Shahid Bahonar University of Kerman and Iranian Biotechnology Society Agricultural Biotechnology Journal 2228-6705 16 1 2024 03 20 Scanning genomic signatures of selection Turkoman and thoroughbred horse breeds Scanning genomic signatures of selection Turkoman and thoroughbred horse breeds 69 86 4155 10.22103/jab.2023.21201.1469 FA Milad Hosseini Department of Animal Science, Faculty of Agriculture and Natural Resources, University of Tehran, Karaj, Iran Hossein Moradi Shahrbabak Journal Article 2023 09 23 Abstract Objective When continuous selection is carried out over years, it creates effects on the genome level, which can be detected by using some strategies. This study was carried out with the aim of scanning the whole genome to identify regions of the genome in Thoroughbred and Turkoman horses that have been targeted by natural or artificial selection. Materials and Methods DNA was extracted from blood samples using the optimal salt method. The quality and quantity of extracted DNA of all samples was determined by nanodrop device with absorption ratio on DNA solution. For this purpose, 44 Thoroughbred horses and 67 Turkoman horses were genotyped by genomic arrays of 60k SNP chips. By two general methods of population differentiation and linkage disequilibrium methods, the selection signatures at the genome level were looked into. In order to identify the population genetic structure of the studied animals, principal component analysis was done in R program. Results The study of population differentiation using the fixation index method (Fst) corrected for the sample size (θ) showed that there are evidences of selection in several loci in these two breeds. A number of five genomic regions were identified in which there were signatures of selection. These areas are located on chromosomes 4, 5, 10, 13 and 15. In order to evaluate the signatures of selection based on linkage disequilibrium methods, the extended haplotype homozygosity test (EHH) was used. The results confirmed the existence of population segregation in these genomic regions. Finally, the investigation of QTLs in the bovine orthologous regions showed that these regions are related to the traits of body length, body weight, chest depth and other important economic traits in horses. Conclusions The present research was effective in identifying regions of the genome of the two breeds of Turkoman and Thoroughbred horses being divergently selected, and identifying the genes that exist in these regions. Also, useful information was obtained on the existence of genetic diversity and signatures of selection between these two horse breeds. Abstract Objective When continuous selection is carried out over years, it creates effects on the genome level, which can be detected by using some strategies. This study was carried out with the aim of scanning the whole genome to identify regions of the genome in Thoroughbred and Turkoman horses that have been targeted by natural or artificial selection. Materials and Methods DNA was extracted from blood samples using the optimal salt method. The quality and quantity of extracted DNA of all samples was determined by nanodrop device with absorption ratio on DNA solution. For this purpose, 44 Thoroughbred horses and 67 Turkoman horses were genotyped by genomic arrays of 60k SNP chips. By two general methods of population differentiation and linkage disequilibrium methods, the selection signatures at the genome level were looked into. In order to identify the population genetic structure of the studied animals, principal component analysis was done in R program. Results The study of population differentiation using the fixation index method (Fst) corrected for the sample size (θ) showed that there are evidences of selection in several loci in these two breeds. A number of five genomic regions were identified in which there were signatures of selection. These areas are located on chromosomes 4, 5, 10, 13 and 15. In order to evaluate the signatures of selection based on linkage disequilibrium methods, the extended haplotype homozygosity test (EHH) was used. The results confirmed the existence of population segregation in these genomic regions. Finally, the investigation of QTLs in the bovine orthologous regions showed that these regions are related to the traits of body length, body weight, chest depth and other important economic traits in horses. Conclusions The present research was effective in identifying regions of the genome of the two breeds of Turkoman and Thoroughbred horses being divergently selected, and identifying the genes that exist in these regions. Also, useful information was obtained on the existence of genetic diversity and signatures of selection between these two horse breeds.

https://jab.uk.ac.ir/article_4155_b0079847e5ba97479884e98879438369.pdf