# Identification of recessive genetic defects in the Abondance regional cattle breed using routine genotyping and life history information

Clémentine Escouflaire, Chris Hozé, Mekki Boussaha, Anne Barbat, Sophie Aguerre, Florian Besnard, Maxime Ben Braiek, Didier Boichard, Foucras G., Sébastien Fritz, et al.

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## To cite this version:

Clémentine Escouflaire, Chris Hozé, Mekki Boussaha, Anne Barbat, Sophie Aguerre, et al. Identification of recessive genetic defects in the Abondance regional cattle breed using routine genotyping and life history information. 76th Annual Meeting of the European Federation of Animal Science, EAAP, Aug 2025, Innsbrück, Austria. **hal-05238714**

HAL Id: hal-05238714

https://hal.inrae.fr/hal-05238714v1

Submitted on 3 Sep 2025

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Opposite inbreeding load for reproductive traits in lines of mice divergently selected population

D. Perdomo-González¹, C. Ojeda-Marín¹, N. Formoso-Rafferty², L. El-Ouazizi El-Kahia¹, L. Varona³, I. Cervantes¹, J. P. Gutiérrez¹

¹ Department of Animal Production, UCM, 28040 Madrid, Spain, ² Department of Producción Agraria, UPM, 28040 Madrid, Spain, ³ Universidad de Zaragoza, Miguel Servet, 177, 50013 Zaragoza, Spain

A divergent selection experiment on the birth weight environmental variability in mice showed that genetic con-
trol of variability is achievable through selection. Homogeneity has been shown to enhance litter size, embryo
survival and fertility, among others, suggesting improvements in robustness and welfare. Nevertheless, related
matings for the selection lead to an increase in inbreeding, which has usually been associated with reduction in
fitness and loss of performance in traits under selection. Some studies have shown that inbreeding has not only a
extensive range of negative effects but also neutral or even positive effects in livestock. Thus, the objective of this
study was to analyse the inbreeding depression load (IL) in three reproductive traits (number of parturitions-NP,
litter size-LS, and fertility-Fert) in a divergently selected mice population. Female mice that acted as breeder and
with both parents known were selected (2829) and the pedigree included 4117 records (1070 males and 3047
females). Partial inbreeding coefficients were estimated for all animals in the population. The genetic model in-
cluded the line (2 levels) and generation (33 levels) as fixed effects and female age as a covariate. Direct additive
genetic and IL variances were estimated using own software. Heritabilities ranged from 0.03 (Fert) to 0.10 (TC)
and IL variance was equivalent to 0.90 times the phenotypic variance in all cases. Even when both lines have
a similar inbreeding level (around 20%), breeding values for IL showed clear differences between lines and, in
all traits, similar divergent trends as the phenotype. The line selected for low environmental variability for birth
weight also showed IL that improved their descendants' phenotype, reaffirming that inbreeding depression not
only depends on the inbreeding level, but also on the common ancestors and the partial inbreeding coefficient
they transmit to their inbred descendants. Understanding these genetic values is crucial to make more informed
selections based on the effects of specific lineages.

Identification of recessive genetic defects in the Abondance regional cattle breed using routine
genotyping and life history information

C. Escouflaire¹, C. Hozé¹, M. Boussaha², A. Barbat², S. Aguerre³, F. Besnard¹, M. Ben-Braiek², D. Boichard², G. Foucras⁴, S. Fritz¹, A. Capitan²

¹ Eliance, 149 rue de Bercy, 75012 Paris, France, ² Université Paris-Saclay, INRAE, GABI, 78350 Jouy-en-Jo-sas, France, ³ IDELE, 149 rue de Bercy, 75012 Paris, France, ⁴ IHAP, Université de Toulouse, INRAE, ENVT, 31076 Toulouse, France

Cattle breeds are genetically small populations prone to recurrent outbreaks of recessive defects, only a fraction of which are detected by on-field observatories and characterized by positional cloning due to lack of specific signs or under-reporting. Here, we present the detection of the first two genetic defects described in a regional cattle breed from the French Alps, the Abondance, using reverse genetic strategies based on life history information for over a hundred thousand animals, 30 000 genotypes collected for genomic evaluation since 2015 and whole genome sequences of 24 influential ancestors. In a first step, a search for homozygous haplotype deficiency identified an haplotype on BTA19 with 142 homozygotes expected versus 0 observed, which was strongly associated with a frameshift variant in the UTP6 gene. Analysis of several fertility traits, large scale genotyping using a custom SNP array and procreation of 7-day embryos from at-risk mating confirmed that this recessive variant was causative and responsible for early embryonic loss. In a second step, we investigated postnatal mortality and searched for haplotype enrichment/depletion in heifers that died of natural causes in comparison with females that completed at least one lactation. One haplotype on BTA4 had an enrichment of +300% of observed versus expected homozygotes in the case group and a complete absence of observed homozygotes in the controls. The best candidate variant for this locus affects a splice donor site in SLC25A13, a gene previously associated in human with citrullinemia type II metabolic disease. Recruitment and clinical examination of homozygous animals is underway. These findings highlight the power of reverse genetics approaches and pave the way for improved genetic management strategies to reduce mortality and enhance herd health in Abondance cattle. This project was funded by APIS-GENE.