Biotechnology Bulletin ›› 2018, Vol. 34 ›› Issue (6): 11-21.doi: 10.13560/j.cnki.biotech.bull.1985.2017-0719
Previous Articles Next Articles
LI Xiao-kai1 ,WANG Gui4 ,QIAO Xian1 ,FAN Yi-xing1 ,ZHANG Lei1 ,MA Yu-hao1 ,NIE Rui-xue1 ,WANG Rui-jun1,5 ,HE Li-bing5 ,SU Rui1,2,3,5
Received:
2017-08-31
Online:
2018-06-26
Published:
2018-07-03
LI Xiao-kai ,WANG Gui ,QIAO Xian ,FAN Yi-xing ,ZHANG Lei ,MA Yu-hao ,NIE Rui-xue ,WANG Rui-jun ,HE Li-bing ,SU Rui. Research Progress on Whole-genome Sequencing on Important Domesticated Animals[J]. Biotechnology Bulletin, 2018, 34(6): 11-21.
[1] Andersson L. Genetic dissection of phenotypic diversity in farm animals[J] . Nat Rev Genet, 2001, 2(2):130-138. [2] Diamond J. Evolution, consequences and future of plant and animal domestication[J] . Nature, 2002, 418(6898):700-707. [3] Bentley DR. Whole-genome re-sequencing[J] . Curr Opin Genet Dev, 2006, 16(6):545-552. [4] Fuentes-Pardo AP, Ruzzante DE. Whole-genome sequencing approaches for conservation biology:Advantages, limitations and practical recommendations[J] . Mol Ecol, 2017, 26(20):5369-5406. [5] Li M, Chen L, Tian S, et al. Comprehensive variation discovery and recovery of missing sequence in the pig genome using multiple De novo assemblies[J] . Genome Res, 2017, 27(5):865-874. [6] Venter JC, Adams MD, Myers EW, et al. The sequence of the human genome[J] . Science, 2001, 291(5507):1304-1351. [7] Lander ES, Linton LM, Birren B, et al. Initial sequencing and analysis of the human genome[J] . Nature, 2001, 409(6822):860-921. [8] Koboldt DC, Steinberg KM, Larson DE, et al. The next-generation sequencing revolution and its impact on genomics[J] . Cell, 2013, 155(1):27-38. [9] Wang GD, Xie HB, Peng MS, et al. Domestication genomics:evidence from animals[J] . Annu Rev Anim Biosci, 2014, 2:65-84. [10] Goodwin S, McPherson JD, McCombie WR. Coming of age:ten years of next-generation sequencing technologies[J] . Nat Rev Genet, 2016, 17(6):333-351. [11] Mardis ER. Next-generation DNA sequencing methods[J] . Annu Rev Genomics Hum Genet, 2008, 9:387-402. [12] Munroe DJ, Harris TJ. Third-generation sequencing fireworks at Marco Island[J] . Nat Biotechnol, 2010, 28(5):426-428. [13] Ono Y, Asai K, Hamada M. PBSIM:PacBio reads simulator--toward accurate genome assembly[J] . Bioinformatics, 2013, 29(1):119-121. [14] Mascher M, Gundlach H, Himmelbach A, et al. A chromosome conformation capture ordered sequence of the barley genome[J] . Nature, 2017, 544(7651):427-433. [15] Clavijo BJ, Venturini L, Schudoma C, et al. An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations[J] . Genome Res, 2017, 27(5):885-896. [16] Bickhart DM, Rosen BD, Koren S, et al. Single-molecule sequencing and chromatin conformation capture enable De novo reference assembly of the domestic goat genome[J] . Nat Genet, 2017, 49(4):643-650. [17] Groenen MA, Archibald AL, Uenishi H, et al. Analyses of pig genomes provide insight into porcine demography and evolution[J] . Nature, 2012, 491(7424):393-398. [18] Li M, Tian S, Jin L, et al. Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars[J] . Nat Genet, 2013, 45(12):1431-1438. [19] Ai H, Fang X, Yang B, et al. Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing[J] . Nat Genet, 2015, 47(3):217-225. [20] Li M, Tian S, Yeung CK, et al. Whole-genome sequencing of Berkshire(European native pig)provides insights into its origin and domestication[J] . Sci Rep, 2013, 4:4678. [21] Ramírez O, Burgos-Paz W, Casas E, et al. Genome data from a sixteenth century pig illuminate modern breed relationships[J] . Heredity(Edinb), 2015, 114(2):175-184. [22] Rubin CJ, Megens HJ, Martinez Barrio A, et al. Strong signatures of selection in the domestic pig genome[J] . Proc Natl Acad Sci USA, 2012, 109(48):19529-19536. [23] Choi JW, Chung WH, Lee KT, et al. Whole-genome resequencing analyses of five pig breeds, including Korean wild and native, and three European origin breeds[J] . DNA Res, 2015, 22(4):259-267. [24] Wang C, Wang H, Zhang Y, et al. Genome-wide analysis reveals artificial selection on coat colour and reproductive traits in Chinese domestic pigs[J] . Mol Ecol Resour, 2015, 15(2):414-424. [25] Groenen MA. A decade of pig genome sequencing:a window on pig domestication and evolution[J] . Genet Sel Evol, 2016, 48:23. [26] Fang X, Mou Y, Huang Z, et al. The sequence and analysis of a Chinese pig genome[J] . Gigascience, 2012, 1(1):16. [27] Wade CM, Giulotto E, Sigurdsson S, et al. Genome sequence, comparative analysis, and population genetics of the domestic horse[J] . Science, 2009, 326(5954):865-867. [28] Myka JL, Lear TL, Houck ML, et al. FISH analysis comparing genome organization in the domestic horse(Equus caballus)to that of the Mongolian wild horse(E. przewalskii)[J] . Cytogenet Genome Res, 2003, 102(1-4):222-225. [29] Orlando L, Ginolhac A, Zhang G, et al. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse[J] . Nature, 2013, 499(7456):74-78. [30] Huang J, Zhao Y, Shiraigol W, et al. Analysis of horse genomes provides insight into the diversification and adaptive evolution of karyotype[J] . Sci Rep, 2014, 4:4958. [31] Doan R, Cohen ND, Sawyer J, et al. Whole-Genome sequencing and genetic variant analysis of a quarter Horse mare[J] . BMC Genomics, 2012, 13:78. [32] Jun J, Cho YS, Hu H, et al. Whole genome sequence and analysis of the Marwari horse breed and its genetic origin[J] . BMC Genomics, 2014, 15(Suppl 9):S4. [33] Metzger J, Gast AC, Schrimpf R, et al. Whole-genome sequencing reveals a potential causal mutation for dwarfism in the Miniature Shetland pony[J] . Mamm Genome, 2017, 28(3-4):143-151. [34] Librado P, Der Sarkissian C, Ermini L, et al. Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments[J] . Proc Natl Acad Sci USA, 2015, 112(50):E6889-E6897. [35] Bovine Genome Sequencing and Analysis Consortium, Elsik CG, Tellam RL, et al. The genome sequence of taurine cattle:a window to ruminant biology and evolution[J] . Science, 2009, 324(5926):522-528. [36] Canavez FC, Luche DD, Stothard P, et al. Genome sequence and assembly of Bos indicus[J] . J Hered, 2012, 103(3):342-348. [37] Qiu Q, Zhang G, Ma T, et al. The yak genome and adaptation to life at high altitude[J] . Nat Genet, 2012, 44(8):946-949. [38] Bovine HapMap Consortium, Gibbs RA, Taylor JF, et al. Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds[J] . Science, 2009, 324(5926):528-532. [39] Kawahara-Miki R, Tsuda K, Shiwa Y, et al. Whole-genome resequencing shows numerous genes with nonsynonymous SNPs in the Japanese native cattle Kuchinoshima-Ushi[J] . BMC Genomics, 2011, 12:103. [40] Wang K, Hu Q, Ma H, et al. Genome-wide variation within and between wild and domestic yak[J] . Mol Ecol Resour, 2014, 14(4):794-801. [41] Choi JW, Choi BH, Lee SH, et al. Whole-Genome Resequencing Analysis of Hanwoo and Yanbian Cattle to Identify Genome-Wide SNPs and Signatures of Selection[J] . Mol Cells, 2015, 38(5):466-473. [42] Stothard P, Choi JW, Basu U, et al. Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery[J] . BMC Genomics, 2011, 12:559. [43] Luikart G, Gielly L, Excoffier L, et al. Multiple maternal origins and weak phylogeographic structure in domestic goats[J] . Proc Natl Acad Sci USA, 2001, 98(10):5927-5932. [44] Chessa B, Pereira F, Arnaud F, et al. Revealing the history of sheep domestication using retrovirus integrations[J] . Science, 2009, 324(5926):532-536. [45] 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. [46] Miller JM, Moore SS, Stothard P, et al. Harnessing cross-species alignment to discover SNPs and generate a draft genome sequence of a bighorn sheep(Ovis canadensis)[J] . BMC Genomics, 2015, 16:397. [47] Kardos M, Luikart G, Bunch R, et al. Whole genome resequencing uncovers molecular signatures of natural and sexual selection in wild bighorn sheep[J] . Mol Ecol, 2015, 24(22):5616-5632. [48] Yang J, Li WR, Lv FH, et al. Whole-genome sequencing of native sheep provides insights into rapid adaptations to extreme environments[J] . Mol Biol Evol, 2016, 33(10):2576-2592. [49] Liu Z, Ji Z, Wang G, et al. Genome-wide analysis reveals signatures of selection for important traits in domestic sheep from different ecoregions[J] . BMC Genomics, 2016, 17(1):863. [50] 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] . Nat Biotechnol, 2013, 31(2):135-141. [51] Du X, Servin B, Womack JE, et al. An update of the goat genome assembly using dense radiation hybrid maps allows detailed analysis of evolutionary rearrangements in Bovidae[J] . BMC Genomics, 2014, 15:625. [52] 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, 16:431. [53] Benjelloun B, Alberto FJ, Streeter I, et al. Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats(Capra hircus)using WGS data[J] . Front Genet, 2015, 6:107. [54] Wang X, Liu J, Zhou G, et al. Whole-genome sequencing of eight goat populations for the detection of selection signatures underlying production and adaptive traits[J] . Sci Rep, 2016, 6:38932. [55] Guan D, Luo N, Tan X, et al. Scanning of selection signature provides a glimpse into important economic traits in goats(Capra hircus)[J] . Sci Rep, 2016, 6:36372. [56] 兰蓉, 朱兰, 邵庆勇, 等. 云南黑山羊全基因组重测序[J] . 草食家畜, 2016, (5):11-17. [57] Lee W, Ahn S, Taye M, et al. Detecting Positive Selection of Korean Native Goat Populations Using Next-Generation Sequencing[J] . Mol Cells, 2016, 39(12):862-868. [58] Erlich Y, Zielinski D. DNA Fountain enables a robust and efficient storage architecture[J] . Science, 2017, 355(6328):950-954. |
[1] | 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. |
[2] | XIAO Liang, WU Zheng-dan, LU Liu-ying, SHI Ping-li, SHANG Xiao-hong, CAO Sheng, ZENG Wen-dan, YAN Hua-bing. Research Progress of Important Traits Genes in Cassava [J]. Biotechnology Bulletin, 2023, 39(6): 31-48. |
[3] | TIAN Li, LI Jun-jiao, DAI Xiao-feng, ZHANG Dan-dan, CHEN Jie-yin. From Functional Genes to Biological Characteristics:The Molecular Basis of Pathogenicity in Verticillium dahliae [J]. Biotechnology Bulletin, 2022, 38(1): 51-69. |
[4] | XUE Qing, DU Hong-rui, XUE Hui-ying, WANG Yi-hao, WANG Xuan, LI Hong-mei. Mitochondrial Genome and Phylogeny of Aphelenchoides medicagus [J]. Biotechnology Bulletin, 2021, 37(7): 98-106. |
[5] | CHEN Yi-dan, ZHANG Yu, YANG Jie, ZHANG Qin, JIANG Li. Exploration of Key Functional Genes Affecting Milk Production Traits in Dairy Cattle Based on RNA-seq [J]. Biotechnology Bulletin, 2020, 36(9): 244-252. |
[6] | LI Xiao-kai, FAN Yi-xing, QIAO Xian, ZHANG Lei, WANG Feng-hong, WANG Zhi-ying, WANG Rui-jun, ZHANG Yan-jun, LIU Zhi-hong, WANG Zhi-xin, HE Li-bing, LI Jin-quan, SU Rui, ZHANG Jia-xin. Research Progress of Goat Genome and Genetic Variation Map [J]. Biotechnology Bulletin, 2020, 36(4): 175-184. |
[7] | ZHANG Hai-miao, LI Yang, LIU Hai-feng, KONG Ling-guang, DING Xin-hua. Research Progress on Regulatory Genes of Important Agronomic Traits and Breeding Utilization in Rice [J]. Biotechnology Bulletin, 2020, 36(12): 155-169. |
[8] | LI Hui ZHA, Jian-jun, SUN Qing-ye. Effects of Acid Mine Drainage on the Abundance of Functional Genes Involved in Nitrogen Cycle in Soil Profiles [J]. Biotechnology Bulletin, 2019, 35(9): 249-256. |
[9] | ZHU Rong-gui, GUAN Tong-wei, JIANG Xiu-juan. Isolation of Rare Actinobacteria in 5 Ecodistricts of Tarim Basin and Distribution of the Genes Synthesizing Antibiotics [J]. Biotechnology Bulletin, 2018, 34(9): 230-236. |
[10] | WANG Zhu-jun, WANG Shang, LIU Yang-ying, FENG Kai, DENG Ye. The Applications of Metagenomics in the Detection of Environmental Microbes Involving in Nitrogen Cycle [J]. Biotechnology Bulletin, 2018, 34(1): 1-14. |
[11] | WANG Yu-xuan, WEI Wei, LI Ping-ping, ZHAO Yun, FU Wei-guo. Study Progress on Microorganism in Constructed Wetlands [J]. Biotechnology Bulletin, 2017, 33(10): 74-79. |
[12] | DAI Xi-lin, GAO Xiang, WANG Hai-yang, MING Lei, JIANG Zong-bing, DING Fu-jiang. Genetic Structure Analysis of Macrobrachiu rosenbergii with Different Developmental Rate at Larval Stage [J]. Biotechnology Bulletin, 2016, 32(2): 192-197. |
[13] | LIU Guo-sheng, ZHANG Da-le. The Application of the Functional Molecular Marker in Wheat Breeding [J]. Biotechnology Bulletin, 2016, 32(11): 18-29. |
[14] | Cao Jianbin, Yu Huiying, Li Xin. Identification of Bacillus sp. LAY and Its Antimicrobial Activity Against Candida albicans [J]. Biotechnology Bulletin, 2015, 31(9): 163-169. |
[15] | Liang Chunhua, Liu Xia, Sun Xuejing, Luo Yuzhu, Gao Xuejin, Du Xiaohua. Genetic Variation Study of NGB Gene Exon 3 of Simmental Cattle Hybrid Taxon in Gansu Hexi Regions [J]. Biotechnology Bulletin, 2015, 31(2): 122-128. |
Viewed | ||||||
Full text |
|
|||||
Abstract |
|
|||||