نوع مقاله : مقاله پژوهشی
نویسندگان
1 گروه علوم دامی، دانشکده علوم دامی و صنایع غذایی، دانشگاه علوم کشاورزی و منابع طبیعی خوزستان، ملاثانی، ایران.
2 گروه علوم دامی، دانشکده کشاورزی و محیط زیست، دانشگاه اراک، اراک، ایران. و گروه علوم دامی، دانشکدگان کشاورزی و منابع طبیعی، دانشگاه تهران، کرج، ایران
3 بخش علوم دامی، دانشکده کشاورزی ,و منابع طبیعی، دانشگاه شهید باهنر کرمان، کرمان. ایران
چکیده
کلیدواژه‌ها
موضوعات
عنوان مقاله [English]
نویسندگان [English]
The selection of novel mutations beneficial only in some subpopulations leads to the retention of signatures across the genome. This study aimed to identify genomic regions, candidate genes, and biological pathways associated with fat deposition in some Asian and African sheep breeds based on selection signatures method and gene set enrichment analysis. A total of 49,034 SNP markers data obtained from 404 animal samples, including 13 fat-tailed and 7 thin-tailed sheep breeds with relatively similar tail and fat-tail dimensions distributed across different regions of Asia and Africa, were used. Principal component analysis (PCA) was utilized for assessing the clustering of animals into their true population, and FST (Theta) statistics was employed for detecting of positive selection signatures. Subsequently, genes reported in the selected regions were identified, and gene set enrichment analysis was performed to identify biological pathways (and candidate genes) associated with fat deposition. PCA analysis showed that all animals clustered into their respective breed groups, and thin and fat tailed sheep breeds could be separated based on different components. In this study, 19 genomic regions were identified to be under selection between thin and fat tailed sheep breeds. Investigation of reported genes in these regions led to the identification of several biological pathways (and candidate genes) directly or indirectly associated with tail morphology (NDUFB, ANO4, ASXL2, ABHD2, and NID2), fat-tail size (ACADL), skeletal or body size (PDGFD, ACAN, HOXC, HOXB, BMP2, and BMP4), immune response (ATG5, IL4, IL5, and IL13), and melanocyte regulation (KITLG). Overall, the findings of this study could play an important role for identifying the genomic regions associated with distinctive phenotypic traits of these breeds, especially fat deposition traits in tails, immunity, and adaptability, which could be of great economic importance in the future considering the observable climatic changes in recent years in various countries.
کلیدواژه‌ها [English]
Extended Abstract
Introduction and Objective
Both natural and artificial selection are among the main driving forces shaping genetic variation across the genome of livestock species. Selection typically leaves signatures in the genome, which are often characterized by high genetic differentiation across breeds and/or a strong reduction in genetic diversity in regions associated with traits under intense selection pressure. Such selections are likely to have imposed distinctive selection signatures on the sheep genome. Therefore, detecting selection signatures across the genome may help elucidate mechanisms of selection and pinpoint candidate genes of interest for further investigation. This study aimed to identify genomic regions, candidate genes, and biological pathways associated with fat deposition in some Asian and African sheep breeds based on selection signatures method and gene set enrichment analysis.
Materials and Methods
A total of 49,034 SNP markers data obtained from 404 animal samples, including 13 fat-tailed and 7 thin-tailed sheep breeds with relatively similar tail and fat-tail dimensions distributed across different regions of Asia and Africa, were used. Quality control of genotypes was performed based on the minor allele frequency (MAF ≤ 0.02), missing genotype (MIND > 10%), and genotyping rate (GENO > 0.05), using PLINK software. Principal component analysis (PCA) was utilized for assessing the clustering of animals into their true population, and FST (Theta) statistics was employed for detecting positive selection signatures. Subsequently, genes reported in the selected regions were identified with the Genome Data Viewer database, and gene set enrichment analysis was performed to identify biological pathways (and candidate genes) associated with fat deposition.
Results
After quality control, 44913 markers and 400 animals (281 fat-tailed and 119 thin-tailed sheep breeds) were remained for the further analysis. PCA analysis showed that all animals clustered into their respective breed groups, and thin and fat tailed sheep breeds could be separated based on different components. In this study, 19 genomic regions were identified to be under selection between thin and fat tailed sheep breeds. Genes associated with selected markers were subsequently identified. Investigation of reported genes in these regions led to the identification of several biological pathways (and candidate genes) directly or indirectly associated with tail morphology (NDUFB, ANO4, ASXL2, ABHD2, and NID2), fat-tail size (ACADL), skeletal or body size (PDGFD, ACAN, HOXC, HOXB, BMP2, and BMP4), immune response (ATG5, IL4, IL5, and IL13), and melanocyte regulation (KITLG).
Conclusion
The results of the present study and identified genomic regions suggest that the selection during the evolution and adaptation to the different environments and geographical conditions led to population differentiation in Asian and African breeds. Overall, the findings of this study could play an important role for identifying the genomic regions associated with distinctive phenotypic traits of these breeds, especially fat deposition traits in tails, immunity, and adaptability, which could be of great economic importance in the future considering the observable climatic changes in recent years in various countries.
Conceptualization, S.R, and M.H.M; methodology, S.R, and M.H.M; software, S.R, and M.H.M; validation, M.H.M, and M.T.B.; formal analysis, S.R; investigation, M.H.M, A.E; resources, M.H.M, A.E; data curation, M.H.M; writing—original draft preparation, S.R; writing—review and editing, M.H.M, M.T.B, A.E; visualization, M.H.M, M.T.B; supervision, M.T.B, M.H.M; project administration, M.H.M, A.E; funding acquisition, M.T.B. All authors have read and agreed to the published version of the manuscript.”
“Not applicable”
The authors gratefully acknowledge the International Sheep Genomics Consortium for access to the Ovine HapMap genotypes and the Animal Breeding Center of Iran (ABCI) for access to the data of the Iranian breeds. We sincerely thank all authors who made their data available for the present research. The authors also acknowledge the supports and contributions of INSF (Project No. 40232205), Animal Science Research Institute of Iran, Mobarakandish Institute and AgResearch, New Zealand.
The study was approved by the Ethics Committee of the Agricultural Science and Natural Resources University of Khuzestan, Iran (Code: 1402.3918). The authors avoided data fabrication, falsification, plagiarism, and misconduct.
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