Subtractive libraries for prospecting differentially expressed genes in the soybean under water deficit

Genetics and Molecular Biology

Volumn 35, Issue SUPPL.1, 2012, Pages 304-314

  Rodrigues, Fabiana Aparecida ^a   Marcolino Gomes, Juliana ^a   de Fátima Corrêa Carvalho, Josirlei ^a   do Nascimento, Leandro Costa ^b   Neumaier, Norman ^a   Farias, José Renato Bouças ^a   Carazzolle, Marcelo Falsarella ^b   Marcelino, Francismar Corrêa ^a   Nepomuceno, Alexandre Lima ^a  

^a EMBRAPA CERRADOS   (Brazil)

^b UNIVERSITY OF CAMPINAS   (Brazil)

Author keywords

Drought; Gene expression; Transcriptome

Indexed keywords

COMPLEMENTARY DNA; TRANSCRIPTOME; PLANT DNA;

ARTICLE; CONTROLLED STUDY; CULTIVAR IDENTIFICATION; DNA LIBRARY; DNA SYNTHESIS; DROUGHT TOLERANCE; GENE EXPRESSION REGULATION; GENETIC LINE; GENETIC VARIABILITY; NONHUMAN; PHOTOSYNTHESIS; PLANT LEAF; PLANT ROOT; PLANT STRESS; PLANT WATER RELATION; POLYMERASE CHAIN REACTION; SENSITIVITY ANALYSIS; SOYBEAN; SUPPRESSION SUBTRACTIVE HYBRIDIZATION; WATER STRESS; CULTIVAR; DROUGHT; GENE EXPRESSION; NUTRIENT; PLANT GENE; PLANT GROWTH; TEMPERATURE; WATER DEFICIT;

GLYCINE MAX;

EID: 84862983664     PISSN: 14154757     EISSN: 16784685     Source Type: Journal    
DOI: 10.1590/S1415-47572012000200011     Document Type: Article

References (55)

1. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W and Lipman DJ (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25:3389-3402.
2. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. (2000) Gene ontology: Tool for the unification of biology. Nat Genet 25:25-29.
3. Bray EA (2004) Genes commonly regulated by water-deficit stress in Arabidopsis thaliana. J Exp Bot 55:2331-2341.
4. Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S, the AmiGO Hub and the Web Presence Working Group (2009) AmiGO: Online access to ontology and annotation data. Bioinformatics 25:288-289.
5. Carvalho MHCD (2008) Drought stress and reactive oxygen species. Plant Signal Behav 3:156-165.
6. Chauhan H, Khurana N, Tyagi AK, Khurana JP and Khurana P (2011) Identification and characterization of high temperature stress responsive genes in bread wheat (Triticum aestivum L.) and their regulation at various stages of development. Plant Mol Biol 75:35-51.
7. Cheung F, Win J, Lang JM, Hamilton J, Vuong H, Leach JE, Kamoun S, Lévesque CA, Tisserat N and Buell CR (2008) Analysis of the Pythium ultimum transcriptome using Sang-er and Pyrosequencing approaches. BMC Genomics 9:e542.
8. Cocozza C, Cherubini P, Regier N, Saurer M, Frey B and Tognetti R (2010) Early effects of water deficit on two parental clones of Populus nigra grown under different environmental conditions. Funct Plant Biol 37:244-254.
9. Daldoul S, Guillaumie S, Reustle GM, Krczal G, Ghorbel A, Delrot S, Mliki A and Hofer MU (2010) Isolation and expression analysis of salt induced genes from contrasting grapevine (Vitis vinifera L.) cultivars. Plant Sci 179:489-498.
10. Diatchenko L, Lau Y-FC, Campbell AP, Chenchik A, Moqadam F, Huang B, Lukyanov S, Lukyanov K, Gurskaya N, Sver-dlov ED, et al. (1996) Suppression subtractive hybridization: A method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc Natl Acad Sci USA 93:6025-6030.
11. Ergen NZ and Budak H (2009) Sequencing over 13,000 expressed sequence tags from six subtractive cDNA libraries of wild and modern wheats following slow drought stress. Plant Cell Environ 32:220-236.
12. Fehr WR, Caviness CE, Burmood DT and Pernnigton JS (1971) Stage of development description for soybeans [Glycine max (L.) Merrill]. Crop Sci 11:929-931.
13. Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, et al. (2010) The Pfam protein families database. Nucleic Acids Res 38:D211-D222.
14. Gao S-Q, Chen M, Xu Z-S, Zhao C-P, Li L, Xu H-j, Tang Y-m, Zhao X and Ma Y-Z (2011) The soybean GmbZIP1 transcription factor enhances multiple abiotic stress tolerances in transgenic plants. Plant Mol Biol 75:537-553.
15. González-Candelas L, Alamar S, Sánchez-Torres P, Zacarías L and Marcos JF (2010) A transcriptomic approach highlights induction of secondary metabolism in citrus fruit in response to Penicillium digitatum infection. BMC Plant Biol 10:e194.
16. Götz S, García-Gómez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, Robles M, Talón M, Dopazo J and Conesa A (2008) High-throughput functional annotation and data min ing with the Blast2GO suite. Nucleic Acids Res 36:3420-3435.
17. Govind G, Thamme-Gowda HV, Kalaiarasi PJ, Iyer DR, Muthap-pa SK, Nese S and Makarla UK (2009) Identication and functional validation of a unique set of drought induced genes preferentially expressed in response to gradual water stress in peanut. Mol Genet Genomics 281:591-605.
18. Harb A, Krishnan A, Ambavaram MMR and Pereira A (2010) Molecular and physiological analysis of drought stress in Arabidopsis reveals early responses leading to acclimation in plant growth. Plant Physiol 154:1254-1271.
19. Harismendy O, Ng PC, Strausberg RL, Wang X, Stockwell TB, Beeson KY, Schork NJ, Murray SS, Topol EJ, Levy S, et al. (2009) Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol 10:R32.
20. Hernandez D, François P, Farinelli L, Østerås M and Schrenzel J (2008) De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer. Genome Res 18:802-809.
21. Hert DG, Fredlake CP and Barron AE (2008) Advantages and limitations of next generation sequencing technologies: A comparison of electrophoresis and non-electrophoresis methods. Electrophoresis 29:4618-4626.
22. Hoagland DR and Arnon DI (1950) The water-culture method for growing for plants without soil. Agric Exp Stn Circ 347:1-32.
23. Jain D and Chattopadhyay D (2010) Analysis of gene expression in response to water deficit of chickpea (Cicer arietinum L.) varieties differing in drought tolerance. BMC Plant Biol 10:e24.
24. Kanehisa M and Goto S (2000) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28:27-30.
25. Khanna-Chopra R and Selote DS (2007) Acclimation to drought stress generates oxidative stress tolerance in drought-resistant than -susceptible wheat cultivar under field conditions. Environ Exp Bot 60:276-283.
26. Kocsy G, Laurie R, Szalai G, Szilágyi V, Simon-Sarkadi L, Galiba G and de Ronde JA (2005) Genetic manipulation of proline levels affects antioxidants in soybean subjected to simultaneous drought and heat stresses. Physiol Plant 124:227-235.
27. Kojima H, Hitomi Y, Numata T, Tanaka C, Imai K and Omokawa H (2009) Analysis of gene expression in rice root tips treated with R-1-a-methylbenzyl-3-p-tolylurea using PCR-based suppression subtractive hybridization. Pestic Biochem Physiol 93:58-64.
28. Koski LB, Gray MW, Lang BF and Burger G (2005) AutoFACT: An automatic functional annotation and classification tool. BMC Bioinformatics 6:e151.
29. Kron AP, Souza GM and Ribeiro RV (2008) Water deficiency at different developmental stages of Glycine max can improve drought tolerance. Bragantia 67:43-49.
30. Li R, Li Y, Kristiansen K and Wang J (2008) SOAP: Short oligonucleotide alignment program. Bioinformatics 24:713-714.
31. Li X-W, Feng Z-G, Yang H-M, Zhu X-P, Liu J and Yuan H-Y (2010) A novel cold-regulated gene from Camellia sinensis, CsCOR1, enhances salt- and dehydration-tolerance in tobacco. Biochem Biophys Res Commun 394:354-359.
32. Marioni JC, Mason CE, Mane SM, Stephens M and Gilad Y (2009) RNA-seq: An assessment of technical reproduci- bility and comparison with gene expression arrays. Genome Res 18:1509-1517.
33. Martins PK, Jordão BQ, Yamanaka N, Farias JRB, Beneventi MA, Binneck E, Fuganti R, Stolf R and Nepomuceno AL (2008) Differential gene expression and mitotic cell analysis of the drought tolerant soybean (Glycine max L. Merrill Fabales, Fabaceae) cultivar MG/BR46 (Conquista) under two water deficit induction systems. Genet Mol Biol 32:512-521.
34. Molina C, Rotter B, Horres R, Udupa SM, Besser B, Bellarmino L, Baum M, Matsumura H, Terauchi R, Kahl G, et al. (2008) SuperSAGE: The drought stress-responsive transcriptome of chickpea roots. BMC Genomics 9:e553.
35. Montero-Barrientos M, Hermosa R, Cardoza RE, Gutiérrez S, Nicolás C and Monte E (2010) Transgenic expression of the Trichoderma harzianum hsp70 gene increases Arabidopsis resistance to heat and other abiotic stresses. J Plant Physiol 167:659-665.
36. Nelson RT and Shoemaker R (2006) Identification and analysis of gene families from the duplicated genome of soybean using EST sequences. BMC Genomics 7:e204.
37. Oya T, Nepomuceno AL, Neumaier N, Farias JRB, Tobita S and Ito O (2004) Drought tolerance characteristics of Brazilian soybean cultivars - Evaluation and characterization of drought tolerance of various Brazilian soybean cultivars in the field. Plant Prod Sci 7:129-137.
38. Pedersen P, Kumudini S, Board J. and Conley S (2005) Soybean growth and development. In: Dorrance AE, Draper MA and Hershman DE (eds) Using Foliar Fungicides to Manage Soybean Rust. Ohio State University, Columbus, pp 41-47.
39. Prentis PJ, Woolfit M, Thomas-Hall SR, Ortiz-Barrientos D, Pavasovic A, Lowe AJ and Schenk PM (2010) Massively parallel sequencing and analysis of expressed sequence tags in a successful invasive plant. Ann Bot 106:1009-1017.
40. Priyanka B, Sekhar K, Reddy VD and Rao KV (2010) Expression of pigeonpea hybrid-proline-rich protein encoding gene (CcHyPRP) in yeast and Arabidopsis affords multiple abiotic stress tolerance. Plant Biotechnol J 8:76-87.
41. Reddy PCO, Sairanganayakulu G, Thippeswamy M, Reddy PS, Reddy MK and Sudhakar C (2008) Identification of stress-induced genes from the drought tolerant semi-arid legume crop horsegram (Macrotyloma uniflorum (Lam.) Verdc.) through analysis of subtracted expressed sequence tags. Plant Sci 175:372-384.
42. Sakuma Y, Maruyama K, Qin F, Osakabe Y, Shinozaki K and Yamaguchi-Shinozaki K (2006) Dual function of an Arabidopsis transcription factor DREB2A in water-stress-responsive and heat-stress-responsive gene expression. Proc Natl Acad Sci USA 103:18822-18827.
43. Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, et al. (2010) Genome sequence of the palaeopolyploid soybean. Nature 463:178-183.
44. Schultz J, Milpetz F, Bork P and Ponting CP (1998) SMART, a simple modular architecture research tool: Identification of signaling domains. Proc Natl Acad Sci USA 95:5857-5864.
45. Sekhar K, Priyanka B, Reddy VD and Rao KV (2010) Isolation and characterization of a pigeonpea cyclophilin (CcCYP) gene, and its over-expression in Arabidopsis confers multiple abiotic stress tolerance. Plant Cell Environ 33:1324-1338.
46. Shendure J and Ji H (2008) Next-generation DNA sequencing. Nat Biotechnol 26:1135-1145.
47. Shinozaki K and Yamaguchi-Shinozaki K (2007) Gene networks involved in drought stress response and tolerance. J Exp Bot 58:221-227.
48. Soria-Guerra RE, Rosales-Mendoza S, Chang S, Haudenshield JS, Zheng D, Rao SS, Hartman GL, Ghabrial SA and Korban SS (2010) Identifying differentially expressed genes in leaves of Glycine tomentella in the presence of the fungal pathogen Phakopsora pachyrhizi. Planta 232:1181-1189.
49. Tedersoo L, Nilsson RH, Abarenkov K, Jairus T, Sadam A, Saar I, Bahram M, Bechem E, Chuyong G and Kõljalg U (2010) 454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases. New Phytol 188:291-301.
50. Türkan I, Bor M, Özdemir F and Koca H (2005) Differential responses of lipid peroxidation and antioxidants in the leaves of drought-tolerant P. acutifolius Gray and drought-sensitive P. vulgaris L. subjected to polyethylene glycol mediated water stress. Plant Sci 168:223-231.
51. Wang Z, Gerstein M and Snyder M (2009) RNA-Seq: A revolutionary tool for transcriptomics. Nat Rev Genet 10:57-63.
52. Xu D, Wei J, Cui H, Gong J, Yan Y, Lai R and Qin Q (2010) Differential profiles of gene expression in grouper Epinephelus coioides, infected with Singapore grouper iridovirus, revealed by suppression subtractive hybridization and DNA microarray. J Fish Biol 77:341-360.
53. Zhang JZ, Li ZM, Liu L, Mei L, Yao JL and Hu CG (2008) Identification of early-flower-related ESTs in an early-flowering mutant of trifoliate orange (Poncirus trifoliata) by suppression subtractive hybridization and macroarray analysis. Tree Physiol 28:1449-1457.
54. Zhang Y, Liu X, Zhang W and Han R (2010) Differential gene expression of the honey bees Apis mellifera and A. cerana induced by Varroa destructor infection. J Insect Physiol 56:1207-1218.
55. Zhao C-X, Shao H-B and Chu L-Y (2008) Aquaporin structure-function relationships: Water flow through plant living cells. Colloids and Surf B Biointerfaces 62:163-172.