"Frontmatter". In: Plant Genomics and Proteomics

Fritillaria assyriaca, genome size of, 2
Full-length cDNAs, 73–75, 75–77
Fungi, mycorrhizal, 138–139
fw2-2 locus, in tomato, 156–160
Gateway
TM
Technology, cloning via,
25–27
GenBank, 170, 173
GenBank dbEST database, 72–73
plant EST numbers in (table), 74
GenBank Nr (nonredundant) database,
63
Gene enrichment strategy, 48–49
Gene expression. See also Expressed
sequence tags (ESTs)
chemically regulated, 99, 100–101
control of, 89–103
enhancer elements and, 91–93
5¢ sequences in, 93
introns in, 94–95
promoters for, 91, 92
proteomics and, 120
3¢ sequences in, 93–94
trans-acting factors controlling, 96–98
translational control in, 103
Gene families, 69–70
in Arabidopsis (table), 97–98
Gene-for-gene interaction, 132–134
Gene indices, 179, 180
Gene knockouts, 80
Arabidopsis, 81
Gene linkage, 18–19
Gene number, counting, 9–10
Gene Ontology (GO) project, 169
Genes. See also Genomes
avirulence, 133–135
bioinformatics and, 167
complex traits and, 147–164
conditioning QTLs via, 156
defined, 69
discovering, 69–87
disease resistance, 133–138
drought stress in plants and, 142–144
encoding ribosomal RNA, 13
identifying, 69–70, 70–73, 78–87
informatics tools for finding, 180
phenotypes and, 147–149
GeneSeqer program, 180, 185
Gene silencing, 16, 24, 80, 86–87
Gene space, 53–54, 65–66
Genetically modified organisms
(GMOs)
bioethics of, 190–191
future of, 197
Genetic maps, in genome sequencing,
50–51
Gene traps, 82
Genome browsers, 182–183
Genome collinearity, 17
Genome contraction, hypothetical
effects of, 15
Genome expansion, hypothetical effects
of, 15
Genomes. See also Genes; Genomics
annotation of, 77–78, 79
automated sequencing strategies for,
38
cellular processes and, 107–109
creating complete sequences of, 47–66
fractionation of, 24–25, 53–58, 61–62
functional data from, 23–43
informatics in analyses of, 171
multiple, 16–19
sequencing strategies for, 58–61
structure of plant, 1–20
tools for investigating, 23–24
Genome size
of plants, 1–3
processes affecting, 13–16
Genomics. See also Genes; Genomes
bioethics of, 189–198
comparative, 182–183
functional, 107–129
goals of, 69
Genomic sequencing, informatics tools
for, 180
Global community, data sharing within,
41

---

2 0 8
I
N D E X
Gramene database, 42, 168, 170, 183
Grasses
gene linkage in, 18–19
genome size increases in, 15
GST (glutathione-S-transferase) genes,
8, 9
GUS (glucuronidase) activity, 82, 83,
84–85, 95
Haplopappus gracilis, chromosome
number of, 3
HarvEST program, 179–180
HB gene family, 98
Heat shock cognate 80 (HSC80) gene,
102
Heterochromatin, 20
High-throughput TILLING, 84
Histone core, in chromatin, 102
HMM profiling, 178
Holocentric chromosomes, 4
Human genome, EST collections for, 54
Human Genome browser, 177
Hybridization. See also Yeast two-hybrid
system
in BAC screening, 30, 31, 32
in microarray experiments, 110–113
RFLPs and, 149–150
Hypermethylation, 57
Hypersensitive response, 133, 134
Hypomethylation, 57
Immobilized pH gradients (IPGs), 124
Ineffective nodulating mutants, of
legumes, 139
Informatics tools, 24, 39–43, 170–180.
See also Bioinformatics; Software
Insertional mutagenesis, 24, 80–82, 83,
84–85
in pathogen resistance studies, 138
International Mapping Consortium, 
63
International Rice Genome Sequencing
Project (IRGSP), 48, 49
International Sequencing Consortium,
63
Intron-mediated enhancement (IME), 95
Introns, in gene expression, 94–95
Isoelectric focusing (IEF), 124
Jasmonic acid/ethylene-mediated
responses, 136–137
Joint Genome Institute, 65
Kinetochore activity, in Luzula, 4
Knockouts, 80