| تعداد نشریات | 282 |
| تعداد نشریات سازمان | 80 |
| تعداد شمارهها | 3,231 |
| تعداد مقالات | 35,790 |
| تعداد مشاهده مقاله | 54,022,312 |
| تعداد دریافت فایل اصل مقاله | 93,182,453 |
برآورد هم خونی ژنومی و ارزیابی هموزیگوسیتی ایجاد شده در گاوهای سرابی و نجدی | ||
| علوم دامی | ||
| دوره 33، شماره 127، شهریور 1399، صفحه 13-30 اصل مقاله (1.74 M) | ||
| نوع مقاله: مقاله پژوهشی | ||
| شناسه دیجیتال (DOI): 10.22092/asj.2019.124197.1819 | ||
| نویسندگان | ||
| احد خصالی اقطاعی1؛ مهدی وفای واله* 2؛ حسین مرادی شهر بابک3؛ غلامرضا داشاب2 | ||
| 1دانش آموخته دکتری ژنتیک و اصلاح نزاد دام، طیور، گروه علوم دامی، دانشکده کشاورزی، دانشگاه زابل، زابل | ||
| 2دانشیار، گروه علوم دامی، دانشکده کشاورزی، دانشگاه زابل، زابل | ||
| 3استادیار، گروه علوم دامی، پردیس کشاورزی و منابع طبیعی، دانشگاه تهران | ||
| چکیده | ||
| مطالعه حاضر به منظور برآورد سطح همخونی ژنومی با استفاده از تجزیه (FROH) ROH در دو توده گاو بومی ایران شامل سرابی و نجدی و همچنین مقایسه برآوردهای FROH با دیگر برآوردهای ضریب همخونی بر اساس ماتریس رابطه ژنوم (FGRM)، درصد SNPs هموزیگوت (FHOM) و اطلاعات شجرهنامه (FPed) انجام شد. برای انجام این کار، به ترتیب تعداد 213 و 211 نمونه به طور تصادفی از جمعیت سرابی و نجدی انتخاب شدند. نمونهها با استفاده از ریز تراشه Illumina BeadChip 40K v2 تعیین ژنوتیپ شدند. علاوه بر این، تعداد 30 نمونه از گاوهای شیری هلشتاین ایران از مرکز اصلاح نژاد ایران، مورد بررسی قرارگرفتند. آنالیز ژنومی با استفاده از برنامههای CFC ، Excel، Plink، SNeP انجام شد. در مجموع 2030 بلوک هاپلوتیپی در جمعیت شناسایی شدند. بیشترین و کمترین تعداد قطعات (ROHs) ROH در بین جمعیت نجدی و سرابی مشاهده شد. علاوه بر این، طول ROH در بین نژادهای مختلف متفاوت بود (۰۵/۰p <). جمعیت نجدی بیشترین تعداد ROH را در دستههای با طول متفاوت Mb ) ROH8-4، Mb16-8 وMb 16<) داشتند. حداکثر ضریب همبستگی بین ضرایب همخونی برآورد شده بین FPed و FROH> 4Mb (592/0) در جمعیت سرابی بدست آمد (۰۰۱/۰p <). نتایج این مطالعه وجود همخونی، حداقل در پنج نسل اخیر جمعیت بومی مورد مطالعه را نشان میدهد و برنامههای حفاظتی باید به منظور مدیریت سطوح همخونی در هر دو جمعیت صورت گیرد. | ||
| کلیدواژهها | ||
| توده های گاو بومی؛ هم خونی ژنومی؛ هموزیگوسیتی ایجاد شده | ||
| عنوان مقاله [English] | ||
| Genomic inbreeding estimation and evaluation of runs of homozygosity in Sarabi and Najdi cattle populations. | ||
| نویسندگان [English] | ||
| Ahad Khasali aghtaei1؛ Mehdi Vafa Valleh2؛ Hossein Moradi Shahrebabak3؛ Golamreza Dashab2 | ||
| 1Agricultural Jahad Organization of Kerman Province, Kerman, Iran | ||
| 2Assistant Professor, Animal Breeding and Genetics, University of Zabol | ||
| 3assistant professor/Department of Animal Sciences, University College of Agriculture and Natural Resources, University of Tehran | ||
| چکیده [English] | ||
| The present study was carried out to estimate levels of genomic inbreeding based on ROH (FROH) analysis in the two Iranian native cattle populations including Sarabi and Najdi, as well as comparing the FROH estimates with other inbreeding estimates obtained based on the genomic relationship matrix (FGRM), percentage of homozygous SNPs (FHOM) and pedigree information (FPed). To do this, 213 and 211 samples were randomly selected from Sarabi and Najdi populations, respectively. The samples were genotyped using the Illumina BeadChip40K v2 microchip. In addition, 30 samples of Holstein dairy cattle of Iran provided by Animal Breeding Center of Iran, were included in the analysis . Genomic analysis was performed using CFC, Excel, Plink, SNeP programs. A total of 2030 haplo-blocks were identified in the populations. The highest and lowest number of ROH segments (ROHs) was observed within Najdi and Sarabi Population, respectively. Furthermore, ROH length were found to be significantly different among breeds (p < 0.05). Najdi population had the highest number of ROH across different categories of ROH length (4-8Mb, 8-16Mb and >16Mb). Maximum correlation coefficient among the estimated inbreeding coefficients was obtained between FPed and FROH>4Mb (0.592) in the Sarabi population (p < 0.001). The results of this study indicate that presence of inbreeding at least in the five early generations of the studied native populations and the conservation programs must be taken to manage the inbreeding levels in both populations. | ||
| کلیدواژهها [English] | ||
| Genomic inbreeding, Local cattle breeds, Runs of homozygosity | ||
| مراجع | ||
|
توکلیان، ج. (1378). ذخائر ژنتیکی دام و طیور بومی ایران. ص . 27-4. Alexander, D.H., Novembre, J. and Lange, K. (2009). Fast model-based estimation of ancestry in unrelated individuals. Genome research, 19(9): 1655-1664. Allendorf, F.W., Hohenlohe, P.A. and Luikart, G. (2010). Genomics and the future ofconservation genetics. Nature Reviews Genetics, 11: 697–709. Barrett, J.C., Fry, B., Maller, J. and Daly, M.J. (2005). Haploview: analysis and visualizationof LD and haplotype maps. Bioinformatics, 21: 263–265. Bjelland, D.W., Weigel, K.A., Vukasinovic, N. and Nkrumah, J.D. (2013). Evaluation of inbreeding depression in Holstein cattle using whole-genome SNP markers and alternative measures of genomic inbreeding. Journal of Dairy Science, 96:4697–4706. Blatt, M., Wiseman, S. and Domany, E. (1996a). Clustering data through an analogy to the Potts model. Advances in Neural Information Processing Systems, 2(3): 416-422. Blatt, M., Wiseman, S. and Domany, E. (1997). Data clustering using a model granular magnet.Neural Computation, 9(8): 1805-1842. Bosse, M., Megens, H.J., Madsen, O., Crooijmans, R.P., Ryder, O.A., Austerlitz, F., et al., (2015). Using genome-wide measures of coancestry to maintain diversity and fitness in endangered and domestic pig opulations. Genome Research, 25: 970–981. Caballero, A. and Toro, M.A. (2002). Analysis of genetic diversity for the management of conserved subdivided pulations. Conservation Genetics, 3: 289–299. considered as ancestors. Molecular Biology Reports, 39: 745–751. Curik, I., Ferenčaković, M. and Sölkner, J. (2014). Inbreeding and runs of homozygosity:a possible solution to an old problem. Livest Science, 166:26–34. De Cara, M.Á.R., Villanueva, B., Toro, M.A. and Fernández, J. (2013). Using genomic tools to maintain diversity and fitness in conservation programmes. Molecular Ecology, 22: 6091–6099. Ferenčaković, M., Hamzić, E., Gredler, B., Solberg, T.R., Klemetsdal, G., Curik, I., et al., (2013a). Estimates of autozygosity derived from runs of homozygosity:empirical evidence from selected cattle populations. Journal of Animal Breeding and Genetics, 130: 286–293. Ferenčaković, M., Solkner, J. and Curik, I. (2013b). Estimating autozygosity from high-throughput information: effects of SNP density and genotyping errors. Genetics Selection Evolution, 2: 42-45. Fernández, J., Meuwissen, T.H.E., Toro, M.A. and Mäki-Tanila, A. (2011). Management of genetic diversity in small farm animal populations. Animal, 5: 1684–1698. Fernández, J., Toro, M.A., and Caballero, A. (2003). Fixed contributions designs vs.minimization of global coancestry to control inbreeding in small populations. Genetics, 165: 885–894. García-Gámez, E., Sahana, G., Gutiérrez-Gil, B. and Arranz, J.J. (2012). Linkagedisequilibrium and inbreeding estimation in Spanish Churra sheep. BMC Genetics, 13: 43. Gaspa, G., Marras, G., Sorbolini, S., Ajmone Marsan, P., Williams, J.L., Valentini, A., et al., (2014). Genome-wide homozygosity in Italian Holstein cattle using HD panel. In Proceedings of the 10th World Congress of Genetics Applied to Livestock Production, 17–22 August, Vancouver,Canada. Gibson, J., Morton, N. and Collins, A. (2006). Extended tracts of homozygosity in outbred human populations. Human Molecular Genetics, 15: 789–795. Gómez-Romano, F., Solkner, J., Villanueva, B., Mészàros, G., De Cara, M.A.R., Pérez O’Brien, A.M. , et al., (2014). Genomic estimates of inbreeding and coancestry in Austrian Brown Swiss cattle. In Proceedings of the 10th World Congress of Genetics Applied to Livestock Production, 17–22 August, Vancouver, Canada. Gómez-Romano, F., Villanueva, B., De Cara, M.A.R. and Fernández, J. (2013). Maintaining genetic diversity using molecular coancestry: the effect of marker density and effective population size. Genetics Selection Evolution, 45: 38. Hayes, B.J., Visscher, P.M., McPartlan, H.C. and Goddard, M.E. (2003). Novel multilocus measure of linkage disequilibrium to estimate past effective population size. Genome Research, 13: 635–643. Howrigan, D.P., Simonson, M.A. and Keller, M.C. (2011). Detecting autozygosity through runs of homozygosity: a comparison of three autozygosity detection algorithms. BMC Genomics, 12: 460. Kadlečík, O., Hazuchová, E., Pavlík, I., Kasarda, R. (2013). Diversity of cattle breeds in Slovakia. Slovak Journal of Animal Science, 46(4): 145-150. Keller, M.C., Visscher, P.M. and Goddard, M.E. (2011). Quantification of inbreeding due to distant ancestors and its detection using dense single nucleotide polymorphism data. Genetics, 189: 237–249. Kim, E.S., Cole, J.B., Huson, H., Wiggans, G.R., Van Tassell, C.P., Crooker, B.A., et al., (2013). Effect of artificial selection on runs of homozygosity in U.S. Holstein cattle. PLoS One, 8: e80813. Kirin, M., McQuillan, R., Franklin, C., Campbell, H., McKeigue, P. and Wilson, J. (2010). Genomic runs of homozygosity record population history and consanguinity. PLoS One, 5: e13996. Leroy, G., Mary-Huard, T., Verrier, E., Danvy, S., Charvolin, E. and Danchin-Burge, C. (2013). Methods to estimate effective population size using pedigree data:examples in dog, sheep, cattle and horse. Genetics Selection Evolution, 45: 1–10. Lush, J.L. (1945). Animal breeding plans. Iowa State College, Ames, pp: 443. Marras, G., Gaspa, G., Sorbolini, S., Dimauro, C., Ajmone-Marsam, P., Valentini, A., et al., (2014). Analysis of runs of homozygosity and their relationship with inbreeding in five cattle breeds farmed in Italy. Animal Genetics, 46: 110–121. Mastrangelo, S. , Tolone, M. , Di Gerlando, R. , Fontanesi, L. , Sardina, M. T. and 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., Sardina, M.T., Riggio, V. and Portolano, B. (2012). Study of polymorphisms in the promoter region of ovine β -lactoglobulin gene and phylogenetic analysis among the Valle del Belice breed and other sheep breeds. Mastrangelo, S., Saura, M., Tolone, M., Salces-Ortiz, J., Di Gerlando, R., Bertolini, F., et al.. (2014). The genome-wide structure of two economically important indigenous Sicilian cattle breeds. Journal of Animal Science, 92: 4833–4842. McQuillan, R., Leutenegger, A.L., Abdel-Rahman, R., Franklin, C.S., Pericic, M., Barac-Lauc, L., et al., (2008). Runs of homozygosity in European populations. The American Journal of Human Genetics, 83: 359–372. Ober, U., Malinowski, A., Schlather, M. and Simianer, H. (2013). The expected linkage disequilibrium in finite opulations revisited. ArXiv Preprint, 1304: 4856. Ouborg, N.J., Pertoldi, C., Loeschcke, V., Bijlsma, R. and Hedrick, P.W. (2010). Conservation genetics in transition to conservation genomics. Trends in Genetics, 26: 177–187. Pertoldi, C., Purfield, D.C., Berg, P., Jensen, T.H., Bach, O.S., Vingborg, R. , et al., (2014). Genetic haracterization of a herd of the endangered Danish Jutland cattle. Journal of Animal Science, 92: 2372–2376. Pritchard, J. K., Stephens, M. and Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics, 155(2): 945-959. Pryce, J.E., Haile-Mariam, M., Goddard, M.E. and Hayes, B.J. (2014). Identification of genomic regions associated with inbreeding depression in Holstein and Jersey dairy cattle. Genetics Selection Evolution, 46: 71. Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M.A., Bender, D., et al., (2007). PLINK: a tool set for wholegenome association and population-based linkage analyses. The American Journal of Human Genetics, 81: 559–575. Purfield, D.C., Berry, D.P., McParland, S. and Bradley, D.G. (2012). Runs of homozygosity and population history in cattle. BMC Genetics, 13: 70. Rodríguez-Ramilo, S.T., Fernández, J., Toro, M.A., Hernández, D. and Villanueva, B. (2015). Genome-wide estimates of coancestry, inbreeding and effective population size in the Spanish Holstein population. PLoS One, 10: 4. Sargolzaei, M., Iwaisaki, H. and Colleau, J.J. (2006). CFC Release 1.0-A software package for pedigree analysis and monitoring genetic diversity comm. Saura, M., Fernández, A., Rodríguez, M.C., Toro, M.A., Barragán, C., Fernández, A.I. et al., (2013). Genome-wide estimates of coancestry and inbreeding depression in an closed herd of ancient Iberian pigs. PLoS One, 8: e78314. Saura, M., Tenesa, A., Woolliams, J.A., Fernández, A. and Villanueva, B. (2015). Evaluation of the linkage-disequilibrium method for the estimation of effective population size when generations overlap: an empirical case. BMC Genomics,16: 922. Saura, M., Woolliams, J.A., Tenesa, A., Fernández, A. and Villanueva, B. (2014).Estimation of ancient and recent effective population size from linkage disequilibrium in a closed herd of Iberian pigs. In Proceedings of the 10th World Congress of Genetics Applied to Livestock Production, 17–22 August,Vancouver, Canada. Silió, L., Rodríguez, M.C., Fernández, A., Barragán, C., Benítez, R., Óvilo, C. et al., (2013). Measuring inbreeding and inbreeding depression on pig growth from pedigree or SNP-derived metrics. Journal of Animal Breeding and Genetics, 130: 349–360. Sved, J.A. (1971). Linkage disequilibrium of chromosome segments. Theoretical Population Biology, 141: 125–141. Tenesa, A., Navarro, P., Hayes, B.J., Duffy, D.L., Clarke, G.M., Goddard, M.E. et al., (2007). Recent human effective population size estimated from linkage disequilibrium. Genome Research, 17: 520–526. Toro, M.A., Meuwissen, T.H.E., Fernández, J., Shaat, I. and Mäki-Tanila, A. (2011). Assessing the genetic diversity in small farm animal populations. Animal, 5:1669–1683. Tsafrir, D., Tsafrir, I., Ein-Dor, L., Zuk, O., Notterman, D.A. and Domany, E. (2005). Sorting points into neighborhoods (SPIN): data analysis and visualization by ordering distance matrices. Bioinformatics, 21(10): 2301-2308. VanRaden, P.M., Olson, K.M., Wiggans, G.R., Cole, J.B. and Tooker, M.E. (2011). Genomic inbreeding and relationships among Holsteins, Jerseys, and Brown Swiss. Journal of Dairy Science, 94: 5673–5682. Waples, R. and England, P.R. (2011). Estimating contemporary effective population size on the basis of linkage disequilibrium in the face of migration. Genetics, 189:633–644. Waples, R.S. and Do, C. (2010). Linkage disequilibrium estimates of contemporary Ne using highly variable genetic markers: a largely untapped resource for applied conservation and evolution. Evolutionary Applications, 3: 244–262. Zavarez, L.B., Utsunomiya, Y.T., Carmo, A.S., Neves, H.H., Carvalheiro, R., Ferenčaković, M., et al., (2015). Assessment of autozygosity in Nellore cows (Bos indicus) through high-density SNP genotypes. Frontiers in Genetics, 6: 5. Zhang, Q., Calus, M.P., Guldbrandtsen, B., Lund, M.S. and Sahana, G. (2015). Estimation of inbreeding using pedigree, 50k SNP chip genotypes and full sequence data in three cattle breeds. BMC Genetics, 16: 88. Zhang, Y., Young, J.M., Wang, C., Sun, X., Wolc, A. and Dekkers, J.C.M. (2014). Inbreeding by pedigree and genomic markers in selection lines of pigs. In Proceedings of the 10th World Congress of Genetics Applied to Livestock Production, 17–22 August, Vancouver, Canada. | ||
|
آمار تعداد مشاهده مقاله: 979 تعداد دریافت فایل اصل مقاله: 641 |
||