A Single-Step Genome-Wide Association Study for Semen Traits of Egyptian Buffalo Bulls.

Simple Summary: A study was conducted to investigate five semen traits in Egyptian buffalo bulls using a single-step genome-wide association study for genomic evaluation. The study aimed to identify associated genomic regions and potential candidate genes. The X-chromosome was the most crucial, accounting for 23.43% of the overall genomic variance observed in these semen traits. Numerous potential candidate genes associated with the examined semen traits were identified within the genomic regions under investigation. In addition, a total of five new candidate genes were discovered within the genomic area examined for semen traits in Egyptian buffalo bulls. The present study aimed to contribute to the limited research on buffalo (Bubalus bubalis) semen traits by incorporating genomic data. A total of 8465 ejaculates were collected. The genotyping procedure was conducted using the Axiom^® Buffalo Genotyping 90 K array designed by the Affymetrix Expert Design Program. After conducting a quality assessment, we utilized 67,282 SNPs genotyped in 192 animals. We identified several genomic loci explaining high genetic variance by employing single-step genomic evaluation. The aforementioned regions were located on buffalo chromosomes no. 3, 4, 6, 7, 14, 16, 20, 22, and the X-chromosome. The X-chromosome exhibited substantial influence, accounting for 4.18, 4.59, 5.16, 5.19, and 4.31% of the genomic variance for ejaculate volume, mass motility, livability, abnormality, and concentration, respectively. In the examined genomic regions, we identified five novel candidate genes linked to male fertility and spermatogenesis, four in the X-chromosome and one in chromosome no. 16. Additional extensive research with larger sample sizes and datasets is imperative to validate these findings and evaluate their applicability for genomic selection. [ABSTRACT FROM AUTHOR]