메뉴 건너뛰기




Volumn 7, Issue 2, 2004, Pages 132-136

Genomics tools for QTL analysis and gene discovery

Author keywords

EST; Expressed sequence tag; Heterogeneous inbred family; HIF; LD; Linkage disequilibrium; Near isogenic line; NIL; QTL; Quantitative trait locus loci; SFP; Single feature polymorphism; Single nucleotide polymorphism; SNP

Indexed keywords

GENE; GENETIC MARKER; GENETICS; GENOME; GENOMICS; METHODOLOGY; QUANTITATIVE TRAIT LOCUS; REVIEW;

EID: 1542351273     PISSN: 13695266     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pbi.2004.01.011     Document Type: Review
Times cited : (100)

References (47)
  • 1
    • 0022449412 scopus 로고
    • Strategies for studying heterogeneous genetic traits in humans by using a linkage map of restriction fragment length polymorphisms
    • Lander E.S., Botstein D. Strategies for studying heterogeneous genetic traits in humans by using a linkage map of restriction fragment length polymorphisms. Proc Natl Acad Sci USA. 83:1986;7353-7357.
    • (1986) Proc Natl Acad Sci USA , vol.83 , pp. 7353-7357
    • Lander, E.S.1    Botstein, D.2
  • 2
    • 0035350685 scopus 로고    scopus 로고
    • Mapping quantitative trait loci in plants: Uses and caveats for evolutionary biology
    • Mauricio R. Mapping quantitative trait loci in plants: uses and caveats for evolutionary biology. Nat Rev Genet. 2:2001;370-381.
    • (2001) Nat Rev Genet , vol.2 , pp. 370-381
    • Mauricio, R.1
  • 3
    • 0033580401 scopus 로고    scopus 로고
    • The limits of selection during maize domestication
    • Wang R.L., Stec A., Hey J., Lukens L., Doebley J. The limits of selection during maize domestication. Nature. 398:1999;236-239.
    • (1999) Nature , vol.398 , pp. 236-239
    • Wang, R.L.1    Stec, A.2    Hey, J.3    Lukens, L.4    Doebley, J.5
  • 4
    • 0035983615 scopus 로고    scopus 로고
    • Arabidopsis map-based cloning in the post-genome era
    • More than 50 000 candidate SNP and indel polymorphisms are revealed by a 2-3× shotgun coverage of the A. thaliana accession Landsberg erecta.
    • Jander G., Norris S.R., Rounsley S.D., Bush D.F., Levin I.M., Last R.L. Arabidopsis map-based cloning in the post-genome era. Plant Physiol. 129:2002;440-450 More than 50 000 candidate SNP and indel polymorphisms are revealed by a 2-3× shotgun coverage of the A. thaliana accession Landsberg erecta.
    • (2002) Plant Physiol , vol.129 , pp. 440-450
    • Jander, G.1    Norris, S.R.2    Rounsley, S.D.3    Bush, D.F.4    Levin, I.M.5    Last, R.L.6
  • 5
    • 0038817772 scopus 로고    scopus 로고
    • Large-scale identification and analysis of genome-wide single-nucleotide polymorphisms for mapping in Arabidopsis thaliana
    • Schmid K.J., Sorensen T.R., Stracke R., Torjek O., Altmann T., Mitchell-Olds T., Weisshaar B. Large-scale identification and analysis of genome-wide single-nucleotide polymorphisms for mapping in Arabidopsis thaliana. Genome Res. 13:2003;1250-1257 The authors release more than 8600 polymorphisms from up to 12 accessions that can be searched at http://www.mpiz-koeln.mpg.de/ masc/.
    • (2003) Genome Res , vol.13 , pp. 1250-1257
    • Schmid, K.J.1    Sorensen, T.R.2    Stracke, R.3    Torjek, O.4    Altmann, T.5    Mitchell-Olds, T.6    Weisshaar, B.7
  • 7
    • 0033988142 scopus 로고    scopus 로고
    • Screening unlabeled DNA targets with randomly ordered fiber-optic gene arrays
    • Steemers F.J., Ferguson J.A., Walt D.R. Screening unlabeled DNA targets with randomly ordered fiber-optic gene arrays. Nat Biotechnol. 18:2000;91-94.
    • (2000) Nat Biotechnol , vol.18 , pp. 91-94
    • Steemers, F.J.1    Ferguson, J.A.2    Walt, D.R.3
  • 8
    • 0035883858 scopus 로고    scopus 로고
    • Matrix-induced fragmentation of P3′-N5′ phosphoramidate- containing DNA: High-throughput MALDI-TOF analysis of genomic sequence polymorphisms
    • Shchepinov M.S., Denissenko M.F., Smylie K.J., Worl R.J., Leppin A.L., Cantor C.R., Rodi C.P. Matrix-induced fragmentation of P3′-N5′ phosphoramidate-containing DNA: high-throughput MALDI-TOF analysis of genomic sequence polymorphisms. Nucleic Acids Res. 29:2001;3864-3872.
    • (2001) Nucleic Acids Res , vol.29 , pp. 3864-3872
    • Shchepinov, M.S.1    Denissenko, M.F.2    Smylie, K.J.3    Worl, R.J.4    Leppin, A.L.5    Cantor, C.R.6    Rodi, C.P.7
  • 9
    • 0033824460 scopus 로고    scopus 로고
    • Determination of single-nucleotide polymorphisms by real-time pyrophosphate DNA sequencing
    • Alderborn A., Kristofferson A., Hammerling U. Determination of single-nucleotide polymorphisms by real-time pyrophosphate DNA sequencing. Genome Res. 10:2000;1249-1258.
    • (2000) Genome Res , vol.10 , pp. 1249-1258
    • Alderborn, A.1    Kristofferson, A.2    Hammerling, U.3
  • 10
    • 0037348718 scopus 로고    scopus 로고
    • Large-scale identification of single-feature polymorphisms in complex genomes
    • The authors describe a method for identifying and genotyping thousands of markers using arrays that are designed for expression analysis. Potential deletions can be predicted and mutations can be quickly mapped with bulk-segregant analysis and array genotyping.
    • Borevitz J.O., Liang D., Plouffe D., Chang H.S., Zhu T., Weigel D., Berry C.C., Winzeler E., Chory J. Large-scale identification of single-feature polymorphisms in complex genomes. Genome Res. 13:2003;513-523 The authors describe a method for identifying and genotyping thousands of markers using arrays that are designed for expression analysis. Potential deletions can be predicted and mutations can be quickly mapped with bulk-segregant analysis and array genotyping.
    • (2003) Genome Res , vol.13 , pp. 513-523
    • Borevitz, J.O.1    Liang, D.2    Plouffe, D.3    Chang, H.S.4    Zhu, T.5    Weigel, D.6    Berry, C.C.7    Winzeler, E.8    Chory, J.9
  • 13
    • 0035671407 scopus 로고    scopus 로고
    • The genetic architecture of quantitative traits
    • Mackay T.F. The genetic architecture of quantitative traits. Annu Rev Genet. 35:2001;303-339.
    • (2001) Annu Rev Genet , vol.35 , pp. 303-339
    • MacKay, T.F.1
  • 14
    • 0035930506 scopus 로고    scopus 로고
    • In silico mapping of mouse quantitative trait loci
    • Darvasi A. In silico mapping of mouse quantitative trait loci. Science. 294:2001;2423.
    • (2001) Science , vol.294 , pp. 2423
    • Darvasi, A.1
  • 18
    • 0142135662 scopus 로고    scopus 로고
    • Structure of linkage disequilibrium in plants
    • A current and comprehensive review of LD mapping approaches in plants.
    • Flint Garcia S.A., Thornsberry J.M., Buckler E.S. IV Structure of linkage disequilibrium in plants. Annu Rev Plant Biol. 54:2003;357-374 A current and comprehensive review of LD mapping approaches in plants.
    • (2003) Annu Rev Plant Biol , vol.54 , pp. 357-374
    • Flint Garcia, S.A.1    Thornsberry, J.M.2    Buckler IV, E.S.3
  • 20
    • 0036950802 scopus 로고    scopus 로고
    • Bay-0 × Shahdara recombinant inbred line population: A powerful tool for the genetic dissection of complex traits
    • Loudet O., Chaillou S., Camilleri C., Bouchez D., Daniel-Vedele F. Bay-0 × Shahdara recombinant inbred line population: a powerful tool for the genetic dissection of complex traits. Theor Appl Genet. 104:2002;1173-1184.
    • (2002) Theor Appl Genet , vol.104 , pp. 1173-1184
    • Loudet, O.1    Chaillou, S.2    Camilleri, C.3    Bouchez, D.4    Daniel-Vedele, F.5
  • 21
    • 0033936751 scopus 로고    scopus 로고
    • Naturally occurring variation in Arabidopsis: An underexploited resource for plant genetics
    • Alonso-Blanco C., Koornneef M. Naturally occurring variation in Arabidopsis: an underexploited resource for plant genetics. Trends Plant Sci. 5:2000;22-29.
    • (2000) Trends Plant Sci , vol.5 , pp. 22-29
    • Alonso-Blanco, C.1    Koornneef, M.2
  • 22
    • 0034712852 scopus 로고    scopus 로고
    • A recombination hotspot delimits a wild-species quantitative trait locus for tomato sugar content to 484 bp within an invertase gene
    • Fridman E., Pleban T., Zamir D. A recombination hotspot delimits a wild-species quantitative trait locus for tomato sugar content to 484 bp within an invertase gene. Proc Natl Acad Sci USA. 97:2000;4718-4723.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 4718-4723
    • Fridman, E.1    Pleban, T.2    Zamir, D.3
  • 23
    • 0035204571 scopus 로고    scopus 로고
    • A gene controlling variation in Arabidopsis glucosinolate composition is part of the methionine chain elongation pathway
    • Kroymann J., Textor S., Tokuhisa J.G., Falk K.L., Bartram S., Gershenzon J., Mitchell-Olds T. A gene controlling variation in Arabidopsis glucosinolate composition is part of the methionine chain elongation pathway. Plant Physiol. 127:2001;1077-1088.
    • (2001) Plant Physiol , vol.127 , pp. 1077-1088
    • Kroymann, J.1    Textor, S.2    Tokuhisa, J.G.3    Falk, K.L.4    Bartram, S.5    Gershenzon, J.6    Mitchell-Olds, T.7
  • 25
    • 0036808829 scopus 로고    scopus 로고
    • Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1 under short-day conditions
    • Kojima S., Takahashi Y., Kobayashi Y., Monna L., Sasaki T., Araki T., Yano M. Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1 under short-day conditions. Plant Cell Physiol. 43:2002;1096-1105.
    • (2002) Plant Cell Physiol , vol.43 , pp. 1096-1105
    • Kojima, S.1    Takahashi, Y.2    Kobayashi, Y.3    Monna, L.4    Sasaki, T.5    Araki, T.6    Yano, M.7
  • 26
    • 0034934225 scopus 로고    scopus 로고
    • Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the alpha subunit of protein kinase CK2
    • Takahashi Y., Shomura A., Sasaki T., Yano M. Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the alpha subunit of protein kinase CK2. Proc Natl Acad Sci USA. 98:2001;7922-7927.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 7922-7927
    • Takahashi, Y.1    Shomura, A.2    Sasaki, T.3    Yano, M.4
  • 27
    • 0034486611 scopus 로고    scopus 로고
    • Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS
    • Yano M., Katayose Y., Ashikari M., Yamanouchi U., Monna L., Fuse T., Baba T., Yamamoto K., Umehara Y., Nagamura Y.et al. Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS. Plant Cell. 12:2000;2473-2484.
    • (2000) Plant Cell , vol.12 , pp. 2473-2484
    • Yano, M.1    Katayose, Y.2    Ashikari, M.3    Yamanouchi, U.4    Monna, L.5    Fuse, T.6    Baba, T.7    Yamamoto, K.8    Umehara, Y.9    Nagamura, Y.10
  • 29
    • 0035059714 scopus 로고    scopus 로고
    • Gene duplication in the diversification of secondary metabolism: Tandem 2-oxoglutarate-dependent dioxygenases control glucosinolate biosynthesis in Arabidopsis
    • Kliebenstein D.J., Lambrix V.M., Reichelt M., Gershenzon J., Mitchell-Olds T. Gene duplication in the diversification of secondary metabolism: tandem 2-oxoglutarate-dependent dioxygenases control glucosinolate biosynthesis in Arabidopsis. Plant Cell. 13:2001;681-693.
    • (2001) Plant Cell , vol.13 , pp. 681-693
    • Kliebenstein, D.J.1    Lambrix, V.M.2    Reichelt, M.3    Gershenzon, J.4    Mitchell-Olds, T.5
  • 30
    • 0030893329 scopus 로고    scopus 로고
    • The evolution of apical dominance in maize
    • Doebley J., Stec A., Hubbard L. The evolution of apical dominance in maize. Nature. 386:1997;485-488.
    • (1997) Nature , vol.386 , pp. 485-488
    • Doebley, J.1    Stec, A.2    Hubbard, L.3
  • 31
    • 0038324415 scopus 로고    scopus 로고
    • Generation and analysis of an artificial gene dosage series in tomato to study the mechanisms by which the cloned quantitative trait locus fw2.2 controls fruit size
    • Liu J., Cong B., Tanksley S.D. Generation and analysis of an artificial gene dosage series in tomato to study the mechanisms by which the cloned quantitative trait locus fw2.2 controls fruit size. Plant Physiol. 132:2003;292-299.
    • (2003) Plant Physiol , vol.132 , pp. 292-299
    • Liu, J.1    Cong, B.2    Tanksley, S.D.3
  • 32
    • 0033101487 scopus 로고    scopus 로고
    • The FLF MADS box gene: A repressor of flowering in Arabidopsis regulated by vernalization and methylation
    • Sheldon C.C., Burn J.E., Perez P.P., Metzger J., Edwards J.A., Peacock W.J., Dennis E.S. The FLF MADS box gene: a repressor of flowering in Arabidopsis regulated by vernalization and methylation. Plant Cell. 11:1999;445-458.
    • (1999) Plant Cell , vol.11 , pp. 445-458
    • Sheldon, C.C.1    Burn, J.E.2    Perez, P.P.3    Metzger, J.4    Edwards, J.A.5    Peacock, W.J.6    Dennis, E.S.7
  • 33
    • 0033133554 scopus 로고    scopus 로고
    • FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering
    • Michaels S.D., Amasino R.M. FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering. Plant Cell. 11:1999;949-956.
    • (1999) Plant Cell , vol.11 , pp. 949-956
    • Michaels, S.D.1    Amasino, R.M.2
  • 34
    • 0036667687 scopus 로고    scopus 로고
    • DNA polymorphism at the FRIGIDA gene in Arabidopsis thaliana: Extensive nonsynonymous variation is consistent with local selection for flowering time
    • Le Corre V., Roux F., Reboud X. DNA polymorphism at the FRIGIDA gene in Arabidopsis thaliana: extensive nonsynonymous variation is consistent with local selection for flowering time. Mol Biol Evol. 19:2002;1261-1271.
    • (2002) Mol Biol Evol , vol.19 , pp. 1261-1271
    • Le Corre, V.1    Roux, F.2    Reboud, X.3
  • 35
    • 0034644643 scopus 로고    scopus 로고
    • Molecular analysis of FRIGIDA, a major determinant of natural variation in Arabidopsis flowering time
    • Johanson U., West J., Lister C., Michaels S., Amasino R., Dean C. Molecular analysis of FRIGIDA, a major determinant of natural variation in Arabidopsis flowering time. Science. 290:2000;344-347.
    • (2000) Science , vol.290 , pp. 344-347
    • Johanson, U.1    West, J.2    Lister, C.3    Michaels, S.4    Amasino, R.5    Dean, C.6
  • 36
    • 0038459045 scopus 로고    scopus 로고
    • Analysis of the molecular basis of flowering time variation in Arabidopsis accessions
    • Gazzani S., Gendall A.R., Lister C., Dean C. Analysis of the molecular basis of flowering time variation in Arabidopsis accessions. Plant Physiol. 132:2003;1107-1114.
    • (2003) Plant Physiol , vol.132 , pp. 1107-1114
    • Gazzani, S.1    Gendall, A.R.2    Lister, C.3    Dean, C.4
  • 38
    • 0037456823 scopus 로고    scopus 로고
    • Genetics of gene expression surveyed in maize, mouse and man
    • This paper describes expression QTL (eQTL) mapping in three species. Variation in gene expression can be attributable to both cis- and trans-acting factors.
    • Schadt E.E., Monks S.A., Drake T.A., Lusis A.J., Che N., Colinayo V., Ruff T.G., Milligan S.B., Lamb J.R., Cavet G.et al. Genetics of gene expression surveyed in maize, mouse and man. Nature. 422:2003;297-302 This paper describes expression QTL (eQTL) mapping in three species. Variation in gene expression can be attributable to both cis- and trans-acting factors.
    • (2003) Nature , vol.422 , pp. 297-302
    • Schadt, E.E.1    Monks, S.A.2    Drake, T.A.3    Lusis, A.J.4    Che, N.5    Colinayo, V.6    Ruff, T.G.7    Milligan, S.B.8    Lamb, J.R.9    Cavet, G.10
  • 39
    • 0037177625 scopus 로고    scopus 로고
    • Genetic dissection of transcriptional regulation in budding yeast
    • The authors demonstrate the genetic mapping of expression-level polymorphisms for the first time and identify both co-regulated genes that are controlled by trans-acting factors and unique loci that are controlled in cis.
    • Brem R.B., Yvert G., Clinton R., Kruglyak L. Genetic dissection of transcriptional regulation in budding yeast. Science. 296:2002;752-755 The authors demonstrate the genetic mapping of expression-level polymorphisms for the first time and identify both co-regulated genes that are controlled by trans-acting factors and unique loci that are controlled in cis.
    • (2002) Science , vol.296 , pp. 752-755
    • Brem, R.B.1    Yvert, G.2    Clinton, R.3    Kruglyak, L.4
  • 40
    • 0036910328 scopus 로고    scopus 로고
    • A high-throughput Arabidopsis reverse genetics system
    • The authors describe a sequence-indexed collection of approximately 53 000 T-DNA lines that have recently been made publicly available.
    • Sessions A., Burke E., Presting G., Aux G., McElver J., Patton D., Dietrich B., Ho P., Bacwaden J., Ko C.et al. A high-throughput Arabidopsis reverse genetics system. Plant Cell. 14:2002;2985-2994 The authors describe a sequence-indexed collection of approximately 53 000 T-DNA lines that have recently been made publicly available.
    • (2002) Plant Cell , vol.14 , pp. 2985-2994
    • Sessions, A.1    Burke, E.2    Presting, G.3    Aux, G.4    McElver, J.5    Patton, D.6    Dietrich, B.7    Ho, P.8    Bacwaden, J.9    Ko, C.10
  • 41
    • 0042768158 scopus 로고    scopus 로고
    • Genome-wide insertional mutagenesis of Arabidopsis thaliana
    • Alonso J.M., Stepanova A.N., Leisse T.J., Kim C.J., Chen H., Shinn P., Stevenson D.K., Zimmerman J., Barajas P., Cheuk R.et al. Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science. 301:2003;653-657 This paper describes the creation of a sequence-indexed collection of knock-out lines for nearly all Arabidopsis genes ( http://signal.salk.edu ). At present, more than 140 000 lines have been sequenced.
    • (2003) Science , vol.301 , pp. 653-657
    • Alonso, J.M.1    Stepanova, A.N.2    Leisse, T.J.3    Kim, C.J.4    Chen, H.5    Shinn, P.6    Stevenson, D.K.7    Zimmerman, J.8    Barajas, P.9    Cheuk, R.10
  • 43
    • 0036787546 scopus 로고    scopus 로고
    • Efficient gene targeting by homologous recombination in rice
    • Terada R., Urawa H., Inagaki Y., Tsugane K., Iida S. Efficient gene targeting by homologous recombination in rice. Nat Biotechnol. 20:2002;1030-1034.
    • (2002) Nat Biotechnol , vol.20 , pp. 1030-1034
    • Terada, R.1    Urawa, H.2    Inagaki, Y.3    Tsugane, K.4    Iida, S.5
  • 44
    • 0345168212 scopus 로고    scopus 로고
    • Ecological adaptation during incipient speciation revealed by precise gene replacement
    • Gene replacement is used to confirm the phenotypic effect of allelic differences at a locus that is involved in speciation.
    • Greenberg A.J., Moran J.R., Coyne J.A., Wu C.-I. Ecological adaptation during incipient speciation revealed by precise gene replacement. Science. 302:2003;1754-1757 Gene replacement is used to confirm the phenotypic effect of allelic differences at a locus that is involved in speciation.
    • (2003) Science , vol.302 , pp. 1754-1757
    • Greenberg, A.J.1    Moran, J.R.2    Coyne, J.A.3    Wu, C.-I.4
  • 45
    • 0038521723 scopus 로고    scopus 로고
    • Quantitative trait loci and comparative genomics of cereal cell wall composition
    • Hazen S.P., Hawley R.M., Davis G.L., Henrissat B., Walton J.D. Quantitative trait loci and comparative genomics of cereal cell wall composition. Plant Physiol. 132:2003;263-271.
    • (2003) Plant Physiol , vol.132 , pp. 263-271
    • Hazen, S.P.1    Hawley, R.M.2    Davis, G.L.3    Henrissat, B.4    Walton, J.D.5
  • 46
    • 0036852098 scopus 로고    scopus 로고
    • Gene expression analysis using oligonucleotide arrays produced by maskless photolithography
    • The authors show that moveable mirrors can be used to synthesize custom oligo-nucleotide arrays in situ, allowing greater flexibility in extension to non-model organisms.
    • Nuwaysir E.F., Huang W., Albert T.J., Singh J., Nuwaysir K., Pitas A., Richmond T., Gorski T., Berg J.P., Ballin J.et al. Gene expression analysis using oligonucleotide arrays produced by maskless photolithography. Genome Res. 12:2002;1749-1755 The authors show that moveable mirrors can be used to synthesize custom oligo-nucleotide arrays in situ, allowing greater flexibility in extension to non-model organisms.
    • (2002) Genome Res , vol.12 , pp. 1749-1755
    • Nuwaysir, E.F.1    Huang, W.2    Albert, T.J.3    Singh, J.4    Nuwaysir, K.5    Pitas, A.6    Richmond, T.7    Gorski, T.8    Berg, J.P.9    Ballin, J.10
  • 47
    • 0042099904 scopus 로고    scopus 로고
    • Molecular characterization of a set of wheat deletion stocks for use in chromosome bin mapping of ESTs
    • Qi L., Echalier B., Friebe B., Gill B.S. Molecular characterization of a set of wheat deletion stocks for use in chromosome bin mapping of ESTs. Funct Integr Genomics. 3:2003;39-55.
    • (2003) Funct Integr Genomics , vol.3 , pp. 39-55
    • Qi, L.1    Echalier, B.2    Friebe, B.3    Gill, B.S.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.