Identification of a cis-acting regulatory polymorphism in a eucalypt COBRA-like gene affecting cellulose content

Genetics

Volumn 183, Issue 3, 2009, Pages 1153-1164

  Thumma, Bala R ^a   Matheson, Bronwyn A ^a   Zhang, Deqiang ^a,b   Meeske, Christian ^a   Meder, Roger ^a   Downes, Geoff M ^a   Southerton, Simon G ^a  

^a CSIRO   (Australia)

^b BEIJING FORESTRY UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CELLULOSE;

ARTICLE; EUCALYPTUS NITENS COBRA GENE; EXON; GENE; GENE EXPRESSION; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENETIC IDENTIFICATION; GENETIC LINKAGE; GENOTYPE; HAPLOTYPE; HETEROZYGOTE; METHYLATION; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS; REGULATOR GENE; SIMPLE SEQUENCE REPEAT; SINGLE NUCLEOTIDE POLYMORPHISM;

ALLELIC IMBALANCE; CELLULOSE; CHROMOSOME MAPPING; CHROMOSOMES, PLANT; CPG ISLANDS; DNA METHYLATION; EUCALYPTUS; GENE EXPRESSION PROFILING; GENE FREQUENCY; GENOTYPE; HAPLOTYPES; LINKAGE DISEQUILIBRIUM; MICROSATELLITE REPEATS; PHYLOGENY; PLANT PROTEINS; POLYMORPHISM, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; REGULATORY SEQUENCES, NUCLEIC ACID;

ARABIDOPSIS; EUCALYPTUS NITENS;

EID: 72449203628     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.109.106591     Document Type: Article

References (60)

1. BARTHEL, K. K. B., and X. LIU, 2008 A transcriptional enhancer from the coding region of ADAMTS5. PLoS ONE 3: e2184.
2. BRADBURY, P. J., Z. ZHANG, D. E. KROON, T. M. CASSTEVENS, Y. RAMDOSS et al., 2007 TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23: 2633-2635.
3. BROWN, D. M., L. A. H. ZEEF, J. ELLIS, R. GOODACRE and S. R. TURNER, 2005 Identification of novel genes in Arabidopsis involved in secondary cell wall formation using expression profiling and reverse genetics. Plant Cell 17: 2281-2295.
4. BROWN, G. R., G. P. GILL, R. J. KUNTZ, C. H. LANGLEY and D. B. NEALE, 2004 Nucleotide diversity and linkage disequilibrium in loblolly pine. Proc. Natl. Acad. Sci. USA 101: 15255-15260.
5. BYRNE, M., J. C. MURRELL, B. ALLEN and G. F. MORAN, 1995 An integrated genetic linkage map for eucalypts using RFLP, RAPD and isozyme markers. Theor. Appl. Genet. 91: 869-875.
6. CHING, A., K. DHUGGA, L. APPENZELLER, R. MEELEY, T. BOURETT et al., 2006 Brittle stalk 2 encodes a putative glycosylphosphatidylinositol- anchored protein that affects mechanical strength of maize tissues by altering the composition and structure of secondary cell walls. Planta 224: 1174-1184.
7. CIRULLI, E. T., and D. B. GOLDSTEIN, 2007 In vitro assays fail to predict in vivo effects of regulatory polymorphisms. Hum. Mol. Genet. 16: 1931-1939.
8. CLARK, R. M., T. N. WAGLER, P. QUIJADA and J. DOEBLEY, 2006 A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture. Nat. Genet. 38: 594-597.
9. EVANS, R., and J. ILIC, 2001 Rapid prediction of wood stiffness from microfibril angle and density. For. Prod. J. 51: 53-57.
10. FAN, J. B., A. OLIPHANT, R. SHEN, B. G. KERMANI, F. GARCIA et al., 2003 Highly parallel SNP genotyping. Cold Spring Harbor Symp. Quant. Biol. 68: 69-78.
11. GONZALGO, M. L., and P. A. JONES, 2002 Quantitative methylation analysis using methylation-sensitive single-nucleotide primer extension (Ms-SNuPE). Methods 27: 128-133.
12. GUO, M., M. A. RUPE, C. ZINSELMEIER, J. HABBEN, B. A. BOWEN et al., 2004 Allelic variation of gene expression in maize hybrids. Plant Cell 16: 1707-1716. (Pubitemid 38908770)
13. GUO, M., M. RUPE, X. YANG, O. CRASTA, C. ZINSELMEIER et al., 2006 Genome-wide transcript analysis of maize hybrids: allelic additive gene expression and yield heterosis. Theor. Appl. Genet. 113: 831-845.
14. HIGO, K., Y. UGAWA, M. IWAMOTO and T. KORENAGA, 1999 Plant cisacting regulatory DNA elements (PLACE) database. Nucleic Acids Res. 27: 297-300.
15. HUDSON, R. R., and N. L. KAPLAN, 1985 Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111: 147-164.
16. KANGASPESKA, S., B. STRIDE, R. METIVIER, M. POLYCARPOU-SCHWARZ, D. IBBERSON et al., 2008 Transient cyclical methylation of promoter DNA. Nature 452: 112-115.
17. KERKEL, K., A. SPADOLA, E. YUAN, J. KOSEK, L. JIANG et al., 2008 Genomic surveys by methylation-sensitive SNP analysis identify sequence-dependent allele-specific DNA methylation. Nat. Genet. 40: 904-908.
18. KIM, S., V. PLAGNOL, T. T. HU, C. TOOMAJIAN, R. M. CLARK et al., 2007 Recombination and linkage disequilibrium in Arabidopsis thaliana. Nat. Genet. 39: 1151-1155.
19. KIRST, M., A. A. MYBURG, J. P. G. DE LEON, M. E. KIRST, J. SCOTT et al., 2004 Coordinated genetic regulation of growth and lignin revealed by quantitative trait locus analysis of cDNA microarray data in an interspecific backcross of Eucalyptus. Plant Physiol. 135: 2368-2378.
20. KIRST, M., C. J. BASTEN, A. A. MYBURG, Z. B. ZENG and R. R. SEDEROFF, 2005 Genetic architecture of transcript-level variation in differentiating xylem of a eucalyptus hybrid. Genetics 169: 2295-2303.
21. KNIGHT, J. C., 2005 Regulatory polymorphisms underlying complex disease traits. J. Mol. Med. 83: 97-109.
22. KNIGHT, J. C., B. J. KEATING, K. A. ROCKETT and D. P. KWIATKOWSKI, 2003 In vivo characterization of regulatory polymorphisms by allele-specific quantification of RNA polymerase loading. Nat. Genet. 33: 469-475.
23. KUMAR, S., K. TAMURA and M. NEI, 2004 MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinform. 5: 150-163.
24. LANG, GEORGINA, W. M. GOMBERT and H. J. GOULD, 2005 A transcriptional regulatory element in the coding sequence of the human Bcl-2 gene. Immunology 114: 25-36. (Pubitemid 40030290)
25. LI, L.-C., and R. DAHIYA, 2002 MethPrimer: designing primers for methylation PCRs. Bioinformatics 18: 1427-1431.
26. LI, Y. H., O. QIAN, Y. H. ZHOU, M. X. YAN, L. SUN et al., 2003 BRITTLE CULM1, which encodes a COBRA-like protein, affects the mechanical properties of rice plants. Plant Cell 15: 2020-2031.
27. MÁTYÁS, G., C. GIUNTA, B. STEINMANN, J. P. HOSSLE and R. HELLWIG, 2002 Quantification of single nucleotide polymorphisms: a novel method that combines primer extension assay and capillary electrophoresis. Hum. Mutat. 19: 58-68.
28. METIVIER, R., R. GALLAIS, C. TIFFOCHE, C. LE PERON, R. Z. JURKOWSKA et al., 2008 Cyclical DNA methylation of a transcriptionally active promoter. Nature 452: 45-50.
29. NEALE, D. B., 2007 Genomics to tree breeding and forest health. Curr. Opin. Genet. Dev. 17: 539-544.
30. NEZNANOV, N., A. UMEZAWA and R. G. OSHIMA, 1997 A regulatory element within a coding exon modulates keratin 18 gene expression in transgenic mice. J. Biol. Chem. 272: 27549-27557.
31. NORDBORG, M., 2000 Linkage disequilibrium, gene trees and selfing: an ancestral recombination graph with partial self-fertilization. Genetics 154: 923-929.
32. PASTINEN, T., and T. J. HUDSON, 2004 Cis-acting regulatory variation in the human genome. Science 306: 647-650. (Pubitemid 39440905)
33. PASTINEN, T., R. SLADEK, S. GURD, A. A. SAMMAK, B. GE et al., 2004 A survey of genetic and epigenetic variation affecting human gene expression. Physiol. Genomics 16: 184-193.
34. PASTINEN, T., B. GE, S. GURD, T. GAUDIN, C. DORE et al., 2005 Mapping common regulatory variants to human haplotypes. Hum. Mol. Genet. 14: 3963-3971.
35. PASTINEN, T., B. GE and T. J. HUDSON, 2006 Influence of human genome polymorphism on gene expression. Hum. Mol. Genet. 15: R9-R16.
36. PIERCE, R. A., C. H. MOORE and M. C. ARIKAN, 2006 Positive transcriptional regulatory element located within exon 1 of elastin gene. Am. J. Physiol. Lung Cell. Mol. Physiol. 291: L391-L399.
37. POLESSKAYA, O. O., C. ASTON and B. P. SOKOLOV, 2006 Allele C-specific methylation of the 5-HT2A receptor gene: evidence for correlation with its expression and expression of DNA methylase DNMT1. J. Neurosci. Res. 83: 362-373.
38. QIU, D., I. W. WILSON, S. GAN, R. WASHUSEN, G. F. MORAN et al., 2008 Gene expression in Eucalyptus branch wood with marked variation in cellulose microfibril orientation and lacking G-layers. New Phytol. 179: 94-103.
39. SALVI, S., G. SPONZA, M. MORGANTE, D. TOMES, X. NIU et al., 2007 Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize. Proc. Natl. Acad. Sci. USA 104: 11376-11381.
40. SAVOLAINEN, O., and T. PYHAJARVI, 2007 Genomic diversity in forest trees. Curr. Opin. Plant Biol. 10: 162-167.
41. SCHIMLECK, L. R., P. S. KUBE and C. A. RAYMOND, 2004 Genetic improvement of kraft pulp yield in Eucalyptus nitens using cellulose content determined by near infrared spectroscopy. Can. J. For. Res. 34: 2363-2370.
42. SCHINDELMAN, G., A. MORIKAMI, J. JUNG, T. I. BASKIN, N. C. CARPITA et al., 2001 COBRA encodes a putative GPI-anchored protein, which is polarly localized and necessary for oriented cell expansion in Arabidopsis. Genes Dev. 15: 1115-1127.
43. SCHOUTEN, J. P., C. J. MCELGUNN, R. WAAIJER, D. ZWIJNENBURG, F. DIEPVENS et al., 2002 Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification. Nucleic Acids Res. 30: e57.
44. SERRE, D., S. GURD, B. GE, R. SLADEK, D. SINNETT et al., 2008 Differential allelic expression in the human genome: a robust approach to identify genetic and epigenetic cis-acting mechanisms regulating gene expression. PLoS Genet. 4: e1000006.
45. SHIRSAT, A., N. WILFORD, R. CROY and D. BOULTER, 1989 Sequences responsible for the tissue specific promoter activity of a pea legumin gene in tobacco. Mol. Gen. Genet. 215: 326-331.
46. SOLE, X., E. GUINO, J. VALLS, R. INIESTA and V. MORENO, 2006 SNPStats: a web tool for the analysis of association studies. Bioinformatics 22: 1928-1929.
47. SOUTHERTON, S. G., H. MARSHALL, A. MOURADOV and R. D. TEASDALE, 1998 Eucalypt MADS-box genes expressed in developing flowers. Plant Physiol. 118: 365-372.
48. SPRINGER, N. M., and R. M. STUPAR, 2007 Allele-specific expression patterns reveal biases and embryo-specific parent-of-origin effects in hybrid maize. Plant Cell 19: 2391-2402.
49. STEPHENS, M., N. J. SMITH and P. DONNELLY, 2001 A new statistical method for haplotype reconstruction from population data. Am. J. Hum. Genet. 68: 978-989.
50. STUPAR, R. M., and N. M. SPRINGER, 2006 Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression patterns in the F1 hybrid. Genetics 173: 2199-2210.
51. TAO, H., D. R. COX and K. A. FRAZER, 2006 Allele-specific KRT1 expression is a complex trait. PLoS Genet. 2: e93.
52. THOMPSON, J. D., D. G. HIGGINS and T. J. GIBSON, 1994 Clustal-W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
53. THORNSBERRY, J. M., M. M. GOODMAN, J. DOEBLEY, S. KRESOVICH, D. NIELSEN et al., 2001 Dwarf8 polymorphisms associate with variation in flowering time. Nat. Genet. 28: 286-289.
54. THUMMA, B. R., M. R. NOLAN, R. EVANS and G. F. MORAN, 2005 Polymorphisms in cinnamoyl CoA reductase (CCR) are associated with variation in microfibril angle in Eucalyptus spp. Genetics 171: 1257-1265.
55. UNOKI, M., and Y. NAKAMURA, 2003 Methylation at CpG islands in intron 1 of EGR2 confers enhancer-like activity. FEBS Lett. 554: 67-72.
56. VEYRIERAS, J.-B., S. KUDARAVALLI, S. Y. KIM, E. T. DERMITZAKIS, Y. GILAD et al., 2008 High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genet. 4: e1000214.
57. YAN, H., W. YUAN, V. E. VELCULESCU, B. VOGELSTEIN and K. W. KINZLER, 2002 Allelic variation in human gene expression. Science 297: 1143. (Pubitemid 36193340)
58. ZAYKIN, D. V., P. H. WESTFALL, S. S. YOUNG, M. A. KARNOUB, M. J. WAGNER et al., 2002 Testing association of statistically inferred haplotypes with discrete and continuous traits in samples of unrelated individuals. Hum. Hered. 53: 79-91.
59. ZHANG, X. Y., J. YAZAKI, A. SUNDARESAN, S. COKUS, S. W. L. CHAN et al., 2006 Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126: 1189-1201. (Pubitemid 44380289)
60. ZHANG, Y., D. WANG, A. D. JOHNSON, A. C. PAPP and W. SADEE, 2005 Allelic expression imbalance of human mu Opioid Receptor (OPRM1) caused by variant A118G. J. Biol. Chem. 280: 32618-32624.