Volume 13, Issue 38 (12-2022)
Res Anim Prod 2022, 13(38): 176-186 |
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Nikmanesh A, Asadi Fozi M, Esmailizadeh A, Asadollahpour Nanaei H, ezedinloo L. (2022). Investigating the Genetic Diversity of the BRCA1 Gene in some of Domestic and Wild Sheep Breeds of the World and Drawing their Phylogenetic Structure. Res Anim Prod. 13(38), 176-186. doi:10.52547/rap.13.38.176
URL: http://rap.sanru.ac.ir/article-1-1319-en.html
URL: http://rap.sanru.ac.ir/article-1-1319-en.html
Alireza Nikmanesh *1, Masood Asadi Fozi2, Ali Esmailizadeh2, Hojjat Asadollahpour Nanaei1, Leila Ezedinloo3
1- Department of Animal Science Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
2- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman,Iran
3- Natural History Museum & Genetic resource Bureau, DOE
2- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman,Iran
3- Natural History Museum & Genetic resource Bureau, DOE
Abstract: (1688 Views)
Extended Abstract
Introduction and Objective: The BRCA1 gene, which is called “gate keeper” It plays an important role in the process of repairing DNA damage, regulating the cell cycle, regulating the transcription process, maintaining chromosome stability, and other important pathways for the maintenance of genome stability. The current research was conducted with the aim of bioinformatic analysis and comparison the genetic diversity and phylogenetic structure of the BRCA1 gene of different breeds of domestic and wild sheep from 49 breeds in 6 geographical regions: Western Asia, Europe, China, North Africa, South Africa and wild (Iran) using the NCBI genome databas.
Material and Methods: The desired sequences were aligned using MEGA11 software and a phylogenetic tree was drawn by Neighbor-Joining method. Also, the number of mutations, nucleotide diversity, haploid diversity, the number of positions in which similar or non-similar substitutions occurred, the percentage of gene differentiation, gene conversion were also analyzed using Dnaspv5 software.
Results: The analyzes related to the comparison of breeds in 6 geographical regions showed 112 polymorphisms, which led to the creation of 19 different haplotypes with a haplotype diversity of 0.035. Nucleotide diversity and average nucleotide differences (k) among breeds were estimated as 0.205 and 0.052, respectively. The genetic differentiation between the Chinese sheep population and the wild sheep population was the lowest. The average genetic distance between all geographical regions was calculated to be 0.29. The average nucleotide ratio (A+T):(G+C) was equal to 38:62%, which indicates the predominance of cytosine and guanine bases. The amount of conserved sequence (c) in this research was 0.313 on average, which indicates the high polymorphism of this gene and the creation of new proteins as well as new functions to adapt to different homeostasis conditions. The effective number of codons (ENC) in this research was calculated to be 56.41. The value of D in the Tajima neutrality test was 0.478, which indicates that the selection pressure is balanced.
Conclusion:The high genetic diversity in the wild population, the reasons for which are the presence of forest and open environments, prevention of genetic drift and reduction of inbreeding, which affects muscle strength, eating habits, aggressive behaviors, defense responses, sensory perception of confrontation with environmental conditions and stress that related to BRCA1 gene expression in these populations.
Introduction and Objective: The BRCA1 gene, which is called “gate keeper” It plays an important role in the process of repairing DNA damage, regulating the cell cycle, regulating the transcription process, maintaining chromosome stability, and other important pathways for the maintenance of genome stability. The current research was conducted with the aim of bioinformatic analysis and comparison the genetic diversity and phylogenetic structure of the BRCA1 gene of different breeds of domestic and wild sheep from 49 breeds in 6 geographical regions: Western Asia, Europe, China, North Africa, South Africa and wild (Iran) using the NCBI genome databas.
Material and Methods: The desired sequences were aligned using MEGA11 software and a phylogenetic tree was drawn by Neighbor-Joining method. Also, the number of mutations, nucleotide diversity, haploid diversity, the number of positions in which similar or non-similar substitutions occurred, the percentage of gene differentiation, gene conversion were also analyzed using Dnaspv5 software.
Results: The analyzes related to the comparison of breeds in 6 geographical regions showed 112 polymorphisms, which led to the creation of 19 different haplotypes with a haplotype diversity of 0.035. Nucleotide diversity and average nucleotide differences (k) among breeds were estimated as 0.205 and 0.052, respectively. The genetic differentiation between the Chinese sheep population and the wild sheep population was the lowest. The average genetic distance between all geographical regions was calculated to be 0.29. The average nucleotide ratio (A+T):(G+C) was equal to 38:62%, which indicates the predominance of cytosine and guanine bases. The amount of conserved sequence (c) in this research was 0.313 on average, which indicates the high polymorphism of this gene and the creation of new proteins as well as new functions to adapt to different homeostasis conditions. The effective number of codons (ENC) in this research was calculated to be 56.41. The value of D in the Tajima neutrality test was 0.478, which indicates that the selection pressure is balanced.
Conclusion:The high genetic diversity in the wild population, the reasons for which are the presence of forest and open environments, prevention of genetic drift and reduction of inbreeding, which affects muscle strength, eating habits, aggressive behaviors, defense responses, sensory perception of confrontation with environmental conditions and stress that related to BRCA1 gene expression in these populations.
Type of Study: Research |
Subject:
ژنتیک و اصلاح نژاد دام
Received: 2022/08/16 | Accepted: 2022/10/9
Received: 2022/08/16 | Accepted: 2022/10/9
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