26 research outputs found
Sugarcane (Saccharum X officinarum): a reference study for the regulation of genetically modified cultivars in Brazil.
Functional markers for gene mapping and genetic diversity studies in sugarcane
<p>Abstract</p> <p>Background</p> <p>The database of sugarcane expressed sequence tags (EST) offers a great opportunity for developing molecular markers that are directly associated with important agronomic traits. The development of new EST-SSR markers represents an important tool for genetic analysis. In sugarcane breeding programs, functional markers can be used to accelerate the process and select important agronomic traits, especially in the mapping of quantitative traits loci (QTL) and plant resistant pathogens or qualitative resistance loci (QRL). The aim of this work was to develop new simple sequence repeat (SSR) markers in sugarcane using the sugarcane expressed sequence tag (SUCEST database).</p> <p>Findings</p> <p>A total of 365 EST-SSR molecular markers with trinucleotide motifs were developed and evaluated in a collection of 18 genotypes of sugarcane (15 varieties and 3 species). In total, 287 of the EST-SSRs markers amplified fragments of the expected size and were polymorphic in the analyzed sugarcane varieties. The number of alleles ranged from 2-18, with an average of 6 alleles per locus, while polymorphism information content values ranged from 0.21-0.92, with an average of 0.69. The discrimination power was high for the majority of the EST-SSRs, with an average value of 0.80. Among the markers characterized in this study some have particular interest, those that are related to bacterial defense responses, generation of precursor metabolites and energy and those involved in carbohydrate metabolic process.</p> <p>Conclusions</p> <p>These EST-SSR markers presented in this work can be efficiently used for genetic mapping studies of segregating sugarcane populations. The high Polymorphism Information Content (PIC) and Discriminant Power (DP) presented facilitate the QTL identification and marker-assisted selection due the association with functional regions of the genome became an important tool for the sugarcane breeding program.</p
Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum
NotificaçÔes aos acordos TBT e SPS: diferentes objetivos e resultados sobre o comércio internacional de agroalimentos
Impactos dos subsĂdios agrĂcolas dos Estados Unidos na expansĂŁo do agronegĂłcio brasileiro
Impacto da regulamentação SPS e TBT nas exportaçÔes brasileiras de uva no perĂodo de 1995 a 2009
Characterization Of New Polymorphic Functional Markers For Sugarcane
Expressed sequence tags (ESTs) offer the opportunity to exploit single, low-copy, conserved sequence motifs for the development of simple sequence repeats (SSRs). The authors have examined the Sugarcane Expressed Sequence Tag database for the presence of SSRs. To test the utility of EST-derived SSR markers, a total of 342 EST-SSRs, which represent a subset of over 2005 SSR-containing sequences that were located in the sugarcane EST database, could be designed from the nonredundant SSR-positive ESTs for possible use as potential genic markers. These EST-SSR markers were used to screen 18 sugarcane (Saccharum spp.) varieties. A high proportion (65.5%) of the above EST-SSRs, which gave amplified fragments of foreseen size, detected polymorphism. The number of alleles ranged from 2 to 24 with an average of 7.55 alleles per locus, while polymorphism information content values ranged from 0.16 to 0.94, with an average of 0.73. The ability of each set of EST-SSR markers to discriminate between varieties was generally higher than the polymorphism information content analysis. When tested for functionality, 82.1% of these 224 EST-SSRs were found to be functional, showing homology to known genes. As the EST-SSRs are within the expressed portion of the genome, they are likely to be associated to a particular gene of interest, improving their utility for genetic mapping; identification of quantitative trait loci, and comparative genomics studies of sugarcane. The development of new EST-SSR markers will have important implications for the genetic analysis and exploitation of the genetic resources of sugarcane and related species and will provide a more direct estimate of functional diversity.522191209Aggarwal, R.K., Hendre, P.S., Varshney, R.K., Bhat, P.R., Krishna-kumar, V., Singh, L., Identification, characterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species (2007) Theor. Appl. Genet, 114, pp. 359-372. , PMID:17115127, doi:10.1007/s00122- 006-0440-xhttp://cran.r-project.org/web/packages/kinship/index.html, Atkinson, B, and Therneau, T. 2007. Kinship: mixed-effects Cox models, sparse matrices, and modeling data from large pedigrees, R package version 1.1.0-17. Available fromBarbosa, A.M.M., Geraldi, I.O., Benchimol, L.L., Garcia, A.A.F., Souza Jr., C.L.S., Souza, A.P., Relationship of intra-and interpopulation tropical maize single cross hybrid performance and genetic distances computed from AFLP and SSR markers (2003) Euphytica, 130, pp. 87-99. , doi:10.1023/A: 1022381008721Barrett, B., Griffiths, A., Schreiber, M., Ellison, N., Mercer, C., Bouton, J., A microsatellite map of white clover (2004) Theor. Appl. Genet, 109, pp. 596-608. , PMID:15103407Bhat, P.R., Krishnakumar, V., Hendre, P.S., Rajendrakumar, P., Varshney, R.K., Aggarwal, R.K., Identification and characterization of expressed sequence tags-derived simple sequence repeats markers from robusta coffee variety 'CxR' (an interespecific hybrid of Coffee canephora Ă Coffee congensis) (2005) Mol. Ecol. Notes, 5, pp. 80-83. , doi:10.1111/j.1471-8286.2004. 00839.xBelaj, A., Satovic, Z., Cipriani, G., Baldoni, L., Testolin, R., Rallo, L., Trujillo, I., Comparative study of the discriminating capacity of RAPD, AFLP and SSR markers and of their effectiveness in establishing genetic relationships in olive (2003) Theor. Appl. Genet, 107, pp. 736-744. , PMID:12819908, doi:10.1007/s00122-003-1301-5Carson, D.L., Botha, F.C., Preliminary analysis of expressed sequence tags for sugarcane (2000) Crop Sci, 40, pp. 1769-1779Casu, R., Dimmock, C., Thomas, M., Bower, N., Knight, D., Grof, C., Genetic and expression profiling in sugarcane (2001) Proc. Int. Soc. Sugarcane Technol, 24, pp. 626-627Casu, R., Manners, J., Bonnett, G., Jackson, P., McIntyre, C., Dunne, R., Genomics approaches for the identification of genes determining important traits in sugarcane (2005) Field Crops Res, 92, pp. 137-147. , doi:10.1016/j.fcr.2005.01.029Chabane, K., Ablett, G.A., Cordeiro, G.M., Valkoun, J., Henry, R.J., EST versus genomics derived microsatellite markers for genotyping wild and cultivated barley (2005) Genet. Resour. Crop Evol, 52, pp. 903-909. , doi:10.1007/s10722-003-6112-7Chee, P.W., Rong, J., Williams-Coplin, D., Schulze, S.R., Paterson, A.H., EST derived PCR-based markers for functional gene homologues in cotton (2004) Genome, 47, pp. 449-462. , PMID:15190362, doi:10.1139/g04-002Chen, C., Zhou, P., Choi, Y.A., Huang, S., Jr-Gmitter, F.G., Mining and characterizing microsatellites from citrus ESTs (2006) Theor. Appl. Genet, 112, pp. 1248-1257. , PMID:16474971, doi:10.1007/ s00122-006-0226-1Cho, Y.G., Ishii, T., Temnykh, S., Chen, X., Lipovich, L., McCouch, S.R., Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.) (2000) Theor. Appl. Genet, 100, pp. 713-722. , doi:10.1007/ s001220051343Cordeiro, G.M., Taylor, G.O., Henry, R.J., Characterization of microsatellite markers from sugarcane (Saccharum spp.), a highly polyploid species (2000) Plant Sci, 155, pp. 161-168. , doi:10. 1016/S0168-9452(00) 00208-9. PMID:10814819Cordeiro, G.M., Casu, R., McIntyre, C.L., Manners, J.M., Henry, R.J., Microsatellite markers from sugarcane (Saccharum spp) ESTs cross-transferable to Erianthus and Sorghum (2001) Plant Sci, 160, pp. 1115-1123. , PMID:11337068, doi:10.1016/S0168-9452(01)00365-XCox, T.S., Kiang, Y.T., Gorman, M.B., Rogers, D.M., Relationships between coefficient of parentage and genetic similarity indices in the soybean (1985) Crop Sci, 25, pp. 529-532Creste, S., Tulmann-Neto, A., Figueira, A., Detection of single repeat polymorphisms in denaturing polyacrylamide sequencing gels by silver staining (2001) Plant Mol. Biol. Rep, 19, pp. 299-306. , doi:10.1007/BF02772828Edwards, K.J., Barker, J.H., Daly, A., Jones, C., Karp, A., Microsatellite libraries enriched for several microsatellite sequences in plants (1996) Biotechniques, 20, pp. 758-760. , PMID:8723911Efron, B., Tibshirani, R.J., (1993) An introduction to the bootstrap, , Chapman & Hall, New YorkEujayl, I., Sorrells, M., Baum, M., Wolters, P., Powell, W., Assessment of genotypic variation among cultivated durum wheat based on EST-SSRs and genomic SSRs (2001) Euphytica, 119, pp. 39-43. , doi:10.1023/A:1017537720475Fraser, L.G., Harvey, C.F., Crowhurst, R.N., De Silva, H.N., EST-derived microsatellites from Actinidia species and their potential for mapping (2004) Theor. Appl. Genet, 108, pp. 1010-1016. , PMID:15067386, doi:10.1007/s00122-003- 1517-4Gao, L.F., Jing, R.L., Huo, N.X., Li, X.P., Zhou, R.H., Chang, X.P., One hundred and one new microsatellite loci derived from ESTs (EST-SSRs) in bread wheat (2004) Theor. Appl. Genet, 108, pp. 1392-1400. , PMID:14968301, doi:10.1007/s00122-003-1554-zGarcia, A.A.F., Kido, E.A., Meza, A.N., Souza, H.M.B., Pinto, L.R., Pastina, M.M., Leite, C.S., Souza, A.P., Development of an integrated genetic map of a sugarcane (Saccharum spp.) commercial cross, based on a maximum-likelihood approach for estimation of linkage and linkage phases (2006) Theor. Appl. Genet, 112, pp. 298-314. , PMID:16307229, doi:10.1007/s00122-005-0129-6Graham, J., Smith, K., MacKenzie, K., Jorgenson, L., Hackett, C., Powell, W., The construction of a genetic linkage map of red raspberry (Rubus idaeus subsp. idaeus) based on AFLPs, genomic-SSR and EST-SSR markers (2004) Theor. Appl. Genet, 109, pp. 740-749. , PMID:15127204, doi:10.1007/s00122- 004-1687-8GuimarĂŁes, P.S., Paterniani, M.E.A.G.Z., LĂŒders, R.R., Souza, A.P., Laborda, P.R., Oliveira, K.M., CorrelacĂŁo da heterose de hĂbridos de milho com divergĂȘncia genĂ©tica entre linhagens. (2007) Pesq. Agropec. Bras, 42, pp. 811-816Gupta, P.K., Varshney, R.K., The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat (2000) Euphytica, 113, pp. 163-185. , doi:10. 1023/A:1003910819967Gupta, P.K., Rutsgi, S., Sharma, S., Singh, R., Kumar, N., Balyan, H.S., Transferable EST-SSR markers for study of polymorphism and genetic diversity in bread wheat (2003) Mol. Genet. Genomics, 270, pp. 315-323. , PMID:14508680, doi:10.1007/s00438-003-0921-4Han, Z.G., Guo, W.Z., Song, X.L., Zhang, T.Z., Genetic mapping of EST-derived microsatellites from the diploid Gossypium arboreum in allotetraploid cotton (2004) Mol. Genet. Genomics, 272, pp. 308-327. , PMID:15368122, doi:10.1007/s00438-004-1059-8Han, Z.G., Wang, C., Song, X., Guo, W., Gou, J., Li, C., Characteristics, development and mapping of Grossypium hirsutum derived EST-SSRs in allotetraploid cotton (2006) Theor. Appl. Genet, 112, pp. 430-439. , PMID:16341684, doi:10.1007/s00122-005-0142-9Hoisington, D., Khairallah, M., GonzĂĄlez-de-LĂ©on, D., (1994) Laboratory protocols, , CIMMYT Applied Molecular Genetics Laboratory. CYMMYT, MĂ©xicoIhaka, R., and Gentleman, R. 1996. R: a language for data analysis and graphics. J. Comput. Graph. Stat. 5: 299-314. doi:10.2307/ 1390807Jaccard, P., (1901) Etude comparative de la distribuition florale dans une portion des Alpes et des Jura. Bull, 37, pp. 547-579. , Soc. Vandoise Sci. NatJannoo, N., Grivet, L., Seguin, M., Paulet, F., Domaingue, R., Rao, P.S., a. Molecular investigation of the genetic base of sugarcane cultivars (1999) Theor. Appl. Genet, 99, pp. 171-184. , doi:10. 1007/s001220051222Kantety, R.V., Rota, M.L., Matthews, D.E., and Sorrells, M.E. 2002. Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol. Biol. 48: 501-510. doi:10.1023/A:1014875206165. PMID:11999831Kempthorne, O., (1957) An introduction to genetic statistics, , John Wiley & Sons, New YorkKhlestkina, E.K., Than, M.H.M., Pestsova, E.G., Röder, M.S., Malyshev, S.V., Korzu, V., Börner, A., Mapping of 99 new microsatellite-derived loci in rye (Secale cereale L.) including 39 expressed sequence tags (2004) Theor. Appl. Genet, 109, pp. 725-732. , PMID:15300380, doi:10.1007/s00122-004-1659-zKing, G., Nienhuis, J., Hussey, C., Genetic similarity among ecotypes of Arabidopsis thaliana estimated by analysis of restriction fragment length polymorphisms (1993) Theor. Appl. Genet, 86, pp. 1028-1032Kota, R., Varshney, R.K., Thiel, T., Dehmer, K.J., Graner, A., Generation and comparison of EST-derived SSRs and SNPs in barley (Hordeum vulgare L.) (2001) Hereditas, 135, pp. 145-151. , PMID:12152327, doi:10.1111/j.1601-5223.2001. 00145.xLima, M.L.A., Garcia, A.A.F., Oliveira, K.M., Matsuoka, S., Souza Jr., C.L., Souza, A.P., Analysis of genetics similarity detected by AFLP and coefficient of parentage among genotypes of sugarcane (Saccharum spp.) (2002) Theor. Appl. Genet, 104, pp. 30-38. , PMID:12579425, doi:10.1007/s001220200003Lu, Y.H., D'Hont, A., Paulet, F., Grivet, L., Arnaud, M., Glaszmann, J.C., Molecular diversity and genome structure in modern sugarcane varieties (1994) Euphytica, 78, pp. 217-226. , doi:10. 1007/BF00027520Mateescu, R.G., Zhang, Z., Tsai, K., Phavaphutanon, J., Burton-Wurster, N.I., Lust, G., Analysis of allele fidelity, polymorphic information content, and density of microsatellites in a genome-wide screening for hip dysplasia in a crossbreed pedigree (2005) J. Hered, 96, pp. 847-853. , PMID:16251522, doi:10.1093/jhered/esi109Nicot, N., Chiquet, V., Gandon, B., Amilhat, L., Legeai, F., Leroy, P., Study of simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs) (2004) Theor. Appl. Genet, 109, pp. 800-805. , PMID:15146317, doi:10.1007/s00122-004-1685-xOliveira, K.M., Pinto, L.R., Marconi, T.G., Margarido, G.R.A., Pastina, M.M., Teixeira, L.H., Functional genetic linkage map based on EST-markers for a sugarcane (Saccharum spp.) commercial cross (2007) Mol. Breed, 20, pp. 189-208. , doi:10.1007/ s11032-007-9082-1Pashley, C.H., Ellis, J.R., McCauley, D.E., Burke, J.M., EST database as a source for molecular markers: Lessons from Helianthus (2006) J. Hered, 97, pp. 381-388. , PMID:16840524, doi:10.1093/jhered/esl013Pflieger, S., Lefebvre, V., Causse, M., The candidate gene approach in plant genetics: A review (2001) Mol. Breed, 7, pp. 275-291. , doi:10.1023/A:1011605013259Pillen, K., Binder, A., Kreuzkam, B., Ramsay, L., Waugh, R., Förster, J., Leon, J., Mapping new EMBL-derived barley microsatellites and their use in differentiating German barley cultivars (2000) Theor. Appl. Genet, 101, pp. 652-660. , doi:10.1007/ s001220051527Pinto, L.R., Oliveira, K.M., Ulian, E.C., Garcia, A.A.F., Souza, A.P., Survey in the expressed sequence tag database (SU-CEST) for simple sequence repeats (2004) Genome, 47, pp. 795-804. , PMID:15499394, doi:10.1139/g04-055Pinto, L.R., Oliveira, K.M., Marconi, T.G., Garcia, A.A.F., Ulian, E.C., Souza, A.P., Characterization of novel sugarcane expressed sequence tag microsatellites and their comparison with genomic SSRs (2006) Plant Breed, 125, pp. 378-384. , doi:10.1111/j. 1439-0523.2006.01227.xPowell, W., Machray, G.C., Provan, J., Polymorphism revealed by simple sequence repeats (1996) Trends Plant Sci, 1, pp. 215-221Powell, W., Morgante, M., Andre, C., Hanafey, M., Vogel, J., Tingey, S., Rafalsky, A., b. The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis (1996) Mol. Breed, 2, pp. 225-238. , doi:10.1007/BF00564200Price, S., Cytology of Chinese and North Indian sugarcanes (1968) Econ. Bot, 22, pp. 155-164Qian, W., Sass, O., Meng, J., Li, M., Frauen, M., and Jung, C. 2007. Heterotic patterns in rapeseed (Brassica napus L.): I. Crosses between spring and Chinese semi-winter lines. Theor. Appl. Genet. 115: 27-34. doi:10.1007/s00122-007-0537-x. PMID:17453172Raboin, L.-M., Oliveira, K.M., Lecunff, L., Telismart, H., Roques, D., Butterfield, M., Genetic mapping in the high polyploid sugarcane using a bi-parental progeny: Identification of a gene controlling stalk colour and new rust resistance gene (2006) Theor. Appl. Genet, 112, pp. 1382-1391. , PMID:16552554, doi:10.1007/s00122-006-0240-3Rossetto, M., McNally, J., Henry, R.J., Evaluating the potential of SSR: Flanking regions examining taxonomic relationships in the Vitaceae (2002) Theor. Appl. Genet, 104, pp. 61-66. , PMID:12579429, doi:10.1007/s001220200007Rudd, S., Expressed sequence tags: Alternative or complement to whole genome sequences? (2003) Trends Plant Sci, 8, pp. 321-329. , PMID:12878016, doi:10.1016/S1360-1385(03)00131-6Rungis, D., BĂ©rubĂ©, Y., Zhang, J., Ralph, S., Ritland, C.E., Ellis, B.E., Robust simple sequence repeat markers for spruce (Picea spp.) from expressed sequence tags (2004) Theor. Appl. Genet, 109, pp. 1283-1294. , PMID:15351929, doi:10.1007/s00122-004-1742-5Russell, J., Booth, A., Fuller, J., Harrower, B., Hedley, P., Machray, G., Powell, W., A comparison of sequence-based polymorphism and haplotype content in transcribed and anonymous regions of the barley (2004) Genome, 47, pp. 389-398. , PMID:15060592Saha, M.C., Mian, M.A.R., Eujayl, I., Zwonitzer, J.C., Wang, L.J., May, G.D., Tall fescue EST-SSR markers with trans-ferability across several grass species (2004) Theor. Appl. Genet, 109, pp. 783-791. , PMID:15205737, doi:10.1007/s00122-004- 1681-1Scott, K.D., Eggler, P., Seaton, G., Rossetto, M., Ablett, E.M., Lee, L.S., Henry, R.J., Analysis of SSRs derived from grape ESTs (2000) Theor. Appl. Genet, 100, pp. 723-726. , doi:10.1007/ s001220051344Sharopova, N., McMullen, M.D., Schultz, L., Schroeder, S., Sanchez-Villeda, H., Gardiner, J., Development and mapping of SSR markers for maize (2002) Plant Mol. Biol, 48, pp. 463-481. , doi:10.1023/A: 1014868625533. PMID:12004892Sneath, P.H.A., Sokal, R.R., (1973) Numerical taxonomy, , Freeman, San Francisco, CalifTeklewold, A., Becker, H.C., Comparison of phenotypic and molecular distance to predict heterosis and F1 performance in Ethiopian mustard (Brassica carinata A. Braum) (2006) Theor. Appl. Genet, 112, pp. 752-759. , PMID:16365759, doi:10.1007/s00122-005-0180-3Temnykh, S., Park, W.D., Ayres, N., Cartinhour, S., Hauck, N., Lipovich, L., Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.) (2000) Theor. Appl. Genet, 100, pp. 697-712. , doi:10.1007/s001220051342Tessier, C., David, J., This, P., Boursiquot, J.M., Charrier, A., Optimization of the choice of molecular markers for varietal identification in Vitis vinifera L (1999) Theor. Appl. Genet, 98, pp. 171-177. , doi:10.1007/s001220051054Gene Ontology: Tool for the unification of biology. Nat.e Genet (2000), 25, pp. 25-29. , The Gene Ontology ConsortiumThiel, T., Michalek, W., Varshney, R.K., Graner, A., Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.) (2003) Theor. Appl. Genet, 106, pp. 411-422. , PMID:12589540Tivang, J.G., Nienhuis, J., Smith, O.S., Estimation of sampling variance of molecular marker data using the bootstrap procedure (1994) Theor. Appl. Genet, 89, pp. 259-264. , doi:10.1007/ BF00225151Varshney, R.K., Thiel, T., Stein, N., Langridge, P., Graner, A., In silico analysis on frequency and distribution of micro-satellites in ESTs of some cereal species (2002) Cell. Mol. Biol. Lett, 7, pp. 537-546. , PMID:12378259Varshney, R.K., Graner, A., Sorrells, M.E., a. Genic microsatellite markers in plants: Features and applications (2005) Trends Biotechnol, 23, pp. 48-55. , PMID:15629858, doi:10.1016/j.tibtech.2004.11.005Varshney, R.K., Sigmund, R., Borner, A., Korzun, V., Stein, N., Sorrells, M.E., Graner, A., b. Interspecific transferability and comparative mapping of barley EST-SSR markers in wheat, rye and rice (2005) Plant Sci, 168, pp. 195-202. , doi:10.1016/j. plantsci.2004.08.001Warnke, S.E., Barker, R.E., Jung, G., Sim, S., Mian, M.A.R., Saha, M.C., Genetic linkage mapping of an annual x perennial ryegrass population (2004) Theor. Appl. Genet, 109, pp. 294-304. , PMID:15071730, doi:10.1007/s00122-004- 1647-3Yu, C.Y., Hu, S.W., Zhao, H.X., Guo, A.G., Genetic distances revealed by morphological characters, isozymes, protein and RAPD markers and their relationships with hybrid performance in oilseed rape (Brassica napus L.) (2005) Theor. Appl. Genet, 110, pp. 511-518. , PMID:15578151, doi:10.1007/s00122-004- 1858-7Yu, J.K., Dake, T.M., Singh, S., Benscher, D., Li, W., Gill, B., Sorrells, E., Development and mapping of EST-derived simple sequence repeat markers for hexaploid wheat (2004) Genome, 47, pp. 805-818. , PMID:15499395, doi:10.1139/g04-05
Plant antimicrobial peptides: an overview of superSAGE transcriptional profile and a functional review.
Defensin, thionin and lipid transfer protein (LTP) gene families, which antimicrobial activity has an attractive use in protein engineering and transgenic production of agronomically important plants, have been here functionally reviewed. Also, a transcriptional overview of plant SuperSAGE libraries and analysis of 26 bp tags possibly annotated for those families are presented. Tags differentially expressed (p < 0.05) or constitutively transcribed were identified from leaves or roots from SuperSAGE libraries from important Brazilian plant crops [cowpea (Vigna unguiculata (L.) Walp.), soybean (Glycine max (L.) Merr.) and modern sugarcane hybrids (Saccharum spp.)] submitted to abiotic [salt (100 mM NaCl) or drought] or biotic stresses [fungus inoculation (Phakopsora pachyrhizi; Asiatic Soybean Rust phytopathogen)]. The diverse transcriptional patterns observed, probably related to the variable range of targets and functions involved, could be the first step to unravel the antimicrobial peptide world and the plant stress response relationship. Moreover, SuperSAGE opens the opportunity to find some SNPs or even rare transcripts that could be important on plant stress resistance mechanisms. Putative defensin or LTPs revealed by SuperSAGE following a specific plant treatment or physiological condition could be useful for future use in genetic improvement of plants
Characterization of new polymorphic functional markers for sugarcane
Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP)[02/01167-1]Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP)[02/00197-4]Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP)[01/14656]Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP)[04/10596-9]CTC (Centro de Tecnologia Canavieira - Piracicaba/SP)CAPES[0181-056]Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq
Characterization of new polymorphic functional markers for sugarcane
Expressed sequence tags (ESTs) offer the opportunity to exploit single, low-copy, conserved sequence motifs for the development of simple sequence repeats (SSRs). The authors have examined the Sugarcane Expressed Sequence Tag database for the presence of SSRs. To test the utility of EST-derived SSR markers, a total of 342 ESTâSSRs, which represent a subset of over 2005 SSR-containing sequences that were located in the sugarcane EST database, could be designed from the nonredundant SSR-positive ESTs for possible use as potential genic markers. These ESTâSSR markers were used to screen 18 sugarcane (Saccharum spp.) varieties. A high proportion (65.5%) of the above ESTâSSRs, which gave amplified fragments of foreseen size, detected polymorphism. The number of alleles ranged from 2 to 24 with an average of 7.55 alleles per locus, while polymorphism information content values ranged from 0.16 to 0.94, with an average of 0.73. The ability of each set of ESTâSSR markers to discriminate between varieties was generally higher than the polymorphism information content analysis. When tested for functionality, 82.1% of these 224 ESTâSSRs were found to be functional, showing homology to known genes. As the ESTâSSRs are within the expressed portion of the genome, they are likely to be associated to a particular gene of interest, improving their utility for genetic mapping; identification of quantitative trait loci, and comparative genomics studies of sugarcane. The development of new ESTâSSR markers will have important implications for the genetic analysis and exploitation of the genetic resources of sugarcane and related species and will provide a more direct estimate of functional diversity522191209CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTĂFICO E TECNOLĂGICO - CNPQCOORDENAĂĂO DE APERFEIĂOAMENTO DE PESSOAL DE NĂVEL SUPERIOR - CAPESFUNDAĂĂO DE AMPARO Ă PESQUISA DO ESTADO DE SĂO PAULO - FAPESPsem informação0181-05602/01167-1; 02/00197-4; 01/14656; 04/10596-