Biotechnology Bulletin ›› 2015, Vol. 31 ›› Issue (11): 35-42.doi: 10.13560/j.cnki.biotech.bull.1985.2015.11.006
• Review • Previous Articles Next Articles
Cheng Hong,JiangYu
Received:
2015-09-27
Online:
2015-11-26
Published:
2015-11-26
Cheng Hong,JiangYu. ProgressandProspects in Domestic Animals and Breeding: a Review of Genomic Copy Number Variations[J]. Biotechnology Bulletin, 2015, 31(11): 35-42.
[1] International Chicken Genome Sequencing, Consortium. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution[J]. Nature, 2004, 432(7018): 695-716. [2] Consortium BH. Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds[J]. Science, 2009, 324(5926): 528-532. [3] Groenen MA, Archibald AL, Uenishi H, et al. Analyses of pig geno-mes provide insight into porcine demography and evolution[J]. Nature, 2012, 491(7424): 393-398. [4] Dong Y, Xie M, Jiang Y, et al. Sequencing and automated whole-genome optical mapping of the genome of a domestic goat(Capra hircus)[J]. Nature Biotechnology, 2013, 31(2): 135-141. [5] Huang Y, Li Y, Burt David W, et al. The duck genome and transcriptome provide insight into an avian influenza virus reservoir species[J]. Nature Genetics, 2013, 45(7): 776-783. [6] Jiang Y, Xie M, Chen W, et al. The sheep genome illuminates biology of the rumen and lipid metabolism[J]. Science, 2014, 344(6188): 1168-1173. [7] Wang Y, Lu Y, Zhang Y, et al. The draft genome of the grass carp(Ctenopharyngodon idellus)provides insights into its evolution and vegetarian adaptation[J]. Nature Genetics, 2015, 47(6): 625-631. [8] MacDonald JR, Ziman R, Yuen R, et al. The Database of Genomic Variants: a curated collection of structural variation in the human genome[J]. Nucleic Acids Research, 2014, 42(D1): D986-D992. [9] Rubin CJ, Zody M, Eriksson J, et al. Whole-genome resequencing reveals loci under selection during chicken domestication[J]. Nature, 2010, 464(7288): 587-591. [10] Daetwyler HD, Capitan A, Pausch H, et al. Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle[J]. Nature Genetics, 2014, 46(8): 858-865. [11] Carneiro M, Rubin CJ, Di Palma F, et al. Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication[J]. Science, 2014, 345(6200): 1074-1079. [12] Sudmant PH, Mallick S, Nelson BJ, et al. Global diversity, population stratification, and selection of human copy-number variation[J]. Science, 2015, 349(6253): aab3761. [13] Bickhart DM, Hou Y, Schroeder SG, et al. Copy number variation of individual cattle genomes using next-generation sequencing[J]. Genome Research, 2012, 22(4): 778-790. [14] Liu GE, Hou Y, Zhu B, et al. Analysis of copy number variations among diverse cattle breeds[J]. Genome Research, 2010, 20(5): 693-703. [15] Fontanesi L, Beretti F, Martelli PL, et al. A first comparative map of copy number variations in the sheep genome[J]. Genomics, 2011, 97(3): 158-165. [16] Ma Y, Zhang Q, Lu Z, et al. Analysis of copy number variations by SNP50 BeadChip array in Chinese sheep[J]. Genomics, 2015, 106(5): 295-300. [17] Chen C, Qiao R, Wei R, et al. A comprehensive survey of copy number variation in 18 diverse pig populations and identification of candidate copy number variable genes associated with complex traits[J]. BMC Genomics, 2012, 13(1): 733. [18] Li Y, Mei S, Zhang X, et al. Identification of genome-wide copy number variations among diverse pig breeds by array CGH[J].BMC Genomics, 2012, 13(1): 725. [19] Crooijmans RP, Fife MS, Fitzgerald TW, et al. Large scale variation in DNA copy number in chicken breeds[J]. BMC Genomics, 2013, 14(1): 398. [20] Yi G, Qu L, Liu J, et al. Genome-wide patterns of copy number variation in the diversified chicken genomes using next-generation sequencing[J]. BMC Genomics, 2014, 15(1): 962. [21] Sebat J, Lakshmi B, Troge J, et al. Large-scale copy number polymorphism in the human genome[J]. Science, 2004, 305(5683): 525-528. [22] Redon R, Ishikawa S, Fitch KR, et al. Global variation in copy number in the human genome[J]. Nature, 2006, 444(7118): 444-454. [23] Perry GH, Ben-Dor A, Tsalenko A, et al. The fine-scale and complex architecture of human copy-number variation[J]. The American Journal of Human Genetics, 2008, 82(3): 685-695. [24] Perry GH, Yang F, Marques-Bonet T, et al. Copy number variation and evolution in humans and chimpanzees[J]. Genome Research, 2008, 18(11): 1698-1710. [25] Perry GH, Ben-Dor A, Tsalenko A, et al. Hotspots for copy number variation in chimpanzees and humans[J]. Proceedings of the National Academy of Sciences, 2006, 103(21): 8006-8011. [26] Meisel RP, Han MV, Hahn MW. A complex suite of forces drives gene traffic from Drosophila X chromosomes[J]. Genome Biology and Evolution, 2009, 1: 176-188. [27] Orozco LD, Cokus SJ, Ghazalpour A, et al. Copy number variation influences gene expression and metabolic traits in mice[J]. Human Molecular Genetics, 2009, 18(21): 4118-4129. [28] Ossowski S, Schneeberger K, Clark RM, et al. Sequencing of natural strains of Arabidopsis thaliana with short reads[J]. Genome Research, 2008, 18(12): 2024-2033. [29] Springer NM, Ying K, Fu Y, et al. Maize inbreds exhibit high levels of copy number variation(CNV)and presence/absence variation(PAV)in genome content[J]. PLoS Genet, 2009, 5(11): e1000734. [30] Maydan JS, Lorch A, Edgley ML, et al. Copy number variation in the genomes of twelve natural isolates of Caenorhabditis elegans[J]. BMC Genomics, 2010, 11(1): 62. [31] Poptsova M, Banerjee S, Gokcumen O, et al. Impact of constitutional copy number variants on biological pathway evolution[J]. BMC Evolutionary Biology, 2013, 13(1): 19. [32] Conrad DF, Pinto D, Redon R, et al. Origins and functional impact of copy number variation in the human genome[J]. Nature, 2010, 464(7289): 704-712. [33] Gonzalez E, Kulkarni H, Bolivar H, et al. The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility[J]. Science, 2005, 307(5714): 1434-1440. [34] Aitman TJ, Dong R, Vyse TJ, et al. Copy number polymorphism in Fcgr3 predisposes to glomerulonephritis in rats and humans[J]. Nature, 2006, 439(7078): 851-855. [35] Theuns J, Brouwers N, Engelborghs S, et al. Promoter mutations that increase amyloid precursor-protein expression are associated with Alzheimer disease[J]. The American Journal of Human Genetics, 2006, 78(6): 936-946. [36] Komura D, Shen F, Ishikawa S, et al. Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays[J]. Genome Research, 2006, 16(12): 1575-1584. [37] Hou Y, Liu GE, Bickhart DM, et al. Genomic regions showing copy number variations associate with resistance or susceptibility to gastrointestinal nematodes in Angus cattle[J]. Functional & Integrative Genomics, 2012, 12(1): 81-92. [38] Flisikowski K, Venhoranta H, Nowacka-Woszuk J, et al. A novel mutation in the maternally imprinted PEG3 domain results in a loss of MIMT1 expression and causes abortions and stillbirths in cattle(Bos taurus)[J]. PLoS One, 2010, 5(11): e15116. [39] Müller D, Kausalya PJ, Claverie-Martin F, et al. A novel claudin 16 mutation associated with childhood hypercalciuria abolishes binding to ZO-1 and results in lysosomal mistargeting[J]. The American Journal of Human Genetics, 2003, 73(6): 1293-1301. [40] Testoni S, Mazzariol S, Dr?gemüller C, et al. Renal dysplasia in grey Alpine breed cattle unrelated to CLDN16 mutations[J]. Veterinary Record, 2012, 170(1): 22. [41] Meyers SN, McDaneld TG, Swist SL, et al. A deletion mutation in bovine SLC4A2 is associated with osteopetrosis in Red Angus cattle[J]. BMC Genomics, 2010, 11(1): 337. [42] Bultman SJ, Michaud EJ, Woychik RP. Molecular characterization of the mouse agouti locus[J]. Cell, 1992, 71(7): 1195-1204. [43] Norris BJ, Whan VA. A gene duplication affecting expression of the ovine ASIP gene is responsible for white and black sheep[J]. Genome Research, 2008, 18(8): 1282-1293. [44] Fontanesi L, Beretti F, Riggio V, et al. Copy number variation and missense mutations of the agouti signaling protein(ASIP)gene in goat breeds with different coat colors[J]. Cytogenetic and Genome Research, 2009, 126(4): 333-347. [45] Dong Y, Zhang X, Xie M, et al. Reference genome of wild goat(Capra aegagrus)and sequencing of goat breeds provide insight into genic basis of goat domestication[J]. BMC Genomics, 2015, 16(1): 431. [46] Fadista J, Nygaard M, Holm LE, et al. A snapshot of CNVs in the pig genome[J]. PLoS One, 2008, 3(12): e3916. [47] Ramayo-Caldas Y, Castelló A, Pena RN, et al. Copy number variation in the porcine genome inferred from a 60 k SNP BeadChip[J]. BMC Genomics, 2010, 11(1): 593. [48] Seo BY, Park EW, Ahn SJ, et al. An accurate method for quantifying and analyzing copy number variation in porcine KIT by an oligonucleotide ligation assay[J]. BMC Genetics, 2007, 8(1): 81. [49] Wang X, Nahashon S, Feaster TK, et al. An initial map of chromosomal segmental copy number variations in the chicken[J]. BMC Genomics, 2010, 11(1): 351. [50] Wang Y, Gu X, Feng C, et al. A genome-wide survey of copy number variation regions in various chicken breeds by array comparative genomic hybridization method[J]. Animal Genetics, 2012, 43(3): 282-289. [51] Wright D, Boije H, Meaclows JR, et al. Copy number variation in intron 1 of SOX5 causes the Pea-comb phenotype in chickens[J]. PLoS Genet, 2009, 5(6): e1000512. [52] Bu G, Huang G, Fu H, et al. Characterization of the novel duplicated PRLR gene at the late-feathering K locus in Lohmann chickens[J]. Journal of Molecular Endocrinology, 2013, 51(2): 261-276. [53] Elferink MG, Vallée A, Jungerius AP, et al. Partial duplication of the PRLR and SPEF2 genes at the late feathering locus in chicken[J]. BMC Genomics, 2008, 9(1): 391. [54] Stuber CW, Polacco M, Senior ML. Synergy of empirical breeding, marker-assisted selection, and genomics to increase crop yield potential[J]. Crop Science, 1999, 39(6): 1571-1583. [55] Moose SP, Mumm RH. Molecular plant breeding as the foundation for 21st century crop improvement[J]. Plant Physiology, 2008, 147(3): 969-977. [56] Schaeffer L. Strategy for applying genome-wide selection in dairy cattle[J]. Journal of Animal Breeding and Genetics, 2006, 123(4): 218-223. [57] 黎裕, 贾继增, 王天宇. 分子标记的种类及其发展[J]. 生物技术通报, 1999(4): 19-22. |
[1] | WANG Teng-hui, GE Wen-dong, LUO Ya-fang, FAN Zhen-yu, WANG Yu-shu. Gene Mapping of Kale White Leaves Based on Whole Genome Re-sequencing of Extreme Mixed Pool(BSA) [J]. Biotechnology Bulletin, 2023, 39(9): 176-182. |
[2] | LI Xue-qi, ZHANG Su-jie, YU Man, HUANG Jin-guang, ZHOU Huan-bin. Establishment of CRISPR/CasX-based Genome Editing Technology in Rice [J]. Biotechnology Bulletin, 2023, 39(9): 40-48. |
[3] | ZHAN Yan, ZHOU Li-bin, JIN Wen-jie, DU Yan, YU Li-xia, QU Ying, MA Yong-gui, LIU Rui-yuan. Research Progress in Plant Leaf Color Mutation Induced by Radiation [J]. Biotechnology Bulletin, 2023, 39(8): 106-113. |
[4] | FANG Lan, LI Yan-yan, JIANG Jian-wei, CHENG Sheng, SUN Zheng-xiang, ZHOU Yi. Isolation, Identification and Growth-promoting Characteristics of Endohyphal Bacterium 7-2H from Endophytic Fungi of Spiranthes sinensis [J]. Biotechnology Bulletin, 2023, 39(8): 272-282. |
[5] | RAO Zi-huan, XIE Zhi-xiong. Isolation and Identification of a Cellulose-degrading Strain of Olivibacter jilunii and Analysis of Its Degradability [J]. Biotechnology Bulletin, 2023, 39(8): 283-290. |
[6] | GUO Shao-hua, MAO Hui-li, LIU Zheng-quan, FU Mei-yuan, ZHAO Ping-yuan, MA Wen-bo, LI Xu-dong, GUAN Jian-yi. Whole Genome Sequencing and Comparative Genome Analysis of a Fish-derived Pathogenic Aeromonas Hydrophila Strain XDMG [J]. Biotechnology Bulletin, 2023, 39(8): 291-306. |
[7] | ZHANG Dao-lei, GAN Yu-jun, LE Liang, PU Li. Epigenetic Regulation of Yield-related Traits in Maize and Epibreeding [J]. Biotechnology Bulletin, 2023, 39(8): 31-42. |
[8] | LENG Yan, MA Xiao-wei, CHEN Guang, REN He, LI Xiang. High-yield Contests in Maize Facilitate the Vitalization of China’s Seed Industry [J]. Biotechnology Bulletin, 2023, 39(8): 4-10. |
[9] | WANG Tian-yi, WANG Rong-huan, WANG Xia-qing, ZHANG Ru-yang, XU Rui-bin, JIAO Yan-yan, SUN Xuan, WANG Ji-dong, SONG Wei, ZHAO Jiu-ran. Research in Maize Dwarf Genes and Dwarf Breeding [J]. Biotechnology Bulletin, 2023, 39(8): 43-51. |
[10] | SHI Jia-xin, LIU Kai, ZHU Jin-jie, QI Xian-tao, XIE Chuan-xiao, LIU Chang-lin. Gene Editing Reshaping Maize Plant Type for Increasing Hybrid Yield [J]. Biotechnology Bulletin, 2023, 39(8): 62-69. |
[11] | DU Dong-dong, QIAN Jing, LI Si-qi, LIU Wen-fei, WEI Xiang-li, LIU Chang-yong, LUO Rui-feng, KANG Li-chao. Whole Genome Sequencing and Analysis of Listeria monocytogenes Strain LMXJ15 [J]. Biotechnology Bulletin, 2023, 39(7): 298-306. |
[12] | LI Yu-zhen, MEI Tian-xiu, LI Zhi-wen, WANG Qi, LI Jun, ZOU Yue, ZHAO Xin-qing. Advances in Genomic Studies and Metabolic Engineering of Red Yeasts [J]. Biotechnology Bulletin, 2023, 39(7): 67-79. |
[13] | LI Yu-ling, MAO Xin, ZHANG Yuan-shuai, DONG Yuan-fu, LIU Cui-lan, DUAN Chun-hua, MAO Xiu-hong. Applications and Perspectives of Radiation Mutagenesis in Woody Plant Breeding [J]. Biotechnology Bulletin, 2023, 39(6): 12-30. |
[14] | ZHU Shao-xi, JIN Zhao-yang, GE Jian-rong, WANG Rui, WANG Feng-ge, LU Yun-cai. High-throughput Specific Detection Methods for Transgenic Maize Based on the KASP Platform [J]. Biotechnology Bulletin, 2023, 39(6): 133-140. |
[15] | YIN Ming-hua, YU Huan-yuan, XIAO Xin-yi, WANG Yu-ting. Chloroplast Genomic Characterization and Phylogenetic Analysis of Colocasia esculenta L. Schoot var. cormosus cv. ‘Hongyayu’ from Jiangxi Yanshan [J]. Biotechnology Bulletin, 2023, 39(6): 233-247. |
Viewed | ||||||
Full text |
|
|||||
Abstract |
|
|||||