شناسایی تنوع در تعداد کپی قطعه ژنومی 15 ‌نژاد گوسفند ایتالیایی با استفاده از چیپ 50‌کی گوسفندی

نوع مقاله : علمی پژوهشی- ژنتیک و اصلاح دام و طیور

نویسندگان

1 دانشگاه علوم و منابع طبیعی گرگان

2 گروه علوم دامی، دانشکده کشاورزی، دانشگاه فردوسی مشهد، مشهد، ایران.

چکیده

در سال‌های اخیر با پیشرفت تکنولوژی توالی‌یابی، مطالعات ژنومی به‌سمت شناسایی تنوع‌های جدید و نحوه تأثیر آن‌ها بر عملکرد صفات اقتصادی معطوف شده است. تنوع در تعداد کپی قطعه ژنومی با طول حداقل یک کیلو جفت‌باز و تشابه بیش از 90 درصد از جمله این تنوع‌ها است. در این پژوهش به هدف شناسایی این تنوع در ژنوم گوسفند از 360‌رأس گوسفند نمونه خون تهیه شد و با استفاده چیپ 50‌ کی گوسفندی شرکت ایلومینا، 54241 جهش تک‌نوکلئوتیدی در سرأسر ژنوم شناسایی شد. تعداد 2180 تنوع در تعداد کپی قطعه ژنومی با استفاده از نرم‌افزار پنسی.ان.وی شناسایی شد. کل طول این تنوع در ژنوم 5/8‌مگا جفت‌باز بود (32/0درصد). پس از ادغام نواحی مشترک 35‌ ناحیه تنوع در تعداد کپی قطعه ژنومی پُرتکرار در کروموزوم‌های اتوزوم با میانگین و میانه طول به‌ترتیب 61/178 و 25/135کیلو جفت‌باز شناسایی شد. توزیع نواحی تنوع در ژنوم بیشتر در مناطق تلومری و سانترومری بود. از 35‌ناحیه شناسایی شده 25‌ناحیه به‌صورت کامل یا جزئی با 152‌ژن مرجع در ژنوم انسان، گاو و گوسفند هم‌پوشانی داشت. این ژن‌ها در مسیرهای متابولیکی ترانس‌دوکسیون بویای، سرطان، متابولیسم پورین و پریمیدین، بیوسنتز استروئیدها و بیماری‌های از قبیل استئوپروسیز و کم‌خونی نقش داشتند. حضور این نواحی در مناطق ژنی این فرضیه را تقویت کرد که احتمالاً این تنوع قادر است مسیرهای متابولیکی را تغییر دهد و منجر به تفاوت در عملکرد فنوتیپی بین افراد یک جمعیت شود. لذا به‌نظر می‌رسد شناسایی این تنوع می‌تواند افق‌های جدیدی را در برنامه‌های اصلاح‌نژادی باز کند.

کلیدواژه‌ها


عنوان مقاله [English]

Copy number variation detection in sheep genome by using ovine BeadChip 50k

نویسندگان [English]

  • Maryam Nosrati 1
  • Mojtaba Tahmoorespur 2
1 Dept. of Animal and Poultry Breeding and Genetics, Faculty of Animal Science, Gorgan University of Agricultural Sciences and Natural Resources,
2 Department of Animal Sciences, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
چکیده [English]

Introduction Recently, genomic research in livestock is focused on genomic variation and its effect on phenotypic performance in economic traits. Copy number variation (CNV) is one of these variations in genome including insertion, deletion and duplication of 1 kb to 1 Mb segment with more than 90% similarity. CNVs can change gene structure and dosage, can regulate gene expression and function and (1, 4). In mammals, it is important source of variability in genomes and it contains 0.4-25% of whole genome variation. Some researches carried out in livestock have been demonstrated that CNV affecting genes or gene regions are associated with several phenotypic traits. For example, CNV in intron 1 of the SOX5 gene causes the pea-comb phenotype in chicken. CNV affects also the Agouti locus in sheep and goats and contributes to the variability of coat color in these two species. The late feathering locus in this avian species includes a partial duplication of the PRLR and SPEF2 genes and Dominant white locus in pigs includes alleles determined by duplications of the KIT gene (2, 5, 6). In spite of, many researches carried out in human represent association between CNV with both complex genetic diseases and traits; however, far too little attention has been paid to CNV in farm animal. This paper will focused on detecting of CNV in sheep genome.
Materials and method The sheep genomic DNA was extracted from blood of 360 Italian ewes using DNA Purification kit (Promega Corporation, Madison, WI). Markers were genotyped by Illumina ovineSNP50 BeadChip according to instructions. It is containing 54,241 markers that uniformly span the entire ovine genome (Illumina, Inc., USA). After completion of the assay, the BeadChips were scanned with a two-color, confocal Bead Array reader. Scanned image intensities were loaded directly into Illumina’s BeadStudio 1.2 software. When normalization was completed, the clustering process was performed to assess cluster position for each marker and to determine individual genotypes. LRR and BAF of sample were reported. The PFB file was calculated based on the BAF of each marker in these populations. The sheep GC model file was generated by calculating the GC content of the1 Mb genomic region surrounding each marker (500 Kb each side). CNVs were inferred using a PennCNV (http: //www.openbioinformatics. org/penncnv/). Penn CNV quality filters were applied after CNV detection. High quality samples with a standard deviation (SD) of LRR < 0.30 and with the default set: BAF drift as 0.01 and waviness factor value between − 0.05 and 0.05, were used respectively. In addition, the program argument: the “lastchr 26” in the “detect” argument were used for specific CNVs. CNVRs were determined by aggregating overlapping CNVs identified in different animals. The UCSC table browser tool was used to identify the gene content located within or partially overlapping with the CNVRs and DAVID Bioinformatics Resources (http://david.abcc.ncif crf.gov) was used for further GO functional analysis, including Gene Ontology.
Results and Discussion After all filtration 184 samples were remained. All CNVs and CNVRs found in one sample were omitted from further analysis. Finally 904 CNVs (599 losses, 111 gains and 194 losses/gains) were detected. The average number of CNVs per sample was 4.91, with an average length and median size of 170 kb and 123.9 kb, respectively. 60% of all CNVs had length between 100 kb to 500 kb. This result was similar to other research (2, and 3). After all CNVs were aggregated for the CNV region (CNVR), 88 CNVRs were identified that 55 event were found just in one sample and were omitted. The average and median size of CNVR were 178.61 kb and 135.25 kb. The profile of CNVRs location on Ovis_aris_3.0 genome were shown distribution of CNVRs was not randomly. The highest percentages covering of CNVRs located on chromosomes 16, 24, 25 and 26 (0.8%, 0.9%, 0.8% and 2%, respectively). It’s similar to result of Liu et al (21). Gene ontology (GO) analysis can provide insight into the functional enrichment of CNVs. For this reason, we ran GO analysis using DAVID http://david.abcc.ncifcrf.gov. Two CNVRs (chr12:481088-180295, chr16: 385305-156698) entirely encompassing MYOG RefSeq gene and Mi103 respectively. The gene content of the 25 CNVR s, we used a BLASTN search for homologous human and cattle sequences using the UCSC table browser tool. There were 110 RefSeq homologous human genes located within or partially overlapping with 16 CNVRs and similarly, there were 40 RefSeq homologous cattle genes located within or partially overlapping with 10 CNVRs.
Conclusion Comparing CNVs and CNVRs identified in sheep genome with CNVRs reported in cattle showed demonstrated low level of similarity, so this genomic variation had great potential detection and using in breeding scheme in sheep industry.

کلیدواژه‌ها [English]

  • CNV
  • Ovine Illumina 50k BeadChip
  • Penncnv
  • Sheep
1- Aboura, A., C. Dupas, G. Tachdjian, M. Portnoi, N. Bourcigaux, D. Dewailly, R. Frydman, B. Fauser, N. Ronci-Chaix, B. Donadille, P. Bouchard, S. Christin-Maitre. 2009. Array Comparative Genomic Hybridization Profiling Analysis Reveals Deoxyribonucleic Acid Copy Number Variations Associated with Premature Ovarian Failure. Journal of Clinical Endocrinology & Metabolism, 94: 4540–4546.
2- Bae, J. S., H. S. Cheong, L. H. Kim, S. NamGung, T. J. Park, J. Y. Chun, J. Y. Kim, C. F. Pasaje, J. S. Lee and H. D. Shin. 2010. Identification of copy number variations and common deletion polymorphisms in cattle. BMC Genomics, 11: 232.
3- Clop, A., O. Vidal and M. Amills. 2012. Copy number variation in the genomes of domestic animals. Animal Genetice, 43: 503–517
4- Conrad, D. F., D. Pinto, R. Redon, L. Feuk, O. Gokcumen, Y. Zhang, J. Aerts, T. D. Andrews, C. Barnes, P. Campbell, T. Fitzgerald, M. Hu, C. H. Ihm, K. Kristiansson, D. G. MacArthur, J. R. MacDonald, I. Onyiah, A. W. C. Pang, S. Robson, K. Stirrups, A. Valsesia, K. Walter, J. Wei, The Wellcome Trust Case Control Consortium, C. Tyler-Smith, N. P. Carter, C. Lee, S. W. Scherer and M. E. Hurles. 2009. Origins and functional impact of copy number variation in the human genome. Nature. 464: 704-712.
5- Diskin, S. J., M. Li, J. Hou, S. Yang, J. Glessner, M. Hakonarson, M. Bucan, J. M. Maris and K. Wang. 2008. Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms. Nucleic Acids Research. 36: e126.
6- Elferink, M. G., A. A. Vallee, A. P. Jungerius, R. P. Crooijmans and M. A. Groenen. 2008. Partial duplication of the PRLR and SPEF2 genes at the late feathering locus in chicken. BMC Genomics 9: 391.
7- Fadista, J., B. Thomsen, L. Holm and C. Bendixen. 2010. Copy number variation in the bovine genome. BMC Genomics. 11:284
8- Fontanesi, L., F. Beretti, P. L. Martelli, M. Colombo, S. Dall'Olio, M. Occidente, B. Portolano, R. Casadio, D. Matassino and V. Russo. 2011. A first comparative map of copy number variations in the sheep genome. Genomics. 97: 158-165
9- Fontanesi, L., P. L. Martelli, F. Beretti, V Riggio, S. Dall'Olio, M. Colombo, R. Casadio, V. Russo and B. Portolano. 2010. An initial comparative map of copy number variations in the goat (Capra hircus) genome. BMC genomics, 11: 639.
10- Huang, D.W., B. T. Sherman and R. A. Lempicki. 2009. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Research, 37(1):1-13.
11- Hastings, P. J., J. R. Lupski, S. M. Rosenberg and G. Ira. 2009. Mechanisms of change in gene copy number. Nature Review Genetic, 10: 551–564.
12- Hou, Y., D. M. Bickhart, M. L. Hvinden, C. Li. J. Song, D. A. Boichard, S. Fritz, A. Eggen, S. DeNise, G. R. Wiggans, T. S. Sonstegard, C. P. Van Tassell and G. E. Liu. 2012. Fine mapping of copy number variations on two cattle genome assemblies using high density SNP array. BMC Genomics, 13: 1471-2164
13- Hou, Y., G. E. Liu, D. M. Bickhart, M. F. Cardone, K. Wang, E. S. Kim, L. K. Matukumalli, M. Ventura, J. Song, P. M. Vanradan, T. S. Sonstegard and C. P. Van Tassell. 2011. Genomic characteristics of cattle copy number variations. BMC genomics, 12:127
14- Kijas, J. W., W. Barendse, W. Barris, B. Harrison, R. McCulloch, S. McWilliam and V. Whan. 2011. Analysis of copy number variants in the cattle genome. Gene, 482: 73–77.
15- Li, X., L. Tan,, X. Liu,, S. Lei,, T. Yang,, X. Chen,, F. Zhang,, Y. Fang, Y. Guo, L. Zhang, H. Yan, F. Pan, Z. Zhang, Y. Peng, Q. Zhou, L. He, X. Zhu, J. Cheng, L. Zhang and Y. Liu. 2010. A genome wide association study between copy number variation (CNV) and human height in Chinese population. Journal of Genetic & Genomics. 37: 779-785
16- Lin, X., J. Luo, L. Zhang, W. Wang and D. Gou. 2013. MiR-103 Controls Milk Fat Accumulation in Goat (Capra hircus) Mammary Gland during Lactation. Plos One, 8(11): e79258
17- Liu, G. E., Y. Hou, B. Zhu, M. F. Cardone, L. Jiang, A. Cellamare, A. Mitra, L. J. Alexander, L. L. Coutinho, M. E. Dell'Aquila, L. C. Gasbarre, G. Lacalandra, R. W. Li, L. K. Matukumalli, D. Nonneman, L. C. Regitano , T. P. Smith, J. Song, T. S. Sonstegard, C. P. Van Tassell, M. Ventura, E. E. Eichler, T. G. McDaneld and J. W. Keele. 2010. Analysis of copy number variations among diverse cattle breeds. Genome Research Journal, 20: 693-703
18- Liu, G. E., C. P. Van Tassel, T. S. Sonstegard, R. W. Li, L. J. Alexander, J. W. Keele, L. K. Matukumalli, T. P. Smith and L. C. Gasbarre. 2008. Detection of germ line and somatic copy number variations in cattle. Journal of Developmental Biology, 132: 231-237.
19- Liu, G. E., M. Ventura, A. Cellamare, L. Chen, Z. Cheng, B. Zhu, C. Li, J. Song and E. E. Eichler. 2009. Analysis of recent segmental duplications in the bovine genome. BMC Genomics, 10:571
20- Liu, Z. J. 2011. Next Generation Sequencing and Whole Genome Selection in Aquaculture. Wiley-Blackwell press.1th Edition. pp. 87-90
21- Liu, J., L. Zhang, L. Xu, H. Ren, J. Lu, X. Zhang, S. Zhang, X. Zhou, C. Wei, F. Zhao and L. Du. 2013. Analysis of copy number variations in the sheep genome using 50K SNP BeadChip array. BMC Genomics, 14:229
22- Mills, R. E., K. Walter, C. Stewart, R. E. Handsaker, K. Chen, C. Alkan, A. Abyzov, S. C. Yoon, K. Ye, R. K. Cheetham, A. Chinwalla, D. F. Conrad, Y. Fu, F. Grubert, I. Hajirasouliha, F. Hormozdiari, L. M. Iakoucheva, Z. Iqbal, S. Kang, M. T. Kidd, M. K. Konkel, J. Korn, E. Khurana, D. Kural, H. Y. Lam, J. Leng, R. Li, Y. Li, C. Y. Lin, R. Luo, X. J. Mu, J. Nemesh, H. E. Peckham, T. Rausch, A. Scally, X. Shi, M. P. Stromberg, A. M. Stütz, A. E. Urban, J. A. Walker, J. Wu, Y. Zhang, Z. D. Zhang, M. A. Batzer, L. Ding, G. T. Marth, G. McVean, J. Sebat, M. Snyder, J. Wang, K. Ye, E. E. Eichler, M. B. Gerstein, M. E. Hurles, C. Lee, S. A. McCarroll, J. O. Korbel.,1000 Genomes Project. 2011. Mapping copy number variation by population-scale genome sequencing. Nature. 470: 59-65
23- Nicholas, T. J., Z. Cheng, M. Ventura, K. Mealey, E. E. Eichler and J. M. Akey. 2009. The genomic architecture of segmental duplications and associated copy number variants in dogs. Genome Research Journal, 19: 491–499
24- Norris, B. J. and V. A. Whan. 2008. A gene duplication affecting expression of the ovine ASIP gene is responsible for white and black sheep. Genome Research Journal, 188: 1282–1293.
25- Pailhoux, E., B. Vigier, S. Chaffaux, N. Servel, S. Taourit, J. P. Furet, M. Fellous, F. Grosclaude, E. P. Cribiu, C. Cotinot and D. Vaiman. 2001. A 11.7-kb deletion triggers intersexuality and polledness in goats. Nature Genetice. 29: 453–458.
26- Redon, R., S. Ishikawa, K. R. Fitch, L. Feuk, G. H. Perry, T. D. Andrews, H. Fiegler, M. H. Shapero, A. R. Carson, W. Chen, E. K. Cho, S. Dallaire, J. L. Freeman, J. R. Gonzalez, M. Gratacòs, J. Huang, D. Kalaitzopoulos, D. Komura, J. R. MacDonald, C. R. Marshall, R. Mei, L. Montgomery, K. Nishimura, K. Okamura, F. Shen, M. J. Somerville, J. Tchinda, A. Valsesia, C. Woodwark, F. Yang, J. Zhang, T. Zerjal, J. Zhang, L. Armengol, D. F. Conrad, X. Estivill, C. Tyler-Smith, N. P. Carter, H. Aburatani, C. Lee, K. W. Jones, S. W. Scherer and M. E. Hurles. 2006. Global variation in copy number in the human genome. Nature. 444: 444-454.
27- Rosengren, P. G., A. Golovko, E. Sundstrom, I. Curik, J. Lennartsson, P. G Rosengren, A. Golovko, E. Sundström, I. Curik, J. Lennartsson, M. H. Seltenhammer, T. Druml, M. Binns, C. Fitzsimmons, G. Lindgren, K. Sandberg, R. Baumung, M. Vetterlein, S. Strömberg, M. Grabherr, C. Wade, K. Lindblad-Toh, F. Ponten, C. H. Heldin, J. Sölkner and L. Andersson. 2008. A cis-acting regulatory mutation causes premature hair greying and susceptibility to melanoma in the horse. Nature Gentice, 40: 1004–1009.
28- Wang, K., M. Li, D. Hadley, R. Liu, J. Glessner, S. F. Grant, H. Hakonarson and M. Bucan. 2007. PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Research Journal, 17:1665-1674.
29- Wang, X., S. Nahashon, T. K. Feaster, A. Bohannon-Stewart and N. Adefope. 2010. Aninitial map of chromosomal segmental copy number variations in the chicken. BMC Genomics, 11: 351.
30- Wright, D., H. Boije, J. R. Meadows, B. Bed’hom, D. Gourichon, A. Vieaud, M. Tixier-Boichard, C. J. Rubin, F. Imsland, F. Hallbook and L. Andersson., 2009. Copy number variation in intron 1 of SOX5 causes the Pea-comb phenotype in chickens. PLoS Genetics, 5: e1000512.
31- Zhang, Z., F. Xu, Y. Zhang, W. Li, Y. Yin, C. Zhu, L. Du, A. K. and B. Li. 2014. Cloning and expression of MyoG gene from Hu sheep and identification of its myogenic specificity. Molecular Biology Reports, 41(2):1003-13.
CAPTCHA Image