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برآورد ضریب همخونی ژنومی و اندازه مؤثر جمعیت در نژادهای مختلف بز | ||
| تولیدات دامی | ||
| مقاله 2، دوره 25، شماره 2، تیر 1402، صفحه 133-143 اصل مقاله (857.83 K) | ||
| نوع مقاله: مقاله پژوهشی | ||
| شناسه دیجیتال (DOI): 10.22059/jap.2023.349362.623707 | ||
| نویسندگان | ||
| حسین محمدی* 1؛ امیر حسین خلت آبادی فراهانی2؛ محمد حسین مرادی2؛ محمد شمس الهی3 | ||
| 1نویسنده مسئول، گروه علوم دامی، دانشکده کشاورزی و منابع طبیعی، دانشگاه اراک، اراک، ایران. رایانامه: H-mohammadi64@araku.ac.ir | ||
| 2گروه علوم دامی، دانشکده کشاورزی و منابع طبیعی، دانشگاه اراک، اراک، ایران. | ||
| 3گروه علوم دامی، دانشکده کشاورزی، دانشگاه ایلام، ایلام، ایران. | ||
| چکیده | ||
| در این پژوهش، میزان همخونی ژنومی و اندازه مؤثر جمعیت در 879 رأس بز نژادهای بیتال، تدی، پهری، نچی، بربری، دیرا دینپناه و پوسوری با استفاده از یک پنل K50 که بعد از کنترل کیفیت 36861 نشانگر SNPو 827 رأس بز بود، بررسی شد. ضریب همخونی با چهار روش ماتریس روابط خویشاوندی (FGRM)، میزان هموزیگوسیتی (FHOM)، همبستگی گامتها (FUNI)، با نرمافزار GCTA (نسخه1/0) و قطعات هموزیگوت ژنومی (FROH) با PLINK (نسخه 1/9) محاسبه شد. اندازه مؤثر جمعیت (Ne) از اطلاعات عدم تعادل پیوستگی با نرمافزار SNeP (نسخه 1/1) محاسبه شد. کم‌ترین ضریب همخونی محاسبه شده با سه روش (FGRM، FHOM، FUNI) مربوط به نژاد بیتال و بیش‌ترین مربوط به نژاد بربری بود. بیش‌ترین میزان FROH (0/159) در نژاد بربری و کم‌ترین مقدار آن (0/028) در نژاد پوسوری برآورد شد. میانگین طول قطعات ROH بین 70/2 تا 391/4 مگاباز و متوسط تعداد قطعات ROH بین 8/19 تا 48/65 متغیر بود. هم‌چنین بیش‌ترین و کم‌ترین تعداد ROH به‌ترتیب روی کروموزومهای دو و 29 مشاهده شدند. اندازه Ne در نسلهای حاضر (نسل پنج) نژادهای موردبررسی در دامنه 365-35 رأس بود. بیش‌ترین Ne در نژاد بیتال (365 رأس) و کم‌ترین در نژاد بربری (35 رأس) برآورد شد. میانگین ضریب همخونی در نژادهای بیتال، تدی، پهری، نچی، بربری، دیرا دینپناه و پوسوری به‌ترتیب 0/035، 0/081، 0/031، 0/052، 0/15، 0/11 و 0/02 بهدست آمد. هم‌چنین Ne اکثر جمعیتهای موردمطالعه کاهش یافت. بنابراین، اقتصادی‌نمودن تولید و طراحی برنامههای مناسب جفت‌گیری برای کنترل همخونی و حفاظت از حیوانات خالص باقیمانده این نژادها ضروری است. | ||
| کلیدواژه‌ها | ||
| ارزیابی ژنومی؛ بز؛ تنوع ژنتیکی؛ قطعات هموزیگوت ژنومی؛ نشانگرهای تک نوکلئوتیدی | ||
| عنوان مقاله [English] | ||
| Estimation of genomic inbreeding coefficient and effective population size in different goat breeds | ||
| نویسندگان [English] | ||
| Hossein Mohammadi1؛ Amir Hossein Khaltabadi Farahani2؛ Mohammad Hossein Moradi2؛ mohammad shamsollahi3 | ||
| 1Assistant Professor, Department of Animal Sciences, Faculty of Agriculture and Natural Resources, Arak University, Arak, Iran. | ||
| 2lecturer | ||
| 3Assistant Professor, Department of Animal Sciences, Faculty of Agriculture, University of Ilam. Ilam, Iran. | ||
| چکیده [English] | ||
| Introduction: The selection of animals by humans left detectable signatures on the genome of modern goat. The identification of these signals can help us to improve the genetic characteristics of economically important traits in goat. Over the last decade, interest in detection of genes or genomic regions that are targeted by selection has been growing. Identifying signatures of selection can provide valuable insights about the genes or genomic regions that are or have been under selection pressure, which in turn leads to a better understanding of genotype-phenotype relationships. A run of homozygosity (ROH) is a consecutive tract of homozygous genotypes in an individual that indicates it has inherited the same ancestral haplotype from both parents. Run of homozygosity one of the most methods were used to detecting the genomic inbreeding. The locations of ROHs which are under positive selection, or laboring favorable allele in population, tend to be fixed in the genome and formation of ROH Island during long times. Genomic regions enriched with ROH may be indicative of selection sweeps and are known as ROH islands. As detecting the ROH Islands, the genomic regions contain economic traits could be detectable. Materials and Methods: In this research, the amount of genomic inbreeding and the effective size of the population were investigated using the information obtained from 879 goats of different breeds including Beetal, Daira Deen Panah, Nachi, Barbari, Teddi, Pahari, and Pothwari. In order to determine the genotype of the samples, Illumina caprine Bead Chip 50K were used. The genomic information of goat breeds was extracted from the figshare database. Quality control was conducted using the Plink software. The markers or individuals were excluded from the further study based on the following criteria: unknown chromosomal or physical location, call rate <0.95, missing genotype frequency >0.05, minor allele frequency (MAF) < 0.05, and a P-value for Hardy–Weinberg equilibrium test less than 10-3. After quality control, 36,861 SNPs from Goat SNP chip 50K on 827 goats were remained for the future analysis. Inbreeding coefficient was calculated using four methods including, genomic relationship matrix (FGRM), excess of homozygosity (FHOM), correlation between uniting gametes (FUNI) using the GCTA 1.0 software and run of homozygosity (FROH) using the PLINK 1.9 software. The effective population size (Ne) was calculated from linkage disequilibrium data with SNeP software (version 1.1). 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 lowest and highest inbreeding coefficient calculated by three methods (FGRM, FHOM, and FUNI) were related to Beetal and Barbari breed, respectively. The highest (0.159) and lowest (0.028) amount of FROH was estimated in the Barbari and Pothwari breeds, respectively. The average length of ROH ranged from 70.2 to 391.4 Mb, and the average number of ROH fragments varied between 8.19 and 48.65. Also, the highest and lowest number of ROH were observed on chromosome 2 and 29, respectively. The size of Ne in in the current generations (fifth generation) of the studied breeds was ranged from 35 to 365. The highest Ne was estimated in the Beetal breed (365 heads) and the lowest in the Barbari breed (35 heads). The average inbreeding coefficient in Beetal, Teddi, Pahari, Nachi, Barbari, Daira Deen Panah and Pothwari breeds was obtained 0.035, 0.081, 0.031, 0.052, 0.15, 0.11 and 0.02, respectively. In addition, the Ne of most of the studied populations has been decreased. The results of this study revealed that, the selection processes in different goat breeds for economic traits during several years, has led to the formation of many ROH islands in goat genome, therefore scanning these regions at the genome level can be an alternative strategy to identify genes and associated loci with economic traits. Conclusions: our findings contribute to the understanding of genetic diversity and population demography, and help design and implement breeding and conservation strategies for study goat breeds. Therefore, it is necessary to economize production and planning a suitable mating scheme to control inbreeding and genetically conserve the remaining pure animals of these breeds. | ||
| کلیدواژه‌ها [English] | ||
| Genetic diversity, Genome wide evaluation, Goat, Runs of homozygosity, Single nucleotide polymorphism | ||
| مراجع | ||
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Al-Mamun, H. A., a Clark, S., Kwan, P., & Gondro, C. (2015). Genome-wide linkage disequilibrium and genetic diversity in five populations of Australian domestic sheep. Genetics Selection Evolution, 47(1), 1-14. Barbato, M., Orozco-terWengel, P., Tapio, M., & Bruford, M. W. (2015). SNeP: a tool to estimate trends in recent effective population size trajectories using genome-wide SNP data. Frontiers in genetics, 6, 109. Bertolini, F., Servin, B., Talenti, A., Rochat, E., Kim, E. S., Oget, C., ... & Crepaldi, P. (2018). Signatures of selection and environmental adaptation across the goat genome post-domestication. Genetics Selection Evolution, 50(1), 1-24. Corbin, L. J., Liu, A. Y. H., Bishop, S. C., & Woolliams, J. A. (2012). Estimation of historical effective population size using linkage disequilibria with marker data. Journal of Animal Breeding and Genetics, 129(4), 257-270. Curik, I., Ferenčaković, M., & Sölkner, J. (2014). Inbreeding and runs of homozygosity: A possible solution to an old problem. Livestock Science, 166, 26-34. Forutan, M., Ansari Mahyari, S., Baes, C., Melzer, N., Schenkel, F. S., & Sargolzaei, M. (2018). Inbreeding and runs of homozygosity before and after genomic selection in North American Holstein cattle. BMC genomics, 19, 1-12. Frankham, R., Bradshaw, C. J., & Brook, B. W. (2014). Genetics in conservation management: revised recommendations for the 50/500 rules, Red List criteria and population viability analyses. Biological Conservation, 170, 56-63. Gomez-Raya, L., Rodríguez, C., Barragán, C., & Silió, L. (2015). Genomic inbreeding coefficients based on the distribution of the length of runs of homozygosity in a closed line of Iberian pigs. Genetics Selection Evolution, 47, 1-15. Islam, R., Li, Y., Liu, X., Berihulay, H., Abied, A., Gebreselassie, G., ... & Ma, Y. (2019). Genome-wide runs of homozygosity, effective population size, and detection of positive selection signatures in six Chinese goat breeds. Genes, 10(11), 938. Luigi-Sierra, M. G., Fernández, A., Martínez, A., Guan, D., Delgado, J. V., Álvarez, J. F., ... & Amills, M. (2022). Genomic patterns of homozygosity and inbreeding depression in Murciano-Granadina goats. Journal of animal science and biotechnology, 13(1), 35. Marquez, G. C., Speidel, S. E., Enns, R. M., & Garrick, D. J. (2010). Genetic diversity and population structure of American Red Angus cattle. Journal of animal science, 88(1), 59-68. Marras, G., Gaspa, G., Sorbolini, S., Dimauro, C., Ajmone‐Marsan, P., Valentini, A., ... & Macciotta, N. P. (2015). Analysis of runs of homozygosity and their relationship with inbreeding in five cattle breeds farmed in Italy. Animal genetics, 46(2), 110-121. Mastrangelo, S., Tolone, M., Di Gerlando, R., Fontanesi, L., Sardina, M. T., & Portolano, B. (2016). Genomic inbreeding estimation in small populations: evaluation of runs of homozygosity in three local dairy cattle breeds. Animal, 10(5), 746-754. Mastrangelo, S., Di Gerlando, R., Sardina, M. T., Sutera, A. M., Moscarelli, A., Tolone, M., ... & Portolano, B. (2021). Genome-wide patterns of homozygosity reveal the conservation status in five italian goat populations. Animals, 11(6), 1510. Mohammadi, H., Rafat, A., Moradi Shahrebabak, H., Shodja, J., & Moradi, M. H. (2018). Estimation of genomic inbreeding coefficient and effective population size in Zandi sheep breed using density SNP markers (50K SNPChip). Animal Sciences Journal, 31(119), 129-142. (In Persian) Mohammadi, H., Rafat, S. A., Moradi Shahrbabak, H., Shodja, J., & Moradi, M. H. (2020). Genome-wide association study and gene ontology for growth and wool characteristics in Zandi sheep. Journal of Livestock Science and Technologies, 8(2), 45-55. Moosanezhad Khabisi, M., Esmailizadeh, A., & Asadi Fozi, M. (2022). Evaluation of Genomic Inbreeding Rate in Iranian Native Sheep using Dense SNP Markers (600K). Research On Animal Production (Scientific and Research), 13(35), 158-167. Pasandideh, M., Gholizadeh, M., & Rahimi Mianji, G. (2020). Estimation of Effective Population Size and Genomic Inbreeding Coefficients in Baluchi Sheep Using Genome-Wide Single Nucleotide Polymorphisms (SNPs). Iranian Journal of Applied Animal Science, 10(2), 287-295. Peripolli, E., Munari, D. P., Silva, M. V. G. B., Lima, A. L. F., Irgang, R., & Baldi, F. (2017). Runs of homozygosity: current knowledge and applications in livestock. Animal genetics, 48(3), 255-271. Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A., Bender, D., ... & Sham, P. C. (2007). PLINK: a tool set for whole-genome association and population-based linkage analyses. The American journal of human genetics, 81(3), 559-575. Purfield, D. C., McParland, S., Wall, E., & Berry, D. P. (2017). The distribution of runs of homozygosity and selection signatures in six commercial meat sheep breeds. PLoS One, 12(5), e0176780. VanRaden, P. M. (2008). Efficient methods to compute genomic predictions. Journal of dairy science, 91(11), 4414-4423. Wright, L. I., Tregenza, T., & Hosken, D. J. (2008). Inbreeding, inbreeding depression and extinction. Conservation Genetics, 9, 833-843. Zhang, Q., Calus, M. P., Guldbrandtsen, B., Lund, M. S., & Sahana, G. (2015). Estimation of inbreeding using pedigree, 50k SNP chip genotypes and full sequence data in three cattle breeds. BMC genetics, 16(1), 1-11. | ||
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