Plant Molecular Breeding

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ISBN: 9781841273211 | 184127321X
Cover: Hardcover
Copyright: 9/1/2003

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The last few years have seen an explosion of new information and resources in the areas of plant molecular genetics and genomics. As a result of developments such as high throughput sequencing, we now have huge amounts of information available on plant genes. But how does this help people charged with the task of improving crop species to create products with altered functions or improved characteristics? This volume considers ways in which the new information, resources and technology can be exploited by the plant breeder. Examples in current use will be quoted wherever possible.

Contributors	p. xi
Preface	p. xiii
Mapping, characterization and deployment of quantitative trait loci	p. 1
Introduction	p. 1
Genetic basis of quantitative trait performance	p. 2
Basic modelling of quantitative traits	p. 3
Statistical principles and methods for mapping QTL	p. 5
Molecular markers for QTL mapping	p. 6
QTL mapping in segregating populations	p. 8
QTL mapping in pedigree populations	p. 13
QTL analysis in natural populations	p. 14
Analysis of variance under an unbalanced nested design	p. 16
Regression analysis	p. 17
Likelihood analysis	p. 17
The application of QTL theory	p. 20
Advanced segregating populations	p. 20
Part chromosome substitution lines (backcross introgression lines) and near-isogenic lines (NILs)	p. 21
Part CSLs	p. 22
NILs	p. 22
STAIRS	p. 24
Cloning QTL	p. 24
Conclusion	p. 25
References	p. 25
Marker-assisted breeding	p. 30
Introduction	p. 30
Marker-assisted backcrossing of a single target gene	p. 31
Foreground selection	p. 32
Target locus is a known locus	p. 32
Target locus is a quantitative trait locus (QTL)	p. 35
Minimal population sizes	p. 36
Background selection	p. 37
Expected genome contents with no selection	p. 38
Marker-based estimate of recipient genome content	p. 40
Reduction of linkage drag (carrier chromosome)	p. 40
Selection on non-carrier chromosomes	p. 45
Example of efficiency for a complete scheme	p. 46
Genotype building strategies for multiple target genes	p. 48
Marker-based population screening	p. 48
Marker-based recurrent selection	p. 48
Marker-based gene pyramiding	p. 49
Marker-assisted backcrossing for several target genes	p. 49
Selection combining molecular and phenotypic information	p. 50
The marker-phenotype index	p. 51
Selection for hybrid performance	p. 52
Experimental results	p. 52
Conclusions	p. 55
References	p. 56
Genomic colinearity and its application in crop plant improvement	p. 60
Introduction	p. 60
A historical perspective	p. 60
Examples of synteny between plant groups	p. 61
The Brassicaceae	p. 61
The Fabaceae	p. 64
The Poaceae	p. 66
The limits to colinearity	p. 68
How can synteny be exploited by those attempting to improve plants?	p. 69
Disease resistance	p. 70
Flowering time	p. 72
Plant height	p. 74
Conclusion	p. 75
References	p. 76
Plant genetic engineering	p. 82
Background	p. 82
Key components of plant genetic engineering	p. 84
Methods for plant transformation	p. 85
Agrobacterium-mediated transformation	p. 86
Agrobacterium rhizogenes	p. 89
Monocot transformation	p. 91
Vectors for Agrobacterium-mediated transformation	p. 93
Integrative vectors	p. 93
Binary vectors	p. 94
Direct DNA delivery	p. 96
Particle bombardment	p. 96
Protoplasts	p. 97
Alternative methods for direct gene transfer	p. 99
Perspectives	p. 99
Alternative approaches to plant genetic engineering	p. 100
In-planta technologies	p. 100
Plastids	p. 104
Selection of transformation events	p. 107
Marker-free transformation	p. 109
Co-transformation	p. 110
Site-specific recombination	p. 112
Transposable elements	p. 113
Perspectives	p. 113
Prospects for improving the efficiency of transformation	p. 113
Genotypic variation for plant transformation	p. 114
Interaction of plant genes with the processes of transformation	p. 116
Cell attachment	p. 116
Transfer and targeting	p. 116
T-DNA integration	p. 117
Conclusions	p. 119
References	p. 120
Plant germplasm collections as sources of useful genes	p. 134
Introduction	p. 134
Germplasm collections as museums	p. 134
The evolution and domestication of crop species	p. 134
The concept of gene pools	p. 135
The classical model	p. 135
Beyond the tertiary gene pool	p. 136
Molecular genetics and genomics	p. 137
RFLP markers	p. 137
PCR-based markers	p. 138
Plant germplasm collections	p. 138
Collection issues: centres of diversity	p. 138
Identification of phylogenetic relationships	p. 139
Management and conservation: rationalization and core collections	p. 139
Utilization requires some sort of screening	p. 141
The challenge for plant breeding: utilization	p. 142
Exploiting the primary gene pool	p. 143
Exploiting the secondary gene pool	p. 143
Beyond the secondary gene pool: how can barriers be broken down?	p. 144
Diploid progenitors	p. 144
Modern techniques: genomics meets bioinformatics	p. 145
Better description and measurement of diversity	p. 145
Better screening of variation for a trait	p. 146
Better management of data: dynamic data sets	p. 146
Beyond the gene pool: redesigning agricultural species with germplasm utilization	p. 147
References	p. 148
The impact of plant genomics on maize improvement	p. 152
Introduction	p. 152
Origins and distribution of maize growing	p. 153
Five small steps for breeding--one giant step for mankind	p. 153
Food and industrial uses of maize	p. 155
Popular maize-based foods	p. 155
Industrial processing of maize	p. 157
Starch uses	p. 158
Oil uses	p. 159
Protein and fibre uses	p. 159
Twentieth-century maize breeding	p. 159
Germplasm resources	p. 160
Gene banks	p. 160
In-situ conservation	p. 161
Breeding methods	p. 161
Inbred lines and hybrid maize	p. 161
Cytoplasmic male sterility	p. 163
Molecular markers and marker-assisted selection	p. 164
Candidate genes: the next generation of molecular markers	p. 165
Foreground and background selection	p. 166
Breeding targets	p. 166
Example 1: Starch synthesis	p. 167
Example 2: Quality protein maize (QPM)	p. 167
Example 3: Chill tolerance	p. 168
'First-wave' maize biotechnology	p. 168
Bt maize	p. 168
Herbicide-resistant maize	p. 169
Engineered male-sterile maize	p. 169
Production of GM maize	p. 169
Maize genomics in the twenty-first century	p. 170
Maize gene function discovery	p. 171
Transcriptomics	p. 171
Functional genomics	p. 171
Genome sequencing/structural genomics	p. 172
Evolutionary genomics	p. 174
Bioinformatics	p. 174
Comparative genomics	p. 174
The grass genome	p. 176
A new paradigm for molecular breeding of maize	p. 177
References	p. 179
Plant genomics and its impact on wheat breeding	p. 184
Introduction	p. 184
Overview of genomics resources in wheat	p. 184
Genetic stocks	p. 185
Genetic and physical maps	p. 186
Gene clustering and density	p. 187
Synteny and comparative mapping	p. 188
Sequence-based homology	p. 189
Will rice genomics contribute to wheat improvement?	p. 189
Gene cloning in wheat	p. 190
Rht1	p. 191
Cre3	p. 191
Leaf rust (Lr10)	p. 191
Transgenics	p. 192
Applications/examples of DNA marker technology in wheat breeding	p. 193
Assessing genetic diversity	p. 193
Marker-assisted selection (MAS)	p. 194
DNA markers for disease resistance genes	p. 195
Limitations to marker-assisted selection in wheat, and possible solutions	p. 199
Beyond MAS: direct allele selection	p. 202
Retrospective breeding and MAS	p. 204
MAS conclusions	p. 205
Acknowledgements	p. 205
References	p. 206
Genomics and molecular breeding for root and tuber crop improvement	p. 216
Root and tuber crop profile	p. 216
The power of comparative mapping for R&T crops	p. 218
The '...ics' technology to unravel R&T gene networks	p. 220
Gene transfer	p. 222
Primary traits for R&T crop improvement	p. 223
Potato late blight disease; mapping and engineering progress	p. 223
Contemporary approaches to durable resistance to potato late blight	p. 228
Candidate gene associations with resistance in mapping populations	p. 229
Use of functional marker loci (genes) to enhance comparative mapping	p. 230
Identification of up- and down-regulated genes as candidate determinants of QTL	p. 231
Molecular approaches to characterizing and improving carbohydrate metabolism in R&T crops	p. 233
Molecular manipulation of starch functional properties through expression of transgenes	p. 234
Starch grain formation and morphology	p. 234
Starch-sugar conversion	p. 235
Starch content	p. 236
Productivity and sink strength	p. 237
Genomics contribution to the improvement of starch yields and quality in R&T crops	p. 238
Future prospects	p. 239
Carbohydrate trait improvement	p. 240
Resistance breeding	p. 240
High-throughput genotyping and association mapping	p. 241
Acknowledgment	p. 242
References	p. 242
Index	p. 255
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