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Weighted Single-Step GWAS Reveals Genomic Regions Associated with Female Fertility in the Spanish Retinta Beef Cattle

R. Morales,Gabriel Anaya Calvo-Rubio,C. Ziadi,María Ángeles Vargas-Pérez,S. Demyda-Peyrás,A. Molina

Published 2025 in Animals

ABSTRACT

Simple Summary Reproductive efficiency in beef cattle remains a limiting factor for productivity, particularly in autochthonous breeds managed under extensive conditions, where traditional phenotypic selection is hindered by low heritability and strong environmental influence. This study addresses the challenge of improving female fertility in the Spanish Retinta breed by applying a weighted single-step genome-wide association study (wssGWAS) that integrates pedigree, phenotypic, and genomic information. Using a comprehensive dataset of the reproductive history of 44,000 cows (over 215,000 calving records) and genomic information of 1030 animals (65K), the analysis identified multiple genomic regions significantly associated with key fertility traits, including age at first calving (AFC), interval between first and second calving (IC12), average calving interval (ACI), and reproductive efficiency (RE). Notably, several candidate genes involved in ovarian function, cell cycle regulation, and hormonal signaling, along with a substantial proportion of lncRNAs, were detected. These findings provide new insights into the genetic architecture of fertility under extensive production systems and offer practical tools for enhancing selection accuracy. By incorporating these genomic markers into breeding programs, it is possible to accelerate genetic progress, improve reproductive performance, and contribute to the long-term sustainability of the Retinta breed.

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