Cold responsive gene expression profiling of sugarcane and Saccharum spontaneum with functional analysis of a cold inducible Saccharum homolog of NOD26-like intrinsic protein to salt and water stress

PLoS ONE

Volumn 10, Issue 5, 2015, Pages

  Park, Jong Won ^a   Benatti, Thiago R ^a,b   Marconi, Thiago ^a   Yu, Qingyi ^a   Solis Gracia, Nora ^a   Mora, Victoria ^a   Da Silva, Jorge A ^a  

^a TEXAS A AND M UNIVERSITY   (United States)

^b Centro de Tecnologia Copersucar   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME; PLANT PROTEIN;

ABIOTIC STRESS; AMINO ACID ANALYSIS; AMINO ACID SEQUENCE; ARTICLE; COLD TOLERANCE; CONTROLLED STUDY; ENZYME SPECIFICITY; EVAPOTRANSPIRATION; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE INDUCTION; GENETIC CONSERVATION; GENETIC DATABASE; GENOTYPE; IRRIGATION (AGRICULTURE); LONG TERM EXPOSURE; MEMBRANE TRANSPORT; MOLECULAR CLONING; MONOCOT; NICOTIANA TABACUM; NONHUMAN; PLANT GENE; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN MOTIF; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; SACCHARUM SPONTANEUM; SALT STRESS; SSPNIP2 GENE; SUGARCANE; TRANSGENIC PLANT; WATER STRESS; WILD TYPE; BIOLOGY; CHEMISTRY; COLD; GENE EXPRESSION REGULATION; GENETICS; HIGH THROUGHPUT SEQUENCING; METABOLISM; MOLECULAR GENETICS; PHENOTYPE; PHYSIOLOGICAL STRESS; SEQUENCE ALIGNMENT; TOBACCO;

NICOTIANA OBTUSIFOLIA; SACCHARUM; SACCHARUM SPONTANEUM;

AMINO ACID SEQUENCE; CLONING, MOLECULAR; COLD TEMPERATURE; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MOLECULAR SEQUENCE ANNOTATION; MOLECULAR SEQUENCE DATA; PHENOTYPE; PLANT PROTEINS; PLANTS, GENETICALLY MODIFIED; SACCHARUM; SEQUENCE ALIGNMENT; STRESS, PHYSIOLOGICAL; TOBACCO; TRANSCRIPTOME;

EID: 84929380261     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0125810     Document Type: Article

References (59)

1. Manners JM. Functional genomics of sugarcane. Adv Bot Res. 2011; 60:89-168.
2. Ramdoyal K, Badaloo GH. Prebreeding in sugarcane with an emphasis on the programme of the Mauritius Sugar Industry Research Institute. In: Engles JMM, Rao VR, Brown AHD, Jackson MT, editors. Managing plant genetic diversity. Wallingford: CABI Publishing; 2001. p. 307-321.
3. Stevenson GC. Genetics and breeding of sugar cane. London: Longman; 1965.
4. Berding N, Roach BT. Germplasm conservation, collection, maintenance and use. In: Heinz DJ, editor. Sugarcane improvement through breeding. Amsteridam: Elsevier; 1987. p. 143-210.
5. Lam E, Shine JJ, Da Silva J, Lawton M, Bonos S, Calvino M, et al. Improving sugarcane for biofuel: engineering for an even better feedstock. GCB Bioenergy. 2009; 1:251-255.
6. Waclawovsky AJ, Sato PM, Lembke CG, Moore PH, Souza GM. Sugarcane for bioenergy production: an assessment of yield and regulation of sucrose content. Plant Biotechnol J. 2010; 8:263-276. doi: 10.1111/j.1467-7652.2009.00491.x PMID: 20388126
7. Heaton EA, Dohleman FG, Long SP. Meeting US biofuel goals with less land: the potential of Miscanthus. Global Change Biol. 2008; 14:2000-2014.
8. Hodnett GL, Hale AL, Packer DJ, Stelly DM, da Silva JA, Rooney WL. Elimination of a reproductive barrier facilitates intergeneric hybridization of Sorghum bicolor and Saccharum. Crop Sci. 2010; 50:1-8.
9. Mukherjee SK. Origin and distribution of Saccharum. Botanical Gazette. 1957; 119:55-61.
10. Amalraj V, Balasundaram N. On the taxonomy of the members of 'Saccharum complex'. Genet Resour Crop Evol. 2006; 53:35-41.
11. Edme SJ, Glynn NG, Comstock JC. Genetic segregation of microsatellite markers in Saccharum officinarum and S. spontaneum. Heredity (Edinb). 2006; 97:366-375. PMID: 16912699
12. Dillon SL, Shapter FM, Henry RJ, Cordeiro G, Izquierdo L, Lee LS. Domestication to crop improvement: genetic resources for sorghum and Saccharum (Andropogoneae). Ann Bot. 2007; 100:975-989. PMID: 17766842
13. Daniels J, Smith P, Paton N, Williams CA. The origin of the genus Saccharum. Sugarcane Breed Newslett. 1975; 36:24-39.
14. Aitken K, McNeil M. Diversity analysis. In: Henry R, Kole C, editors. Genetics, Genomics and Breeding of Sugarcane. New York: CRC Press; 2010. p. 419-442.
15. Daniels J, Roach BT. Taxonomy and evolution. In: Heinz DJ, editor. Sugarcane improvement through breeding. Amsterdam: Elsevier; 1987. p. 7-84.
16. Martin F. Survey of germplasm needs for Saccharum species in the United States 1996. Available from: http://www.ars-grin.gov/npgs/cgc-reports/sugar.html.
17. Kawar PG, Devarumath RM, Nerkar Y. Use of RAPD markers for assessment of genetic diversity in sugarcane cultivars. Indian J Biotech. 2009; 8:67-71. doi: 10.1007/s10237-008-0121-6 PMID: 18293021
18. Khan FA, Khan A, Azhar FM, Rauf S. Genetic diversity of Saccharum officinarum accessions in Pakistan as revealed by random amplified polymorphic DNA. Genetics and Molecular Research. 2009; 8:1376-1382. doi: 10.4238/vol8-4gmr665 PMID: 19937582
19. Nair NV, Selvi A, Sreenivasan TV, Push-palatha KN. Molecular diversity in Indian sugarcane cultivars as revealed by randomly amplified DNA polymorphisms. Euphytica. 2002; 127:219-225.
20. Ma JF, Yamaji N. Functions and transport of silicon in plants. Cell Mol Life Sci. 2008; 65:3049-3057. doi: 10.1007/s00018-008-7580-x PMID: 18560761
21. Hsieh TH, Lee JT, Yang PT, Chiu LH, Charng YY, Wang YC, et al. Heterology expression of the Arabidopsis C-repeat/dehydration response element binding factor 1 gene confers elevated tolerance to chilling and oxidative stresses in transgenic tomato. Plant Physiol. 2002; 129:1086-1094. PMID: 12114563
22. Dugas DV, Monaco MK, Olsen A, Klein RR, Kumari S, Ware D, et al. Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid. BMC Genomics. 2011; 12:514. doi: 10.1186/1471-2164-12-514 PMID: 22008187
23. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013; 30:2725-2729. doi: 10.1093/molbev/mst197 PMID: 24132122
24. Danielson JA, Johanson U. Phylogeny of major intrinsic proteins. Adv Exp Med Biol. 2010; 679:19-31. PMID: 20666221
25. Ma JF. Silicon transporters in higher plants. Adv Exp Med Biol. 2010; 679:99-109. PMID: 20666227
26. Mitani N, Yamaji N, Ma JF. Identification of maize silicon influx transporters. Plant Cell Physiol. 2009; 50:5-12. doi: 10.1093/pcp/pcn110 PMID: 18676379
27. Danielson JAH, Johanson U. Phylogeny of major intrinsic proteins. In: Jahn TP, Bienert GP, editors. MIPs and their role in the exchange of metalloids. New York: Springer Science+Business Media, LLC; 2010. p. 19-31. PMID: 20666219
28. Gong HJ, Randall DP, Flowers TJ. Silicon deposition in the root reduces sodium uptake in rice (Oryza sativa L.) seedlings by reducing bypass flow. Plant Cell Environ. 2006; 29:1970-1979. PMID: 16930322
29. Baker SS, Wilhelm KS, Thomashow MF. The 5'-region of Arabidopsis thaliana cor15a has cis-acting elements that confer cold-, drought- and ABA-regulated gene expression. Plant Mol Biol. 1994; 24:701-713. PMID: 8193295
30. Shinozaki K, Yamaguchi-Shinozaki K, Seki M. Regulatory network of gene expression inn the drought and cold stress responses. Current Opinion in Plant Biology. 2003; 6:410-417. PMID: 12972040
31. Yamaguchi-Shinozaki K, Shinozaki K. Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses. Annu Rev Plant Biol. 2006; 57:781-803. PMID: 16669782
32. Qi X, Xie S, Liu Y, Yi F, Yu J. Genome-wide annotation of genes and noncoding RNAs of foxtail millet in response to simulated drought stress by deep sequencing. Plant Mol Biol. 2013; 83:459-473. doi: 10.1007/s11103-013-0104-6 PMID: 23860794
33. Perrone I, Pagliarani C, Lovisolo C, Chitarra W, Roman F, Schubert A. Recovery from water stress affects grape leaf petiole transcriptome. Planta. 2012; 235:1383-1396. doi: 10.1007/s00425-011-1581-y PMID: 22241135
34. Giordano A, Cogan NO, Kaur S, Drayton M, Mouradov A, Panter S, et al. Gene discovery and molecular marker development, based on high-throughput transcript sequencing of Paspalum dilatatum Poir. PLoS One. 2014; 9:e85050. doi: 10.1371/journal.pone.0085050 PMID: 24520314
35. Priest HD, Fox SE, Rowley ER, Murray JR, Michael TP, Mockler TC. Analysis of global gene expression in Brachypodium distachyon reveals extensive network plasticity in response to abiotic stress. PLoS One. 2014; 9:e87499. doi: 10.1371/journal.pone.0087499 PMID: 24489928
36. Wspalz T, Fujiyoshi Y, Engel A. The AQP structure and functional implications. In: Beitz E, editor. Aquaporins, Handbook of Experimental Pharmacology. 190. Heidelberg: Springer-Verlag Berlin; 2009. p. 31-56.
37. Johanson U, Gustavsson S. A new subfamily of major intrinsic proteins in plants. Mol Biol Evol. 2002; 19:456-461. PMID: 11919287
38. Ma JF. Silicon transporters in higher plants. In: Jahn TP, editor. MIPs and their role in the exchange of metalloids. New York: Landes Bioscience and Springer Science+Business Media; 2010. p. 99-109. PMID: 20666219
39. Wallace IS, Roberts DM. Distinct transport selectivity of two structural subclasses of the nodulin-like intrinsic protein family of plant aquaglyceroporin channels. Biochemistry. 2005; 44:16826-16834. PMID: 16363796
40. Forrest KL, Bhave M. Major intrinsic proteins (MIPs) in plants: a complex gene family with major impacts on plant phenotype. Funct Integr Genomics. 2007; 7:263-289. PMID: 17562090
41. Ma JF, Tamai K, Yamaji N, Mitani N, Konishi S, Katsuhara M, et al. A silicon transporter in rice. Nature. 2006; 440:688-691. PMID: 16572174
42. Ma JF, Tamai K, Ichii M, Wu GF. A rice mutant defective in Si uptake. Plant Physiol. 2002; 130: 2111-2117. PMID: 12481095
43. Yamaji N, Mitatni N, Ma JF. A transporter regulating silicon distribution in rice shoots. Plant Cell. 2008; 20:1381-1389. doi: 10.1105/tpc.108.059311 PMID: 18515498
44. Yamaji N, Chiba Y, Mitani-Ueno N, Feng Ma J. Functional characterization of a silicon transporter gene implicated in silicon distribution in barley. Plant Physiol. 2012; 160:1491-1497. doi: 10.1104/pp.112.204578 PMID: 22992512
45. Kvedaras OL, Keeping MG, Goebel FR, Byrne MJ. Water stress augments silicon-mediated resistance of susceptible sugarcane cultivars to the stalk borer Eldana saccharina (Lepidoptera: Pyralidae). Bulletin of entomological research. 2007; 97:175-183. PMID: 17411480
46. de Camargo MS, Amorim L, Gomes AR Jr. Silicon fertilisation decreases brown rust incidence in sugarcane. Crop Protection. 2013; 53:72-79.
47. Savant NK, Korndoerfer GH, Datnoff LE, Snyder GH. Silicon nutrition and sugarcane production: A review. J Plant Nutrition. 1999; 22:1853-1903.
48. Sacala E. Role of silicon in plant resistance to water stress. J Elementol. 2009; 14:619-630.
49. Fauteux F, Remus-Borel W, Menzies JG, Belanger RR. Silicon and plant disease resistance against plant pathogenic fungi. FEMS Microbiol Lett. 2005; 249:1-6. PMID: 16006059
50. Gao X, Zou CH, Wang L, Zhang F. Silicon decreases tranpiration rate and conductance from stomata of maize plants. J Plant Nutrition. 2006; 29:1637-1647.
51. Tuna AL, Kaya C, Higgs D, Murillo-Amador B, Aydemir S, Girgin AR. Silicon improves salinity tolerance in wheat plants. Environ Exp Bot. 2008; 62:10-16.
52. Savvas D, Giotis D, Chatzieustratiou E, Bakea M, Patakioutas G. Silicon supply in soilless cultivation of zucchini alleviates stress induced by salinity and powdery mildew infections. Environ Exp Bot. 2009; 65:11-17.
53. Keeping MG, Miles N, Sewpersad C. Silicon reduces impact of plant nitrogen in promoting stalk borer (Eldana saccharina) but not sugarcane thrips (Fulmekiola serrata) infestations in sugarcane. Front Plant Sci. 2014; 5:289. doi: 10.3389/fpls.2014.00289 PMID: 24999349
54. Keeping MG, Meyer JH, Sewpersad C. Soil silicon amendments increase resistance of sugarcane to stalk borer Eldana saccharina Walker (Lepidoptera: Pyralidae) under field conditions. Plant Soil. 2013; 363:297-318.
55. Liang Y, Sun W, Zhu Y-G, Christie P. Mechanisms of silicon alleviation of abiotic stresses in higher plants: A review. Environ Pollut. 2007; 147:422-428. PMID: 16996179
56. Gunes A, Inal A, Bagci EG, Pilbeam DJ. Silicon-mediated changes of some physiological and enzymatic parameters symptomatic for oxidative stress in spinach and tomato grown in sodic-B toxic soil. Plant Soil. 2007; 290:103-114.
57. Zuccarini P. Effects of silicon on photosynthesis, water relations and nutrient uptake of Phaseolus vulgaris under NaCl stress. Biol Plant. 2008; 52:157-160. doi: 10.1387/ijdb.072316jk PMID: 18311705
58. Liang Y, Zhang W, Chen Q, Liu Y, Ding R. Effect of exogenous silicon (Si) on H+-ATPase activity, phospholipids and fluidity of plasma membrane in leaves of salt-stressed barley (Hordeum vulgare L.). Environ Exp Bot. 2006; 57:212-219.
59. Liang Y. Effects of silicon on enzyme activity and sodium, potassium and calcium concentration in barley under salt stress. Plant soil. 1999; 209:217-224.