Estimation & Prediction

Towards an international genetic evaluation in dairy sheep: the ARDI2 project

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Abstract

Latxa and Manech are closely related dairy sheep breeds, raised in Spain and France respectively, each with a blonde (Latxa Cara Rubia, LCR; Manech Tàªte Rousse, MTR) and a black (Latxa Cara Negra, LCN; Manech Tàªte Noire, MTN) strain. Over the last 20 years, artificial insemination doses have been exchanged within colour strains, primarily from France to Spain, establishing a genetic link between the breeds. Consequently, an international genomic evaluation within-colour could improve genomic precision by using a larger reference population and accelerate genetic progress by increasing the selection base. The genetic connection across countries includes 292 animals common to LCN and MTN, and 1,055 common to LCR and MTR. Among these, 25 in LCN/MTN and 224 in LCR/MTR were AI rams with more than 10 daughters in each country. Genotyped animals comprised 813 LCN, 1,618 MTN, 1,975 LCR, and 9,337 MTR; however, they were obtained using different technologies. Manech animals were genotyped with low-density (18K) and mid-density (50K) Illumina chips, whereas Latxa animals were genotyped using both Illumina and Affymetrix mid-density chips. This study aimed to outline the integration of genotypes required for the across-country, within-colour genomic evaluation.Comparing and merging SNP data from different technologies is challenging, and its complexity is usually underestimated. Using SNP position proved inadequate, as SNPs at the same locus can have different locations depending on the genome assembly version, even within the same technology. In this study, we relied on SNP names (or IDs) to ensure consistency between Affymetrix and Illumina SNP data. However, this information is not always easily accessible across different array providers. After a thorough harmonization procedure, 38,516 SNPs from the Affymetrix chip were found to have a clear correspondence with Illumina IDs. These SNPs were used as a "customized" reference map. Although it is based on the Illumina 50K chip, it is not identical to any commercial SNP array. Genotypes from the four breeds were uploaded to Interbull Centre's Genotype Exchange platform (GenoEx). Interbull Centre also performed the alignment and imputation using an adaptation of InterGenomics pipeline. Affymetrix genotypes included Illumina IDs to ensure unequivocal correspondence across chips. Two reference maps were used for the imputation: the "customized" map and the Illumina OvineSNP50_v1, the latter due to having the largest number of genotyped animals. Accuracy of imputation, evaluated as the average percent of correctly imputed SNPs, ranged from 91.7% to 93.0% for LCN/MTN, and from 94.7% to 95.8% for LCR/MTR.This work produced one final genotype dataset for each reference map, ready for genomic evaluation: one including 13,743 animals and 38,032 SNPs, and the other including 13,736 animals and 52,017 SNPs. The ARDI2 project enables progress toward a unified, across-country breeding programme for Latxa and Manech dairy sheep breeds.

Keywords: 2026

How to Cite:

Zubiri-Gaitán, A., Aguilar, I., Pineda-Quiroga, C., Astruc, J., Granado-Tajada, I., Ugarte, E., Haugaard, K., Macedo, F., Roozen, T., Rodriguez-Ramilo, S. & Vitezica, Z., (2026) “Towards an international genetic evaluation in dairy sheep: the ARDI2 project”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2285362. doi: https://doi.org/10.31274/wcgalp.23656

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