Extensive allelic variation in gene expression in populus F1 hybrids

Genetics

Volumn 177, Issue 4, 2007, Pages 1987-1996

  Zhuang, Yan ^a   Adams, Keith L ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; ASPEN; GENE CONTROL; GENE EXPRESSION; GENE REARRANGEMENT; GENE SILENCING; GENETIC ANALYSIS; GENETIC VARIABILITY; HETEROSIS; HYBRID; NUCLEOTIDE SEQUENCE; PHENOTYPIC VARIATION; PLANT LEAF; PLANT STEM; PRIORITY JOURNAL; SPECIES DIFFERENTIATION;

ALLELES; CHIMERA; ENHANCER ELEMENTS (GENETICS); GENE EXPRESSION REGULATION, PLANT; PLANT COMPONENTS; POPULUS; TRANS-ACTIVATION (GENETICS); VARIATION (GENETICS);

POPULUS; POPULUS DELTOIDES; POPULUS TRICHOCARPA X POPULUS DELTOIDES;

EID: 37249069878     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.107.080325     Document Type: Article

References (51)

1. ADAMS, K. L., 2007 Evolution of duplicate gene expression in polyploid and hybrid plants. J. Hered. 98: 136-141.
2. ADAMS, K. L., R. CRONN, R. PERCIFIELD and J. F. WENDEL, 2003 Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing. Proc. Natl. Acad. Sci. USA 100: 4649-4654.
3. ADAMS, K. L., R. PERCIFIELD and J. F. WENDEL, 2004 Organ-specific silencing of duplicated genes in a newly synthesized cotton allotetraploid. Genetics 168: 2217-2226.
4. ADAMS, K. L., and J. F. WENDEL, 2005 Allele-specific, bidirectional silencing of an alcohol dehydrogenase gene in different organs of interspecific diploid cotton hybrids. Genetics 171: 2139-2142.
5. ARNOLD, M. L., 2004 Natural hybridization and the evolution of domesticated, pest and disease organisms. Mol. Ecol. 13: 997-1007.
6. AUGER, D. L., A. D. GRAY, T. S. REAM, A. KATO, E. H. COE, JR. et al., 2005 Nonadditive gene expression in diploid and triploid hybrids of maize. Genetics 169: 389-397.
7. BAO, J., S. LEE, C. CHEN, X. ZHANG, Y. ZHANG et al., 2005 Serial analysis of gene expression study of a hybrid rice strain (LYP9) and its parental cultivars. Plant Physiol. 138: 1216-1231.
8. BIRCHLER, J. A., D. L. AUGER and N. C. RIDDLE, 2003 In search of the molecular basis of heterosis. Plant Cell 15: 2236-2239.
9. BIRCHLER, J. A., H. YAO and S. CHUDALAYANDI, 2006 Unraveling the genetic basis of hybrid vigor. Proc. Natl. Acad. Sci. USA 103: 12957-12958.
10. BRADSHAW, JR., H. D., and R. F. STETTLER, 1995 Molecular genetics of growth and development in populus. IV. Mapping QTLs with large effects on growth, form, and phenology traits in a forest tree. Genetics 139: 963-973.
11. BRAY, N. J., P. R. BUCKLAND, M. J. OWEN and M. C. O'DONOVAN, 2003 Cis-acting variation in the expression of a high proportion of genes in human brain. Hum. Genet. 113: 149-153.
12. COMAI, L., A. P. TYAGI, K. WINTER, R. HOLMES-DAVIS, S. H. REYNOLDS et al., 2000 Phenotypic instability and rapid gene silencing in newly formed Arabidopsis allotetraploids. Plant Cell 12: 1551-1568.
13. COWLES, C. R., J. N. HIRSCHHORN, D. ALTSHULER and E. S. LANDER, 2002 Detection of regulatory variation in mouse genes. Nat. Genet. 32: 432-437.
14. GILCHRIST, E. J., G. W. HAUGHN, C. C. YING, S. P. OTTO, J. ZHUANG et al., 2006 Use of ecotilling as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa. Mol. Ecol. 15: 1367-1378.
15. GUO, M., M. A. RUPE, O. N. DANILEVSKAYA, X. YANG and Z. HU, 2003 Genome-wide mRNA profiling reveals heterochronic allelic variation and a new imprinted gene in hybrid maize endosperm. Plant J. 36: 30-44.
16. GUO, M., M. A. 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.
17. 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.
18. HEGARTY, M. J., G. L. BARKER, I. D. WILSON, R. J. ABBOTT, K. J. EDWARDS et al., 2006 Transcriptome shock after interspecific hybridization in senecio is ameliorated by genome duplication. Curr. Biol. 16: 1652-1659.
19. HEGARTY, M. J., and S. J. HISCOCK, 2005 Hybrid speciation in plants: new insights from molecular studies. New Phytol. 165: 411-423.
20. HEGARTY, M. J., J. M. JONES, I. D. WILSON, G. L. BARKER, J. A. COGHILL et al., 2005 Development of anonymous cDNA microarrays to study changes to the Senecio floral transcriptome during hybrid speciation. Mol. Ecol. 14: 2493-2510.
21. KASHKUSH, K., M. FELDMAN and A. A. LEVY, 2002 Gene loss, silencing, and activation in a newly synthesized wheat allotetraploid. Genetics 160: 1651-1659.
22. LANDRY, C. R., P. J. WITTKOPP, C. H. TAUBES, J. M. RANZ, A. G. CLARK et al., 2005 Compensatory cis-trans evolution and the dysregulation of gene expression in interspecific hybrids of Drosophila. Genetics 171: 1813-1822.
23. LI, B., G. T. HOWE and R. WU, 1998 Developmental factors responsible for heterosis in aspen hybrids (Populus tremuloides X P. tremula). Tree Physiol. 18: 29-36.
24. LIU, B., and J. F. WENDEL, 2000 Retrotransposon activation followed by rapid repression in introgressed rice plants. Genome 43: 874-880.
25. MEYER, S., H. POSPISIL and S. SCHOLTEN, 2007 Heterosis associated gene expression in maize embryos 6 days after fertilization exhibits additive, dominant and overdominant pattern. Plant Mol. Biol. 63: 381-391.
26. NORTON, N., N. M. WILLIAMS, H. J. WILLIAMS, G. SPURLOCK, G. KIROV et al., 2002 Universal, robust, highly quantitative SNP allele frequency measurement in DNA pools. Hum. Genet. 110: 471-478.
27. PINSONNEAULT, J., C. U. NIELSEN and W. SADEE, 2004 Genetic variants of the human H+/dipeptide transporter PEPT2: analysis of haplotype functions. J. Pharmacol. Exp. Ther. 311: 1088-1096.
28. RIDDLE, N. C., and J. A. BIRCHLER, 2003 Effects of reunited diverged regulatory hierarchies in allopolyploids and species hybrids. Trends Genet. 19: 597-600.
29. RIESEBERG, L. H., 1997 Hybrid origins of plant species. Annu. Rev. Ecol. Syst. 28: 359-389.
30. RIESEBERG, L. H., M. A. ARCHER and R. K. WAYNE, 1999 Transgressive segregation, adaptation and speciation. Heredity 83 (Pt 4): 363-372.
31. RIESEBERG, L. H., O. RAYMOND, D. M. ROSENTHAL, Z. LAI, K. LIVINGSTONE et al., 2003a Major ecological transitions in wild sunflowers facilitated by hybridization. Science 301: 1211-1216.
32. RIESEBERG, L. H., B. SINERVO, C. R. LINDER, M. C. UNGERER and D. M. ARIAS, 1996 Role of gene interactions in hybrid speciation: evidence from ancient and experimental hybrids. Science 272: 741-745.
33. RIESEBERG, L. H., A. WIDMER, A. M. ARNTZ and J. M. BURKE, 2003b The genetic architecture necessary for transgressive segregation is common in both natural and domesticated populations. Philos. Trans. R. Soc. Lond. B Biol. Sci. 358: 1141-1147.
34. RONALD, J., J. M. AKEY, J. WHITTLE, E. N. SMITH, G. YVERT et al., 2005 Simultaneous genotyping, gene-expression measurement, and detection of allele-specific expression with oligonucleotide arrays. Genome Res. 15: 284-291.
35. SALMON, A., M. L. AINOUCHE and J. F. WENDEL, 2005 Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae). Mol. Ecol. 14: 1163-1175.
36. SHAKED, H., K. KASHKUSH, H. OZKAN, M. FELDMAN and A. A. LEVY, 2001 Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. Plant Cell 13: 1749-1759.
37. SHAN, X., Z. LIU, Z. DONG, Y. WANG, Y. CHEN et al., 2005 Mobilization of the active MITE transposons mPing and Pong in rice by introgression from wild rice (Zizania latifolia Griseb.). Mol. Biol. Evol. 22: 976-990.
38. SONG, R., G. SEGAL and J. MESSING, 2004 Expression of the sorghum 10-member kafirin gene cluster in maize endosperm. Nucleic Acids Res. 32: e189.
39. SPRINGER, N. M., and R. M. STUPAR, 2007a Allelic variation and heterosis in maize: How do two halves make more than a whole? Genome Res. 17: 264-275.
40. SPRINGER, N. M., and R. M. STUPAR, 2007b Allele-specific expression patterns reveal biases and embryo-specific parent-of-origin effects in hybrid maize. Plant Cell 19: 2391-2402.
41. STUPAR, R. M., P. J. HERMANSON and N. M. SPRINGER, 2007 Non-additive expression and parent-of-origin effects identified by microarray and allele-specific expression profiling of maize endosperm. Plant Physiol. (in press).
42. 1 hybrid. Genetics 173: 2199-2210.
43. SWANSON-WAGNER, R. A., Y. JIA, R. DECOOK, L. A. BORSUK, D. NETTLETON et al., 2006 All possible modes of gene action are observed in a global comparison of gene expression in a maize F1 hybrid and its inbred parents. Proc. Natl. Acad. Sci. USA 103: 6805-6810.
44. TUSKAN, G. A., S. DIFAZIO, S. JANSSON, J. BOHLMANN, I. GRIGORIEV et al., 2006 The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313: 1596-1604.
45. UZAROWSKA, A., B. KELLER, H. P. PIEPHO, G. SCHWARZ, C. INGVARDSEN et al., 2007 Comparative expression profiling in meristems of inbred-hybrid triplets of maize based on morphological investigations of heterosis for plant height. Plant Mol. Biol. 63: 21-34.
46. VUYLSTEKE, M., F. VAN EEUWIJK, P. VAN HUMMELEN, M. KUIPER and M. ZABEAU, 2005 Genetic analysis of variation in gene expression in Arabidopsis thaliana. Genetics 171: 1267-1275.
47. WANG, D., A. D. JOHNSON, A. C. PAPP, D. L. KROETZ and W. SADEE, 2005 Multidrug resistance polypeptide 1 (MDR1, ABCB1) variant 3435C>Taffects mRNA stability. Pharmacogenet. Genomics 15: 693-704.
48. WANG, Z., Z. NI, H. WU, X. NIE and Q. SUN, 2006 Heterosis in root development and differential gene expression between hybrids and their parental inbreds in wheat (Triticum aestivum L.). Theor. Appl. Genet. 113: 1283-1294.
49. WITTKOPP, P. J., B. K. HAERUM and A. G. CLARK, 2004 Evolutionary changes in cis and trans gene regulation. Nature 430: 85-88.
50. WU, L. M., Z. F. NI, F. R. MENG, Z. LIN and Q. X. SUN, 2003 Cloning and characterization of leaf cDNAs that are differentially expressed between wheat hybrids and their parents. Mol. Genet. Genomics 270: 281-286.
51. YAN, H., W. YUAN, V. E. VELCULESCU, B. VOGELSTEIN and K. W. KINZLER, 2002 Allelic variation inhumangeneexpression. Science 297: 1143.