A physical map of the short arm of wheat chromosome 1A

PLoS ONE

Volumn 8, Issue 11, 2013, Pages

  Breen, James ^a   Wicker, Thomas ^a   Shatalina, Margarita ^a   Frenkel, Zeev ^b   Bertin, Isabelle ^c   Philippe, Romain ^c   Spielmeyer, Wolfgang ^d   Šimková, Hana ^e   Šafář, Jan ^e   Cattonaro, Federica ^f   Scalabrin, Simone ^f   Magni, Federica ^f   Vautrin, Sonia ^g   Bergès, Hélène ^g   Paux, Etienne ^c   Fahima, Tzion ^b   Doležel, Jaroslav ^e   Korol, Abraham ^b   Feuillet, Catherine ^c   Keller, Beat ^a  

^a UNIVERSITY OF ZURICH   (Switzerland)

^b UNIVERSITY OF HAIFA   (Israel)

^c Diversity and Ecophysiology of Cereals   (France)

^d CSIRO   (Australia)

^e INSTITUTE OF EXPERIMENTAL BOTANY   (Czech Republic)

^f Istituto di Genomica Applicata   (Italy)

^g CEMAGREF   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTOSOME; BACTERIAL ARTIFICIAL CHROMOSOME; BRACHYPODIUM; CENTROMERE; CHROMOSOME 1A; CHROMOSOME MAP; CHROMOSOME SIZE; CONTIG MAPPING; DNA FINGERPRINTING; DNA HYBRIDIZATION; GENE ASSIGNMENT; GENE SEQUENCE; GENE STRUCTURE; GENETIC MARKER; NONHUMAN; RICE; SORGHUM; SYNTENY; TRITICUM AESTIVUM;

CHROMOSOME MAPPING; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CHROMOSOMES, PLANT; GENETIC MARKERS; MULTIGENE FAMILY; NUCLEIC ACID HYBRIDIZATION; POLYMERASE CHAIN REACTION;

EID: 84894379312     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0080272     Document Type: Article

References (70)

1. Gill BS, Appels R, Botha-Oberholster AM, Buell CR, Bennetzen JL, et al. (2004) A workshop report on wheat genome sequencing: International genome research on wheat consortium. Genetics 168: 1087-1096.
2. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436: 793-800.
3. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, et al. (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457: 551-556.
4. International Brachypodium Initiative (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463: 763-768.
5. International Barley Genome Sequencing Consortium (2012) A physical, genetic and functional sequence assembly of the barley genome. Nature 491: 711-716.
6. Mayer KFX, Taudien S, Martis M, Simkova H, Suchankova P, et al. (2009) Gene content and virtual gene order of barley chromosome 1H. Plant Physiol 151: 496-505.
7. Mayer KFX, Martis M, Hedley PE, Simkovaa H, Liu H, et al. (2011) Unlocking the barley genome by chromosomal and comparative genomics. Plant Cell 23: 1249-1263.
8. Wicker T, Mayer KFX, Gundlach H, Martis M, Steuernagel B, et al. (2011) Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives. Plant Cell 23: 1706-1718.
9. Choulet F, Wicker T, Rustenholz C, Paux E, Salse J, et al. (2010) Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces. Plant Cell. 22: 1686-1701.
10. Bennett MD, Smith JB (1976) Nuclear DNA amounts in angiosperms. Philos Trans R Soc Lond B Biol Sci 274: 227-274.
11. Paux E, Roger D, Badaeva E, Gay G, Bernard M, et al. (2006) Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through BAC-end sequencing on chromosome 3B. Plant J 48: 463-474.
12. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.
13. Wei F, Coe E, Nelson W, Bharti AK, Engler F, et al. (2007) Physical and genetic structure of the maize genome reflects its complex evolutionary history. PLoS Genet 3: e123.
14. Wei F, Stein JC, Liang C, Zhang J, Fulton RS, et al. (2009) Detailed analysis of a contiguous 22-Mb region of the maize genome. PLoS Genet 5: e1000728.
15. Šafář J, Šimková H, Kubaláková M, Číhalíková J, Suchánková P, et al. (2010) Development of chromosome-specific BAC resources for genomics of bread wheat. Cytogenet Genome Res 129: 211-223.
16. Kubaláková M, Kovařová P, Suchánková P, Číhalíková J, Bartoš J, et al. (2005) Chromosome sorting in tetraploid wheat and its potential for genome analysis. Genetics 170: 823-829.
17. Doležel J, Kubaláková M, Paux E, Bartoš J, Feuillet C (2007) Chromosome-based genomics in the cereals. Chromosome Res 15: 51-66.
18. Paux E, Sourdille P, Salse J, Saintenac C, Choulet F, et al. (2008) A physical map of the 1-gigabase bread wheat chromosome 3B. Science 322: 101-104.
19. Brenchley R, Spannagl M, Pfeifer M, Barker GL, D'Amore R, et al. (2012) Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature. 491: 705-710.
20. Soderlund C, Longden I, Mott R (1997) FPC: a system for building contigs from restriction fingerprinted clones. Comput Appl Biosci 13: 523-535.
21. Frenkel Z, Paux E, Mester D, Feuillet C, Korol A (2010) LTC: a novel algorithm to improve the efficiency of contig assembly for physical mapping in complex genomes. BMC Bioinformatics 11: 584.
22. Rustenholz C, Choulet F, Laugier C, Šafaář J, Šimková H, et al. (2011) A 3,000-loci transcription map of chromosome 3B unravels the structural and functional features of gene islands in hexaploid wheat. Plant Physiol 157: 1596-1608.
23. Lazo GR, Chao S, Hummel DD, Edwards H, Crossman CC, et al. (2004) Development of an expressed sequence tag (EST) resource for wheat (Triticum aestivum l.): EST generation, UniGene analysis, probe selection and bioinformatics for a 16,000-locus bin-delineated map. Genetics 168: 585-593.
24. Qi LL, Echalier B, Chao S, Lazo GR, Butler GE, et al. (2004) A chromosome bin map of 16,000 expressed sequence tag loci and distribution of genes among the three genomes of polyploid wheat. Genetics 168: 701-712.
25. Rustenholz C, Hedley PE, Morris J, Choulet F, Feuillet C, et al. (2010) Specific patterns of gene space organisation revealed in wheat by using the combination of barley and wheat genomic resources. BMC Genomics 11: 714.
26. Gill KS, Gill BS, Endo TR, Boyko EV (1996) Identification and high-density mapping of gene-rich regions in chromosome group 5 of wheat. Genetics 143: 1001-1012.
27. Breen J, Wicker T, Kong X, Zhang J, Ma W, et al. (2010) A highly conserved gene island of three genes on chromosome 3B of hexaploid wheat: diverse gene function and genomic structure maintained in a tightly linked block. BMC Plant Biol 10: 98.
28. Gill KS, Gill BS (1991) A DNA fragment mapped within the submicroscopic deletion of Ph1, a chromosome pairing regulator gene in polyploid wheat. Genetics 129: 257-259.
29. Yahiaoui N, Srichumpa P, Dudler R, Keller B (2004) Genome analysis at different ploidy levels allows cloning of the powdery mildew resistance gene Pm3b from hexaploid wheat. Plant J 37: 528-538.
30. Feuillet C, Travella S, Stein N, Albar L, Nublat A, et al. (2003) Map-based isolation of the leaf rust disease resistance gene Lr10 from the hexaploid wheat (Triticum aestivum L.) genome. Proc Natl Acad Sci U S A 100: 15253-15258.
31. Ozdemir N, Cloutier S (2005) Expression analysis and physical mapping of low-molecular-weight glutenin loci in hexaploid wheat (Triticum aestivum L.). Genome 48: 401-410.
32. Spielmeyer W, Richards RA (2004) Comparative mapping of wheat chromosome 1AS which contains the tiller inhibition gene (tin) with rice chromosome 5S. Theor Appl Genet 109: 1303-1310.
33. McFadden HG, Lehmensiek A, Lagudah ES (2006) Resistance gene analogues of wheat: molecular genetic analysis of ESTs. Theor Appl Genet 113: 987-1002.
34. Vrána J, Kubaláková M, Šimková H, Číhalíková J, Lysák MA, et al. (2000) Flow-sorting of mitotic chromosomes in common wheat (Triticum aestivum L.). Genetics 156: 2033-2041.
35. Šimková H, Číhalíková J, Vrána J, Lysák MA, Doležel J (2003) Preparation of HMW DNA from plant nuclei and chromosomes isolated from root tips. Biol. Plant. 46: 369-373.
36. Janda J, Šafář J, Kubaláková M, Bartoš J, Kovářová P, et al. (2006) Advanced resources for plant genomics: BAC library specific for the short arm of wheat chromosome 1B. Plant J. 47: 977-986.
37. Šimková H, Šafář J, Kubaláková M, Suchánková P, Čí halíková J, et al. (2011) BAC libraries from wheat chromosome 7D: efficient tool for positional cloning of aphid resistance genes. J. Biomed. Biotechnol. 2011: 302543.
38. Ding Y, Johnson MD, Chen WQ, Wong D, Chen YJ, et al. (2001) Five-color-based high-information-content fingerprinting of bacterial artificial chromosome clones using type IIS restriction endonucleases. Genomics 74: 142-154.
39. Scalabrin S, Morgante M, Policriti A (2009) Automated fingerprint background removal: FPB. BMC Bioinformatics 10: 127.
40. You FM, Luo MC, Gu YQ, Lazo GR, Deal K, et al. (2007) GenoProfiler: batch processing of high-throughput capillary fingerprinting data. Bioinformatics 23: 240-242.
41. Nelson W, Soderlund C (2009) Integrating sequence with FPC fingerprint maps. Nucleic Acids Res 37: e36.
42. Paux E, Legeai F, Guilhot N, Adam-Blondon AF, Alaux M, et al. (2008) Physical mapping in large genomes: accelerating anchoring of BAC contigs to genetic maps through in silico analysis. Funct Integr Genomics 8: 29-32.
43. Peng JH, Zadeh H, Lazo GR, Gustafson JP, Chao S, et al. (2004) Chromosome bin map of expressed sequence tags in homoeologous group 1 of hexaploid wheat and homoeology with rice and Arabidopsis. Genetics 168: 609-623.
44. Nelson WM, Bharti AK, Butler E, Wei F, Fuks G, et al. (2005) Whole-genome validation of high-information-content fingerprinting. Plant Physiol 139: 27-38.
45. Vitulo N, Albiero A, Forcato C, Campagna D, Pero FD, et al. (2011) First survey of the wheat chromosome 5A composition through a next generation sequencing approach. PLoS One 6: e26421.
46. Presting GG, Malysheva L, Fuchs J, Schubert I (1998) A Ty3/gypsy retro-transposon-like sequence localizes to the centromeric regions of cereal chromosomes. Plant J 16: 721-728.
47. Houben A, Schroeder-Reiter E, Nagaki K, Nasuda S, Wanner G, et al. (2007) CENH3 interacts with the centromeric retrotransposon Cereba and GC-rich satellites and locates to centromeric substructures in barley. Chromosoma 116: 275-283.
48. Vicient CM, Kalendar R, Anamthawat-Jansson K, Schulman AH (1999) Structure, functionality, and evolution of the BARE-1 retrotransposon of barley. Genetica 107: 53-63.
49. Kalendar R, Tanskanen J, Immonen S, Nevo E, Schulman AH (2000) Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence. Proc Natl Acad Sci U S A 97: 6603-6607.
50. Soleimani VD, Baum BR, Johnson DA (2006) Quantification of the retrotransposon BARE-1 reveals the dynamic nature of the barley genome. Genome 49: 389-396.
51. Wicker T, Taudien S, Houben A, Keller B, Graner A, et al. (2009) A wholegenome snapshot of 454 sequences exposes the composition of the barley genome and provides evidence for parallel evolution of genome size in wheat and barley. Plant J 59: 712-722.
52. Middleton CP, Stein N, Keller B, Kilian B, Wicker T (2012) Comparative analysis of genome composition in Triticeae reveals strong variation in transposable element dynamics and nucleotide diversity. Plant J.
53. Somers DJ, Isaac P, Edwards K (2004) A high-density microsatellite consensus map for bread wheat (Triticum aestivum L.). Theor Appl Genet 109: 1105-1114.
54. Ronin Y, Mester D, Minkov D, Belotserkovski R, Jackson BN, et al. (2012) Two-phase analysis in consensus genetic mapping. G3 (Bethesda). 2: 537-549.
55. Wicker T, Stein N, Albar L, Feuillet C, Schlagenhauf E, et al. (2001) Analysis of a contiguous 211 kb sequence in diploid wheat (Triticum monococcum L.) reveals multiple mechanisms of genome evolution. Plant J 26: 307-316.
56. Yan H, Jin W, Nagaki K, Tian S, Ouyang S, et al. (2005) Transcription and histone modifications in the recombination-free region spanning a rice centromere. Plant Cell 17: 3227-3238.
57. Akhunov ED, Goodyear AW, Geng S, Qi LL, Echalier B, et al. (2003) The organization and rate of evolution of wheat genomes are correlated with recombination rates along chromosome arms. Genome Res 13: 753-763.
58. Kalavacharla V, Hossain K, Gu Y, Riera-Lizarazu O, Vales MI, et al. (2006) High-resolution radiation hybrid map of wheat chromosome 1D. Genetics 173: 1089-1099.
59. Wicker T, Yahiaoui N, Keller B (2007) Contrasting rates of evolution in Pm3 loci from three wheat species and rice Genetics 177: 1207-1216.
60. Wang ZN, Huang XQ, Cloutier S (2010) Recruitment of closely linked genes for divergent functions: the seed storage protein (GLU-3) and powdery mildew (Pm3) genes in wheat (Triticum aestivum L.). Funct Integr Genomics 10: 241-251.
61. m genomes of wheat. Plant Cell 15: 1186-1197.
62. Allen AM, Barker GLA, Berry ST, Coghill JA, Gwilliam R, et al. (2011) Transcript-specific, single-nucleotide polymorphism discovery and linkage analysis in hexaploid bread wheat (Triticum aestivum L.). Plant Biotechnol J 9: 1086-1099.
63. Griffiths S, Sharp R, Foote TN, Bertin I, Wanous M, et al. (2006) Molecular characterization of Ph1 as a major chromosome pairing locus in polyploid wheat. Nature 439: 749-752.
64. Febrer M, Goicoechea JL, Wright J, McKenzie N, Song X, et al. (2010) An integrated physical, genetic and cytogenetic map of Brachypodium distachyon, a model system for grass research. PLoS One 5: e13461.
65. Brkljacic J, Grotewold E, Scholl R, Mockler T, Garvin DF, et al. (2011) Brachypodium as a model for the grasses: today and the future. Plant Physiol 157: 3-13.
66. Shatalina M, Wicker T, Buchmann JP, Oberhaensli S, Simkovaa H, et al. (2013) Genotype-specific SNP map based on whole chromosome 3B sequence information from wheat cultivars Arina and Forno. Plant Biotechnol J 11: 23-32.
67. m of Triticum monococcum and its recognition by the wheat Ph1 locus. Proc Natl Acad Sci U S A 92: 6645-6649.
68. Paillard S, Schnurbusch T, Winzeler M, Messmer M, Sourdille P, et al. (2003) An integrative genetic linkage map of winter wheat (Triticum aestivum L.). Theor Appl Genet 107: 1235-1242.
69. Xue S, Zhang Z, Lin F, Kong Z, Cao Y, et al. (2008) A high-density intervarietal map of the wheat genome enriched with markers derived from expressed sequence tags. Theor Appl Genet 117: 181-189.
70. Nelson JC, Sorrells ME, Deynze AEV, Lu YH, Atkinson M, et al. (1995) Molecular mapping of wheat : major genes and rearrangements in homoeologous groups 4, 5, and 7. Genetics 141: 721-731.