Genomic resources and tools for gene function analysis in potato

International Journal of Plant Genomics

Volumn 2008, Issue , 2008, Pages

  Bryan, Glenn J ^a   Hein, Ingo ^a  

^a SCOTTISH CROP RESEARCH INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

LYCOPERSICON ESCULENTUM; MAGNOLIOPHYTA; SOLANACEAE; SOLANUM TUBEROSUM;

EID: 58049192548     PISSN: 16875370     EISSN: 16875389     Source Type: Journal    
DOI: 10.1155/2008/216513     Document Type: Article

References (67)

1. Gebhardt C., Vreugdenhil D., Molecular markers, maps, and population genetics Potato Biology and Biotechnology: Advances and Perspectives 2007 chapter 5 Amsterdam, The Netherlands Elsevier 77 89
2. van Os H., Andrzejewski S., Bakker E., Construction of a 10,000-marker ultradense genetic recombination map of potato: providing a framework for accelerated gene isolation and a genomewide physical map Genetics 2006 173 2 1075 1087
3. Hackett C. A., Pande B., Bryan G. J., Constructing linkage maps in autotetraploid species using simulated annealing Theoretical and Applied Genetics 2003 106 6 1107 1115
4. Bradshaw J. E., Pande B., Bryan G. J., Interval mapping of quantitative trait loci for resistance to late blight [ Phytophthora infestans (Mont.) de bary], height and maturity in a tetraploid population of potato (Solanum tuberosum subsp. tuberosum) Genetics 2004 168 2 983 995
5. Simko I., Jansky S., Stephenson S., Spooner D., Vreugdenhil D., Genetics of resistance to pests and disease Potato Biology and Biotechnology: Advances and Perspectives 2007 chapter 7 Amsterdam, The Netherlands Elsevier 117 155
6. van Eck H. J., Vreugdenhil D., Genetics of morphological and tuber traits Potato Biology and Biotechnology: Advances and Perspectives 2007 Amsterdam, The Netherlands Elsevier 91 115
7. Arumuganathan K., Earle E. D., Nuclear DNA content of some important plant species Plant Molecular Biology Reporter 1991 9 4 415
8. Gavrilenko T., Vreugdenhil D., Potato cytogenetics Potato Biology and Biotechnology: Advances and Perspectives 2007 chapter 10 Oxford, UK Elsevier 203 216
9. Tanksley S. D., Ganal M. W., Prince J. P., High density molecular linkage maps of the tomato and potato genomes Genetics 1992 132 4 1141 1160
10. Zamir D., Tanksley S. D., Tomato genome is comprised largely of fast-evolving, low copy-number sequences Molecular General Genetics 1988 213 2-3 254 261
11. Schweizer G., Borisjuk N., Borisjuk L., Molecular analysis of highly repeated genome fractions in Solanum and their use as markers for the characterization of species and cultivars Theoretical and Applied Genetics 1993 85 6-7 801 808
12. Wang Y., van der Hoeven R. S., Nielsen R., Mueller L. A., Tanksley S. D., Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments Theoretical and Applied Genetics 2005 112 1 72 84
13. Zhu W., Ouyang S., Iovene M., Analysis of 90Mb of the potato genome reveals conservation of gene structures and order with tomato but divergence in repetitive sequence composition BMC Genomics 2008 9, article 286 1 14
14. Crookshanks M., Emmersen J., Welinder K. G., Nielsen K. L., The potato tuber transcriptome: analysis of 6077 expressed sequence tags FEBS Letters 2001 506 2 123 126
15. Ronning C. M., Stegalkina S. S., Ascenzi R. A., Comparative analyses of potato expressed sequence tag libraries Plant Physiology 2003 131 2 419 429
16. Flinn B., Rothwell C., Griffiths R., Potato expressed sequence tag generation and analysis using standard and unique cDNA libraries Plant Molecular Biology 2005 59 3 407 433
17. Tang J., Vosman B., Voorrips R. E., van der Linden C. G., Leunissen J. A. M., QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species BMC Bioinformatics 2006 7, article 438 1 15
18. Kanyuka K., Bendahmane A., van der Voort J. N. A. M. R., van der Vossen E. A. G., Baulcombe D. C., Mapping of intra-locus duplications and introgressed DNA: aids to map-based cloning of genes from complex genomes illustrated by physical analysis of the Rx locus in tetraploid potato Theoretical and Applied Genetics 1999 98 5 679 689
19. Song J., Dong F., Jiang J., Construction of a bacterial artificial chromosome (BAC) library for potato molecular cytogenetics research Genome 2000 43 1 199 204
20. Chen Q., Sun S., Ye Q., McCuine S., Huff E., Zhang H.-B., Construction of two BAC libraries from the wild Mexican diploid potato, Solanum pinnatisectum, and the identification of clones near the late blight and Colorado potato beetle resistance loci Theoretical and Applied Genetics 2004 108 6 1002 1009
21. Kuang H., Wei F., Marano M. R., The R1 resistance gene cluster contains three groups of independently evolving, type I R1 homologues and shows substantial structural variation among haplotypes of Solanum demissum The Plant Journal 2005 44 1 37 51
22. Dong F., Song J., Naess S. K., Helgeson J. P., Gebhardt C., Jiang J., Development and applications of a set of chromosome-specific cytogenetic DNA markers in potato Theoretical and Applied Genetics 2000 101 7 1001 1007
23. Bendahmane A., Kanyuka K., Baulcombe D. C., The Rx gene from potato controls separate virus resistance and cell death responses Plant Cell 1999 11 5 781 791
24. van der Vossen E. A. G., van der Voort J. N. A. M. R., Kanyuka K., Homologues of a single resistance-gene cluster in potato confer resistance to distinct pathogens: a virus and a nematode The Plant Journal 2000 23 5 567 576
25. Huang S., Vleeshouwers V. G. A. A., Werij J. S., The R3 resistance to Phytophthora infestans in potato is conferred by two closely linked R genes with distinct specificities Molecular Plant-Microbe Interactions 2004 17 4 428 435
26. Huang S., van der Vossen E. A. G., Kuang H., Comparative genomics enabled the isolation of the R3a late blight resistance gene in potato The Plant Journal 2005 42 2 251 261
27. Park T.-H., Gros J., Sikkema A., The late blight resistance locus Rpi-blb3 from Solanum bulbocastanum belongs to a major late blight R gene cluster on chromosome 4 of potato Molecular Plant-Microbe Interactions 2005 18 7 722 729
28. Park T. H., Vleeshouwers V. G. A. A., Huigen D. J., van der Vossen E. A.G., van Eck H. J., Visser R. G. F., Characterization and high-resolution mapping of a late blight resistance locus similar to R2 in potato Theoretical and Applied Genetics 2005 111 3 591 597
29. Hein I., McLean K., Chalhoub B., Bryan G. J., Generation and screening of a BAC library from a diploid potato clone to unravel durable late blight resistance on linkage group IV International Journal of Plant Genomics 2007 2007 5
30. Pflieger S., Lefebvre V., Causse M., The candidate gene approach in plant genetics: a review Molecular Breeding 2001 7 4 275 291
31. Paal J., Henselewski H., Muth J., Molecular cloning of the potato Gro1-4 gene conferring resistance to pathotype Ro1 of the root cyst nematode Globodera rostochiensis, based on a candidate gene approach The Plant Journal 2004 38 2 285 297
32. Jung C. S., Griffiths H. M., De Jong D. M., Cheng S., Bodis M., De Jong W. S., The potato P locus codes for flavonoid 3′,5′ -hydroxylase Theoretical and Applied Genetics 2005 110 2 269 275
33. Li L., Strahwald J., Hofferbert H.-R., DNA variation at the invertase locus invGE/GF is associated with tuber quality traits in populations of potato breeding clones Genetics 2005 170 2 813 821
34. Bachem C. W. B., van der Hoeven R. S., de Bruijn S. M., Vreugdenhil D., Zabeau M., Visser R. G. F., Visualization of differential gene expression using a novel method of RNA fingerprinting based on AFLP: analysis of gene expression during potato tuber development The Plant Journal 1996 9 5 745 753
35. Bachem C., van der Hoeven R. S., Lucker J., Functional genomic analysis of potato tuber life-cycle Potato Research 2000 43 4 297 312
36. Brugmans B., del Carmen A. F., Bachem C. W. B., van Os H., van Eck H. J., Visser R. G. F., A novel method for the construction of genome wide transcriptome maps The Plant Journal 2002 31 2 211 222
37. Trindade L. M., Horvath B. M., van Berloo R., Visser R. G. F., Analysis of genes differentially expressed during potato tuber life cycle and isolation of their promoter regions Plant Science 2004 166 2 423 433
38. Ritter E., Ruiz de Galarreta J. I., van Eck H. J., Snchez I., Construction of a potato transcriptome map based on the cDNA-AFLP technique Theoretical and Applied Genetics 2008 116 7 1003 1013
39. Velculescu V. E., Zhang L., Vogelstein B., Kinzler K. W., Serial analysis of gene expression Science 1995 270 5235 484 487
40. Saha S., Sparks A. B., Rago C., Using the transcriptome to annotate the genome Nature Biotechnology 2002 20 5 508 512
41. Nielsen K. L., Grnkjr K., Welinder K. G., Emmersen J., Global transcript profiling of potato tuber using LongSAGE Plant Biotechnology Journal 2005 3 2 175 185
42. Emrich S. J., Barbazuk W. B., Li L., Schnable P. S., Gene discovery and annotation using LCM-454 transcriptome sequencing Genome Research 2007 17 1 69 73
43. Rensink W., Hart A., Liu J., Ouyang S., Zismann V., Buell C. R., Analyzing the potato abiotic stress transcriptome using expressed sequence tags Genome 2005 48 4 598 605
44. Kloosterman B., Vorst O., Hall R. D., Visser R. G. F., Bachem C. W., Tuber on a chip: differential gene expression during potato tuber development Plant Biotechnology Journal 2005 3 5 505 519
45. Kloosterman B., De Koeyer D., Griffiths R., The potato transcriptome: a new look at transcriptional changes during tuber development using the POCI array Functional Integrative Genomics 2008 8 329 340
46. Muth J., Hartje S., Twyman R. M., Hofferbert H.-R., Tacke E., Prfer D., Precision breeding for novel starch variants in potato Plant Biotechnology Journal 2008 6 6 576 584
47. Simko I., Haynes K. G., Jones R. W., Assessment of linkage disequilibrium in potato genome with single nucleotide polymorphism markers Genetics 2006 173 4 2237 2245
48. Lu R., Martn-Hernndez A. M., Peart J. R., Malcuit I., Baulcombe D. C., Virus-induced gene silencing in plants Methods 2003 30 4 296 303
49. Faivre-Rampant O., Gilroy E. M., Hrubikova K., Potato virus X-induced gene silencing in leaves and tubers of potato Plant Physiology 2004 134 4 1308 1316
50. Brigneti G., Martn-Hernndez A. M., Jin H., Virus-induced gene silencing in Solanum species The Plant Journal 2004 39 2 264 272
51. Jones L., Hamilton A. J., Voinnet O., Thomas C. L., Maule A. J., Baulcombe D. C., RNA-DNA interactions and DNA methylation in post-transcriptional gene silencing Plant Cell 1999 11 12 2291 2302
52. Lu R., Malcuit I., Moffett P., High throughput virus-induced gene silencing implicates heat shock protein 90 in plant disease resistance The EMBO Journal 2003 22 21 5690 5699
53. Ryu C.-M., Anand A., Kang L., Mysore K. S., Agrodrench: a novel and effective agroinoculation method for virus-induced gene silencing in roots and diverse Solanaceous species The Plant Journal 2004 40 2 322 331
54. Goodin M. M., Zaitlin D., Naidu R. A., Lommel S. A., Nicotiana benthamiana: its history and future as a model for plant-pathogen interactions Molecular Plant-Microbe Interactions 2008 21 8 1015 1026
55. Godge M. R., Purkayastha A., Dasgupta I., Kumar P. P., Virus-induced gene silencing for functional analysis of selected genes Plant Cell Reports 2008 27 2 209 219
56. Gilroy E. M., Hein I., van der Hoorn R., Involvement of cathepsin B in the plant disease resistance hypersensitive response The Plant Journal 2007 52 1 1 13
57. Gabrils S. H. E. J., Takken F. L. W., Vossen J. H., cDNA-AFLP combined with functional analysis reveals novel genes involved in the hypersensitive response Molecular Plant-Microbe Interactions 2006 19 6 567 576
58. Gabrils S. H. E. J., Vossen J. H., Ekengren S. K., An NB-LRR protein required for HR signalling mediated by both extra- and intracellular resistance proteins The Plant Journal 2007 50 1 14 28
59. Dong Y., Burch-Smith T. M., Liu Y., Mamillapalli P., Dinesh-Kumar S. P., A ligation-independent cloning tobacco rattle virus vector for high-throughput virus-induced gene silencing identifies roles for NbMADS4-1 and -2 in floral development Plant Physiology 2007 145 4 1161 1170
60. Kamoun S., Goodwin S. B., Fungal and oomycete genes galore New Phytologist 2007 174 4 713 717
61. Armstrong M. R., Whisson S. C., Pritchard L., An ancestral oomycete locus contains late blight avirulence gene Avr3a, encoding a protein that is recognized in the host cytoplasm Proceedings of the National Academy of Sciences of the United States of America 2005 102 21 7766 7771
62. Rehmany A. P., Gordon A., Rose L. E., Differential recognition of highly divergent downy mildew avirulence gene alleles by RPP1 resistance genes from two Arabidopsis lines Plant Cell 2005 17 6 1839 1850
63. Whisson S. C., Boevink P. C., Moleleki L., A translocation signal for delivery of oomycete effector proteins into host plant cells Nature 2007 450 7166 115 118
64. Torto T. A., Li S., Styer A., EST mining and functional expression assays identify extracellular effector proteins from the plant pathogen Phytophthora Genome Research 2003 13 7 1675 1685
65. Vleeshouwers V. G. A. A., Driesprong J.-D., Kamphuis L. G., Agroinfection-based high-throughput screening reveals specific recognition of INF elicitins in Solanum Molecular Plant Pathology 2006 7 6 499 510
66. Champouret N., Rietman H., Bos J. I., Functional allele mining: a new approach to identify R-gene homologues in Solanum Proceedings of the 13th International Congress on Molecular Plant-Microbe Interactions July 2007 Sorrento, Italy 177
67. Hein I., Squires J., Birch P., Bryan G. J., Screening wild potato accessions for resistance to the virulent allele of the Phytophthora infestans effector Avr3a Proceedings of the 13th International Congress on Molecular Plant-Microbe Interactions July 2007 Sorrento, Italy 259