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Review
Review
555
Origin of DNA
sequence
Function of
polymorphic site
Marker
development
costs
Quality of
markera
RDM
GTM
IFM
DFM
Unknown
Gene
Gene
Gene
Not known
Not known
Functional motif
Functional motif
Association studies
Isogenic lines
Low
Low
Medium
High
Low
Medium
High
High
Abbreviations: DFM, direct functional marker; GTM, gene-targeted marker; IFM, indirect functional marker; RDM, random DNA marker.
a
Based on risk of recombination and functional characterization of marker.
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556
Review
Gene(s)
Species
Refs
Plant height
Plant stature
Flowering time
Vernalization requirements
Fruit size
Food quality
Feed quality
Disease resistance
General stress response
Dwarf8 orthologs
tb1
Dwarf8
VFR2
fw2.2
GBSS
Genes in the lignin biosynthesis pathway
NBS LRR class of resistance genes
ERF transcription factors
Cereals
Maize (Zea mays)
Maize (Zea mays)
Oilseed (Brassica rapa)
Tomato (Lycopersicon ssp.)
Rice (Oryza sativa)
Several
Several
Several
[64 66]
[67]
[29]
[68]
[69]
[70]
[71]
[72]
[73]
Abbreviations: ERF, ethylene-responsive element binding factor; NBSLRR, nucleotide binding site leucine-rich repeat.
Review
557
Number of alleles
sequenced per
marker gene
No
alleles
Marker type
RDM
Sequencing
One
allele
Expression profiling,
sequence comparisons,
synteny studies
GTM
Sequencing
At least
two
alleles
Association studies
IFM
Mutant studies,
EMS/TILLING,
HR
DFM
Figure 1. Definition of marker types based on the level of functional characterization. Increasing thickness of arrow indicates increasing functional characterization of polymorphisms monitored by markers. Random DNA markers (RDM), gene-targeted markers (GTM) and functional markers (FM) are defined based on this level of functional
characterization. RDMs are derived at random from polymorphic sites in the genome whereas GTMs are markers derived from polymorphism within genes. Both RDMs
and GTMs can be established independently of the relationship of the underlying sequence polymorphisms to phenotypic characters. By contrast, FMs are derived from
polymorphic sites within genes causally involved in phenotypic trait variation. Indirect and direct FMs (IFM) and DFM) differ in development procedures and thus in the
degree of the functional characterization of polymorphisms. The list of methods for marker development is not comprehensive. Abbreviations: EMS, ethylmethane sulfonate; HR, homologous recombination; TILLING, targeting-induced local lesions in genomes.
558
Review
References
1 Sturtevant, A.H. (1913) The linear arrangement of six sex-linked
factors in Drosophila, as shown by their mode of association. J. Exp.
Zool. 14, 43 59
2 Sax, K. (1923) The association of size differences with seed-coat pattern
and pigmentation in Phaseolus vulgaris. Genetics 8, 552 560
3 Henry, R.J. ed. (2001) Plant Genotyping CABI Publishing
4 Poehlman, J.M. and Sleper, D.A. (1995) Breeding Field Crops, Iowa
State University Press
5 Botstein, D. et al. (1980) Construction of a genetic linkage map in man
using restriction fragment length polymorphisms. Am. J. Hum. Genet.
32, 314 331
6 Gupta, P.K. et al. (2002) Molecular markers: principles and methodology. In Molecular Techniques in Crop Improvement (Jain, S.M. et al.,
eds), pp. 9 54, Kluwer Academic Publishers
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560
Review
71
72
73
74
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