Linkage mapping of putative regulator genes of barley grain development characterized by expression profiling

BMC Plant Biology

Volumn 9, Issue , 2009, Pages

  Pietsch, Christof ^a   Sreenivasulu, Nese ^a   Wobus, Ulrich ^a   Röder, Marion S ^a  

^a LEIBNIZ INSTITUTE OF PLANT GENETICS AND CROP PLANT RESEARCH IPK   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

HORDEUM; HORDEUM VULGARE SUBSP. VULGARE; TRITICUM AESTIVUM;

PLANT DNA; TRANSCRIPTION FACTOR;

ARTICLE; BARLEY; CHROMOSOME MAP; CLUSTER ANALYSIS; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE LIBRARY; GENETIC MARKER; GENETICS; GENOTYPE; GROWTH, DEVELOPMENT AND AGING; PLANT GENE; PLANT SEED; REGULATOR GENE; SINGLE NUCLEOTIDE POLYMORPHISM; SYNTENY;

CHROMOSOME MAPPING; CLUSTER ANALYSIS; DNA, PLANT; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE EXPRESSION REGULATION, PLANT; GENE LIBRARY; GENES, PLANT; GENES, REGULATOR; GENETIC MARKERS; GENOTYPE; HORDEUM; POLYMORPHISM, SINGLE NUCLEOTIDE; SEEDS; SEQUENCE ANALYSIS, DNA; SYNTENY; TRANSCRIPTION FACTORS;

EID: 61849112317     PISSN: None     EISSN: 14712229     Source Type: Journal    
DOI: 10.1186/1471-2229-9-4     Document Type: Article

References (49)

1. The barley Mlo gene: A novel control element of plant pathogen resistance. R Büschges K Hollricher R Panstruga G Simons M Wolter A Frijters R van Daelen T van der Lee P Diergaarde J Groenendijk S Töpsch P Vos F Salamini P Schulze-Lefert, Cell 1997 88 695 705 10.1016/S0092-8674(00) 81912-1 9054509
2. The barley stem rust-resistance gene RPG1 is a novel disease-resistance gene with homology to receptor kinases. R Brueggeman N Rostoks D Kudrna A Kilian F Han J Chen A Druka B Steffenson A Kleinhofs, Proc Natl Acad Sci USA 2002 99 9328 9333 12077318 10.1073/pnas.142284999
3. The pseudo-response regulator Ppd-H1 provides adaption to photoperiod in barley. A Turner J Beales S Faure RP Dunford DA Laurie, Science 2005 310 1031 1034 10.1126/science.1117619 16284181
4. Six-rowd barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene. T Komatsuda M Pourkheinrandish C He P Azhaguval H Kanamori D Perovic N Stein A Graner T Wicker A Tagiri U Lundqvist T Fujimura M Matsuoka T Matsumoto M Yano, Proc Natl Acad Sci USA 2007 104 1424 1429 17220272 10.1073/pnas.0608580104
5. Molecular physiology and genomics of developing barley grains. U Wobus N Sreenivasulu L Borisjuk H Rolletschek RS Panitz S Gubatz W Weschke, Recent Research Developments in Plant Molecular Biology 2005 2 1 29
6. Genetical genomics: the added value from segregation. RC Jansen JP Nap, Trends in Genet 2001 17 388 391 11418218 10.1016/S0168-9525(01)02310-1
7. Large-scale analysis of the barley transcriptome based on expressed sequence tags. H Zhang N Sreenivasulu W Weschke N Stein S Rudd V Radchuk E Potokina U Scholz P Schweizer U Zierold P Langridge RK Varshney U Wobus A Graner, Plant J 2004 40 276 290 10.1111/j.1365-313X.2004.02209.x 15447653
8. Gene expression patterns reveal tissue-specific signaling networks controlling programmed cell death and ABA-regulated maturation in developing barley seeds. N Sreenivasulu V Radchuk M Strickert O Miersch W Weschke U Wobus, Plant J 2006 47 310 327 10.1111/j.1365-313X.2006.02789.x 16771774
9. Barley grain maturation and germination: Metabolic pathway and regulatory network commonalities and differences highlighted by new MapMan/PageMan profiling tools. N Sreenivasulu B Usadel A Winter V Radchuk U Scholz N Stein W Weschke M Strickert TJ Close M Stitt A Graner U Wobus, Plant Physiol 2008 146 1738 1758 18281415 10.1104/pp.107.111781
10. An atlas of gene expression from seed to seed through barley development. A Druka G Muehlbauer I Druka R Caldo U Baumann N Rostoks A Schreiber R Wise T Close A Kleinhofs A Graner A Schulman P Langridge K Sato P Hayes J McNicol D Marshall R Waugh, Funct Integr Gen 2006 6 202 211 16547597 10.1007/s10142-006- 0025-4
11. Activation of CRABS CLAW in the Nectaries and Carpels of Arabidopsis. JY Lee SF Baum J Alvarez A Patel DH Chitwood JL Bowman, Plant Cell 2005 17 25 36 15598802 10.1105/tpc.104.026666
12. Spatially and temporally regulated expression of the MADS-box gene AGL2 in wild-type and mutant arabidopsis flowers. CA Flanagan H Ma, Plant Mol Biol 1994 26 581 595 10.1007/BF00013745 7948914
13. Complexes of MADS-box proteins are sufficient to convert leaves into floral organs. T Honma K Goto, Nature 2001 409 525 529 10.1038/35054083 11206550
14. An endosperm-specific DOF protein from barley, highly conserved in wheat, binds to and activates transcription from the prolamin-box of a native B-hordein promoter in barley endosperm. M Mena J Vicente-Carbajosa RJ Schmidt P Carbonero, Plant J 1998 16 53 62 10.1046/j.1365-313x.1998.00275.x 9807827
15. A network of local and redundant gene regulation governs Arabidopsis seed maturation. A To C Valon G Savino J Guilleminot M Devic J Giraudat F Parcy, Plant Cell 2006 18 1642 16451 16731585 10.1105/tpc.105.039925
16. CHR11, a chromatin-remodeling factor essential for nuclear proliferation during female gametogenesis in Arabidopsis thaliana. W Huanca-Mamani M Garcia-Aguilar G Len-Martínez U Grossniklaus JP Vielle-Calzada, Proc Natl Acad Sci USA 2005 102 17231 17236 16286646 10.1073/pnas.0508186102
17. The Arabidopsis gene PROLIFERA is required for proper cytokinesis during seed development. DR Holding PS Springer, Planta 2002 214 373 382 10.1007/s00425-001-0686-0 11855642
18. KNOX action in Arabidopsis is mediated by coordinate regulation of cytokinin and gibberellin activities. S Jasinski P Piazza J Craft A Hay L Woolley I Rieu A Phillips P Hedden M Tsiantis, Curr Biol 2005 15 1560 1565 10.1016/j.cub.2005.07.023 16139211
19. FILAMENTOUS FLOWER controls the formation and development of arabidopsis inflorescences and floral meristems. S Sawa T Ito Y Shimura K Okada, Plant Cell 1999 11 69 86 9878633 10.1105/tpc.11.1.69
20. A molecular, isozyme and morphological map of the barley (Hordeum vulgare) genome. A Kleinhofs A Kilian MA Saghai Maroof RM Biyashev P Hayes FQ Chen N Lapitan Fenwick TK Blake V Kanazin E Ananiev L Dahleen D Kudrna J Bollinger SJ Knapp B Liu M Sorrells M Heun JD Franckowiak D Hoffman R Skadsen BJ Steffenson, Theor Appl Genet 1993 86 705 712 10.1007/BF00222660
21. Molecular mapping of the Oregon Wolfe Barleys: a phenotypically polymorphic doubled-haploid population. JM Costa A Corey PM Hayes C Jobet A Kleinhofs Kopisch-Obusch SF Kramer D Kudrna M Li O Riera-Lizarazu K Sato P Szucs T Toojinda MI Vales RI Wolfe, Theor Appl Genet 2001 103 415 424 10.1007/s001220100622
22. Analysis of QTLs for yield, yield components, and malting quality in a BC3-DH population of spring barley. JZ Li XQ Huang F Heinrichs MW Ganal MS Röder, Theor Appl Genet 2005 110 356 363 10.1007/s00122-004-1847-x 15549229
23. Analysis of QTLs for yield components, agronomic traits and disease resistance in an advanced backcross population of spring barley. J Li XQ Huang F Heinrichs MW Ganal MS Röder, Genome 2006 49 454 466 10.1139/G05-128 16767170
24. A 1000-loci transcript map of the barley genome: new anchoring points for integrative grass genomics. N Stein M Prasad U Scholz T Thiel H Zhang M Wolf R Kota RK Varshney D Perovic I Grosse A Graner, Theor Appl Genet 2007 114 823 839 10.1007/s00122-006-0480-2 17219208
25. A common RNA structural motif involved in the internal initiation of translation of cellular mRNAs. SY Le JV Maizel Jr, Nucleic Acids Res 1997 25 362 69 9016566 10.1093/nar/25.2.362
26. Isolation and characterization of euplasmic wheat-barley chromosome addition lines. AKMR Islam KW Shepard DHB Sparrow, Heredity 1981 46 161 174 10.1038/hdy.1981.24
27. Genome relationships: the grass model in current research. K Devos M Gale, Plant Cell 2000 12 637 646 10810140 10.1105/tpc.12.5.637
28. Updating the 'crop circle'. K Devos, Curr Opin Plant Biol 2005 8 155 162 10.1016/j.pbi.2005.01.005 15752995
29. Grasses, line up and form a circle. G Moore K Devos Z Wang M Gale, Curr Biol 1995 5 737 739 10.1016/S0960-9822(95)00148-5 7583118
30. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. G Smyth, Stat Appl Genet Mol Biol 2004 3 16646809
31. Genesis: cluster analysis of microarray data. A Sturn J Quackenbush Z Trajanoski, Bioinformatics 2002 18 207 208 10.1093/bioinformatics/18.1.207 11836235
32. Detection of genetic diversity in closely related bread wheat using microsatellite markers. J Plaschke MW Ganal MS Röder, Theor Appl Genet 1995 91 1001 1007 10.1007/BF00223912
33. Primer3 on the WWW for general users and for biologist programmers. S Rozen H Skaletsky, Bioinformatics Methods and Protocols: Methods in Molecular Biology Humana Press, Totowa, NJ, Krawetz S, Misener S, 2000 365 386
34. Base-calling of automated sequencer traces using Phred. II. Error probabilities. B Ewing P Green, Genome Res 1998 8 186 194 9521922
35. Consed: a graphical tool for sequence finishing. D Gordon C Abajian P Green, Genome Res 1998 8 195 202 9521923
36. PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing. D Nickerson V Tobe S Taylor, Nucl Acids Res 1997 25 2745 2751 9207020 10.1093/nar/25.14.2745
37. DNA SEQUENCING: A Sequencing Method Based on Real-Time Pyrophosphate. M Ronaghi M Uhlén P Nyrén, Science 1998 281 363 365 10.1126/science.281.5375.363 9705713
38. Single-nucleotide polymorphism analysis by pyrosequencing. A Ahmadian B Gharizadeh A Gustafsson F Sterky P Nyrén J Lundeberg, Analyt Biochem 2000 280 103 110 10.1006/abio.2000.4493 10805527
39. Development of SNP assays for genotyping the Puroindoline b gene for grain hardness in wheat using pyrosequencing. XQ Huang MS Röder, J Agric Food Chem 2005 53 2070 2075 10.1021/jf047955b 15769137
40. SNP2CAPS: a SNP and INDEL analysis tool for CAPS marker development. T Thiel R Kota I Grosse N Stein A Graner, Nucl Acids Res 2004 32 e5 14704362 10.1093/nar/gnh006
41. SNP Cutter: a comprehensive tool for SNP PCR-RFLP assay design. R Zhang Z Zhu H Zhu T Nguyen F Yao K Xia D Liang C Liu, Nucl Acids Res 2005 33 489 492 15980518 10.1093/nar/gki358
42. A high-density consensus map of barley to compare the distribution of QTLs for partial resistance to Puccinia hordei and of defence gene homologues. TC Marcel RK Varshney M Barbieri H Jafary MJD de Kock A Graner RE Niks, Theor Appl Genet 2007 114 487 500 10.1007/s00122-006-0448-2 17115126
43. MapChart: software for graphical presentation of linkage maps and QTLs. RE Voorrips, J Hered 2002 93 77 78 10.1093/jhered/93.1.77 12011185
44. RiceGAAS: an automated annotation system and database for rice genome sequence. K Sakata Y Nagamura H Numa B Antonio H Nagasaki A Idonuma W Watanabe Y Shimizu I Horiuchi T Matsumoto T Sasaki K Higo, Nucl Acids Res 2002 30 98 102 11752265 10.1093/nar/30.1.98
45. RiceHMM: gene domain prediction program for rice genome sequence. K Sakata H Nagasaki A Idonuma W Watanabe M Kise T Sasaki, Abstracts of 4th Annual Conference on Computational Genomics 2000 31
46. Using MZEF to find internal coding exons. M Zhang, Current Protocols in Bioinformatics John Wiley & Sons, Inc, Baxevanis A, Davison D, 2003 1,4.2 1 18 18792940
47. Logitlinear models for the prediction of splice sites in plant pre-mRNA sequences. J Kleffe K Hermann W Vahrson B Wittig V Brendel, Nucl Acids Res 1996 24 4709 4718 8972857 10.1093/nar/24.23.4709
48. GeneSeqer@PlantGDB: gene structure prediction in plant genomes. SD Schlueter Q Dong V Brendel, Nucl Acids Res 2003 31 3597 3600 12824374 10.1093/nar/gkg533
49. Internet resources for the functional analysis of 5' and 3' untranslated regions of eukaryotic mRNAs. G Pesole S Liuni, Trends in Genet 1999 15 378 10.1016/S0168-9525(99)01795-3