Development of a system to analyse the mitochondrial genome region (Cyt B) from cattle samples of different time periods

Relevance. Population genetic diversity studies shed light on the genetic composition of different breeds and can provide valuable information about the evolution of breeds and species. Among the numerous available molecular markers, mitochondrial DNA (mtDNA) is widely used to study genetic diversity and analyze phylogenetic relationships in various breeds and populations of livestock. Cytochrome b (Cyt B) is an mtDNA gene that is widely used to determine phylogenetic relationships in domestic animals due to its sequence variability.

The aim of the work is to develop a test system that makes it possible to obtain the complete sequence of the Cyt В gene for further assessment of the genetic diversity and phylogenetic relationships of various breeds and populations of cattle.

Methods. To develop the test system, DNA extracts obtained from archaeological samples of cattle dated the 13^th–14^th centuries were used (n = 10). To amplify the Cyt B (Cytochrome b) mtDNA gene of cattle, four pairs of primers were selected, overlapping each other, with a total length of 1189 bp. between positions 14480–15669 mtDNA.

Results. Analysis of the phylogenetic tree showed that archaeological samples grouped with haplogroups T1, T2, T3 and T5. The median network allowed the archaeological samples to be confidently classified as Bos Taurus rather than Bos Indicus. As a result of the study, it was revealed that the power of analysis using the Cyt B sequence is not enough to separate haplogroups within taurine cattle, because the Сytochrome b sequence is more conserved compared to other regions of the mitochondrial genome. More polymorphic regions of the mitochondrial genome, such as the sequence of the D-loop, should be used to confidently identify haplogroup membership.

1. Zinovieva N.A. et al. Animal genetic resources: developing the research of allele pool of Russian cattle breeds — minireview. Agricultural Biology. 2019; 54(4): 631–641. https://doi.org/10.15389/agrobiology.2019.4.631eng

2. Marsoner T., Vigl L.E., Manck F., Jaritz G., Tappeiner U., Tasser E. Indigenous livestock breeds as indicators for cultural ecosystem services: A spatial analysis within the Alpine Space. Ecological Indicators. 2018; 94(2): 55–63. https://doi.org/10.1016/j.ecolind.2017.06.046

3. Zinovieva N.A. et al. Genome-wide SNP analysis clearly distinguished the Belarusian Red cattle from other European cattle breeds. Animal Genetics. 2021; 52(5): 720–724. https://doi.org/10.1111/age.13102

4. Sharma R. et al. Microsatellite and mitochondrial DNA analyses unveil the genetic structure of native sheep breeds from three major agro-ecological regions of India. Scientific Reports. 2020; 10: 20422. https://doi.org/10.1038/s41598-020-77480-6

5. Hartatik T., Hariyono D.N.H., Adinata Yu. Short Communication: Genetic diversity and phylogenetic analysis of two Indonesian local cattle breeds based on cytochrome b gene sequences. Biodiversitas. 2019; 20(1): 17–22. https://doi.org/10.13057/biodiv/d200103

6. Xia X. et al. Abundant Genetic Diversity of Yunling Cattle Based on Mitochondrial Genome. Animals. 2019; 9(9): 641. https://doi.org/10.3390/ani9090641

7. Abdelmanova A.S. et al. Comparative Study of the Genetic Diversity of Local Steppe Cattle Breeds from Russia, Kazakhstan and Kyrgyzstan by Microsatellite Analysis of Museum and Modern Samples. Diversity. 2021; 13(8): 351. https://doi.org/10.3390/d13080351

8. Boronetskaya O.I., Chikurova E.A., Nikiforov A.I. Strain breeding features and conservation practice of White park cattle breeds. Izvestiya of Timiryazev Agricultural Academy. 2017; (6): 68–84 (in Russian). https://doi.org/10.26897/0021-342X-2017-6-68-84

9. Bro-Jørgensen M.H. et al. Ancient DNA analysis of Scandinavian medieval drinking horns and the horn of the last aurochs bull. Journal of Archaeological Science. 2018; 99: 47–54. https://doi.org/10.1016/j.jas.2018.09.001

10. Delsol N., Stucky B.J., Oswald J.A., Cobb C.R., Emery K.F. Guralnick R. Ancient DNA confirms diverse origins of early post-Columbian cattle in the Americas. Scientific Reports. 2023; 13: 12444. https://doi.org/10.1038/s41598-023-39518-3

11. Robin E.D., Wong R. Mitochondrial DNA molecules and virtual number of mitochondria per cell in mammalian cells. Journal of Cellular Physiology. 1988; 136(3): 507–513. https://doi.org/10.1002/jcp.1041360316

12. Zhang X., Yang L., Zhao X., Xiang H. The complete mitochondrial genome of an ancient cattle (Bos taurus) from Taosi site, China, and its phylogenetic assessment. Mitochondrial DNA Part B. 2022; 7(5): 804–806. https://doi.org/10.1080/23802359.2022.2073834

13. Luikart G., Gielly L., Excoffier L., Vigne J.-D., Bouvet J., Taberlet P. Multiple maternal origins and weak phylogeographic structure in domestic goats. Proceedings of the National Academy of Sciences. 2001; 98(10): 5927–5932. https://doi.org/10.1073/pnas.091591198

14. Dong Z., Wang Y., Li C., Li L., Men X. Mitochondrial DNA as a Molecular Marker in Insect Ecology: Current Status and Future Prospects. Annals of the Entomological Society of America. 2021; 114(4): 470–476. https://doi.org/10.1093/aesa/saab020

15. Shi L. et al. Effect of locomotor preference on the evolution of mitochondrial genes in Bovidae. Scientific Reports. 2024; 14: 12944. https://doi.org/10.1038/s41598-024-63937-5

16. Prihandini P.W., Primasari A., Luthfi M., Efendy J., Pamungkas D. Genetic Diversity of Mitochondrial DNA Cytochrome b in Indonesian Native and Local Cattle Populations. Jurnal Ilmu Ternak dan Veteriner. 2020; 25(2): 39–47.

17. Tarekegn G.M. et al. Variations in mitochondrial cytochrome b region among Ethiopian indigenous cattle populations assert Bos taurus maternal origin and historical dynamics. Asian-Australasian Journal of Animal Sciences. 2018; 31(9): 1393–1400. https://doi.org/10.5713/ajas.17.0596

18. Rahmatullaili S., Fatmawati D., Nisa C., Winaya A., Chamisijatin L., Hindun I. Genetic Diversity of Bali Cattle: Cytochrome b Sequence Variation. IOP Conference Series: Earth and Environmental Science. 2019; 276: 012048. https://doi.org/10.1088/1755-1315/276/1/012048

19. Kocher T.D. et al. Dynamics of mitochondrial DNA evolution in mammals: amplification and sequencing with conserved primers. Proceedings of the National Academy of Sciences. 1989; 86(16): 6196–6200. https://doi.org/10.1073/pnas.86.16.6196

20. Irwin D.M., Kocher T.D., Wilson A.C. Evolution of the cytochrome b gene of mammals. Journal of Molecular Evolution. 1991; 32(2): 128–144. https://doi.org/10.1007/BF02515385

21. Zhang Y. et al. Strong and stable geographic differentiation of swamp buffalo maternal and paternal lineages indicates domestication in the China/Indochina border region. Molecular Ecology. 2016; 25(7): 1530–1550. https://doi.org/10.1111/mec.13518

22. Mkize L.S., Zishiri O.T. Population genetic structure and maternal lineage of South African crossbred Nguni cattle using the cytochrome b gene in mtDNA. Tropical Animal Health and Production. 2020; 52(4): 2079–2089. https://doi.org/10.1007/s11250-020-02231-8

23. Çiftci Y., Eroğlu O., Firidin Ş. Mitochondrial Cytochrome b Sequence Variation in Three Sturgeon Species (A. stellatus Pallas, 1771, A. gueldenstaedtii Brandt, 1833, H. huso Linnaeus, 1758) from the Black Sea Coasts of Turkey. Turkish Journal of Fisheries and Aquatic Sciences. 2013; 13(2): 291–303.