In Silico and Quantitative Analyses of the Putative FLC-like Homologue in Coffee (Coffea arabica L.)

Plant Molecular Biology Reporter

Volumn 30, Issue 1, 2012, Pages 29-35

  Barreto, Horllys Gomes ^a   Lazzari, Fabiane ^a   Ságio, Solange Aparecida ^a   Chalfun Junior, Antonio ^a   Paiva, Luciano Vilela ^a   Benedito, Vagner Augusto ^b  

^a FEDERAL UNIVERSITY OF LAVRAS   (Brazil)

^b WEST VIRGINIA UNIVERSITY   (United States)

Author keywords

Bioinformatics; Flowering regulation; Gene expression; Real time polymerase chain reaction

Indexed keywords

COFFEA ARABICA; DICOTYLEDONEAE;

EID: 84856094054     PISSN: 07359640     EISSN: 15729818     Source Type: Journal    
DOI: 10.1007/s11105-011-0310-9     Document Type: Article

References (37)

1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI BLAST: a new generation of protein database search programs. Nucleic Acids Res 25(17): 3389-3402. doi: 10. 1093/nar/25. 17. 3389.
2. Alvim PT (1960) Moisture stress as a requirement for flowering of coffee. Science 3423(132): 354. doi: 10. 1126/science. 132. 3423. 354.
3. Barsalobres-Cavallari CF, Severino FE, Maluf MP, Maia IG (2009) Identification of suitable internal control genes for expression studies in Coffea arabica under different experimental conditions. BMC Mol Biol 10(1): 1-11. doi: 10. 1186/1471-2199-10-1.
4. Becker A, Theissen G (2003) The major clades of MADS-box genes and their role in the development and evolution of flowering plants. Mol Phylogenet Evol 29(3): 464-489. doi: 10. 1016/S1055-7903(03)00207-0.
5. Blazquez MA (2000) Flower development pathways. J Cell Sci 113(20): 3547-3548.
6. Camargo AP (1985) Florescimento e frutificação do café arábica nas diferentes regiões cafeeiras do Brasil. Pesqui Agropecu Bras 20(7): 831-839.
7. Chalfoun SM (2010) Controle biológico e metabólitos microbianos bioativos: uma perspectiva da qualidade do café. Ciên Agrotec 34(5): 1071-1085. doi: 10. 1590/S1413-70542010000500001.
8. Ciannamea S (2007) Molecular characterization of the vernalization response in lolion perenne. Dissertation (PhD in Plant Sciences) Wageningen University.
9. Du N, Pijut PM (2010) Isolation and characterization of an AGAMOUS homolog from Fraxinus pennsylvanica. Plant Mol Biol Rep 28(2): 344-351. doi: 10. 1007/s11105-009-0163-7.
10. Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95(25): 14863-14868.
11. Farnezi MMM, Silva EB, Guimarães PTG, Pinto NAVD (2010) Levantamento da qualidade da bebida do café e avaliação do estado nutricional dos cafeeiros do Alto Jequitinhonha, Minas Gerais, através do DRIS. Ciên Agrotec 34(5): 1191-1198. doi: 10. 1590/S1413-70542010000500016.
12. Hou JH, Gao ZH, Zhang Z, Chen SM, Ando T, Zhang JY, Wang XW (2011) Isolation and characterization of an AGAMOUS homologue PmAG from the japanese apricot (Prunus mume Sieb. et Zucc.). Plant Mol Biol Rep 29(2): 473-480. doi: 10. 1007/s11105-010-0248-3.
13. Johanson U, West J, Lister C, Michaels S, Amasino R, Dean C (2000) Molecular analysis of FRIGIDA, a major determinant of natural variation in Arabidopsis flowering time. Science 290(5490): 344-347. doi: 10. 1126/science. 290. 5490. 344.
14. Liu X, Anderson JM, Pijut PM (2010) Cloning and characterization of prunus serotina AGAMOUS, a putative flower homeotic Gene. Plant Mol Biol Rep 28(2): 193-203. doi: 10. 1007/s11105-009-0140-1.
15. Masarirambi MT, Chingwara V, Shongwe VD (2009) The effect of irrigation on synchronization of coffee (Coffea arabica L.) flowering and berry ripening at Chipinge, Zimbabwe. Phys Chem Earth 34(13): 786-789. doi: 10. 1016/j. pce. 2009. 06. 013.
16. Michaels SD, Amasino RM (1999) FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering. Plant Cell 11(5): 949-956. doi: 10. 1105/tpc. 11. 5. 949.
17. Mondego JM, Vidal RO, Carazzolle MF, Tokuda EK, Parizzi LP, Costa GG, Pereira LF, Andrade AC, Colombo CA, Vieira LG, Pereira GA, Genome Project Consortium BC (2011) An EST-based analysis identifies new genes and reveals distinctive gene expression features of Coffea arabica and Coffea canephora. BMC Plant Biol 11(1): 30. doi: 10. 1186/1471-2229-11-30.
18. Morais H, Caramori PH, Koguishi MS, Ribeiro AMA (2008) Escala fenológica detalhada da fase reprodutiva de Coffea arabica. Bragantia 67(1): 257-260. doi: 10. 1590/S0006-87052008000100031.
19. Oliveira RR, Chalfun-Junior A, Paiva LV, Andrade AC (2010) In silico and quantitative analyses of MADS-Box genes in Coffea arabica. Plant Mol Biol Rep 28(3): 460-472. doi: 10. 1007/s11105-009-0173-5.
20. Privat I, Bardil A, Gomez AB, Severac D, Dantec C, Fuentes I, Mueller L, Joët T, Pot D, Foucrier S, Dussert S, Leroy T, Journot L, de Kochko A, Campa C, Combes MC, Lashermes P, Bertrand B (2011) The 'PUCE CAFE' Project: the first 15K coffee microarray, a new tool for discovering candidate genes correlated to agronomic and quality traits. BMC Genomics 12(1): 5. doi: 10. 1186/1471-2164-12-5.
21. Reeves PA, He Y, Schimitz RJ, Amasino RM, Panella LM, Richards CM (2007) Evolutionary conservation of the FLC-mediated vernalization response: evidence from the sugarbeet (Beta vulgaris). Genetics 176(1): 295-307. doi: 10. 1534/genetics. 106. 069336.
22. Rena AB, Maestri M (1985) Fisiologia do cafeeiro. Informe Agropecuário Belo Horizonte 11(126): 26-40.
23. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4(4): 406-425.
24. Silva FM, Alves MC, Souza JCS, Oliveira MS (2010) Efeitos da colheita manual na bienalidade do cafeeiro em Ijaci, Minas Gerais. Ciên Agrotec 34(3): 625-632. doi: 10. 1590/S1413-70542010000300014.
25. Simpson GG, Dean C (2002) Arabidopsis, the rosetta stone of flowering time. Science 296(5566): 285-289. doi: 10. 1126/science. 296. 5566. 285.
26. Sitnikova T, Rzhetsky A, Nei M (1995) Interior-branch and bootstrap tests of phylogenetics trees. Mol Biol Evol 13(4): 319-333.
27. Song JJ, Ma W, Tang YJ, Chen ZY, Liao JP (2010) Isolation and characterization of three MADS-box genes from Alpinia hainanensis (Zingiberaceae). Plant Mol Biol Rep 28(2): 264-276. doi: 10. 1007/s11105-009-0147-7.
28. Tamura K, Dudley J, Nei M, Kumar SH (2007) MEGA4: molecular evolutionary genetics analysis: software: version 4. 0. Mol Biol Evol 24(8): 1596-1599. doi: 10. 1093/molbev/msm092.
29. Tan FC, Swain SM (2007) Functional characterization of AP3, SOC1 and WUS homologues from citrus (Citrus sinensis). Physiol Plant 131(3): 481-595. doi: 10. 1111/j. 1399-3054. 2007. 00971. x.
30. Thompson JD, Higgins DG, Gibson TJ, Clustal W (1994) Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22(22): 4673-4680.
31. Vidal RO, Mondego JMC, Pot D, Ambrosio AB, Andrade AC, Pereira LFP, Colombo CA, Vieira LGE, Carazzolle MF, Pereira GAG (2010) A high-throughput data mining of single nucleotide polymorphisms in Coffea species expressed sequence tags suggests differential homeologous gene expression in the allotetraploid Coffea Arabica. Plant Physiol 154(3): 1053-1066. doi: 10. 1104/pp. 110. 162438.
32. Vieira LGE, Andrade AC, Colombo CA, Pereira LFP, Santos SN, Moraes AHA, Metha A, Oliveira AC, Labate CA, Marino CL (2006) Brazilian coffee genome project: an EST-based genomic resource. Braz J Plant Physiol 18(1): 95-108. doi: 10. 1590/S1677-04202006000100008.
33. Wang R, Farrona S, Vincent C, Joecker A, Schoof H, Turck F, Alonso-Blanco C, Coupland G, Albani MC (2009) PEP1 regulates perennial flowering in Arabis alpina. Nature 459(7245): 423-427. doi: 10. 1038/nature07988.
34. Wu X, Shi J, Xi M, Luo Z, Hu X (2010) A B functional gene cloned from lily encodes an ortholog of Arabidopsis PISTILLATA (PI). Plant Mol Biol Rep 28(4): 684-691. doi: 10. 1007/s11105-010-0193-1.
35. Xu J, Zhong X, Zhang Q, Li H (2010) Overexpression of the GmGAL2 gene accelerates flowering in Arabidopsis. Plant Mol Biol Rep 28(4): 704-711. doi: 10. 1007/s11105-010-0201-5.
36. Yan Z, Liang D, Liu H, Zheng G (2010) FLC: a key regulator of flowering time in Arabidopsis. Russ J Plant Physiol 57(2): 166-174. doi: 10. 1134/S1021443710020020.
37. Zhang JZ, Li ZM, Mei L, Yao JL, Hu CG (2009) PtFLC homolog from trifoliate orange (Poncirus trifoliata) is regulated by alternative splicing and experiences seasonal fluctuation in expression level. Planta 299(4): 847-859. doi: 10. 1007/s00425-008-0885-z.