Legume Crop Genomics

Legume Crop Genomics......Page 1
Preface......Page 3
Contents......Page 5
Introduction......Page 7
Development of the Initiative......Page 9
Activities of the USLCGI......Page 11
References......Page 13
What Is Plant Genomics?......Page 15
Molecular Markers......Page 16
Molecular Marker Technologies......Page 17
Use of Molecular Markers to Construct Genetic Maps......Page 19
Marker-Assisted Breeding......Page 20
DNA Sequencing......Page 21
Genetic Libraries......Page 22
Sequencing Methods......Page 23
Transcriptomics: Studying Expression of the Genome......Page 24
RT-PCR......Page 25
Nuclease Protection Assays......Page 26
Microarray Analysis......Page 27
Bioinformatics: Interpreting the Findings of Genomic Science......Page 28
Transformation: Direct Modification of the Plant Genome......Page 29
References......Page 31
Introduction......Page 36
Phylogenetic Analysis of Sequence Data: What It Can and Cannot Do......Page 37
The Context: Where Legumes Fit in the Flowering Plants......Page 38
Major Evolutionary Lineages in Leguminosae: Two Natural Groups and One Paraphyletic Assemblage......Page 40
The Familiar Legumes: Subfamily Papilionoideae......Page 44
The Peanut and Its Allies: The Aeschynomenoid-Dalbergiod Group......Page 45
The Lupine and Its Allies: The Genistoids......Page 46
Medicago, Lotus, and Much More: The Hologalegina......Page 47
Soybean, Common Bean, and Many Minor Domesticates: The Phaseoloid-Millettioid Group......Page 51
Model Species and the Diversity of the Leguminosae......Page 55
The Value of Sampling Legume Diversity: Genome Size as an Example......Page 56
Another Argument for More Legume Models: Nodulation......Page 57
References......Page 59
The Agronomic and Experimental Importance of Phaseolus Vulgaris......Page 66
Phaseolus Phylogeny......Page 67
DNA Sequencing......Page 68
Genetic Markers......Page 71
Bacterial Artificial Chromosome Libraries......Page 74
Summary......Page 77
References......Page 78
Introduction......Page 89
Genomic Applications and Limitations in Cool Season Pulses......Page 91
Genomics in Pea?Possibilities in Both Basic and Applied Research......Page 93
Genomics in Lentil?Dependence on Other Genera as Models......Page 96
Genomics in Chickpea?a Potential Intermediate Model Species for Pulse Crops......Page 97
Summary......Page 98
References......Page 99
Introduction......Page 103
Genetic Diversity and Chromosomal Relationships of Cultivated and Wild Arachis......Page 104
Conventional Genetic Improvement of Peanut......Page 105
Genetic Mapping of Peanut......Page 106
Marker-Assisted Selection......Page 107
Tools and Strategies for Physical Mapping of Peanut......Page 109
Prospects for Sequencing the Peanut Genome......Page 110
Acknowledgments......Page 111
References......Page 112
Introduction......Page 116
Genetic Markers......Page 117
Genetic Diversity......Page 118
Map Development......Page 120
Mapping Traits......Page 122
Genetic Distance and Trait Expression......Page 124
Gene Expression Analyses......Page 125
Transformation......Page 126
Prospects......Page 134
References......Page 137
Introduction......Page 149
Genetic Maps and Synteny......Page 151
The Medicago truncatula Transcriptome......Page 153
Proteomics......Page 157
Transformation, Insertional Mutagenesis, RNAi......Page 159
Summary......Page 162
References......Page 164
Introduction......Page 168
Genome Duplications in Legumes......Page 169
Gene Clustering in Legume Genomes......Page 170
Comparative Genomics of Soybean and Other Legumes......Page 171
Summary......Page 173
References......Page 174
Introduction......Page 176
Identification of Potential Duplicates......Page 177
Evolutionary Distances and Mixtures of Normal Distributions......Page 178
Results......Page 179
Coalescence Estimates......Page 180
Selection on Duplicated Genes......Page 181
Duplicate Gene Expression......Page 182
Legumes......Page 187
Distance Measures......Page 188
References......Page 189
Composition of Plant Genomes......Page 193
Approaches to Determining Gene Space in Complex Genomes......Page 194
The Soybean Genome......Page 195
References......Page 198
Introduction......Page 200
Subtraction Libraries Identify Important Genes......Page 201
TILLING Permits the Function of Important Genes to Be Determined......Page 202
Summary......Page 206
References......Page 207
Introduction......Page 210
Soybean Transformation Using Organogenic In Vitro Cultures......Page 211
Soybean Transformation Using Somatic Embryo In Vitro Cultures......Page 215
Quality and Quantity of Transgenic Soybean......Page 218
Transformation for Functional Genomics......Page 221
Transformation for Novel Trait Development......Page 223
References......Page 228
Importance of Soybean Genomics......Page 240
Genetic Map......Page 241
Soybean Transformation and Mutagenesis......Page 242
DNA Methylation and Plant Genome Structure......Page 243
Synteny......Page 246
Physical Mapping......Page 247
Capture of Gene-Rich Regions......Page 250
Methylfiltration MF......Page 251
A Strategy for the Soybean Genome......Page 252
Acknowledgments......Page 254
References......Page 255
Introduction......Page 261
Genome Informatics......Page 262
Spliced Alignment......Page 263
A Prototype Syntenic Browser......Page 264
Applications......Page 265
Gene Annotation......Page 267
Summary......Page 269
References......Page 270
Introduction......Page 273
Soybean Microarray Construction......Page 274
Microarray Use......Page 275
Mutation and Transgene Analysis......Page 278
Tissue-Specific Expression Profiles......Page 279
Gene Expression Changes During Tissue and Organ Differentiation......Page 280
Identifying Genes Governing Quantitative Traits......Page 281
Genotyping......Page 282
Summary......Page 283
References......Page 284
Introduction......Page 289
Oil Concentration......Page 290
Fatty Acids......Page 298
Function of Genes Governing Lower Linolenic and Palmitic Acid Concentration......Page 309
Summary......Page 312
References......Page 313
Introduction......Page 318
A Case Study of Traditional Strategies: SCN Plant Resistance......Page 319
Application of Genomics to Broaden Resistance Using Plant Breeding......Page 321
New Strategies for Broadening Resistance......Page 323
Future Directions......Page 328
Summary......Page 329
References......Page 330
Manifestation of Clinical Allergies......Page 332
Preventing Allergic Reactions......Page 334
Soybean and Other Legume Allergens......Page 335
Allergens and Seed Oil......Page 337
Food Processing Affects Allergenicity......Page 338
Occupational Legume Allergies......Page 339
Hypoallergenic Seed Lines......Page 340
Biotechnology and Allergens......Page 341
Introduction of an Allergen Brazil Nut 2S Protein into Soybean......Page 342
Targeted Suppression of Food Allergens......Page 343
References......Page 346