Document Type : Research Articles
Authors
1
Ferdowsi University of Mashhad
2
Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad
3
Department of Medicine Massachusetts General Brigham Harvard Medical School Boston, MA, 02115, USA
Abstract
Introduction The genetic mutations that occur in the populations of domestic animals, will be added to the merits of animals who contain these genetic mutations and they will have more breeds. These mutations are also repeated in their breeds. If a new SNP in population increases the competence of its carriers compared to other members of society, this choice will make the more deserving individual more involved in shaping the next generation. The most important statistical tests based on demographic differentiation are the FST statistics, which identify distinct positions under positive selection, which are of particular importance for economic characteristics. One of the best ways to understand physiological processes is to analyze gene regulation networks. Identification of genes involved in economic traits as molecular markers in breeding is of special importance. Gene regulation networks enable the researcher to study all of the genes together. The aim of this study was to identify selection signature regions and candidate genes related to economic traits.
Materials and Methods downloaded the needed data of this research from two sites of NEXTGEN and HAPMAP. These breeds included Afshari (41 heads), Ghezel (35 heads), Moghani (35 heads) breeds and eight wild sheep in order to check the quality and filtration of raw data Finally, for the remaining SNPs, those that are not in Hardy-Weinberg equilibrium is considered as a measure of genotyping error. The probability level is equal to 106, which will be obtained using the Bonferroni correction. Different stages of quality control were performed using the PLINK v1.9. study and identify the animals outside their group to have a general perspective on population structure of the two groups. Principal component analysis (PCA) were done in R software. The FST index was proposed to study the distinction between subpopulations and identification of selection signature. the population structure of wild and domestic sheep breeds was analyzed. PCA analysis was performed using genotype information of the samples to investigate how the animals were grouped Investigation of identified genes using SNPs in the upper 1% range of FST were identified by Plink v1.9 software. In addition, the DAVID database (http://david.abcc.ncifcrf.gov) was used to determine biological routes. At this stage, it is assumed that genes that belong to a functional class can be considered as a group of genes that have some specific and common characteristics. GeneCards (http://www.genecards.org) and UniProtKB (http://www.uniprot.org) databases were also used to interpret the function of the obtained genes.
Results and Discussion The results showed that adjacent SNPs are highly dispersed in several genomic regions. From 34556 SNPs after filtration above 1%, SNPs with higher FST stabilization index (340 SNP) with FST range from 0.304 to 0.472 were selected. Selected SNPs consisted of 95 genomic regions on 23 chromosomes between domestic and wild sheep. Most regions were located on chromosomes 13 and 7 had 14 and 9 gene regions, respectively. Examination of the relationship between QTLs and important genes in selected areas showed that 95 genes related to economic traits were identified. QTLs with important economic characteristics including quality and quantity of meat, milk, fat, bone, immune system and parasite resistance were reported. Most QTLs were located on chromosomes 2, 3, 5, 6, and 7, indicating that the most positive mutations occurred on these chromosomes. Most of the identified biological pathways related to ion channels through cell membranes are neuromuscular processes, Brain and cerebellum growth, metencephalon growth, membrane ion membrane transport, and pathways involved in regulating ion transport in cell membranes. Genes identified in different genomic regions can be considered as selective candidates. A number of genes studied as selection signatures reported were consistent with previous studies. Important genes were included: GABRB1, GRM3, HERC1, HERC3 and KCND2.
Conclusion The study of genomic regions showed that these regions are directly and indirectly related to the quality and quantity of meat, milk, fat, bone, immune system and parasite resistance. Identifying important economic traits and locating parts of the genome that have changed as a result of selection could be used in sheep breeding programs. However, in this research we had limitations such as the incompleteness of information related to functional annotation of genes in sheep species and also the small sample size of this study. Therefore, in subsequent studies with more samples and more breeds of domestic and wild sheep in Iran, a better understanding of candidate genes for important economic traits in domestic and wild species would be achieved.
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