Equine

EQUIGENE 90K Array increases breeding values reliability in Purebred Spanish Horses genomic selecction.

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Abstract

The Pura Raza Española (PRE) is a native Spanish breed with over 290,000 registered horses distributed across 71 countries, supported by a structured breeding program focused on morphological conformation, reproductive efficiency, and dressage performance. While genomic selection has revolutionized genetic improvement in livestock species, its adoption in horse breeding remains limited due to long generation intervals and the challenge of obtaining reliable breeding value predictions for young animals without progeny records. To address these limitations, the Royal Purebred Spanish Horse Breeders' Association (ANCCE) developed the custom Axiom EQUIGENE 90K medium-density array, incorporating 90,926 SNPs including the complete recommended parentage panel (859 SNPs), breed-specific informative markers selected for maximum variability capture, SNPs from equine GWAS literature, and high imputation accuracy markers. The objective was to quantify breeding value reliability improvements using single-step genomic evaluation (ssGBLUP) compared to traditional pedigree-based BLUP across morphological, reproductive, and dressage performance traits in the PRE breed. A total of 6,916 animals were genotyped using the EQUIGENE 90K array, with 82,542 informative SNPs retained after quality control. Genetic evaluations encompassed 21 traits across three categories: 14 morphological traits (7,152 phenotyped animals; h²=0.08-0.76), 7 fertility traits (47,502 females; h²=0.07-0.35), and dressage performance including classical evaluation and young horse selection trials for walk, trot, canter, and submission. Pedigrees comprised 41,888-57,316 animals traced across 8-11 equivalent generations. Variance components and breeding values were estimated using multivariate animal models with BLUPF90+ software, comparing pedigree-based A-matrix (REML) versus combined genomic H-matrix (ssGREML) approaches. Reliability (R²) gains were stratified by trait category, heritability, genotype status, sex, and progeny group size. Single-step genomic evaluation demonstrated substantial reliability improvements over pedigree-based methods across all trait categories. Morphological traits gained 1.56% to 13.30% (mean 8.09%), fertility traits 2.20% to 3.71% (mean 2.98%), and classical dressage performance 2.96%. Young horse selection trials showed exceptional gains of 17.8% to 48.4%, with canter achieving the highest improvement. Critically, genotyped animals demonstrated dramatically higher benefits compared to non-genotyped relatives: morphological traits gained 6.93-22.70% versus 0.82-12.37%, and fertility traits 17.81-24.04% versus 0.80-2.34%. Young breeding candidates without progeny records showed the most substantial improvements (14.47-35.34% across morphological traits), while stallions with limited progeny ( < 40 offspring) gained 5.96-19.25% compared to minimal improvements in extensively progeny-tested stallions (≥40 offspring). These results demonstrate that genomic selection using medium-density SNP genotyping significantly improves breeding value reliability in horses, particularly for young animals and low-heritability traits. The EQUIGENE 90K array provides the genomic infrastructure necessary for implementing ssGBLUP in PRE horses, enabling earlier and more accurate selection decisions with potential to reduce generation intervals by 40-50%, thereby accelerating genetic progress while maintaining the dual functionality of parentage verification and genomic evaluation within a single genotyping platform.

Keywords: 2026

How to Cite:

Srihi, H., Valera, M., Ziadi, C., Laseca, N., Rodríguez Sainz de los Terreros, A., Azor, P., González, I., Gil-Gálvez, A., Perdomo-González, D., Poyato-Bonilla, J., Encina, A., Demyda-Peyrás, S. & Molina, A., (2026) “EQUIGENE 90K Array increases breeding values reliability in Purebred Spanish Horses genomic selecction.”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286833. doi: https://doi.org/10.31274/wcgalp.24138

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