Volume 9, Issue 20 (10-2018)                   rap 2018, 9(20): 88-99 | Back to browse issues page

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mosavi kashani M, Rahimi mianji G, Moradi shahrbabak H. Genome-Wide Scan for Selection Signatures in Iranian Sarabi and Taleshi Indigenous Breed. rap. 2018; 9 (20) :88-99
URL: http://rap.sanru.ac.ir/article-1-720-en.html
Department of animal science of University of Tehran
Abstract:   (98 Views)

The aim of this study was to find the footprint of selection in native Sarabi and Taleshi cattle breeds 296 cattle from two breeds were sampled and genotyped. by 40 k microarray of illumine company. 43 animals were removed because their ACR was below 0.09. Markers were filtered with minor allele frequency (MAF) equal 0.01 and Hardy-Weinberg equilibrium test (10-6). After filtering, 28782 markers remained. To study the genetic structure of population and sub-population principal component analysis (PCA) was used. To identify selective signals for Sarabi and Taleshi pure population theta parameter was calculated. To reduce error theta values was averaged with near marker and Manhattans graph were obtained by haploview software. Chromosomes 2, 5, 6, 7, 10, 22, 25 and 27 had selection signatures. To searching for selection signatures in both population, extended haplotype homozygosity statistics (EHH) was calculated using R software. In addition, for each chromosome LD erosion rate for ancestral and mutant alleles were calculated. To study of positions that showed signature selection, bioinformatics web site were searched. EIF4G3 gene was identified on chromosome 2. This gene have fundamental role in transfering RNA from nucleus to the cytoplasm and gene expression. ANK2 gene was identified on chromosome 6 which encodes polypeptide ankirin B expressed in all tissues. On chromosome 7 the gene ARHGAP26 was found which is a tumor suppressor genes. On chromosome 10, a gene identified that encodes protein SYNJ2BP that suppress activing protein. On chromosome 22, FAM3D protein coding gene detected that plays a role in cyto sckeleton actin biochemical pathway. This gene is expressed in the placenta and plays a role in biological functions such as migration and function of leukocyte, temperature regulation, cell survival and hematopoiesis differentiation.
 

 

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