RAD-seq技术在基因组研究中的现状及展望
收稿日期: 2013-07-16
修回日期: 2013-08-15
网络出版日期: 2013-12-20
基金资助
国家重点基础研究发展规划(973计划)项目(编号：2011CB109300)资助
Current status and perspective of RAD-seq in genomic research
Received date: 2013-07-16
Revised date: 2013-08-15
Online published: 2013-12-20
Supported by
supported by grants from the Major State Basic Research Development Program of China (973 Program)
Restriction-site associated DNA sequencing(RAD-seq)技术是在二代测序基础上发展起来的一项基于全基因组酶切位点的简化基因组测序技术。该方法技术流程简单, 不受有无参考基因组的限制, 可大大简化基因组的复杂性, 减少实验费用, 通过一次测序就可以获得数以万计的多态性标记。目前, RAD-seq技术已成功应用于超高密度遗传图谱的构建、重要性状的精细定位、辅助基因组序列组装、群体基因组学以及系统发生学等基因组研究热点领域。文章主要介绍了RAD-seq的技术原理、技术发展及其在基因组研究中的广泛应用。鉴于RAD-seq方法的独特性, 该技术必将在复杂基因组研究领域具有广泛的应用前景。
关键词： RAD-seq; 基因组; 遗传图谱; SNP; 双酶系统的RAD(ddRAD)测序
王洋坤, 胡艳, 张天真 . RAD-seq技术在基因组研究中的现状及展望[J]. 遗传, 2014 , 36(1) : 41 -49 . DOI: 10.3724/SP.J.1005.2014.00041
The restriction-site associated DNA sequencing (RAD-seq) is a high-throughput sequencing technique developed from the next-generation sequencing (NGS). This method can reduce the representation of the complex genome while mapping thousands of polymorphic markers with or without a reference genome. It has been extensively used for high-density genetic map construction, fine mapping of important genes, genome sequence assembly, population genomic research, as well as phylogenetic research and so on. Here, we introduce the technological principle and development of RAD-seq combined with the sequencing applications in various species. Due to its uniqueness, RAD-seq will have a wide application in genetic analysis of complex genomic research in the future.
[1] Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM. Genome sequencing in microfabricated high-density picolitre reactors. Nature, 2005, 437(7057): 376–380. <\p>
[2] Altshuler D, Pollara VJ, Cowles CR, van Etten WJ, Baldwin J, Linton L, Lander ES. An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature, 2000, 407(6803): 513–516. <\p>
[3] Davey JL, Blaxter MW. RADSeq: next-generation popu-lation genetics. Brief Funct Genomic, 2010, 9(5?6): 416– 423. <\p>
[4] Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE. A robust, simple genotyping- by-sequencing (GBS) approach for high diversity species. PloS ONE, 2011, 6(5): e19379. <\p>
[5] Miller MR, Dunham JP, Amores A, Cresko WA, Johnson EA. Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Res, 2007, 17(2): 240–248. <\p>
[6] van Tassell CP, Smith TP, Matukumalli LK, Taylor JF, Schnabel RD, Lawley CT, Haudenschild CD, Moore SS, Warren WC, Sonstegard TS. SNP discovery and allele frequency estimation by deep sequencing of reduced re-presentation libraries. Nat Methods, 2008, 5(3): 247–252. <\p>
[7] Emerson KJ, Merz CR, Catchen JM, Hohenlohe PA, Cresko WA, Bradshaw WE, Holzapfel CM. Resolving postglacial phylogeography using high-throughput sequencing. Proc Natl Acad Sci USA, 2010, 107(37): 16196– 16200. <\p>
[8] Hohenlohe PA, Amish JS, Catchen MJ, Allendorf WF, Luikart G. Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout. Mol Ecol Resour, 2011, 11(Suppl. 1): 117–122. <\p>
[9] Pfender WF, Saha MC, Johnson EA, Slabaugh MB. Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne. Theor Appl Genet, 2011, 122(8): 1467–1480. <\p>
[10] Poland JA, Brown PJ, Sorrells ME, Jannink JL. Develop-ment of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing ap-proach. PloS ONE, 2012, 7(2): e32253. <\p>
[11] Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Johnson EA. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE, 2008, 3(10): e3376. <\p>
[12] Catchen JM, Amores A, Hohenlohe P, Cresko W, Post-lethwait JH. Stacks: building and genotyping Loci de novo from short-read sequences. G3, 2011, 1(3): 171–182. <\p>
[13] Catchen JM, Hohenlohe P, Bassham S, Amores A, Cresko WA. Stacks: an analysis tool set for population genomics. Mol Ecol, 2013, 22(11): 3124–3140. <\p>
[14] Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res, 2004, 32(5): 1792–1797. <\p>
[15] Altschul SF, Madden TL, Schäffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res, 1997, 25(17): 3389–3402. <\p>
[16] Kent WJ. BLAT-the BLAST-like alignment tool. Genome Res, 2002, 12(4): 656–664. <\p>
[17] Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Durbin R. The sequence alignment/map format and SAM
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