Work

238 Applying the algorithm for proven and young in genome-wide association studies for reproductive traits in Nellore cattle.

Year: 2025

Type: article

Abstract: Due to their significant economic impact, reproductive traits are crucial in beef cattle breeding programs. However, identifying the genomic regions associated with these traits requires large datasets to capture the complex genetic architecture underlying their variability. Traits such as age at first calving (AFC), stayability (STAY), and scrotal circumference measured at 365 and 450 days (SC365 and SC450, respectively) are highly polygenic, making it essential to leverage robust genomic methodologies to uncover meaningful associations. In this study we aimed to identify candidate genes and genomic regions associated with reproductive traits in Nellore cattle. A dataset containing genomic estimated breeding values (GEBVs) for 304,782 Nellore animals genotyped with 437,650 SNPs (after quality control) was made available by the Brazilian Association of Zebu Breeders (ABCZ). The Algorithm for Proven and Young (APY), implemented in the PREGSF90 software, was used to compute the matrix using 36,000 core animals. Subsequently, the SNP solutions were estimated by back-solving the GEBVs predicted by ABCZ using the single-step GBLUP method. We identified genomic regions associated with these traits using sliding windows of 175 consecutive SNPs, and the top 1% of genomic windows were used to annotate positional candidate genes. The top 1% genomic windows for these traits explained between 2.8% (STAY) to 3.0% (AFC) of the additive genetic variance, highlighting their polygenic nature. Functional analysis of the candidate genes within these genomic regions provided valuable insights into the genetic architecture underlying reproductive traits in Nellore cattle. For instance, our results revealed genes with important functions for each trait, such as SERPINA14 (plays a key role for the endometrial epithelium) and CCNB1 (essential for spindle checkpoint regulation, meiosis, and mitosis) identified for AFC. ARHGAP18 (involved in maintaining endothelial cell alignments) and KCNC1 (regulates potassium ion flow crucial for animal longevity) were identified for STAY. Additionally, genes such as EVI5 (important for centrosome stability), BRDT (essential for male germ cell differentiation), KIT (associated with the male germ cells), and (involved in spermatogenesis and intraflagellar transport) were identified for both SC365 and SC450. We identified genomic regions and candidate genes, some of which have been previously reported in the literature, while others are novel discoveries that warrant further investigation. These findings contribute to gene prioritization efforts, facilitating the identification of functional candidate genes that can enhance genomic selection strategies for economically important traits in Nellore cattle.

Source: Journal of Animal Science

DOI: 10.1093/jas/skaf300.033