Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Dec 5;13(24):3758.
doi: 10.3390/ani13243758.

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

Ayman G El Nagar  1 , Mohamed M I Salem  2 , Amin M S Amin  3 , Maher H Khalil  1 , Ayman F Ashour  3 , Mohammed M Hegazy  3 , Hamdy Abdel-Shafy  4
Affiliations

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

Ayman G El Nagar et al. Animals (Basel). .

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.

PubMed Disclaimer

Conflict of interest statement

The authors declare that they have no competing interest.

Figures

Figure 1
Figure 1
ssGWAS results of ejaculate volume (VOL) in the Egyptian buffalo bulls. Single nucleotide polymorphisms on different chromosomes are denoted by different colors. Each dot represents one SNP. The X-axis represents 25 chromosomes. The Y-axis represents the percentage of the explained variance by SNP.
Figure 2
Figure 2
ssGWAS results of mass motility (MM) in the Egyptian buffalo bulls. Single nucleotide polymorphisms on different chromosomes are denoted by different colors. Each dot represents one SNP. The X-axis represents 25 chromosomes. The Y-axis represents the percentage of the explained variance by SNP.
Figure 3
Figure 3
ssGWAS results of sperm livability (LS) in the Egyptian buffalo bulls. Single nucleotide polymorphisms on different chromosomes are denoted by different colors. Each dot represents one SNP. The X-axis represents 25 chromosomes. The Y-axis represents the percentage of the explained variance by SNP.
Figure 4
Figure 4
ssGWAS results of percentage of abnormal sperms (AS) in the Egyptian buffalo bulls. Single nucleotide polymorphisms on different chromosomes are denoted by different colors. Each dot represents one SNP. The X-axis represents 25 chromosomes. The Y-axis represents the percentage of the explained variance by SNP.
Figure 5
Figure 5
ssGWAS results of sperm concentration (CONC) in the Egyptian buffalo bulls. Single nucleotide polymorphisms on different chromosomes are denoted by different colors. Each dot represents one SNP. The X-axis represents 25 chromosomes. The Y-axis represents the percentage of the explained variance by SNP.
See this image and copyright information in PMC

References

    1. Humberto A., Minervino H., Zava M., Vecchio D., Borghese A. Bubalus Bubalis: A Short Story. Front. Vet. Sci. 2020;7:570413. doi: 10.3389/fvets.2020.570413. - DOI - PMC - PubMed
    1. Vale W.G. Effects of Environment on Buffalo Reproduction. Ital. J. Anim. Sci. 2007;6:130–142. doi: 10.4081/ijas.2007.s2.130. - DOI
    1. Abdel-Shafy H., Awad M.A.A., El-Regalaty H., Ismael A., El-Assal S.E.D., Abou-Bakr S. A Single-Step Genomic Evaluation for Milk Production in Egyptian Buffalo. Livest. Sci. 2020;234 doi: 10.1016/j.livsci.2020.103977. - DOI
    1. Do D.N., Janss L.L.G., Jensen J., Kadarmideen H.N. SNP Annotation-Based Whole Genomic Prediction and Selection: An Application to Feed Efficiency and Its Component Traits in Pigs. J. Anim. Sci. 2015;93:2056–2063. doi: 10.2527/jas.2014-8640. - DOI - PubMed
    1. Fulton J.E. Genomic Selection for Poultry Breeding. Anim. Front. 2012;2:30–36. doi: 10.2527/af.2011-0028. - DOI

LinkOut - more resources