Genetic variation at the OLR1, ANXA9, MYF5, LTF, IGF1, LGB, CSN3, PIT1, MBL1, CACNA2D1, and ABCG2 loci in Turkish Grey Steppe, Anatolian Black, and East Anatolian Red cattle

Native breeds are excellent sources of genetic variation. Anatolian native breeds are relatives of the first cattle domesticated and are ancestors of many European breeds. Therefore, this study aimed to evaluate the genetic variation of OLR1, ANXA9, MYF5, LTF, IGF1, LGB, CSN3, PIT1, MBL1, CACNA2D1, and ABCG2 markers in Turkish Grey Steppe, Anatolian Black, and East Anatolian Red cattle. The analysis included 367 cattle and the genotyping was performed by the PCR-RFLP. Population genetics indices including heterozygosity, the number of effective alleles, the polymorphism information content, fixation index, and the level of possible variability realization, and moreover, the genetic diversity parameters including Shannon–Weaver diversity index and Simpson dominance index were estimated. Hardy–Weinberg equilibrium was evaluated based on the number of individuals per genotype. Native breeds exhibited admissible population genetics and diversity levels. There was no animal with the MYF5-AA, IGF1-CC, LGB-BB, CSN3-BB, CACNA2D1- GG, and ABCG2-AC genotypes in the Anatolian Black breed. The frequencies of the genotypes/alleles favorable for milk production traits were remarkably low in all breeds. These findings could provide useful information on the genetic variation of Anatolian native cattle and the genetic investigations of resistance and health traits in bovine breeding and genetics.

PDF

___

1. Demir E, Karslı T, Balcıoğlu MS. A comprehensive review on genetic diversity and phylogenetic relationships among native Turkish cattle breeds based on microsatellite markers. Turkish Journal of Veterinary and Animal Sciences 2021; 45 (1): 1-10.
2. Ardıçlı S. The analysis of FSH beta-subunit gene genotypes in East Anatolian Red, East Anatolian Red×Holstein, and Zavot bulls. Open Veterinary Science 2021; 2 (1): 91-97.
3. Özşensoy Y, Kurar E, Doğan M, Bulut Z, Nizamlıoğlu M et al. Phylogenetic relationships of native Turkish cattle breeds using microsatellite markers. Turkish Journal of Veterinary and Animal Sciences 2019; 43 (1): 23-29.
4. Ardıçlı S, Çobanoğlu O. Genetic variation in the bovine myogenic determination factor 1 (g. 782G> A polymorphism) and its influence on carcass traits in Turkish Grey Steppe cattle. Turkish Journal of Veterinary and Animal Sciences 2021; 45 (3): 380-387.
5. Ardıçlı S, Şamlı H, Vatansever B, Soyudal B, Dinçel D, Balcı F. Comprehensive assessment of candidate genes associated with fattening performance in Holstein–Friesian bulls. Archives Animal Breeding 2019; 62 (1): 9-32.
6. Curi RA, Oliveira HNd, Gimenes MA, Silveira AC, Lopes CR. Effects of CSN3 and LGB gene polymorphisms on production traits in beef cattle. Genetics and Molecular Biology 2005; 28 (2): 262-266.
7. Sharma A, Tiwari M, Singh SP, Sharma D, Kumar S et al. Study of ABCG2 gene polymorphism in Sahiwal and Hariana Cattle by PstI/PCR-RFLP assay. Journal of Animal Research 2016; 6 (3): 475-477.
8. Soyudal B, Ardıçlı S, Samlı H, Dinçel D, Balcı F. Association of polymorphisms in the CSN2, CSN3, LGB and LALBA genes with milk production traits in Holstein cows raised in Turkey. Journal of the Hellenic Veterinary Medical Society 2019; 69 (4)
9. Zhao Q, Davis M, Hines H. Associations of polymorphisms in the Pit-1 gene with growth and carcass traits in Angus beef cattle. Journal of Animal Science 2004; 82 (8): 2229-2233.
10. Zhou G, Cao Y, Li M, Zhang L, Yu Y, Jin H. Meat quality and carcass traits in relation to HGD-BstXI and HGD-HaeIII PCR– RFLP polymorphism in Chinese red cattle. Meat Science 2010; 85 (2): 270-273.
11. Yuan ZR, Li J, Liu L, Zhang LP, Zhang LM et al. Single nucleotide polymorphism of CACNA2D1 gene and its association with milk somatic cell score in cattle. Molecular Biology Reports 2011; 38 (8): 5179-5183.
12. El‐Domany WB, Radwan HA, Ateya AI, Ramadan HH, Marghani BH, Nasr SM. Genetic Polymorphisms in LTF/EcoRI and TLR4/AluI loci as candidates for milk and reproductive performance assessment in Holstein cattle. Reproduction in Domestic Animals 2019; 54 (4): 678-686.
13. Kulig H, Kowalewska-Łuczak I, Kmieć M, Wojdak-Maksymiec K. ANXA9, SLC27A3, FABP3 and FABP4 single nucleotide polymorphisms in relation to milk production traits in Jersey cows. Czech Journal of Animal Science 2010; 55 (11): 463-467.
14. Yuan Z, Li J, Li J, Gao X, Xu S. SNPs identification and its correlation analysis with milk somatic cell score in bovine MBL1 gene. Molecular Biology Reports 2013; 40 (1): 7-12.
15. Özdemir M, Doğru U. Determination of phylogenetic relationships of Turkish native cattle breeds with other cattle breeds using mitochondrial DNA D-loop sequence polymorphism. Asian-Australasian Journal of Animal Sciences 2009; 22: 955-961.
16. Doğan M, Nizamlıoğlu M, Özşensoy Y, Kurar E, Bulut Z et al. Maternal Phylogenetics of Some Anatolian Cattle Breeds. Universal Journal of Agricultural Research 2017; 5: 79-84.
17. Green M, Sambrook J. Isolation of high-molecular-weight DNA from mammalian cells using proteinase K and phenol. Molecular Cloning: A Laboratory Manual. 4th ed. ed. Cold Spring Harbor Laboratory Press 2012: 47-48.
18. Nei M, Roychoudhury AK. Sampling variances of heterozygosity and genetic distance. Genetics 1974; 76 (2): 379-390.
19. Botstein D, White RL, Skolnick M, Davis RW. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics 1980; 32 (3): 314.
20. Crow JF, Kimura M. Properties of a finite population. An introduction to population genetics theory. The Blackburn Press 1970: 319-365.
21. Ortiz-Burgos S. Shannon-weaver diversity index. Encyclopedia of Estuaries 2016: 572-573.
22. Morris EK, Caruso T, Buscot F, Fischer M, Hancock C et al. Choosing and using diversity indices: insights for ecological applications from the German Biodiversity Exploratories. Ecology and Evolution 2014; 4 (18): 3514-3524.
23. Zeder MA. Archaeological approaches to documenting animal domestication. In: Zeder MA, Bradley DG, Emshwiller E, Smith BD (editors). Documenting domestication: New genetic and archaeological paradigms. 1st ed. London, England: University of California Press; 2006. pp. 171-180.
24. Zeder MA. Domestication and early agriculture in the Mediterranean Basin: Origins, diffusion, and impact. Proceedings of the National Academy of Sciences 2008; 105: 11597-11604.
25. Soysal M, Kök S. The last survivors of Grey cattle resisting extinction. A case study of characteristics and sustainability of traditional systems of native Grey cattle breeds. Options Méditerranéenes A 2006; 78: 55-63.
26. Heringstad B, Klemetsdal G, Steine T. Selection responses for disease resistance in two selection experiments with Norwegian red cows. Journal of Dairy Science 2007; 90 (5): 2419-2426.
27. Khatib H, Leonard S, Schutzkus V, Luo W, Chang Y. Association of the OLR1 gene with milk composition in Holstein dairy cattle. Journal of Dairy Science 2006; 89 (5): 1753-1760.
28. Siadkowska E, Zwierzchowski L, Oprzadek J, Strzalkowska N, Bagnicka E, Krzyzewski J. Effect of polymorphism in IGF-1 gene on production traits in Polish Holstein-Friesian cattle. Animal Science Papers and Reports 2006; 24 (3): 225-37.
29. Kucerova J, Matejicek A, Jandurová O, Sorensen P, Nemkova E et al. Milk protein genes CSN1S1, CSN2, CSN3, LGB and their relation to genetic values of milk production parameters in Czech Fleckvieh. Czech Journal of Animal Science 2006; 51 (6): 241.
30. Olsen HG, Nilsen H, Hayes B, Berg PR, Svendsen M et al. Genetic support for a quantitative trait nucleotide in the ABCG2 gene affecting milk composition of dairy cattle. BMC Genetics 2007; 8 (1): 1-9.
31. Martínez-Royo A, Ordovas L, Zaragoza P, Altarriba J, Serrano M et al. The bovine annexin 9 gene (ANXA9) is significantly associated with milk-fat yield in a Spanish Holstein–Friesian population. Research in Veterinary Science 2010; 88 (3): 452- 455.
32. Viorica C. RFLP/HinfI polymorphism between exon 5 and exon 6 of the PIT-1 gene in Romanian Simmental cattle. Usamv Journal-Cn 2006; 63: 219-222.
33. Wojdak-Maksymiec K, Kmiec M, Ziemak J. Associations between bovine lactoferrin gene polymorphism and somatic cell count in milk. Veterinarni Medicina-Praha 2006; 51 (1): 14.
34. Konopiński MK. Shannon diversity index: a call to replace the original Shannon’s formula with unbiased estimator in the population genetics studies. PeerJ 2020; 8:e9391.
35. Sherwin WB, Chao A, Jost L, Smouse PE. Information theory broadens the spectrum of molecular ecology and evolution. Trends in Ecology & Evolution 2017; 32 (12): 948-963.
36. Akyüz B, Ağaoğlu ÖK, Ertuğrul O. Genetic polymorphism of kappa‐casein, growth hormone and prolactin genes in Turkish native cattle breeds. International Journal of Dairy Technology 2012; 65 (1): 38-44.
37. Komisarek J, Dorynek Z. Effect of ABCG2, PPARGC1A, OLR1 and SCD1 gene polymorphism on estimated breeding values for functional and production traits in Polish Holstein-Friesian bulls. Journal of Applied Genetics 2009; 50: 125–132.
38. Özdemir M. Determination of Pit-1/Hinf1 polymorphism in holstein and native EAR cattle raised as genetic resource in Turkey. The Journal of Animal and Plant Sciences 2012; 22: 25- 28.