Polymorphism of Alpha S1-Casein Gene in Yankasa Sheep Breed of Mubi, Adamawa State of Nigeria

Yıl 2020, , 275 - 290, 15.12.2020

İsmaila Yada Sudi , Shuaibu Mohammed Malachi Tizhe Clément Augustine

https://doi.org/10.38001/ijlsb.740103

Öz

Present study was conducted on five Yankasa breeds of sheep to determine alpha S1-CSNISI casein gene polymorphism. Five blood samples were collected using sterile needle and syringe. All the samples were collected into sample tubes containing ethylene diamine tetraacetic acid (EDTA), placed on an ice in cold-chain container and immediately transported to the laboratory for analysis. Gene extraction was carried out using Quick-DNA Miniprep TM kit. Reverse and forward primers were designed and used to amplify the isolated DNA. Nucleotide sequence was subjected to BLAST search against the NCBI database and a similar sequence NC-0040257.1 was retrieved for comparison. Single nucleotide polymorphism was analysed to ascertain the variation. Multiple sequence alignment was performed using Clustal W and was reconstructed using Multalin. A MEGAx Program incorporated in GenAleX 6.503 was used to construct phylogenetic tree using Nei’s genetic distance and multiple sequence alignment generated in muscle (3.8) which was also used to construct phylogenetic tree within as well as with the reference (NC-040257.1). Results from the analysis revealed that, the extracted DNA were found on chromosome 6, intron 16 and exon 17. The breeds showed total number of polymorphic and monomorphic site of 68 and 600 respectively, and percentage polymorphism of 10.18%. High frequency of 0.733 was observed at position 201. Amino acid substitution in Yankasa sheep breed was 4 at positions 161, 163, 164 and 201, showing the existence of variation in Yankasa species possibly indicating long term chances of survival. CSN1S1 isolated in Yankasa sheep showed polymorphism, genetic variation within and between breeds. In further studies, it is therefore of interest to characterize, genotype and find the allele frequencies of casein gene of Yankasa sheep breed, provide a complete picture about milk protein gene and milk protein variation in order to improve consumer preference.

Anahtar Kelimeler

Alpha S1-casein, milk protein, Mubi, polymorphism, yankasa sheep breeds

Kaynakça

• Adebayo, A. A. Mubi Region. A Geographic synthesis, Paraclete Publisher, Yola. 2004. pp. 17- 37.
• Arif, I. A., and Khan, H. A. Molecular markers for biodiversity analysis of wildlife animals: A brief review. Animal Biodiversity and Conservation. 2009. 32(1): p. 9-17. Tropical Animal Health and Production. (2010).
• Boettcher, P. J., et al., Effects of casein haplotypes on milk production traits in Italian Holstein and Brown Swiss cattle. Journal of Dairy Science, 2004. 87(12): p. 4311-4317.
• Calvo, J.H., et al., (2013). Structural and functional characterization of the αs1- casein gene and association studies with milk traits in Assaf sheep breed. Livestock Science, 2013. p. 01-08.
• Ceriotti, G., et al., Single nucleotide polymorphisms in the ovine casein genes detected by Polymerase chain reaction-single strand conformation polymorphism. Journal of Dairy Science, 2004. 87: p. 2606-2613.
• Corpet, F. Multiple sequence alignment with hierarchical clustering". Nucleic Acids Research, 1988. 16 (22): p.10881-10890.
• Degerforsertr, A. M. Climate Mubi. Climate-Data.Org. 2019. http://en.climate-data.org/info/sources Retrieved on 30.09.2019.
• Edgar, R. C. MUSCLE: Muscle multiple sequence alignment with high accuracy and throughput. Nucleic acid Research, 2004. 32(5): p. 1792-1797.
• Gencheva, D. and Georgieva, S. Genetic diversity and population structure of Bulgerian authochthonous sheep breeds based on nucleotide variation in alpha SI-casein gene. Bulgarian Journal of Agricultural Science. 2019. 25(Suppl. 3): p. 95-102.
• Hall, T. A. BioEdit: A user- friendly biological sequence alignment editor and and analysis programmed windows 95/98nt. Nucleic acids. Symposium. 1999. Ser.41: p. 95- 98.
• Ikonen, T., et al., Genetic parameters for the milk coagulation properties and prevalence of non-coagulating milk in Finnish dairy cows. Journal of Dairy Science, 1999. 82: p. 205- 214.
• Ilori, B. M., et al., Assessment of OvineSNP50 in Nigerian and Kenyan sheep populations. Nigerian Journal of Biotechnology. 2018. 35(2): p. 176-183.
• Kumar, S, et al., MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Molecular Biology and Evolution, 2018. 35: p. 1547-1549.
• Martin, P., et al., The impact of genetic polymorphisms on the protein composition of ruminant milks. Reproduction Nutrition Development. EDP Sciences, 2002. 42: p. 433-459.
• Peakall, R. and Smouse, P.E. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research – an update. Bioinformatics, 2012. 28(19): p. 2537-2539.
• Ramunno, L., et al., Characterization of two new alleles at the goat CSN1S2 locus. Animal Genetics, 2001. 32(5): p. 264-268.
• Sanger, F; and Coulson, A. R. A rapid method for determining sequence in DNA by primed synthesis with DNA polymerase Journal of Molecular Biology, 1975. 94 (3): p. 441-448.
• Sudi, I. Y., et al., Alpha S1 casein gene polymorphism in Ouda sheep breed of Mubi, Nigeria. Nigerian Journal of Genetics, 2019a. 33(1): p. 110-116.
• Sudi, I. Y., et al., Alpha S1 casein gene polymorphism in Balami sheep breed indigenous to Mubi. International Journal of Applied Sciences and Biotechnology. 2019b. 2(3): p. 231-242.