Transcriptomic and proteomic analysis reveals mechanisms of embryo abortion during chrysanthemum cross breeding

Scientific Reports

Volumn 4, Issue , 2014, Pages

  Zhang, Fengjiao ^a,b   Wang, Zhiquan ^a   Dong, Wen ^c   Sun, Chunqing ^a   Wang, Haibin ^a   Song, Aiping ^a   He, Lizhong ^a   Fang, Weimin ^a   Chen, Fadi ^a,b   Teng, Nianjun ^a,b  

^a NANJING AGRICULTURAL UNIVERSITY   (China)

^b Jiangsu Province Engineering Lab for Modern Facility Agriculture Technology and Equipment   (China)

^c CHINA RURAL TECHNOLOGY DEVELOPMENT CENTER   (China)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME; VEGETABLE PROTEIN;

BIOSYNTHESIS; BREEDING; CHRYSANTHEMUM; CROSS BREEDING; EMBRYOLOGY; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; NUCLEOTIDE SEQUENCE; PLANT SEED; PROTEOMICS;

BASE SEQUENCE; BREEDING; CHRYSANTHEMUM; CROSSES, GENETIC; GENE EXPRESSION REGULATION, PLANT; PLANT PROTEINS; PROTEOMICS; SEEDS; TRANSCRIPTOME;

EID: 84923313963     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep06536     Document Type: Article

References (56)

1. Bawa, K. S. Embryo and seed abortion in plants. Nature 342, 625 (1989
2. Batygina, R. B. Generative organs of flower Embryology of flowering plants: Terminology and concepts Batygina, R. B. (ed.) (Science Publishers Inc, USA, 2002
3. Arathi, H. S., Ganeshaiah, K. N., Shaanker, R. U. & Hegde, S. G. Factors affecting embryo abortion in Syzygium cuminii (L.) Skeels (Myrtaceae). Int. J. Plant Sci. 157, 49-52 (1996
4. Ndoutoumou, P. N., Toussaint, A. & Baudoin, J. P. Embryo abortion and histological features in the interspecific cross between Phaseolus vulgaris L. and P. coccineus L. Plant Cell Tissue Organ Cult. 88, 329-332 (2007
5. Wang, Z., Gerstein, M. & Snyder, M. RNA-Seq: A revolutionary tool for transcriptomics. Nat. Rev. Genet. 10, 57-63 (2009
6. Palmieri, M. C. et al. Proteomic analysis of grapevine resistance induced by Trichoderma harzianum T39 reveals specific defence pathways activated against downy mildew. J. Exp. Bot. 63, 6237-6251 (2012
7. Robertson, F. P. et al. Proteome changes in tomato lines transformed with phytoene synthase-1 in the sense and antisense orientations. J. Exp. Bot. 63, 6035-6043 (2012
8. Raherison, E. et al. Transcriptome profiling in conifers and the PiceaGenExpress database show patterns of diversification within gene families and interspecific conservation in vascular gene expression. BMC Genomics 13, 434 (2012
9. Q?iu, Z. B. et al. The regulation of cambial activity in Chinese fir (Cunninghamia lanceolata) involves extensive transcriptome remodeling. New Phytol. 199, 708-719 (2013
10. Palovaara, J., Saiga, S. & Weijers, D. Transcriptomics approaches in the early Arabidopsis embryo. Trends Plant Sci. 18, 514-521 (2013
11. Chen, X. P. et al. Deep sequencing analysis of the transcriptomes of peanut aerial and subterranean young pods identifies candidate genes related to early embryo abortion. Plant Biotechnol. J. 11, 115-127 (2013
12. Teixeira da Silva, J. A. et al. Chrysanthemum Biotechnology: Quo vadis? Crit. Rev. Plant Sci. 32, 21-52 (2013
13. Anderson, N. O. Chrysanthemum. Flower Breeding and Genetics Anderson, N. O. (ed.) 389-437 (Springer, Netherlands, 2006
14. Sun, C. Q. et al. Interspecific hybrids between Chrysanthemum grandiflorum (Ramat.) Kitamura and C. indicum (L.) Des Moul. and their drought tolerance evaluation. Euphytica 174, 51-60 (2010
15. Sun, C. Q. et al. Factors affecting seed set in the crosses between Dendranthema grandiflorum (Ramat.) Kitamura and its wild species. Euphytica 171, 181-192 (2010
16. Sun, C. Q. et al. Overcoming pre-fertilization barriers in the wide cross between Chrysanthemum grandiflorum (Ramat.) Kitamura and C. nankingense (Nakai) Tzvel. by using special pollination techniques. Euphytica 178, 195-202 (2011
17. Lafon-Placette, C. & Köhler, C. Embryo and endosperm, partners in seed development. Curr. Opin. Plant Biol. 17, 64-69 (2014
18. Köhler, C. & Kradolfer, D. Epigenetic mechanisms in the endosperm and their consequences for the evolution of flowering plants. BBA-Gene Regul. Mech. 1809, 438-443 (2011
19. Costa, L. M. et al. Maternal control of nutrient allocation in plant seeds by genomic imprinting. Curr. Biol. 22, 160-165 (2012
20. Kradolfer, D., Wolff, P., Jiang, H., Siretskiy, A. & Köhler, C. An imprinted gene underlies postzygotic reproductive isolation in Arabidopsis thaliana. Dev. cell 26, 525-535 (2013
21. Bochenek, M. et al. Transcriptome analysis of the sulfate deficiency response in the marine microalga Emiliania huxleyi. New Phytol. 199, 650-662 (2013
22. Guggisberg, A., Lai, Z., Huang, J. & Rieseberg, L. H. Transcriptome divergence between introduced and native populations of Canada thistle, Cirsium arvense. New Phytol. 199, 595-608 (2013
23. Muth, T. et al. TraqX: A free, platform independent tool for isobaric tag quantitation at the protein level. Proteomics 10, 1223-1225 (2010
24. Hou, S. Y., Jones, S. W., Choe, L. H., Papoutsakis, E. T. & Lee, K. H. Workflow for quantitative proteomic analysis of Clostridia acetobutylicum ATCC 824 using iTRAQ tags. Methods 61, 269-276 (2013
25. Tse, W. K. F. et al. Transcriptomic and iTRAQ proteomic approaches reveal novel short-term hyperosmotic stress responsive proteins in the gill of the Japanese eel (Anguilla japonica). J. Proteomics 89, 81-94 (2013
26. Wang, H. B. et al. Next-generation sequencing of the Chrysanthemum nankingense (Asteraceae) transcriptome permits large-scale unigene assembly and SSR marker discovery. PloS one 8, e62293 (2013
27. Mortazavi, A.,Williams, B. A.,McCue, K., Schaeffer, L. &Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. methods 5, 621-628 (2008
28. Oliveros, J. C. VENNY. An interactive tool for comparing lists with Venn Diagrams.,http://bioinfogp.cnb.csic.es/tools/venny/index.html. (2007) Date of access: 06/06/2014.
29. Zhao, P. et al. A bipartite molecular module controls cell death activation in the basal cell lineage of plant embryos. PLoS Biol. 11, e1001655 (2013
30. Thomas, S. G. & Franklin-Tong, V. E. Self-incompatibility triggers programmed cell death in Papaver pollen. Nature 429, 305-309 (2004
31. Rogers, H. J. Cell death and organ development in plants. Curr. Top. Develop. Biol. 71, 225-261 (2005
32. Ge, X. C. et al. An Arabidopsis aspartic protease functions as an anti-cell-death component in reproduction and embryogenesis. EMBO Rep. 6, 282-288 (2005
33. Bosch, M. & Franklin-Tong, V. E. Temporal and spatial activation of caspase-like enzymes induced by self-incompatibility in Papaver pollen. Proc. Natl. Acad. Sci. USA 104, 18327-18332 (2007
34. Wilkins, K. A. et al. Reactive oxygen species and nitric oxide mediate actin reorganization and programmed cell death in the self-incompatibility response of papaver. Plant Physiol. 156, 404-416 (2011
35. Xue, Z. Q. et al. Changes of Endogenous Hormones in Relation to Embryo Abortion in Seedless Watermelon. Acta Agr. Boreali-Occidentalis Sinica 3, 044 (2007
36. Ma, K. F. et al. The low fertility of Chinese white poplar: Dynamic changes in anatomical structure, endogenous hormone concentrations, and key gene expression in the reproduction of a naturally occurring hybrid. Plant Cell Rep. 32, 401-414 (2013
37. Hays, D. B., Do, J. H., Mason, R. E., Morgan, G. & Finlayson, S. A. Heat stress induced ethylene production in developing wheat grains induces kernel abortion and increased maturation in a susceptible cultivar. Plant Sci. 172, 1113-1123 (2007
38. Facucho-Oliveira, J. M. & John, J. S. The relationship between pluripotency and mitochondrial DNA proliferation during early embryo development and embryonic stem cell differentiation. Stem Cell Rev. Rep. 5, 140-158 (2009
39. Speakman, J. R. Body size, energy metabolism and lifespan. J. Exp. Biol. 208, 1717-1730 (2005
40. Wu, X. Q. et al. Integrative proteomic and cytological analysis of the effects of extracellular Ca21 influx on Pinus bungeana pollen tube development. J. Proteome Res. 7, 4299-4312 (2008
41. Clark, B. F. C. et al. Prokaryotic and eukaryotic translation actors: International union of biochemistry and molecular biology (IUBMB). Biochimie 78, 1119-1122 (1996
42. Drake, T. & Vavylonis, D. Cytoskeletal dynamics in fission yeast: A review of models for polarization and division. HFSP J. 4, 122-130 (2010
43. Verma, R. et al. Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome. Science 298, 611-615 (2002
44. Guo, X. et al. UBLCP1 is a 26S proteasome phosphatase that regulates nuclear proteasome activity. Proc. Natl. Acad. Sci. USA 108, 18649-18654 (2011
45. Teixeira, L. K. & Reed, S. I. Ubiquitin ligases and cell cycle control. Annu. Rev. Biochem. 82, 387-414 (2013
46. Kim, D. H. et al. SOMNUS, a CCCH-type zinc finger protein in Arabidopsis, negatively regulates light-dependent seed germination downstream of PIL5. Plant Cell 20, 1260-1277 (2008
47. Xu, Z. S., Chen, M., Li, L. C.&Ma, Y. Z. Functions and application of the AP2/ERF transcription factor family in crop improvement. J. Integr. Plant Biol. 53, 570-585 (2011
48. Schmitz, R. J., Hong, L., Michaels, S. & Amasino, R. M. FRIGIDA-ESSENTIAL 1 interacts genetically with FRIGIDA and FRIGIDA-LIKE 1 to promote the winterannual habit of Arabidopsis thaliana. Develpment 132, 5471-5478 (2005
49. Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29, 644-652 (2011
50. Iseli, C., Jongeneel, C. V. & Bucher, P. ESTScan: A program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. ISMB 99, 138-148 (1999
51. Ashburner, M. et al.Gene Ontology: Tool for the unification of biology. Nat. Genet. 25, 25-29 (2000
52. Ye, J. et al. WEGO: A web tool for plotting GO annotations. Nucl. Acid. Res. 34, W293-W297 (2006
53. Audic, S. & Claverie, J. M. The significance of digital gene expression profiles. Genome Res. 7, 986-995 (1997
54. Song, A. P. et al. Isolation and characterisation of Chrysanthemum crassum SOS1, encoding a putative plasma membrane Na1/H1 antiporter. Plant Biol. 14, 706-713 (2012
55. Rozen, S. &Skaletsky, H. Primer3 on theWWWfor general users and for biologist programmers. Bioinformatics methods and protocols Misener, S. & Krawetz, S. A. (eds.) 365-386 (Humana Press, New York, 1999
56. Liu, S. Y. et al. iTRAQ-based quantitative proteomic analysis for identification of oligodendroglioma biomarkers related with loss of heterozygosity on chromosomal arm 1p. J. Proteomics. 77, 480-491 (2012).