Open Access

Integration of EST-CAPS markers into genetic maps of Eucalyptus urophylla and E. tereticornis and their alignment with E. grandis genome sequence


Cite

BRONDANI, R. P. V., E. R. WILLIAMS, C. BRONDANI and D. GRATTAPAGLIA (2006): A microsatellite-based consensus linkage map for species of Eucalyptus and a novel set of 230 microsatellite markers for the genus. BMC Plant Biol 6: 20.10.1186/1471-2229-6-20159973316995939Search in Google Scholar

CHA, R. S. and W. G. THILLY (1995): Specificity, efficiency, and fidelity of PCR, pp. 37-52. In: PCR primer: a laboratory manual, edited by C. W. DIEFFENBACH and G. S. DVEKSLER, Cold Spring Harbor Press, New York.Search in Google Scholar

CHAGNÉ, D., K. GASIC, R. N. CROWHURST, Y. HAN, H. C. BASSETT, D. R. BOWATTE, T. J. LAWRENCE, E. H. A. RIKKERINK, S. E. GARDINER and S. S. KORBAN (2008): Development of a set of SNP markers present in expressed genes of the apple. Genomics 92: 353-358.10.1016/j.ygeno.2008.07.00818721872Search in Google Scholar

CHO, R. J., M. MINDRINOS, D. R. RICHARDS, R. J. SAPOLSKY, M. ANDERSON, E. DRENKARD, J. DEWDNEY, N. FEDERSPIEL, A. THEOLOGIS, W. H. YANG, E. HUBBELL, M. AU, E. Y. CHUNG, D. LASHKARI, B. Lemieux, C. DEAN, R. J. LIPSHUTZ, F. M. AUSUBEL, R. W. DAVIS and P. J. OEFNER (1999): Genome-wide mapping with biallelic markers in Arabidopsis thaliana. Nat Genet 23: 203-207.10.1038/1383310508518Search in Google Scholar

ELLIS, J. R. and J. M. BURKE (2007): EST-SSRs as a resource for population genetic analyses. Heredity 99: 125-132.10.1038/sj.hdy.680100117519965Search in Google Scholar

FAO (2000): Global forest resources assessment 2000 - main report. FAO forestry paper No. 140. FAO, Rome. Search in Google Scholar

GAN, S., J. SHI, M. LI, K. WU, J. WU and J. BAI (2003): Moderate-density molecular maps of Eucalyptus urophylla S. T. Blake and E. tereticornis Smith genomes based on RAPD markers. Genetica 118: 59-67.10.1023/A:1022966018079Search in Google Scholar

GRATTAPAGLIA, D. and H. D. BRADSHAW JR (1994): Nuclear DNA content of commercially important Eucalyptus species and hybrids. Can J For Res 24: 1074-1078.10.1139/x94-142Search in Google Scholar

GUJARIA, N., A. KUMAR, P. DAUTHAL, A. DUBEY, P. HIREMATH, A. B. PRAKASH, A. FARMER, M. BHIDE, T. SHAH, P. M. GAUR, H. D. UPADHYAYA, S. BHATIA, D. R. COOK, G. D. MAY, J. K. VARSHNEY (2011): Development and use of genic molecular markers (GMMs) for construction of a transcript map of chickpea (Cicer arietinum L.). Theor Appl Genet 122: 1577-1589.10.1007/s00122-011-1556-1308204021384113Search in Google Scholar

HARRY, D. E., B. TEMESGEN and D. B. NEALE (1998): Codominant PCR-based markers for Pinus taeda developed from mapped cDNA clones. Theor Appl Genet 97: 327-336.10.1007/s001220050903Search in Google Scholar

HEESACKER, A., V. K. KISHORE, W. GAO, S. TANG, J. M. KOLKMAN, A. GINGLE, M. MATVIENKO, A. KOZIK, R. M. MICHELMORE, Z. LAI, L. H. RIESEBERG and S. J. KNAPP (2008): SSRs and INDELs mined from the sunflower EST database: abundance, polymorphisms, and crosstaxa utility. Theor Appl Genet 117: 1021-1029.10.1007/s00122-008-0841-018633591Search in Google Scholar

HUDSON, C. J., A. R. K. KULLAN, J. S. FREEMAN, D. A. FARIA, D. GRATTAPAGLIA, A. KILIAN, A. A. MYBURG, B. M. POTTS and R. E. VAILLANCOURT (2012): High synteny and colinearity among Eucalyptus genomes revealed by high-density comparative genetic mapping. Tree Genet Genomes 8: 339-352.10.1007/s11295-011-0444-9Search in Google Scholar

IWATA, H., T. UJINO-IHARA, K. YOSHIMURA, K. NAGASAKA, Y. MUKAI and Y. TSUMURA (2001): Cleaved amplified polymorphic sequence markers in sugi, Cryptomeria japonica D. Don, and their locations on a linkage map. Theor Appl Genet 103: 881-895.10.1007/s001220100732Search in Google Scholar

JONES, N., H. OUGHAM, H. THOMAS and I. PAS˘AKINSKIENË (2009): Markers and mapping revisited: finding your gene. New Phytol 183: 935-966.10.1111/j.1469-8137.2009.02933.x19594696Search in Google Scholar

KELLER, G., T. MARCHAL, H. SANCLEMENTE, M. NAVARRO, N. LADOUCE, P. WINCKER, A. COULOUX, C. TEULIÈRES and C. MARQUE (2009): Development and functional annotation of an 11,303-EST collection from Eucalyptus for studies of cold tolerance. Tree Genet Genomes 5: 317-327.10.1007/s11295-008-0184-7Search in Google Scholar

KIM, S. and A. MISRA (2007): SNP Genotyping: technologies and biomedical applications. Annu Rev Biomed Eng 9: 7.1-7.32.10.1146/annurev.bioeng.9.060906.15203717391067Search in Google Scholar

KONIECZNY, A. and F. M. AUSUBEL (1993): A procedure for mapping Arabidopsis mutations using co-dominant ecotype- specific PCR-based markers. Plant J 4: 403-410.10.1046/j.1365-313X.1993.04020403.xSearch in Google Scholar

KULLAN, A. R. K., M. M. DYK VAN, N. JONES, A. KANZLER, A. BAYLEY and A. A. MYBURG (2012): High-density genetic linkage maps with over 2,400 sequence-anchored DArT markers for genetic dissection in an F2 pseudobackcross of Eucalyptus grandis × E. urophylla. Tree Genet Genomes 8: 163-175.10.1007/s11295-011-0430-2Search in Google Scholar

KUNKEL, T. A. and K. BEBENIK (2000): DNA replication fidelity. Annu Rev Biochem 69: 497-529.10.1146/annurev.biochem.69.1.49710966467Search in Google Scholar

LI, F. and S. GAN (2011): An optimised protocol for fluorescent- dUTP based SSR genotyping and its application to genetic mapping in Eucalyptus. Silvae Genet 60: 18-25.10.1515/sg-2011-0003Search in Google Scholar

LINCOLN, S., M. DALY and E. LANDER (1992): Constructing genetic maps with MAPMAKER/EXP 3.0. Whitehead Institute technical report, 3rd edition. Whitehead Institute, Cambridge, Massachusetts.Search in Google Scholar

MIURA, Y., M. HIRATA and M. FUJIMORI (2007): Mapping of EST-derived CAPS markers in Italian ryegrass (Lolium multiflorum Lam.). Plant Breed 126: 353-360.10.1111/j.1439-0523.2007.01386.xSearch in Google Scholar

NELSON, M. N., P. M. MOOLHUIJZEN, J. G. BOERSMA, M. CHUDY, K. LESNIEWSKA, M. BELLGARD, R. P. OLIVER, W. S´WIE˛CICKI, B. WOLKO, W. A. COWLING and S. R. ELLWOOD (2010): Aligning a new reference genetic map of Lupinus angustifolius with the genome sequence of the model legume, Lotus japonicus. DNA Res 17: 73-83.10.1093/dnares/dsq001285338120133394Search in Google Scholar

NELSON, M. N., H. T. T. PHAN, S. R. ELLWOOD, P. M. MOOLHUIJZEN, J. HANE, A. WILLIAMS, C. E. O’LONE, J. FOSU-NYARKO, M. SCOBIE, M. CAKIR, M. G. K. JONES, M. BELLGARD, M. KSIA˛Z · KIEWICZ, B. WOLKO, S. J. BARKER, R. P. OLIVER AND W. A. COWLING (2006): The first genebased map of Lupinus angustifolius L. - location of domestication genes and conserved synteny with Medicago truncatula. Theor Appl Genet 113: 225-238.10.1007/s00122-006-0288-0Search in Google Scholar

NEVES, L. G., E. M. C. MAMANI, A. C. ALFENAS, M. KIRST and D. GRATTAPAGLIA (2011): A high-density transcript linkage map with 1,845 expressed genes positioned by microarray-based Single Feature Polymorphisms (SFP) in Eucalyptus. BMC Genomics 12: 189.10.1186/1471-2164-12-189Search in Google Scholar

PETROLI, C. D., C. P. SANSALONI, J. CARLING, D. A. STEANE, R. E. VAILLANCOURT, A. A. MYBURG, O. B. SILVA, G. J. PAPPAS, A. KILIAN and D. GRATTAPAGLIA (2012): Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus genome. PLoS One 7: e44684.10.1371/journal.pone.0044684Search in Google Scholar

RAFALSKI, A. (2002): Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5: 94-100.10.1016/S1369-5266(02)00240-6Search in Google Scholar

ROZEN, S. and H. J. SKALETSKY (2000): Primer3 on the WWW for general users and for biologist programmers, pp. 365-386. In: Bioinformatics methods and protocols: methods in molecular biology, edited by S. KRAWETZ and S. MISENER, Humana Press, Totowa, New Jersey.10.1385/1-59259-192-2:365Search in Google Scholar

SHERRY, S. T., M.-H. WARD, M. KHOLODOV, J. BAKER, L. PHAN, E. M. SMIGIELSKI and K. SIROTKIN (2001): dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 29: 308-311.10.1093/nar/29.1.3082978311125122Search in Google Scholar

SLATE, J., J. GRATTEN, D. BERALDI, J. STAPLEY, M. HALE and J. M. PEMBERTON (2009): Gene mapping in the wild with SNPs: guidelines and future directions. Genetica 136: 97-107.10.1007/s10709-008-9317-z18780148Search in Google Scholar

STANIASZEK, M., E. U. KOZIK and W. MARCZEWSKI (2007): A CAPS marker TAO1902 diagnostic for the I-2 gene conferring resistance to Fusarium oxysporum f. sp. lycopersici race 2 in tomato. Plant Breed 126: 331-333.10.1111/j.1439-0523.2007.01355.xSearch in Google Scholar

VARSHNEY, R. K., A. GRANER and M. E. SORRELLS (2005): Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23: 48-55.10.1016/j.tibtech.2004.11.00515629858Search in Google Scholar

VARSHNEY, R. K., S. NAYAK, B. JAYASHREE, K. ESHWAR, H. D. UPADHYAYA and D. A. HOISINGTON (2007): Development of cost-effective SNP assays for chickpea genome analysis and breeding. SAT eJournal 3: 1-3.Search in Google Scholar

ZHANG, X., F. LI, Y. WANG, L. XU, M. LI and S. GAN (2009): An optimized protocol for sequencing EST-PCR products in Eucalyptus. Genomics Appl Biol 28: 535-543.Search in Google Scholar

eISSN:
2509-8934
Language:
English
Publication timeframe:
Volume Open
Journal Subjects:
Life Sciences, Molecular Biology, Genetics, Biotechnology, Plant Science