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

Abstract

Improving reproductive efficiency in beef cattle remains a key objective for sustainable genetic progress, particularly in extensively managed autochthonous breeds such as the Spanish Retinta. In this study, we applied a weighted single-step genome-wide association approach (wssGWAS) to identify genomic regions associated with four fertility-related traits: age at first calving (AFC), interval between first and second calving (IC12), average calving interval (ACI), and reproductive efficiency (RE). A total of 215,125 calving records from 44,032 cows and the genomic information of 1030 animals (Axiom™ Bovine Genotyping v3 Array 65k) were analyzed. Heritability was estimated using a single-step genomic best linear unbiased prediction (ssGBLUP) that incorporated both pedigree and genomic data, and estimates ranged from 0.15 (0.008) for AFC to 0.27 (0.012) for ACI. The wssGWAS identified 96 1 Mb-windows explaining over 1% of additive genetic variance (40 of them are common for more than one trait and 46 windows are unique), notably on chromosomes 2 and 5. Candidate genes related to folliculogenesis, steroidogenesis, immune modulation, and cell cycle control were identified, including ACVR1B, AMHR2, CYP27B1, CDK2, and IFNG. Additionally, a significant proportion of lncRNAs were detected, suggesting regulatory roles in reproductive processes through the modulation of gene expression at different levels. These findings enhance our understanding of the genetic architecture underlying female fertility in beef cattle and provide valuable markers for incorporation into genomic selection programs aimed at improving reproductive performance and long-term sustainability in the Retinta breed.