Mitogenomic Analysis of Western Baggara Cattle Breed-Nyalawi Population Revealed High Level of Haplotype Diversity and Population Expansion

Sumaya Kambal¹, Bashir Salim²
¹Faculty of Animal Production Science and Technology, Sudan University of Science and Technology; ²Department of Parasitology, Faculty of Veterinary Medicine, University of Khartoum

Western Baggara cattle breed is naturally inhabiting the western regions of the Sudan, primarily raised by nomadic pastoralists in Darfur and Kurdofan states and ranked the best beef producing cattle breed in the country. This breed had structured phenotypically into three populations, Nyalawi, Rezaigi and Messairi. Decades to date, western Baggara cattle breed-Nyalawi population (WBCB-NP) is the most reputable beef cattle among the other types by its large size that contribute significantly to local meat consumption as well as to the export revenue. Knowledge-based breeding programs and conservation strategies are necessarily needed to aid in sustainable production and preservation of such population.
This study was undertaken to investigate the maternal genetic diversity and the demography dynamic by addressing whether this population had undergone demographic expansion, decline or equilibrium.

Genomic DNA was extracted from blood of 30 animals selected WBCB-NP and subjected to PCR targeting the entire mitochondrial DNA D-loop region and subsequently to DNA sequencing. This resulted in 43 polymorphic sites that defined 28 haplotypes of which 4 signatures of breed specific transition were detected when compared to bovine reference sequence. Genetic diversity indices revealed high level of haplotype diversity (1.000 ± 0.0091) and low level of nucleotide diversity (0.005 ± 0.0028) between these haplotypes that agreed with the Median Joining and Minimum Spanning networks' pattern, and the Neighbor Joining phylogenetic tree. The revealed unimodal pattern of the mismatch distribution among the haplotypes was in a good accordance with both the negative values of Tajima's D (-2.259; P= 0.000) and Fu's Fs (-25.671; P= 0.000) results that are significantly deviated from the neutral model, suggesting population demographic expansion event.

It is concluded that WBCB-NP is highly divers and had experienced a demographic growth. This study has raised important queries about the nature and the factors of this demographic expansion that can be compared with other populations of cattle for historical dynamics tracing purpose. Therefore, this research lays the groundwork for future research enhancing our understanding of Baggara breed as well as the other local cattle breeds. Further Bayesian analysis is required to trace the time series and nature of this population expansion.

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