Parallel domestication, convergent evolution and duplicated gene recruitment in allopolyploid cotton

Genetics

Volumn 179, Issue 3, 2008, Pages 1725-1733

  Hovav, Ran ^a   Chaudhary, Bhupendra ^a   Udall, Joshua A ^a,b   Flagel, Lex ^a   Wendel, Jonathan F ^a  

^a IOWA STATE UNIVERSITY   (United States)

^b BRIGHAM YOUNG UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALLOPOLYPLOIDY; ARTICLE; CONTROLLED STUDY; COTTON; DOMESTICATION; EVOLUTION; GENE DUPLICATION; GENE EXPRESSION; GENE MUTATION; GENOME; GOSSYPIUM BARBADENSE; GOSSYPIUM HIRSUTUM; HIGH THROUGHPUT SCREENING; MICROARRAY ANALYSIS; MORPHOLOGY; NONHUMAN; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; DUPLICATE GENE; GENE; GENE EXPRESSION REGULATION; GENETICS; POLYPLOIDY;

GOSSYPIUM HIRSUTUM;

COTTON FIBER; EVOLUTION; GENE EXPRESSION REGULATION, PLANT; GENES, DUPLICATE; GENES, PLANT; GOSSYPIUM; POLYPLOIDY;

EID: 52049088237     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.108.089656     Document Type: Article

References (36)

1. ADAMS, K. L., and J. F. WENDEL, 2005 Novel patterns of gene expression in polyploid plants. Trends Genet. 21: 539-543.
2. APPLEQUIST, W. L., R. CRONN and J. F. WENDEL, 2001 Comparative development of fiber in wild and cultivated cotton. Evol. Dev. 3: 3-17.
3. BLUTHGEN, N., K. BRAND, B. CAJAVEC, M. SWAT, H. HERZEL et al., 2005 Biological profiling of gene groups utilizing gene ontology. Genome Inform. Ser. Workshop Genome Inform. 16: 106-115.
4. BRUBAKER, C. L., F. M. BOURLAND and J. F. WENDEL, 1999 The origin and domestication of cotton, pp. 3-31 in Cotton: Origin, History, Technology and Production, edited by C. W. SMITH and J. T. COTHREN. John Wiley & Sons, New York.
5. BRUBAKER, C. L., and J. F. WENDEL, 1994 Reevaluating the origin of domesticated cotton (Gossypium-hirsutum Malvaceae) using nuclear restriction-fragment-length-polymorphisms (Rflps). Am. J. Bot. 81: 1309-1326.
6. CHEN, Z. J., 2007 Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids. Annu. Rev. Plant. Biol. 58: 377-406.
7. CHEN, Z. J., M. HA and D. SOLTIS, 2007 Polyploidy: genome obesity and its consequences. New Phytol. 174: 717-720.
8. DILLEHAY, T. D., J. ROSSEN, T. C. ANDRES and D. E. WILLIAMS, 2007 Preceramic adoption of peanut, squash, and cotton in northern Peru. Science 316: 1890-1893.
9. ENDRIZZI, J. E., E. L. TURCOTTE and R. J. KOHEL, 1985 Genetics, cytology, and evolution of Gossypium. Adv. Genet. 23: 271-375.
10. FLAGEL, L., J. A. UDALL, D. NETTLETON and J. F. WENDEL, 2008 Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution. BMC Biol. 6: 16.
11. FORCE, A., M. LYNCH, F. B. PICKETT, A. AMORES, Y. L. YAN et al., 1999 Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531-1545.
12. FRYXELL, P. A., 1979 The Natural History of the Cotton Tribe. Texas A&M University Press, College Station, TX.
13. GAETA, R. T., J. C. PIRES, F. INIGUEZ- LUY, E. LEON and T. C. OSBORN, 2007 Genomic changes in resynthesized Brassica napus and their effect on gene expression and phenotype. Plant Cell 19:3403-3417.
14. HONG-BIN, L., Y.-M. QIN, P. YU, S. WEN-QIANG, M. WEN-QIAN et al., 2007 A cotton ascorbate peroxidase is involved in hydrogen peroxide homeostasis during fibre cell development. New Phytol. 175: 462-471.
15. HOVAV, R., J. A. UDALL, B. CHAUDHARY, L. FLAGEL, R. RAPP et al., 2008a Partitioned expression of duplicated genes during development and evolution of a single cell in a polyploid plant. Proc. Natl. Acad. Sci. USA 105: 6191-6195.
16. HOVAV, R., J. A. UDALL, B. CHAUDHARY, E. HOVAV, L. FLAGEL et al., 2008b The evolution of spinable cotton fiber entailed natural selection for prolonged development and a novel metabolism. PLoS Genet. 4: e25.
17. HOVAV, R., J. A. UDALL, E. HOVAV, R. A. RAPP, L. FLAGEL et al., 2008c A majority of genes are expressed in the single-celled seed trichome of cotton. Planta 227: 319-329.
18. JIANG, C. X., R. J. WRIGHT, K. M. EL-ZIK and A. H. PATERSON, 1998 Polyploid formation created unique avenues for response to selection in Gossypium (cotton). Proc. Natl. Acad. Sci. USA 95: 4419-4424.
19. KIM, H. J., and B. A. TRIPLETT, 2001 Cotton fiber growth in planta and in vitro. Models for plant cell elongation and cell wall biogenesis. Plant Physiol. 127: 1361-1366.
20. LIU, B., and J. F. WENDEL, 2003 Epigenetic phenomena and the evolution of plant allopolyploids. Mol. Phylogenet. Evol. 29: 365-379.
21. LYNCH, M., and J. S. CONERY, 2000 The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155.
22. OSBORN, T. C., 2004 The contribution of polyploidy to variation in Brassica species. Plant Physiol. 121: 531-536.
23. PERCY, R. G., and J. F. WENDEL, 1990 Allozyme evidence for the origin and diversification of Gossypium-barbadense L. Theor. Appl. Genet. 79: 529-542.
24. RABINOWICZ, P. D., R. CITEK, M. A. BUDIMAN, A. NUNBERG, J. A. BEDELL et al., 2005 Differential methylation of genes and repeats in land plants. Genome Res. 15: 1431-1440.
25. RONG, J., E. A. FELTUS, V. N. WAGHMARE, G. J. PIERCE, P. W. CHEE et al., 2007 Meta-analysis of polyploid cotton QTL shows unequal contributions of subgenomes to a complex network of genes and gene clusters implicated in lint fiber development. Genetics 176: 2577-2588.
26. STOREY, J. D., and R. TIBSHIRANI, 2003 SAM thresholding and false discovery rates for detecting differential gene expression in DNA microarrays, pp. 272-290 in The Analysis of Gene Expression Data: Methods and Software, edited by G. PARMIGIANI, E. S. GARRETT, R. A. IRIZARRY and S. L. ZEGER. Springer, New York.
27. TALIERCIO, E. W., and D. BOYKIN, 2007 Analysis of gene expression in cotton fiber initials. BMC Plant Biol. 7: 22.
28. UDALL, J. A., and J. F. WENDEL, 2006 Polyploidy and crop improvement. Crop Sci. 46: S3-S14.
29. UDALL, J. A., J. M. SWANSON, D. NETTLETON, R. J. PERCIFIELD and J. F. WENDEL, 2006 A novel approach for characterizing expression levels of genes duplicated by polyploidy. Genetics 173: 1823-1827.
30. WENDEL, J. F., 1995 Cotton, pp. 358-366 in Evolution of Crop Plants, edited by N. Simmonds and J. Smartt. Longman, London.
31. WENDEL, J. F., 2000 Genome evolution in polyploids. Plant Mol. Biol. 42: 225-249.
32. WENDEL, J. F., and R. C. CRONN, 2003 Polyploidy and the evolutionary history of cotton. Adv. Agron. 78: 139-186.
33. WESTENGEN, O., Z. HUAMAN and M. HEUN, 2005 Genetic diversity and geographic pattern in early South American cotton domestication. Theor. Appl. Genet. 110: 392-402.
34. WHITTAKER, D. J., and B. A. TRIPLETT, 1999 Gene-specific changes in alpha-tubulin transcript accumulation in developing cotton fibers. Plant Physiol. 121: 181-188.
35. XIANG, Y., X. HUANG, T. WANG, Y. ZHANG, Q. W. LIU et al., 2007 ACTIN BINDING PROTEIN29 from Lilium pollen plays an important role in dynamic actin remodeling. Plant Cell 19: 1930-1946.
36. ZHAO, G. R., J. Y. LIU and X. M. DU, 2001 Molecular cloning and characterization of cotton cDNAs expressed in developing fiber cells. Biosci. Biotechnol. Biochem. 65: 2789-2793.