메뉴 건너뛰기




Volumn 4, Issue 1, 2014, Pages 29-37

A high-density gene map of loblolly pine (pinus taeda l.) based on exome sequence capture genotyping

Author keywords

Copy number; Exome; Genetic map; Genotyping; High density; High throughput; Loblolly pine; Sequencing; Variation

Indexed keywords

GENOMIC DNA;

EID: 84892706794     PISSN: None     EISSN: 21601836     Source Type: Journal    
DOI: 10.1534/g3.113.008714     Document Type: Article
Times cited : (65)

References (40)
  • 1
    • 0002159550 scopus 로고
    • Genetic of allozyme variants in loblolly pine
    • Adams, W. T., and R. J. Joly, 1980 Genetic of allozyme variants in loblolly pine. J. Hered. 71: 33-40.
    • (1980) J. Hered. , vol.71 , pp. 33-40
    • Adams, W.T.1    Joly, R.J.2
  • 2
    • 79958151996 scopus 로고    scopus 로고
    • BamTools: a C++ API and toolkit for analyzing and managing BAM files
    • Barnett, D., E. Garrison, A. Quinlan, M. Stromberg, and G. Marth, 2011 BamTools: a C++ API and toolkit for analyzing and managing BAM files. Bioinformatics 27: 1691-1692.
    • (2011) Bioinformatics , vol.27 , pp. 1691-1692
    • Barnett, D.1    Garrison, E.2    Quinlan, A.3    Stromberg, M.4    Marth, G.5
  • 3
    • 75849136053 scopus 로고    scopus 로고
    • Allelic genome structural variations in maize detected by array comparative genome hybridization
    • Belo, A., M. K. Beatty, D. Hondred, K. A. Fengler, B. Li et al., 2010 Allelic genome structural variations in maize detected by array comparative genome hybridization. Theor. Appl. Genet. 120: 355-367.
    • (2010) Theor. Appl. Genet. , vol.120 , pp. 355-367
    • Belo, A.1    Beatty, M.K.2    Hondred, D.3    Fengler, K.A.4    Li, B.5
  • 4
    • 54949113665 scopus 로고    scopus 로고
    • Molecular markers and selection for complex traits in plants: Learning from the last 20 years
    • Bernardo, R., 2008 Molecular markers and selection for complex traits in plants: Learning from the last 20 years. Crop Sci. 48: 1649- 1664.
    • (2008) Crop Sci. , vol.48
    • Bernardo, R.1
  • 6
    • 84863597153 scopus 로고    scopus 로고
    • Enrichment of genomic DNA for polymorphism detection in a non-model highly polyploid crop plant
    • Bundock, P. C., R. E. Casu, and R. J. Henry, 2012 Enrichment of genomic DNA for polymorphism detection in a non-model highly polyploid crop plant. Plant Biotechnol. J. 10: 657-667.
    • (2012) Plant Biotechnol. J. , vol.10 , pp. 657-667
    • Bundock, P.C.1    Casu, R.E.2    Henry, R.J.3
  • 7
    • 84861137137 scopus 로고    scopus 로고
    • Exploring diversification and genome size evolution in extant gymnosperms through phylogenetic synthesis
    • Burleigh, J. G., W. B. Barbazuk, J. M. Davis, A. M. Morse, and P. S. Soltis, 2012 Exploring diversification and genome size evolution in extant gymnosperms through phylogenetic synthesis. J. Bot. 2012: 292857.
    • (2012) J. Bot. , vol.2012 , pp. 292857
    • Burleigh, J.G.1    Barbazuk, W.B.2    Davis, J.M.3    Morse, A.M.4    Soltis, P.S.5
  • 8
    • 0025872337 scopus 로고
    • A maximum likelihood method for estimating genome length using genetic linkage data
    • Chakravarti, A., L. K. Lasher, and J. E. Reefer, 1991 A maximum likelihood method for estimating genome length using genetic linkage data. Genetics 128: 175-182.
    • (1991) Genetics , vol.128 , pp. 175-182
    • Chakravarti, A.1    Lasher, L.K.2    Reefer, J.E.3
  • 9
    • 79959435199 scopus 로고    scopus 로고
    • Genome-wide genetic marker discovery and genotyping using next-generation sequencing
    • Davey, J. W., P. A. Hohenlohe, P. D. Etter, J. Q. Boone, J. M. Catchen et al., 2011 Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat. Rev. Genet. 12: 499-510.
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 499-510
    • Davey, J.W.1    Hohenlohe, P.A.2    Etter, P.D.3    Boone, J.Q.4    Catchen, J.M.5
  • 10
    • 65549156994 scopus 로고    scopus 로고
    • A microarray-based genotyping and genetic mapping approach for highly heterozygous outcrossing species enables localization of a large fraction of the unassembled Populus trichocarpa genome sequence
    • Drost, D. R., E. Novaes, C. Boaventura-Novaes, C. I. Benedict, R. S. Brown et al., 2009 A microarray-based genotyping and genetic mapping approach for highly heterozygous outcrossing species enables localization of a large fraction of the unassembled Populus trichocarpa genome sequence. Plant J. 12: 1054-1067.
    • (2009) Plant J. , vol.12 , pp. 1054-1067
    • Drost, D.R.1    Novaes, E.2    Boaventura-Novaes, C.3    Benedict, C.I.4    Brown, R.S.5
  • 11
    • 79251581865 scopus 로고    scopus 로고
    • An annotated genetic map of loblolly pine based on microsatellite and cDNA markers
    • Echt, C. S., S. Saha, K. V. Krutovsky, K. Wimalanathan, J. E. Erpelding et al., 2011 An annotated genetic map of loblolly pine based on microsatellite and cDNA markers. BMC Genet. 12: 17.
    • (2011) BMC Genet. , vol.12 , pp. 17
    • Echt, C.S.1    Saha, S.2    Krutovsky, K.V.3    Wimalanathan, K.4    Erpelding, J.E.5
  • 12
    • 57349107224 scopus 로고    scopus 로고
    • High-throughput genotyping and mapping of single nucleotide polymorphisms in loblolly pine (Pinus taeda L.)
    • Eckert, A. J., B. Pande, E. S. Ersoz, M. H. Wright, V. K. Rashbrook et al., 2009 High-throughput genotyping and mapping of single nucleotide polymorphisms in loblolly pine (Pinus taeda L.). Tree Genet. Genomes 5: 225-234.
    • (2009) Tree Genet. Genomes , vol.5 , pp. 225-234
    • Eckert, A.J.1    Pande, B.2    Ersoz, E.S.3    Wright, M.H.4    Rashbrook, V.K.5
  • 13
    • 77956090475 scopus 로고    scopus 로고
    • Patterns of population structure and environmental associations to aridity across the range of loblolly pine (Pinus taeda L., Pinaceae)
    • Eckert, A. J., J. van Heerwaarden, J. L. Wegrzyn, C. D. Nelson, J. Ross-Ibarra et al., 2010 Patterns of population structure and environmental associations to aridity across the range of loblolly pine (Pinus taeda L., Pinaceae). Genetics 185: 969-982.
    • (2010) Genetics , vol.185 , pp. 969-982
    • Eckert, A.J.1    van Heerwaarden, J.2    Wegrzyn, J.L.3    Nelson, C.D.4    Ross-Ibarra, J.5
  • 14
    • 0035678654 scopus 로고    scopus 로고
    • Low-copy microsatellite recovery from a conifer genome
    • Elsik, C. G., and C. G. Williams, 2001 Low-copy microsatellite recovery from a conifer genome. Theor. Appl. Genet. 103: 1189-1195.
    • (2001) Theor. Appl. Genet. , vol.103 , pp. 1189-1195
    • Elsik, C.G.1    Williams, C.G.2
  • 15
    • 59849113821 scopus 로고    scopus 로고
    • Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing
    • Gnirke, A., A. Melnikov, J. Maguire, P. Rogov, E. M. LeProust et al., 2009 Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat. Biotechnol. 27: 182-189.
    • (2009) Nat. Biotechnol. , vol.27 , pp. 182-189
    • Gnirke, A.1    Melnikov, A.2    Maguire, J.3    Rogov, P.4    LeProust, E.M.5
  • 17
    • 79953839352 scopus 로고    scopus 로고
    • High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species
    • Grattapaglia, D., O. B. Silva-Junior, M. Kirst, B. M. de Lima, D. A. Faria et al., 2011 High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species. BMC Plant Biol. 11: 65.
    • (2011) BMC Plant Biol. , vol.11 , pp. 65
    • Grattapaglia, D.1    Silva-Junior, O.B.2    Kirst, M.3    de Lima, B.M.4    Faria, D.A.5
  • 18
    • 0037284041 scopus 로고    scopus 로고
    • Effects of genotyping errors, missing values and segregation distortion in molecular marker data on the construction of linkage maps
    • Hackett, C. A., and L. B. Broadfoot, 2003 Effects of genotyping errors, missing values and segregation distortion in molecular marker data on the construction of linkage maps. Heredity 90: 33-38.
    • (2003) Heredity , vol.90 , pp. 33-38
    • Hackett, C.A.1    Broadfoot, L.B.2
  • 19
    • 17444388556 scopus 로고    scopus 로고
    • Genetic dissection of fusiform rust and pitch canker disease traits in loblolly pine
    • Kayihan, G. C., D. A. Huber, A. M. Morse, T. L. White, and J. M. Davis, 2005 Genetic dissection of fusiform rust and pitch canker disease traits in loblolly pine. Theor. Appl Genet. 110: 948-958.
    • (2005) Theor. Appl Genet. , vol.110 , pp. 948-958
    • Kayihan, G.C.1    Huber, D.A.2    Morse, A.M.3    White, T.L.4    Davis, J.M.5
  • 20
    • 77954270761 scopus 로고    scopus 로고
    • The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences
    • Kovach, A., J. L. Wegrzyn, G. Parra, C. Holt, G. E. Bruening et al., 2010 The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences. BMC Genomics 11: 420.
    • (2010) BMC Genomics , vol.11 , pp. 420
    • Kovach, A.1    Wegrzyn, J.L.2    Parra, G.3    Holt, C.4    Bruening, G.E.5
  • 22
    • 0020262869 scopus 로고
    • How many polymorphic genes will it take to span the human genome? Am
    • Lange, K., and M. Boehnke, 1982 How many polymorphic genes will it take to span the human genome? Am. J. Hum. Genet. 34: 842-845.
    • (1982) J. Hum. Genet. , vol.34 , pp. 842-845
    • Lange, K.1    Boehnke, M.2
  • 25
    • 84888128019 scopus 로고    scopus 로고
    • Combination of multipoint maximum likelihood (MML) and regression mapping algorithms to construct a high-density genetic linkage map for loblolly pine (Pinus taeda L.)
    • Martinez-Garcia, P., K. Stevens, J. Wegrzyn, J. Liechty, M. Crepeau et al., 2013 Combination of multipoint maximum likelihood (MML) and regression mapping algorithms to construct a high-density genetic linkage map for loblolly pine (Pinus taeda L.). Tree Genet. Genomes 1-7.
    • (2013) Tree Genet. Genomes , pp. 1-7
    • Martinez-Garcia, P.1    Stevens, K.2    Wegrzyn, J.3    Liechty, J.4    Crepeau, M.5
  • 26
    • 79953882464 scopus 로고    scopus 로고
    • A high-density transcript linkage map with 1,845 expressed genes positioned by microarray-based Single Feature Polymorphisms (SFP) in Eucalyptus
    • Neves, L. G., E. M. 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.
    • (2011) BMC Genomics , vol.12 , pp. 189
    • Neves, L.G.1    Mamani, E.M.2    Alfenas, A.C.3    Kirst, M.4    Grattapaglia, D.5
  • 27
    • 84879233990 scopus 로고    scopus 로고
    • Whole-exome targeted sequencing of the uncharacterized pine genome
    • Neves, L. G., J. M. Davis, W. B. Barbazuk, and M. Kirst, 2013 Whole-exome targeted sequencing of the uncharacterized pine genome. Plant J. 75: 146- 156.
    • (2013) Plant J. , vol.75
    • Neves, L.G.1    Davis, J.M.2    Barbazuk, W.B.3    Kirst, M.4
  • 28
    • 0032788294 scopus 로고    scopus 로고
    • Construction of an AFLP genetic map with nearly complete genome coverage in Pinus taeda
    • Remington, D. L., R. W. Whetten, B. H. Liu, and D. M. O'Malley, 1999 Construction of an AFLP genetic map with nearly complete genome coverage in Pinus taeda. Theor. Appl. Genet. 98: 1279-1292.
    • (1999) Theor. Appl. Genet. , vol.98 , pp. 1279-1292
    • Remington, D.L.1    Whetten, R.W.2    Liu, B.H.3    O'Malley, D.M.4
  • 29
    • 84855802587 scopus 로고    scopus 로고
    • Accelerating the domestication of trees using genomic selection: accuracy of prediction models across ages and environments
    • Resende, M. F., Jr., P. Munoz, J. J. Acosta, G. F. Peter, J. M. Davis et al., 2012 Accelerating the domestication of trees using genomic selection: accuracy of prediction models across ages and environments. New Phytol. 193: 617-624.
    • (2012) New Phytol. , vol.193 , pp. 617-624
    • Resende, M.F.1    Munoz, P.2    Acosta, J.J.3    Peter, G.F.4    Davis, J.M.5
  • 30
    • 80052831072 scopus 로고    scopus 로고
    • Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome
    • Saintenac, C., D. Jiang, and E. D. Akhunov, 2011 Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome. Genome Biol. 12: R88.
    • (2011) Genome Biol. , vol.12
    • Saintenac, C.1    Jiang, D.2    Akhunov, E.D.3
  • 31
    • 84863693752 scopus 로고    scopus 로고
    • The tomato genome sequence provides insights into fleshy fruit evolution
    • Sato, S., S. Tabata, H. Hirakawa, E. Asamizu, K. Shirasawa et al., 2012 The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485: 635-641.
    • (2012) Nature , vol.485 , pp. 635-641
    • Sato, S.1    Tabata, S.2    Hirakawa, H.3    Asamizu, E.4    Shirasawa, K.5
  • 32
    • 84856733475 scopus 로고    scopus 로고
    • Bidirectional introgression between loblolly pine (Pinus taeda L.) and shortleaf pine (P. echinata Mill.) has increased since the 1950s
    • Stewart, J. F., C. G. Tauer, and C. D. Nelson, 2012 Bidirectional introgression between loblolly pine (Pinus taeda L.) and shortleaf pine (P. echinata Mill.) has increased since the 1950s. Tree Genet. Genomes 8: 725-735.
    • (2012) Tree Genet. Genomes , vol.8 , pp. 725-735
    • Stewart, J.F.1    Tauer, C.G.2    Nelson, C.D.3
  • 33
    • 78549273825 scopus 로고    scopus 로고
    • Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor
    • Swanson-Wagner, R. A., S. R. Eichten, S. Kumari, P. Tiffin, J. C. Stein et al., 2010 Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor. Genome Res. 20: 1689-1699.
    • (2010) Genome Res. , vol.20 , pp. 1689-1699
    • Swanson-Wagner, R.A.1    Eichten, S.R.2    Kumari, S.3    Tiffin, P.4    Stein, J.C.5
  • 34
    • 84868016827 scopus 로고    scopus 로고
    • Statistical challenges associated with detecting copy number variations with nextgeneration sequencing
    • Teo, S. M., Y. Pawitan, C. S. Ku, K. S. Chia, and A. Salim, 2012 Statistical challenges associated with detecting copy number variations with nextgeneration sequencing. Bioinformatics 28: 2711-2718.
    • (2012) Bioinformatics , vol.28 , pp. 2711-2718
    • Teo, S.M.1    Pawitan, Y.2    Ku, C.S.3    Chia, K.S.4    Salim, A.5
  • 35
    • 33748760611 scopus 로고    scopus 로고
    • The genome of black cottonwood, Populus trichocarpa (Torr.& Gray)
    • Tuskan, G. A., S. Difazio, S. Jansson, J. Bohlmann, I. Grigoriev et al., 2006 The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313: 1596-1604.
    • (2006) Science , vol.313 , pp. 1596-1604
    • Tuskan, G.A.1    Difazio, S.2    Jansson, S.3    Bohlmann, J.4    Grigoriev, I.5
  • 37
    • 0004110466 scopus 로고    scopus 로고
    • JoinMap 3.0, Software for the Calculation of Genetic Linkage Maps
    • Plant Research International, Wageningen, The Netherlands.
    • Van Ooijen, J. W., and R. E. Voorrips, 2001 JoinMap 3.0, Software for the Calculation of Genetic Linkage Maps. Plant Research International, Wageningen, The Netherlands.
    • (2001)
    • Van Ooijen, J.W.1    Voorrips, R.E.2
  • 38
    • 0036256695 scopus 로고    scopus 로고
    • MapChart: software for the graphical presentation of linkage maps and QTLs
    • Voorrips, R. E., 2002 MapChart: software for the graphical presentation of linkage maps and QTLs. J. Hered. 93: 77-78.
    • (2002) J. Hered. , vol.93 , pp. 77-78
    • Voorrips, R.E.1
  • 39
    • 0012600238 scopus 로고    scopus 로고
    • The southern forest resource assessment summary report
    • USDA Forest Service, Southern Research Station. Asheville, NC.
    • Wear, D. N., and J. G. Greis, 2002 The southern forest resource assessment summary report. USDA Forest Service, Southern Research Station. Asheville, NC.
    • (2002)
    • Wear, D.N.1    Greis, J.G.2
  • 40
    • 84870860897 scopus 로고    scopus 로고
    • Targeted enrichment of the black cottonwood (Populus trichocarpa) gene space using sequence capture
    • Zhou, L., and J. A. Holliday, 2012 Targeted enrichment of the black cottonwood (Populus trichocarpa) gene space using sequence capture. BMC Genomics 13: 703.
    • (2012) BMC Genomics , vol.13 , pp. 703
    • Zhou, L.1    Holliday, J.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.