Exploring genetic diversity and variation of Ovar-DRB1 gene in Sudan Desert Sheep using targeted next-generation sequencing

Salim, Bashir; Nakao, Ryo; Chatanga, Elisha; Marcuzzi, Olivia; Eissawi, Muna Ahmed; Almathen, Faisal; Hanotte, Olivier; Giovambattista, Guillermo

Abstract

Introduction
The Ovar-DRB1 gene, a crucial element of the Major Histocompatibility Complex (MHC) Class II region, initiates adaptive immunity by presenting antigens to T-cells. Genetic diversity in sheep, particularly in MHC Class II genes like Ovar-DRB1, directly influences the specturm of presented antigens impacting immune responses and disease susceptability. Understanding the allelic diversity of Ovar-DRB1 gene in Sudan Desert Sheep (SDS) is essential for uncovering the genetic basis of immune responses and disease resistance, given the the breeds significance in Sudan's unique environment.

Methods
Utilizing Targeted Next-Generation Sequencing (NGS) we explore allelic diversity in Ovar-DRB1 gene within SDS. Successfully ampliying and and sequencing the second exon of this gene in 288 SDS samples representing six breeds provided a comprehensive allelic profile, enabling a detalied examination of the gene's genetic makeup.

Results
We identifed forty-six alleles, including four previously unreported, enrichness the genetic diversity of SDS breeds. These alleles exhibiting non-uniform distribution, varying frequencies across breeds, indicating a breed-specific genetic landscape. Certain alleles, known and novel, show higher frequencies in specific populations, suggesting potential associations with adaptive immune responses. Identifying these alleles sets the stage for investigating their functional roles and implications for disease resistance. Genetic differentiation among SDS breeds, as indicated by FST values and clustering analyses, highlights a unique genetic makeup shaped by geographic and historical factors. These differentiation patterns among SDS breeds have broader implications for breed conservation and targeted breeding to enhance disease resistance in specific populations.

Conclusion
This study unveils Ovar-DRB1 gene allelic diversity in SDS breeds through targeted NGS and genetic analyses, revealing new alleles that underscore the breeds’ unique genetic profile. Insights into the genetic factors governing immune responses and disease resistance emerge, promising for optimization of breeding strategies for enhanced livestock health in Sudan’s unique environment.

Citation

Salim, B., Nakao, R., Chatanga, E., Marcuzzi, O., Eissawi, M. A., Almathen, F., …Giovambattista, G. (2024). Exploring genetic diversity and variation of Ovar-DRB1 gene in Sudan Desert Sheep using targeted next-generation sequencing. BMC Genomics, 25(1), Article 160. https://doi.org/10.1186/s12864-024-10053-3

• Journal Article Type: Article
• Acceptance Date: Jan 25, 2024
• Online Publication Date: Feb 8, 2024
• Publication Date: Feb 8, 2024
• Deposit Date: Apr 23, 2024
• Publicly Available Date: Apr 23, 2024
• Journal: BMC Genomics
• Electronic ISSN: 1471-2164
• Publisher: Springer Verlag
• Peer Reviewed: Peer Reviewed
• Volume: 25
• Issue: 1
• Article Number: 160
• DOI: https://doi.org/10.1186/s12864-024-10053-3
• Keywords: Genetic diversity, Sudan Desert Sheep, Ovar-DRB1 gene, Next-generation sequencing
• Public URL: https://nottingham-repository.worktribe.com/output/31435781
• Publisher URL: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-024-10053-3
• Additional Information: Received: 12 November 2023; Accepted: 25 January 2024; First Online: 8 February 2024; : ; : We confirm that the study is reported in accordance with ARRIVE guidelines (ExternalRef removed). The study protocol was reviewed and approved by the Faculty of Veterinary Medicine, University of Khartoum. The research was conducted in accordance with their guidelines for sampling domestic animals in Sudan, ensuring ethical compliance in the collection and use of the samples.; : Not applicable.; : The authors declare no competing interests.