"Frontmatter". In: Plant Genomics and Proteomics

See also Amplified fragment length
polymorphisms (AFLPs); Random
amplified polymorphic DNAs
(RAPDs); Single-nucleotide
polymorphisms (SNPs)
Polyploidy, 1
consequences of, 16–19
genome size and, 13–14
Poplar, as sequencing target, 65
“Prey” plasmids, 126, 127
Promoters
conserved sequences in, 95–96
eukaryotic, 95–96
for gene expression, 91, 92
MAS, 93, 94
organ- and tissue-specific, 148
Prosite, 178, 180–181
Protein homology searches, 183–185
Protein identification, in proteomics
experiments, 125
Protein isolation, in proteomics
experiments, 123–124
Protein-protein interactions, in
proteomics experiments, 125–126
Proteins. See also Proteomes; Proteomics
cellular processes and, 107–109
drought stress in plants and, 142–143
informatics tools for, 180–181
in proteomics, 120–128
recognition of pathogen, 135
sequencing of, 38–39, 40
Protein separation, in proteomics
experiments, 124–125
Protein sequences, BLAST
®
and, 175,
176
Protein tags, in proteomics, 126–128
Proteomes. See also Protein entries;
Proteomics
analysis of, 39, 40
cellular processes and, 107–109
Proteomics, 109, 120–128. See also
Proteomes
informatics tools for, 180–181
in pathogen resistance studies, 138
in plant stress studies, 132
transgenics in, 126, 128
yeast two-hybrid systems in, 126, 
127
Public data archives, 170
Public perception, of genetically
modified organisms, 193–196
Public policy, toward genetically
modified organisms, 196–197
Pumilio-like protein, 8, 9
Quantitative trait loci (QTLs), 48, 148
genes conditioning, 156
identification of, 152–160
in tomato, 156–160
Random amplified polymorphic DNAs
(RAPDs), 149, 151
Reactive oxygen species (ROS), 141
Real-time PCR, 129
Reassociation kinetics, genome
fractionation via, 54–56
Recognition, of plant pathogens, 135
Recombinant DNA, 23
Recombination, genetic maps and,
50–51

---

2 1 2
I
N D E X
Regulation, of genetically modified
organisms, 191, 193–196
Relational databases, 167
Resistance (R) genes, 133–138
Restriction enzymes, methylation-
sensitive, 57
Restriction fragment length
polymorphisms (RFLPs), 149–150
Retrotransposons, 10–11
in genome size increase, 15
Reverse transcriptase, in cDNA cloning,
32
Reverse transcription PCR (RT-PCR),
173
R genes. See Resistance (R) genes
Rhizobia, as sequencing target, 65
Rhizobium, 139–140
Ribosomal RNA (rRNA), 11, 13, 16
Rice
annotated DNA sequence of, 79
centromeres of, 12–13
drought-stress proteins in, 143
genome sequencing of, xiii, 48, 53
genome variation in, 7–8, 10
GUS activity in, 82, 83
RNA, 129. See also Double-stranded
RNA (dsRNA); Messenger RNA
(mRNA); Ribosomal RNA (rRNA)
abnormal, 70
in cells, 107–108
in controlling gene expression, 89–91
counting molecules of, 113
in expression profiling, 109–110,
111–113
in generating ESTs, 71, 73
mutagenesis and, 78–80
in proteomics experiments, 121
RNA interference (RNAi), 24, 80, 86–
87
RNA polymerase, 90
RNA polymerase III products, 15
Rosa, genome size of, 2
Royal Botanic Gardens, 2
Safener-inducible In2-2 system, 101
Safety, of genetically modified
organisms, 190, 191–192, 193–196
SAGE tags, 114–115, 116
Salicylic acid-mediated responses
(SAR), 136–137
SCF file format, 42