencia
Encina, Ana
Demyda Peyrás, Sebastián
author_sort Laseca, Nora
title Fine-scale analysis of runs of homozygosity islands affecting fertility in mares
title_short Fine-scale analysis of runs of homozygosity islands affecting fertility in mares
title_full Fine-scale analysis of runs of homozygosity islands affecting fertility in mares
title_fullStr Fine-scale analysis of runs of homozygosity islands affecting fertility in mares
title_full_unstemmed Fine-scale analysis of runs of homozygosity islands affecting fertility in mares
title_sort fine-scale analysis of runs of homozygosity islands affecting fertility in mares
publishDate 2022
url http://sedici.unlp.edu.ar/handle/10915/156291
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