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2012
G. C. Sant’Ana, Ferreira, J. L., Rocha, H. S., Borém, A., Pasqual, M., and Cançado, G. M. A., Comparison of a retrotransposon-based marker with microsatellite markers for discriminating accessions of Vitis vinifera, vol. 11, pp. 1507-1525, 2012.
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Development and characterization of additional microsatellite DNA markers for grape. Am. J. Enol. Viticult. 50: 243-246.   Casacuberta JM, Vernhettes S, Audeon C and Grandbastien MA (1997). Quasispecies in retrotransposons: a role for sequence variability in Tnt1 evolution. Genetica 100: 109-117. http://dx.doi.org/10.1023/A:1018309007841 PMid:9440263   Cavalli-Sforza LL and Edwards AW (1967). Phylogenetic analysis. Models and estimation procedures. Am. J. Hum. Genet. 19: 233-257. PMid:6026583 PMCid:1706274   Chakraborty R and Jin L (1993). Determination of relatedness between individuals using DNA fingerprinting. Hum. Biol. 65: 875-895. PMid:8300084   Cipriani G, Marrazzo MT, Di Gaspero G, Pfeiffer A, et al. (2008). A set of microsatellite markers with long core repeat optimized for grape (Vitis spp.) genotyping. BMC Plant Biol. 8: 127. http://dx.doi.org/10.1186/1471-2229-8-127 PMid:19087321 PMCid:2625351   Cordaux R and Batzer MA (2009). The impact of retrotransposons on human genome evolution. Nat. Rev. Genet. 10: 691-703. http://dx.doi.org/10.1038/nrg2640 PMid:19763152 PMCid:2884099   Creste S, Tulmann-Neto A and Figueira A (2001). Detection of simple sequence repeat polymorphisms in denaturing polyacrilamide sequencing gels by silver staining. Plant Mol. Biol. Rep. 4: 299-306. http://dx.doi.org/10.1007/BF02772828   Dettweiler E, Jung A, Zyprian E and Töpfer R (2000). Grapevine cultivar Müller-Thurgau its true to type descent. Vitis 39: 63-65.   Doyle JJ and Doyle JL (1990). Isolation of plant DNA from fresh tissue. Focus 12: 13-15.   Evanno G, Regnaut S and Goudet J (2005). Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14: 2611-2620. http://dx.doi.org/10.1111/j.1365-294X.2005.02553.x PMid:15969739   Excoffier L, Laval G and Schneider S (2005). Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol. Bioinform. Online 1: 47-50.   Glaubitz JC (2004). A user-friendly program to reformat diploid genotypic data for commonly used population genetic software packages. Mol. Ecol. Notes 4: 309-310. http://dx.doi.org/10.1111/j.1471-8286.2004.00597.x   Hocquigny S, Pelsy F, Dumas V, Kindt S, et al. (2004). Diversification within grapevine cultivars goes through chimeric states. Genome 47: 579-589. http://dx.doi.org/10.1139/g04-006 PMid:15190375   Kumar A and Bennetzen JL (1999). Plant retrotransposons. Annu. Rev. Genet. 33: 479-532. http://dx.doi.org/10.1146/annurev.genet.33.1.479 PMid:10690416   Laucou V, Boursiquot JM, Lacombe T, Bordenav L, et al. (2009). Parentage of grapevine rootstock 'Fercal' finally elucidated. Vitis 47: 163-167.   Leão PCS, Riaz S, Graziani R, Dangl GS, et al. (2009). Characterization of a Brazilian grape germplasm collection using microsatellite markers. Am. J. Enol. Viticult. 60: 517-524.   Liu KJ and Muse SV (2005). PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21: 2128-2129. http://dx.doi.org/10.1093/bioinformatics/bti282 PMid:15705655   Lopes MS, Sefc KM, Eiras ED, Steinkellner H, et al. (1999). The use of microsatellites for germplasm management in a Portuguese grapevine collection. Theor. Appl. Genet. 99: 733-739. http://dx.doi.org/10.1007/s001220051291 PMid:22665212   Moncada X, Pelsy F, Merdinoglu D and Hinrichsen P (2006). Genetic diversity and geographical dispersal in grapevine clones revealed by microsatellite markers. Genome 49: 1459-1472. http://dx.doi.org/10.1139/g06-102 PMid:17426761   Peakall R and Smouse PE (2006). GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol. Ecol. Notes 6: 288-295. http://dx.doi.org/10.1111/j.1471-8286.2005.01155.x   Pelsy F (2007). Untranslated leader region polymorphism of Tvv1, a retrotransposon family, is a novel marker useful for analyzing genetic diversity and relatedness in the genus Vitis. Theor. Appl. Genet. 116: 15-27. http://dx.doi.org/10.1007/s00122-007-0643-9 PMid:17926019   Pelsy F and Merdinoglu D (2002). The complete sequence of Tvv1 a family of Ty1 copia-like retrotransposon of Vitis vinifera L., reconstructed by chromosome walking. Theor. Appl. Genet. 105: 614-621. http://dx.doi.org/10.1007/s00122-002-0969-2 PMid:12582512   Pritchard J, Stephens M and Donnelly P (2000). Inference of population structure using multilocus genotype data. Genetics 155: 945-959. PMid:10835412 PMCid:1461096   Riaz S, Garrison KE, Dangl GS, Boursiquot JM, et al. (2002). Genetic divergence and chimerism within ancient asexually propagated winegrape cultivars. J. Am. Soc. Hort. Sci. 127: 508-514.   Saitou N and Nei M (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425. PMid:3447015   Sanmiguel P and Bennetzen JL (1998). Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons. Ann. Bot. 82: 37-44. http://dx.doi.org/10.1006/anbo.1998.0746   SanMiguel P, Tikhonov A, Jin YK, Motchoulskaia N, et al. (1996). Nested retrotransposons in the intergenic regions of the maize genome. Science 274: 765-768. http://dx.doi.org/10.1126/science.274.5288.765 PMid:8864112   Santana JC, Hidalgo E, de Lucas AI, Recio P, et al. (2008). Identification and relationships of accessions grown in the grapevine (Vitis vinifera L.) Germplasm Bank of Castilla y Léon (Spain) and the varieties authorized in the VQPRD areas of the region by SSR-marker analysis. Genet. Res. Crop Evol. 55: 573-583.   Schuck MR, Moreira FM, Guerra MP, Voltolini JA, et al. (2009). Molecular characterization of grapevine from Santa Catarina, Brazil, using microsatellite markers. Pesq. Agropec. Bras. 44: 487-495. http://dx.doi.org/10.1590/S0100-204X2009000500008   Sefc KM, Regner F, Turetschek E, Glossl J, et al. (1999). Identification of microsatellite sequences in Vitis riparia and their applicability for genotyping of different Vitis species. Genome 42: 367-373. PMid:10382286   Sefc KM, Lopes MS, Lefort F, Botta R, et al. (2000). Microsatellite variability in grapevine cultivars from different European regions and evaluation of assignment testing to assess the geographic origin of cultivars. Theor. Appl. Genet. 100: 498-505. http://dx.doi.org/10.1007/s001220050065   Sousa JSI (1959). Mutações somáticas na videira niagara. Bragantia 18: 387-423. http://dx.doi.org/10.1590/S0006-87051959000100027   Tessier C, David J, This P, Boursiquot JM, et al. (1999). Optimization of the choice of molecular markers for varietal identification in Vitis vinifera L. Theor. Appl. Genet. 89: 171-177. http://dx.doi.org/10.1007/s001220051054   This P, Jung A, Boccacci P, Borrego J, et al. (2004). Development of a standard set of microsatellite reference alleles for identification of grape cultivars. Theor. Appl. Genet. 109: 1448-1458. http://dx.doi.org/10.1007/s00122-004-1760-3 PMid:15565426   Thomas MR and Scott NS (1993). Microsatellites repeats in grapevine reveal DNA polymorphisms when analysis as sequenced-tagged sites (STSs). Theor. Appl. Genet. 86: 985-990. http://dx.doi.org/10.1007/BF00211051   Waits LP, Luikart G and Taberlet P (2001). Estimating the probability of identity among genotypes in natural populations: cautions and guidelines. Mol. Ecol. 10: 249-256. http://dx.doi.org/10.1046/j.1365-294X.2001.01185.x PMid:11251803
A. D. Bdo Val, Ferreira, J. L., J. Neto, V., Pasqual, M., de Oliveira, A. F., Borém, A., and Cançado, G. M. A., Genetic diversity of Brazilian and introduced olive germplasms based on microsatellite markers, vol. 11, pp. 556-571, 2012.
Alba V, Montemurro C, Sabetta W, Pasqualone A, et al. (2009). SSR-based identification key of cultivars of Olea europaea L. diffused in Southern-Italy. Sci. Horticult. 123: 11-16. http://dx.doi.org/10.1016/j.scienta.2009.07.007 Albertini E, Torricelli R, Bitocchi E, Raggi L, et al. (2011). Structure of genetic diversity in Olea europaea L. cultivars from central Italy. Mol. Breed. 27: 533-547. http://dx.doi.org/10.1007/s11032-010-9452-y Baldoni L, Cultrera NG, Mariotti R, Ricciolini C, et al. (2009). A consensus list of microsatellite markers for olive genotyping. Mol. Breed. 24: 213-231. http://dx.doi.org/10.1007/s11032-009-9285-8 Besnard G, Baali-Cherif D, Bettinelli-Riccardi S, Parietti D, et al. (2009). Pollen-mediated gene flow in a highly fragmented landscape: consequences for defining a conservation strategy of the relict Laperrine’s olive. C R Biol. 332: 662-672. http://dx.doi.org/10.1016/j.crvi.2009.02.003 PMid:19523606 Bracci T, Busconi M, Fogher C and Sebastiani L (2011). Molecular studies in olive (Olea europaea L.): overview on DNA markers applications and recent advances in genome analysis. Plant Cell Rep. 30: 449-462. http://dx.doi.org/10.1007/s00299-010-0991-9 PMid:21212959 Cadalen T, Mörchen M, Blassiau C, Clabaut A, et al. (2010). Development of SSR markers and construction of a consensus genetic map for chicory (Cichorium intybus L.). Mol. Breed. 25: 699-722. http://dx.doi.org/10.1007/s11032-009-9369-5 Carriero F, Fontanazza G, Cellini F and Giorio G (2002). Identification of simple sequence repeats (SSRs) in olive (Olea europaea L.). Theor. Appl. Genet. 104: 301-307. http://dx.doi.org/10.1007/s001220100691 PMid:12582701 Cavalli-Sforza LL and Edwards AW (1967). Phylogenetic analysis. Models and estimation procedures. Am. J. Hum. Genet. 19: 233-257. PMid:6026583    PMCid:1706274 Chafari J, Meziane AE, Moukhli A, Boulouha B, et al. (2008). Menara gardens: a Moroccan olive germplasm collection identified by a SSR locus-based genetic study. Genet. Resour. Crop Evol. 55: 893-900. http://dx.doi.org/10.1007/s10722-007-9294-6 Cipriani G, Marrazzo MT, Marconi R, Cimato A, et al. (2002). Microsatellite markers isolated in olive (Olea europaea L.) are suitable for individual fingerprinting and reveal polymorphism within ancient cultivars. Theor. Appl. Genet. 104: 223-228. http://dx.doi.org/10.1007/s001220100685 PMid:12582690 Cordeiro AI, Sanchez-Sevilla JF, Alvarez-Tinaut MC and Gomez-Jimenez MC (2008). Genetic diversity assessment in Portugal accessions of Olea europaea by RAPD markers. Bio. Plant 52: 642-647. http://dx.doi.org/10.1007/s10535-008-0125-1 Creste S, Tulmann-Neto A and Figueira A (2001). Detection of single sequence repeat polymorphisms in denaturing polyacrylamide sequencing gels by silver staining. Plant Mol. Biol. Rep. 4: 299-306. http://dx.doi.org/10.1007/BF02772828 Doyle JJ and Doyle JL (1990). Isolation of plant DNA from fresh tissue. Focus 12: 13-15. Erre P, Chessa I, Umñoz-Diez C, Belaj A, et al. (2010). Genetic diversity and relationships between wild and cultivated olives (Olea europaea L.) in Sardinia as assessed by SSR markers. Genet. Resour. Crop Evol. 57: 41-54. http://dx.doi.org/10.1007/s10722-009-9449-8 Evanno G, Regnaut S and Goudet J (2005). Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14: 2611-2620. http://dx.doi.org/10.1111/j.1365-294X.2005.02553.x PMid:15969739 Excoffier L, Laval G and Schneider S (2005). Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol. Bioinform. Online 1: 47-50. Glaubitz JC (2004). Convert: a user-friendly program to reformat diploid genotypic data for commonly used population genetic software packages. Mol. Ecol. Not 4: 309-310. http://dx.doi.org/10.1111/j.1471-8286.2004.00597.x Gorji AH and Zolnoori M (2011). Genetic diversity in hexaploid wheat genotypes using microsatellite markers. Asian J.l Biotechnol. 3: 368-377. http://dx.doi.org/10.3923/ajbkr.2011.368.377 Gouveia JMNB (2008). O Azeite da “Galega Vulgar”, Patrimônio Nacional. Available at [http://www.esa.ipsantarem.pt/newsletter/N6Marco2008/index_ficheiros/JoseGouveia.pdf]. Accessed June 9, 2011. Grati-Kamoun N, Mahmoud FL, Rebaï A, Gargouri A, et al. (2006). Genetic diversity of Tunisian olive tree (Olea europaea L.) cultivars assessed by AFLP markers. Genet. Resour. Crop Evol. 53: 265-275. http://dx.doi.org/10.1007/s10722-004-6130-0 Hakim IR, Kammoun NG, Makhloufi E and Rebaï A (2010). Discovery and potential of snp markers in characterization of tunisian olive germplasm. Diversity 2: 17-27. http://dx.doi.org/10.3390/d2010017 Khadari B, Charafi J, Moukhli A and Ater M (2008). Substantial genetic diversity in cultivated Moroccan olive despite a single major cultivar: a paradoxical situation evidenced by the use of SSR loci. Tree Gen. Gen. 4: 213-221. http://dx.doi.org/10.1007/s11295-007-0102-4 Liu K and Muse SV (2005). PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21: 2128-2129. http://dx.doi.org/10.1093/bioinformatics/bti282 PMid:15705655 Martins-Lopes P, Gomes S, Lima-Brito J, Lopes J, et al. (2009). Assessment of clonal genetic variability in Olea europaea L. “Cobrançosa” by molecular markers. Sci. Horticult. 123: 82-89. http://dx.doi.org/10.1016/j.scienta.2009.08.001 Mookerjee S, Guerin J, Collins G, Ford C, et al. (2005). Paternity analysis using microsatellite markers to identify pollen donors in an olive grove. Theor. Appl. Genet. 111: 1174-1182. http://dx.doi.org/10.1007/s00122-005-0049-5 PMid:16133312 Muzzalupo I, Stefanizzi F, Salimonti A, Falabella R, et al. (2009). Microsatellite markers for identification of a group of italian olive accessions. Sci. Agric. 66: 685-690. http://dx.doi.org/10.1590/S0103-90162009000500014 Noormohammadi Z, Hosseini-Mazinani M, Trujillo I and Angjelina B (2009). Study of intracultivar variation among main Iranian olive cultivars using SSR markers. Acta Biol. Szegediensis 53: 27-32. Pasqualone A, Montemurro C, Summo C, Sabetta W, et al. (2007). Effectiveness of microsatellite DNA markers in checking the identity of protected designation of origin extra virgin olive oil. J. Agric. Food Chem. 55: 3857-3862. http://dx.doi.org/10.1021/jf063708r PMid:17439146 Peakall R and Smouse PE (2006). Genalex 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol. Ecol. Not 6: 288-295. http://dx.doi.org/10.1111/j.1471-8286.2005.01155.x Poljuha D, Sladonja B, Šetić E, Milotić A, et al. (2008). DNA fingerprinting of olive varieties in Istria (Croatia) by microsatellite markers. Sci. Horticult. 115: 223-230. http://dx.doi.org/10.1016/j.scienta.2007.08.018 Pritchard JK, Stephens M and Donnelly P (2000). Inference of population structure using multilocus genotype data. Genetics 155: 945-959. PMid:10835412    PMCid:1461096 Rony C, Baalbaki R, Kalaitzis P and Talhouk SN (2009). Molecular characterization of Lebanese olive germplasm. Tree Gen. Gen. 5: 109-115. http://dx.doi.org/10.1007/s11295-008-0170-0 Roubos K, Moustakas M and Aravanopoulos FA (2010). Molecular identification of Greek olive (Olea europaea) cultivars based on microsatellite loci. Genet. Mol. Res. 9: 1865-1876. http://dx.doi.org/10.4238/vol9-3gmr916 PMid:20882482 Saitou N and Nei M (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425. PMid:3447015 Sarri V, Baldoni L, Porceddu A, Cultrera NG, et al. (2006). Microsatellite markers are powerful tools for discriminating among olive cultivars and assigning them to geographically defined populations. Genome 49: 1606-1615. http://dx.doi.org/10.1139/g06-126 PMid:17426775 Spennemann DHR and Allen LR (2000). Feral olives (Olea europaea) as future woody weeds in Australia: A review. Aust. J. Exp. Agricult. 40: 889-901. http://dx.doi.org/10.1071/EA98141 Waits LP, Luikart G and Taberlet P (2001). Estimating the probability of identity among genotypes in natural populations: cautions and guidelines. Mol. Ecol. 10: 249-256. http://dx.doi.org/10.1046/j.1365-294X.2001.01185.x PMid:11251803 Weber JL (1990). Informativeness of human (dC-dA)n.(dG-dT)n polymorphisms. Genomics 7: 524-530. http://dx.doi.org/10.1016/0888-7543(90)90195-Z