Mapping-by-sequencing accelerates forward genetics in barley
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- 作者：Martin Mascher (1)
Matthias Jost (1)
Joel-Elias Kuon (1)
Axel Himmelbach (1)
Axel A?falg (1)
Sebastian Beier (1)
Uwe Scholz (1)
Andreas Graner (1)
Nils Stein (1) - 刊名：Genome Biology
- 出版年：2014
- 出版时间：June 2014
- 年：2014
- 卷：15
- 期：6
- 全文大小：1,053 KB
- 参考文献：1. Huang X, Han B: Natural variations and genome-wide association studies in crop plants. / Annu Rev Plant Biol 2013, 65:531-51. CrossRef
2. Michael TP, Jackson S: The first 50 plant genomes. / Plant Genome 2013., 6: doi:10.3835/plantgenome2013.03.0001in CrossRef
3. Schneeberger K, Weigel D: Fast-forward genetics enabled by new sequencing technologies. / Trends Plant Sci 2011, 16:282-88. CrossRef
4. Michelmore RW, Paran I, Kesseli RV: Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. / Proc Natl Acad Sci U S A 1991, 88:9828-832. CrossRef
5. Schneeberger K, Ossowski S, Lanz C, Juul T, Petersen AH, Nielsen KL, Jorgensen JE, Weigel D, Andersen SU: SHOREmap: simultaneous mapping and mutation identification by deep sequencing. / Nat Methods 2009, 6:550-51. CrossRef
6. Lindner H, Raissig MT, Sailer C, Shimosato-Asano H, Bruggmann R, Grossniklaus U: SNP-Ratio Mapping (SRM): identifying lethal alleles and mutations in complex genetic backgrounds by next-generation sequencing. / Genetics 2012, 191:1381-386. CrossRef
7. Hartwig B, James GV, Konrad K, Schneeberger K, Turck F: Fast isogenic mapping-by-sequencing of ethyl methanesulfonate-induced mutant bulks. / Plant Physiol 2012, 160:591-00. CrossRef
8. Abe A, Kosugi S, Yoshida K, Natsume S, Takagi H, Kanzaki H, Matsumura H, Yoshida K, Mitsuoka C, Tamiru M, Innan H, Cano L, Kamoun S, Terauchi R: Genome sequencing reveals agronomically important loci in rice using MutMap. / Nat Biotechnol 2012, 30:174-78. CrossRef
9. Liu S, Yeh CT, Tang HM, Nettleton D, Schnable PS: Gene mapping via bulked segregant RNA-Seq (BSR-Seq). / PLoS One 2012, 7:e36406. CrossRef
10. Leshchiner I, Alexa K, Kelsey P, Adzhubei I, Austin-Tse CA, Cooney JD, Anderson H, King MJ, Stottmann RW, Garnaas MK, Ha S, Drummond IA, Paw B, North TE, Beier DR, Goessling W, Sunyaev SR: Mutation mapping and identification by whole-genome sequencing. / Genome Res 2012, 22:1541-548. CrossRef
11. Galvao VC, Nordstrom KJ, Lanz C, Sulz P, Mathieu J, Pose D, Schmid M, Weigel D, Schneeberger K: Synteny-based mapping-by-sequencing enabled by targeted enrichment. / Plant J 2012, 71:517-26.
12. Nordstrom KJ, Albani MC, James GV, Gutjahr C, Hartwig B, Turck F, Paszkowski U, Coupland G, Schneeberger K: Mutation identification by direct comparison of whole-genome sequencing data from mutant and wild-type individuals using k-mers. / Nat Biotechnol 2013, 31:325-30. CrossRef
13. Scholz F, Lehmann CO: Die Gaterslebener Mutanten der Saatgerste in Beziehung zur Formenmannigfaltigkeit der Art Hordeum vulgare L. III. / Die Kulturpflanze 1961, 9:230-72. CrossRef
14. Ehrenberg L, Lundqvist U, Osterman S, Sparrman B: On the mutagenic action of alkanesulfonic esters in barley. / Hereditas 1966, 56:277-05. CrossRef
15. Gustafsson ?, Hagberg A, Lundqvist U, Persson G: A proposed system of symbols for the collection of barley mutants at Sval?v. / Hereditas 1969, 62:409-14. CrossRef
16. Gustafsson ?, Hagberg A, Persson G, Wiklund K: Induced mutations and barley improvement. / Theor Appl Genet 1971, 41:239-48. CrossRef
17. Druka A, Franckowiak J, Lundqvist U, Bonar N, Alexander J, Houston K, Radovic S, Shahinnia F, Vendramin V, Morgante M, Stein N, Waugh R: Genetic dissection of barley morphology and development. / Plant Physiol 2011, 155:617-27. CrossRef
18. Gottwald S, Bauer P, Komatsuda T, Lundqvist U, Stein N: TILLING in the two-rowed barley cultivar ‘Barke-reveals preferred sites of functional diversity in the gene HvHox1. / BMC Res Notes 2009, 2:258. CrossRef
19. Caldwell DG, McCallum N, Shaw P, Muehlbauer GJ, Marshall DF, Waugh R: A structured mutant population for forward and reverse genetics in Barley (Hordeum vulgare L.). / Plant J 2004, 40:143-50. CrossRef
20. Koppolu R, Anwar N, Sakuma S, Tagiri A, Lundqvist U, Pourkheirandish M, Rutten T, Seiler C, Himmelbach A, Ariyadasa R, Youssef HM, Stein N, Sreenivasulu N, Komatsuda T, Schnurbusch T: Six-rowed spike4 (Vrs4) controls spikelet determinacy and row-type in barley. / Proc Natl Acad Sci U S A 2013, 110:13198-3203. CrossRef
21. Comadran J, Kilian B, Russell J, Ramsay L, Stein N, Ganal M, Shaw P, Bayer M, Thomas W, Marshall D, Hedley P, Tondelli A, Pecchioni N, Francia E, Korzun V, Walther A, Waugh R: Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and environmental adaptation in cultivated barley. / Nat Genet 2012, 44:1388-392. CrossRef
22. Schulte D, Close TJ, Graner A, Langridge P, Matsumoto T, Muehlbauer G, Sato K, Schulman AH, Waugh R, Wise RP, Stein N: The international barley sequencing consortium–at the threshold of efficient access to the barley genome. / Plant Physiol 2009, 149:142-47. CrossRef
23. International Barley Genome Sequencing Consortium T: A physical, genetic and functional sequence assembly of the barley genome. / Nature 2012, 491:711-16.
24. Mascher M, Muehlbauer GJ, Rokhsar DS, Chapman J, Schmutz J, Barry K, Munoz-Amatriain M, Close TJ, Wise RP, Schulman AH, Himmelbach A, Mayer KFX, Scholz U, Poland JA, Stein N, Waugh R: Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). / Plant J 2013, 76:718-27. CrossRef
25. Mascher M, Richmond TA, Gerhardt DJ, Himmelbach A, Clissold L, Sampath D, Ayling S, Steuernagel B, Pfeifer M, D’Ascenzo M, Akhunov ED, Hedley PE, Gonzales AM, Morrell PL, Kilian B, Blattner FR, Scholz U, Mayer KF, Flavell AJ, Muehlbauer GJ, Waugh R, Jeddeloh JA, Stein N: Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond. / Plant J 2013, 76:494-05. CrossRef
26. Nelson SL, Giver CR, Grosovsky AJ: Spectrum of X-ray-induced mutations in the human hprt gene. / Carcinogenesis 1994, 15:495-02. CrossRef
27. Miyoshi K, Ahn BO, Kawakatsu T, Ito Y, Itoh J, Nagato Y, Kurata N: PLASTOCHRON1, a timekeeper of leaf initiation in rice, encodes cytochrome P450. / Proc Natl Acad Sci U S A 2004, 101:875-80. CrossRef
28. Mayer KF, Martis M, Hedley PE, Simkova H, Liu H, Morris JA, Steuernagel B, Taudien S, Roessner S, Gundlach H, Kubaláková M, Suchánková P, Murat F, Felder M, Nussbaumer T, Graner A, Salse J, Endo T, Sakai H, Tanaka T, Itoh T, Sato K, Platzer M, Matsumoto T, Scholz U, Dolezel J, Waugh R, Stein N: Unlocking the barley genome by chromosomal and comparative genomics. / Plant Cell 2011, 23:1249-263. CrossRef
29. Ariyadasa R, Mascher M, Nussbaumer T, Schulte D, Frenkel Z, Poursarebani N, Zhou R, Steuernagel B, Gundlach H, Taudien S, Felder M, Platzer M, Himmelbach A, Schmutzer T, Hedley PE, Muehlbauer GJ, Scholz U, Korol A, Mayer KF, Waugh R, Langridge P, Graner A, Stein N: A sequence-ready physical map of barley anchored genetically by two million SNPs. / Plant Physiol 2013, 164:412-23. CrossRef
30. Takagi H, Uemura A, Yaegashi H, Tamiru M, Abe A, Mitsuoka C, Utsushi H, Natsume S, Kanzaki H, Matsumura H, Saitoh H, Yoshida K, Cano LM, Kamoun S, Terauchi R: MutMap-Gap: whole-genome resequencing of mutant F2 progeny bulk combined with de novo assembly of gap regions identifies the rice blast resistance gene Pii. / New Phytol 2013, 200:276-83. CrossRef
31. Masumura K, Kuniya K, Kurobe T, Fukuoka M, Yatagai F, Nohmi T: Heavy-ion-induced mutations in the gpt delta transgenic mouse: comparison of mutation spectra induced by heavy-ion, X-ray, and gamma-ray radiation. / Environ Mol Mutagen 2002, 40:207-15. CrossRef
32. Laitinen RA, Schneeberger K, Jelly NS, Ossowski S, Weigel D: Identification of a spontaneous frame shift mutation in a nonreference Arabidopsis accession using whole genome sequencing. / Plant Physiol 2010, 153:652-54. CrossRef
33. James GV, Patel V, Nordstrom KJ, Klasen JR, Salome PA, Weigel D, Schneeberger K: User guide for mapping-by-sequencing in Arabidopsis. / Genome Biol 2013, 14:R61. CrossRef
34. Okagaki RJ, Cho S, Kruger WM, Xu WW, Heinen S, Muehlbauer GJ: The barley UNICULM2 gene resides in a centromeric region and may be associated with signaling and stress responses. / Funct Integr Genomics 2013, 13:33-1. CrossRef
35. Shahinnia F, Druka A, Franckowiak J, Morgante M, Waugh R, Stein N: High resolution mapping of Dense spike-ar (dsp.ar) to the genetic centromere of barley chromosome 7H. / Theor Appl Genet 2012, 124:373-84. CrossRef
36. Acevedo-Garcia J, Collins NC, Ahmadinejad N, Ma L, Houben A, Bednarek P, Benjdia M, Freialdenhoven A, Altmuller J, Nurnberg P, Reinhardt R, Schulze-Lefert P, Panstruga R: Fine mapping and chromosome walking towards the Ror1 locus in barley (Hordeum vulgare L.). / Theor Appl Genet 2013, 126:2969-982. CrossRef
37. Poland JA, Brown PJ, Sorrells ME, Jannink JL: Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. / PLoS One 2012, 7:e32253. CrossRef
38. Mascher M, Wu S, Amand PS, Stein N, Poland J: Application of genotyping-by-sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley. / PLoS One 2013, 8:e76925. CrossRef
39. Meyer M, Kircher M: Illumina sequencing library preparation for highly multiplexed target capture and sequencing. / Cold Spring Harb Protoc 2010, 2010:pdb prot5448. CrossRef
40. Mizutani M, Ohta D: Diversification of P450 genes during land plant evolution. / Annu Rev Plant Biol 2010, 61:291-15. CrossRef
41. Imaishi H, Matsuo S, Swai E, Ohkawa H: CYP78A1 preferentially expressed in developing inflorescences of Zea mays encoded a cytochrome P450-dependent lauric acid 12-monooxygenase. / Biosci Biotechnol Biochem 2000, 64:1696-701. CrossRef
42. Kai K, Hashidzume H, Yoshimura K, Suzuki H, Sakurai N, Shibata D, Ohta D: Metabolomics for the characterization of cytochromes P450-dependent fatty acid hydroxylation reactions in Arabidopsis. / Plant Biotechnol 2009, 26:175-82. CrossRef
43. Helliwell CA, Chin-Atkins AN, Wilson IW, Chapple R, Dennis ES, Chaudhury A: The Arabidopsis AMP1 gene encodes a putative glutamate carboxypeptidase. / Plant Cell 2001, 13:2115-125. CrossRef
44. Kawakatsu T, Taramino G, Itoh J, Allen J, Sato Y, Hong SK, Yule R, Nagasawa N, Kojima M, Kusaba M, Sakakibara H, Sakai H, Nagato Y: PLASTOCHRON3/GOLIATH encodes a glutamate carboxypeptidase required for proper development in rice. / Plant J 2009, 58:1028-040. CrossRef
45. Nagasawa N, Hibara KI, Heppard EP, Vander Velden KA, Luck S, Beatty M, Nagato Y, Sakai H: GIANT EMBRYO encodes CYP78A13, required for proper size balance between embryo and endosperm in rice. / Plant J 2013, 75:592-05. CrossRef
46. Fang WJ, Wang ZB, Cui RF, Li J, Li YH: Maternal control of seed size by EOD3/CYP78A6 in Arabidopsis thaliana. / Plant J 2012, 70:929-39. CrossRef
47. Adamski NM, Anastasiou E, Eriksson S, O’Neill CM, Lenhard M: Local maternal control of seed size by KLUH/CYP78A5-dependent growth signaling. / Proc Nat Acad Sci U S A 2009, 106:20115-0120. CrossRef
48. Chakrabarti M, Zhang N, Sauvage C, Munos S, Blanca J, Canizares J, Diez MJ, Schneider R, Mazourek M, McClead J, Causse M, van der Knaap E: A cytochrome P450 regulates a domestication trait in cultivated tomato. / Proc Natl Acad Sci U S A 2013, 110:17125-7130. CrossRef
49. Doyle JJ: Isolation of plant DNA from fresh tissue. / Focus 1990, 12:13-5.
50. Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform. / Bioinformatics 2009, 25:1754-760. CrossRef
51. Li H: A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. / Bioinformatics 2011, 27:2987-993. CrossRef
52. The R project. [http://www.r-project.org]
53. Nussbaumer T, Martis MM, Roessner SK, Pfeifer M, Bader KC, Sharma S, Gundlach H, Spannagl M: MIPS PlantsDB: a database framework for comparative plant genome research. / Nucleic Acids Res 2013, 41:D1144-D1151. CrossRef
54. Anchoring information of barley WGS assemblies [ftp://ftpmips.helmholtz-muenchen.de/plants/barley/public_data/anchoring/wgs_anc/WGS_ANC.TXT]
55. Quinlan AR, Hall IM: BEDTools: a flexible suite of utilities for comparing genomic features. / Bioinformatics 2010, 26:841-42. CrossRef
56. GFF file of barley HC genes [ftp://ftpmips.helmholtz-muenchen.de/plants/barley/public_data/genes/barley_HighConf_genes_MIPS_23Mar12_HumReadDesc.txt]
57. Barley POPSEQ results [ftp://ftp.ipk-gatersleben.de/barley-popseq/]
58. Barley gene expression data [ftp://ftpmips.helmholtz-muenchen.de/plants/barley/public_data/expression/]
59. Thiel T, Kota R, Grosse I, Stein N, Graner A: SNP2CAPS: a SNP and INDEL analysis tool for CAPS marker development. / Nucleic Acids Res 2004, 32:e5. CrossRef
60. Taylor NE, Greene EA: PARSESNP: A tool for the analysis of nucleotide polymorphisms. / Nucleic Acids Res 2003, 31:3808-811. CrossRef
61. CLC bio website. [http://www.clcbio.com]
62. Chevreux B, Wetter T, Suhai S: Genome Sequence Assembly Using Trace Signals and Additional Sequence Information. / Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 1999, 99:45-6.
63. Zhang Z, Schwartz S, Wagner L, Miller W: A greedy algorithm for aligning DNA sequences. / J Comput Biol 2000, 7:203-14. CrossRef
64. Schmutzer T, Ma L, Pousarebani N, Bull F, Stein N, Houben A, Scholz U: Kmasker - A Tool for in silico Prediction of Single-Copy FISH Probes for the Large-Genome Species Hordeum vulgare. / Cytogenet Genome Res 2014, 142:66-8. CrossRef
65. Stanke M, Steinkamp R, Waack S, Morgenstern B: AUGUSTUS: a web server for gene finding in eukaryotes. / Nucleic Acids Res 2004, 32:W309-W312. CrossRef
66. Source code of AHRD. [https://github.com/groupschoof/AHRD]
67. Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R, Muller R, Dreher K, Alexander DL, Garcia-Hernandez M, Karthikeyan AS, Lee CH, Nelson WD, Ploetz L, Singh S, Wensel A, Huala E: The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. / Nucleic Acids Res 2012, 40:D1202-D1210. CrossRef
68. UniProt C: Update on activities at the Universal Protein Resource (UniProt) in 2013. / Nucleic Acids Res 2013, 41:D43-D47. CrossRef
69. Huang X, Madan A: CAP3: A DNA sequence assembly program. / Genome Res 1999, 9:868-77. CrossRef
70. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. / J Mol Biol 1990, 215:403-10. CrossRef
71. Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA, 1000 Genomes Project Consortium: An integrated map of genetic variation from 1,092 human genomes. / Nature 2012, 491:56-5. CrossRef
72. Swarbreck D, Wilks C, Lamesch P, Berardini TZ, Garcia-Hernandez M, Foerster H, Li D, Meyer T, Muller R, Ploetz L, Radenbaugh A, Singh S, Swing V, Tissier C, Zhang P, Huala E: The Arabidopsis Information Resource (TAIR): gene structure and function annotation. / Nucleic Acids Res 2008, 36:D1009-D1014. CrossRef
73. Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, Childs K, Thibaud-Nissen F, Malek RL, Lee Y, Zheng L, Orvis J, Haas B, Wortman J, Buell CR: The TIGR Rice Genome Annotation Resource: improvements and new features. / Nucleic Acids Res 2007, 35:D883-D887. CrossRef
74. International Brachypodium Initiative T: Genome sequencing and analysis of the model grass Brachypodium distachyon. / Nature 2010, 463:763-68. CrossRef
75. Jia J, Zhao S, Kong X, Li Y, Zhao G, He W, Appels R, Pfeifer M, Tao Y, Zhang X, Jing R, Zhang C, Ma Y, Gao L, Gao C, Spannagl M, Mayer KF, Li D, Pan S, Zheng F, Hu Q, Xia X, Li J, Liang Q, Chen J, Wicker T, Gou C, Kuang H, He G, Luo Y, / et al.: Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. / Nature 2013, 496:91-5. CrossRef
76. Ling HQ, Zhao S, Liu D, Wang J, Sun H, Zhang C, Fan H, Li D, Dong L, Tao Y, Gao C, Wu H, Li Y, Cui Y, Guo X, Zheng S, Wang B, Yu K, Liang Q, Yang W, Lou X, Chen J, Feng M, Jian J, Zhang X, Luo G, Jiang Y, Liu J, Wang Z, Sha Y, / et al.: Draft genome of the wheat A-genome progenitor Triticum urartu. / Nature 2013, 496:87-0. CrossRef
77. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S: MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. / Mol Biol Evol 2011, 28:2731-739. CrossRef
78. Hall BG: Building phylogenetic trees from molecular data with MEGA. / Mol Biol Evol 2013, 30:1229-235. CrossRef
79. Jones DT, Taylor WR, Thornton JM: The rapid generation of mutation data matrices from protein sequences. / Comput Appl Biosci 1992, 8:275-82.
80. Felsenstein J: Confidence-limits on phylogenies - an approach using the bootstrap. / Evolution 1985, 39:783-91. CrossRef - 作者单位：Martin Mascher (1)
Matthias Jost (1)
Joel-Elias Kuon (1)
Axel Himmelbach (1)
Axel A?falg (1)
Sebastian Beier (1)
Uwe Scholz (1)
Andreas Graner (1)
Nils Stein (1)
1. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstra?e 3, 06466, Stadt Seeland, Germany - ISSN：1465-6906
文摘
Mapping-by-sequencing has emerged as a powerful technique for genetic mapping in several plant and animal species. As this resequencing-based method requires a reference genome, its application to complex plant genomes with incomplete and fragmented sequence resources remains challenging. We perform exome sequencing of phenotypic bulks of a mapping population of barley segregating for a mutant phenotype that increases the rate of leaf initiation. Read depth analysis identifies a candidate gene, which is confirmed by the analysis of independent mutant alleles. Our method illustrates how the genomic resources of barley together with exome resequencing can underpin mapping-by-sequencing.