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

Ayman G El Nagar; Mohamed M I Salem; Amin M S Amin; Maher H Khalil; Ayman F Ashour; Mohammed M Hegazy; Hamdy Abdel-Shafy

doi:10.3390/ani13243758

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

Animals (Basel). 2023 Dec 5;13(24):3758. doi: 10.3390/ani13243758.

Authors

Ayman G El Nagar¹, Mohamed M I Salem², Amin M S Amin³, Maher H Khalil¹, Ayman F Ashour³, Mohammed M Hegazy³, Hamdy Abdel-Shafy⁴

Affiliations

¹ Department of Animal Production, Faculty of Agriculture at Moshtohor, Benha University, Benha 13736, Egypt.
² Department of Animal and Fish Production, Faculty of Agriculture (El-Shatby), Alexandria University, Alexandria 21545, Egypt.
³ Animal Production Research Institute, Agricultural Research Center, Dokki, Giza 12619, Egypt.
⁴ Department of Animal Production, Faculty of Agriculture, Cairo University, El-Gamma Street, Giza 12613, Egypt.

Abstract

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.

Keywords: X-chromosome; buffalo; candidate genes; genomic selection; semen traits; ss-GWAS.

Grants and funding

The work was funded by project No. 33531, entitled “A Genomic Approach to Improve Production and Reproduction Traits in Egyptian Buffalo” from the Science, Technology & Innovation Funding Authority (STDF), Egyptian Ministry for Scientific Research, Egypt.