"Frontmatter". In: Plant Genomics and Proteomics

See also Bt crops; Plants; Transgenic
crops
Crossbreeding, bioethics of, 189–190
Cucumis melo, BLAST
®
sequences for,
183–185
Cy3 fluorochrome, 111
Cy5 fluorochrome, 111
Cypripedium calceolus, DNA content of,
2–3
Cytosine, methylated, 57, 62
Data
analyzing genomic, 23–43, 167
expression, 179
gene identification from sequence,
70–73
interpreting, 183–185
static and dynamic, 169
Database-independent software, 4
Databases, 167, 168–170
for Arabidopsis gene insertions, 81
creation of, 39–42
critique of, 41–42
developing, 168–169
from NCBI (table), 176
protein, 181
in proteomics experiments, 123
specialized, 170
Data management, 168
Data mining, 168
Data processing, of shotgun sequence
data, 63
Data storage, 169–1701
Delayed nodulation mutants, of
legumes, 139
Deletion lines, 150
Dexamethasone-inducible GR fusions,
100
Dexamethasone-inducible GVG system,
100
Dex-inducible and tet-repressible TGV
system, 101
DICER enzyme complex, 86, 87
Dicots, intron-mediated enhancement
in, 95
Differential display technology, 36–37
Diploid plants, 1
Diseases, 131
plant resistance to, 132–138
Dispersed repetitive sequences, DNA
variation via, 10–11
Distributed Annotation System (DAS),
177
DNA, 129. See also Recombinant DNA;
T-DNA insertion
annotated sequences of, 79
in cells, 107–108
in centromeres, 12–13
in chromatin, 102
controlling gene expression via, 89–91
enhancers in, 91–93
in Luzula chromosomes, 4
methylation and, 57
mutagenesis and, 78
of plants, ix–x, xi
in reassociation experiments, 55, 56
of rice, 79

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N D E X
sequencing of, 23, 39
single-nucleotide polymorphisms in,
152
DNA fingerprinting, physical mapping
and, 51–53
DNA markers, 48, 149–152. See also
Marker-assisted selection (MAS)
DNA microarrays, 37–38. See also
Microarray technology
advantages and disadvantages of,
119–120
error estimating in, 112–113
types of, 110
DNA polymerase, in cDNA cloning, 32
DNA-Protein Search program, 179
DNA values, table of selected, 2
DNA variation
origin of, 7–16
in plants, 1–3
Dof gene family, 98
Double-stranded RNA (dsRNA), 86, 87
Doubling, of chromosomes, 13–14,
14–15
Downstream element (DST), 99
Downstream processing, 24
Drought stress, 131, 142–144
Ds transposon, 84
Dynamic data, 169
EDS1 gene, 136
Electrospray ionization (ESI), 39
Enhancement, intron-mediated, 95
Enhancer elements, effect on gene
expression, 91–93
Enhancers, defined, 91–93
Enhancer traps, 82, 84–85
Environment, plant interactions with,
131–144
Enzymes
gene families and, 69
methylation-sensitive, 57
of plants, ix
Error estimating, in microarray
experiments, 112–113
Escherichia coli, 29, 57, 61
EST assembly, in informatics, 172–173
EST clustering, informatics for, 42–43,
179–180
EST Databases, 63
EST libraries, in informatics, 172–173
EST markers, 52–53
EST numbers, table of, 74
Estradiol-inducible ER-C1 system, 100
Estradiol-inducible XVE system, 100
Ethanol-inducible AlcR system, 101
Ethics, plant genomics and, 189–198
Euchromatin, 57
Eukaryotic promoters, conserved
sequences in, 95–96
European Union (EU), moratorium on
GMOs by, 192, 193–196
Evolution, chromosomal gene
distribution and, 16–19
Expressed sequence tags (ESTs), 30. See
also EST entries
in cDNA cloning, 32–33
cDNAs versus, 77
in gene expression analysis, 110,
113–114, 119
in gene identification, 70–73, 74
generating, 71–73, 74
genome fractionation via, 54, 55
RFLPs and, 149–150
software for clustering, 42–43,
179–180
Expression data, 179
Expression profiling, 108, 109–120
in pathogen resistance studies,
137–138
Expression vectors, 25
Extracellular LRR proteins, 133, 134,
136, 137
Extraction, isolating source DNA via, 28
FASTA file format, 42
FASTA system, 178
Fingerprint contigs (FPC) software,
51–53
Fingerprinting
BAC end sequencing and, 59–60
physical mapping and, 51–53
5¢ sequences, in gene expression, 93
Flax
BLAST
®
sequences for, 183–185
disease resistance in, 132–133
Miropeats analysis of, 177

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I
N D E X
2 0 7
Flax polyubiquitin gene, BLAST
®
sequences for, 183–185
Floral Genome Project, xi
Flowering plants, origin of, xi
Fluorescent dyes, in protein separation,
124–125
FootPrinter program, 182
Fractionation, of genomes, 53–58, 61–62