Genetics, Genomics and Breeding of Potato

Contents......Page 13
Dedication......Page 5
Preface to the Series......Page 6
Preface to the Volume......Page 11
List of Contributors......Page 20
Abbreviations......Page 23
1. Introduction to Potato......Page 27
1.1 A Brief History of the Potato......Page 28
1.3 Potato Taxonomy, Related Species, and Crossability......Page 30
1.3.2 The Endosperm Balance Number EBN......Page 33
1.3.3 Predicted Phylogenetic Relationships......Page 35
1.4 Potato Production Statistics......Page 36
1.5 Potato Nutritional Content......Page 39
References......Page 41
2. Classical Genetics and Traditional Breeding......Page 46
2.1.1 Genetic Characteristics......Page 47
2.1.2 Reproductive Characteristics Relevant for Breeding......Page 50
2.2.1 The Tetraploid 4EBN Level......Page 54
2.2.2 The Diploid 2EBN Level......Page 57
2.3 Breeding Objectives......Page 60
References......Page 63
3. Molecular Breeding for Potato Improvement......Page 67
3.1 Introduction: Molecular Breeding—The Beginning of a New Era......Page 68
3.2.1 Characterization of Solanum Gene Pools......Page 69
3.2.2 Genealogy and Diversity of Modern Varieties......Page 70
3.2.3 Distinctiveness, Uniformity, and Stability......Page 71
3.3.1 Genome-wide Markers for Negative Selection......Page 72
3.3.3 Marker-assisted Selection in Potato......Page 73
3.4 Breeding Strategies Incorporating DNA Markers......Page 76
3.4.2 Parent Development with DNA Markers......Page 77
3.4.4 Advanced-generation Selection with DNA Markers......Page 80
3.5 Transgenic Breeding......Page 81
3.6 Conclusions......Page 84
References......Page 85
4. Molecular Linkage Maps: Strategies, Resources and Achievements......Page 94
4.2 Brief History of Mapping Efforts in Potato......Page 95
4.3.1 RFLP Markers......Page 98
4.3.3 DArT Markers......Page 101
4.4 Potato Mapping Populations: Structures and Strategies......Page 102
4.5.1 Wild Potato Species as Sources of Genes for Potato Improvement......Page 104
4.5.2 Documenting and Capitalizing upon Genome Synteny......Page 105
4.5.3 Genome Mapping in S. bulbocastanum......Page 106
References......Page 112
5. Mapping and Tagging of Simply Inherited Traits......Page 116
5.1 Introduction......Page 117
5.2 Virus Resistance......Page 122
5.3 Nematode Resistance......Page 127
5.4 Late Blight Resistance......Page 130
5.5 Conclusions......Page 133
References......Page 134
6. Mapping Complex Potato Traits......Page 139
6.2 Complex Traits in Potato......Page 140
6.3 Quantitative Pest and Disease Resistance......Page 141
6.3.1 Late Blight Resistance......Page 142
6.3.2 Potato Cyst Nematode Resistance......Page 145
6.3.3 Trichome-mediated Insect Resistance......Page 147
6.3.4 Glycoalkaloid-mediated Insect Resistance......Page 148
6.4 Tuber Life-cycle Traits: Dormancy and Tuberization......Page 149
6.5 Tuber Morphological Traits: Tuber Shape and Eye Depth......Page 151
6.6.2 Cold Sweetening......Page 153
6.6.3 Tuber Yield and Starch Content......Page 154
6.7 How Can the Genes for Potato Quantitative Traits be Identified?......Page 155
References......Page 156
7.1 Introduction......Page 159
7.2 Potato Populations for Association Mapping......Page 162
7.4 Detection and Scoring of DNA Variation......Page 165
7.4.1 Microsatellite Markers......Page 166
7.4.2 Single Strand Conformational Polymorphism Markers SSCP......Page 167
7.4.4 Candidate Gene Markers: Nucleotide Binding Site NBS Profiling......Page 168
7.4.6 Other PCR-based Markers......Page 169
7.5 Association Test Statistics......Page 170
7.6 Association Studies in Potato......Page 171
7.7 Conclusions and Outlook......Page 173
References......Page 174
8. Cloning of Late Blight Resistance Genes: Strategies and Progress......Page 179
8.1 Introduction......Page 180
8.2.1 Large Insert Chromosome Walking Approaches......Page 181
8.2.2 Candidate Gene Approaches......Page 183
8.2.3 Cross-species Comparative Genomics Approaches......Page 188
8.3.1 The Cloning of R1?2002......Page 191
8.3.2 The Cloning of RB?2003......Page 193
8.3.3 The Cloning of Rpi-blb1, an Allele of the RB Locus?2003......Page 195
8.3.4 The Cloning of R3a?2005......Page 196
8.3.5 The Cloning of Rpi-blb2?2005......Page 197
8.3.6 The Cloning of RBver, Rpi-sto1, and Rpi-pta1?2006, 2008......Page 198
8.3.7 The Cloning of Rpi-vnt1.1 and Rpi-vnt1.3?2009......Page 200
8.3.8 The Cloning of Rpi-blb3, Rpi-abpt, R2, and R2-like?2009......Page 202
8.3.9 The Cloning of Rpi-bt1?2009......Page 203
8.4 Future Prospects......Page 204
References......Page 205
9.1 Introduction......Page 210
9.2.1 FISH-based Chromosome Identification and Integration of Chromosomal and Genetic Maps of Potato......Page 211
9.2.3 FISH Mapping of Chromosomal Domains and Various Repetitive Sequences......Page 214
9.3 Studying Natural and Artificial Polyploids by Genomic In Situ Hybridization......Page 217
9.3.1 Studying Polyploidy in Potato Species—Traditional and Molecular Cytogenetics......Page 218
9.4 Practical Applications of Molecular Cytogenetics......Page 227
References......Page 228
10.1 Introduction......Page 233
10.2.1 Expressed Sequence Tags......Page 235
10.2.2 Microarrays......Page 239
10.2.3 PCR-Based Methods......Page 242
10.2.4 Emerging Technologies......Page 243
10.2.5 Online Resources......Page 244
10.3.2 Gene Ontogeny Categories of Genes Expressed at Different Ploidies and under Different Environments......Page 246
10.4.1 Transcriptome QTL Mapping......Page 247
10.4.2 Gene Discovery......Page 248
10.4.3 Functional Genomics-Assisted Breeding......Page 249
10.5 Concluding Remarks and Prospects......Page 250
References......Page 251
11.1 Introduction......Page 255
11.2 Methodology......Page 256
11.2.1 Proteomics......Page 257
11.2.2 Metabolomics......Page 262
11.3.1 Proteomics......Page 265
11.3.2 Metabolomics......Page 269
11.4.1 Tuber Quality Traits?by Fingerprinting......Page 272
11.4.2 Tuber Quality Traits?by Metabolic Profiling......Page 273
11.4.3 Biotic and Abiotic Stress......Page 276
11.5 Evaluation of Potato Tuber Nutrition, Safety and Genetic Modifications......Page 278
References......Page 279
12.1 Introduction......Page 286
12.2 Challenges......Page 287
12.3 Prospects......Page 289
12.3.1 In Response to Climate Change......Page 290
12.3.2 In Response to Increasing Management Costs......Page 291
12.3.4 In Response to Legislative Issues......Page 292
12.3.5 Novel Applications......Page 294
12.4 Conclusion......Page 296
References......Page 298