Wild Crop Relatives: Genomic and Breeding Resources (eBook)

Wild Crop Relatives: Genomic and Breeding Resources 3
Dedication 5
Preface 9
Contents 15
Abbreviations 17
List of Contributors 21
Chapter 1: Agrostis 25
1.1 Introduction 25
1.2 Three Major Bentgrass Species 25
1.2.1 Creeping Bentgrass (A. stolonifera L.) 25
1.2.2 Colonial Bentgrass (A. capillaris L.) 26
1.2.3 Velvet Bentgrass (A. canina L.) 26
1.3 Three Minor Bentgrass Species 27
1.3.1 Redtop (A. gigantea Roth) 27
1.3.2 Highland Bentgrass (A. castellana Boiss. and Reuter) 27
1.3.3 Idaho Bentgrass (Agrostis idahoensis Nash) 27
1.4 Marker Systems 27
1.5 Heat Stress and Drought Tolerance 28
1.6 Salt Tolerance 30
1.7 Invasion Properties and Weed Control Invasion 30
1.8 Diseases in Agrostis Species 30
1.9 Plant Transformation in Agrostis Species 31
1.10 Hybridization Studies and Gene Escape 33
References 34
Chapter 2: Bromus 38
2.1 Introduction 38
2.2 Evolution and Systematics 38
2.3 Agricultural Status 39
2.4 Mediterranean and SW Asian Annual Species of Section Genea 40
2.5 Section Pnigma 40
2.5.1 B. inermis (Smooth Bromegrass, Russian Brome) 41
2.5.1.1 Genetic Diversity in B. inermis 42
2.5.1.2 Breeding Progress 43
2.5.2 B. riparius Rehm. (Meadow Bromegrass) 43
2.5.3 B. erectus (Erect Bromegrass) 44
2.5.4 B. variegatus 44
2.5.5 B. pumpellianus (Arctic Bromegrass) 44
2.5.6 Other North American Species in Section Pnigma 44
2.5.7 South American Species in Section Pnigma 45
2.6 Section Bromus 45
2.6.1 B. arvensis (Field Bromegrass) and Its Close Relatives 46
2.6.2 B. hordeaceus 46
2.7 Section Ceratochloa 47
2.7.1 The Hexaploid B. catharticus Complex (2n=42) 47
2.7.2 Two Disjunct Octoploid Groups 47
2.7.2.1 B. carinatus (California Brome) 48
2.7.2.2 B. marginatus (Mountain Brome) 48
2.7.2.3 B. sitchensis (Sitka or Alaska Brome) 48
2.7.3 B. arizonicus (2n=84) (Arizona Brome) 48
2.7.4 Duodecaploid (2n=84) Accessions Found in Andean Regions of South America 48
2.8 Section Neobromus 49
2.9 Section Nevskiella 49
2.10 Role of Bromus Species in Crop Improvement Using Biotechnology 49
2.10.1 Tissue Culture 49
2.10.2 Cell Culture 49
2.10.3 Protoplast Fusion 49
2.10.4 Genome Mapping 49
2.11 Bromus Species in Genetic Research 49
2.11.1 Herbicide Resistance 49
2.11.2 Genetic Diversity and Weediness 49
2.12 Endophytic Fungi in Bromus 50
2.13 Recommendations for Future Action 50
References 50
Chapter 3: Cenchrus 54
3.1 Introduction 54
3.2 Morphology, Taxonomy, and Geographical Distribution of Genetic Diversity 54
3.3 Cytology and Cytogenetics 60
3.4 Phylogenetic Relationship 62
3.5 Ecological Behavior 64
3.6 Traits of Agronomic Importance and Scope for Domestication 64
3.7 Breeding and Crop Improvement 65
3.8 Application of Molecular Techniques in Crop Improvement 65
3.9 Genetic Map 66
3.10 BAC Libraries 70
3.11 Genetics and Molecular Mechanism of Apomixis in Buffelgrass 70
3.12 Genomic Database 71
3.13 Germplasm Banks 72
3.14 Potential and Pitfalls 72
References 73
Chapter 4: Cynodon 76
4.1 Introduction 76
4.2 Basic Botany of the Species 77
4.2.1 Taxonomy, Morphology, and Distribution 77
4.2.2 Cytology, Karyotype, and Genome Size 80
4.2.3 Agriculture Uses 81
4.3 Conservation Initiatives 82
4.3.1 Species for Forage 82
4.3.2 Germplasm Collection and Conservation 83
4.4 Origin and Evolution 86
4.5 Cynodon Genetic Diversity Revealed by Molecular Markers 88
4.6 Breeding Interspecific Hybrid Cultivars 90
4.7 Recommendations for Future Actions 91
References 92
Chapter 5: Dactylis 95
5.1 Introduction 95
5.2 Agricultural Status 95
5.3 Basic Botany of the Species 95
5.3.1 Morphology 95
5.3.2 Taxonomy of D. glomerata L 95
5.3.2.1 Diploid D. glomerata Forms 96
5.3.2.2 Origin of Diploids 96
5.3.2.3 The Diploid Subspecies 98
Himalayensis 98
Sinensis 98
Altaica 98
Aschersoniana 99
Parthiana 99
Reichenbachii 99
Lusitanica 99
Iscoi 99
Woronowii 100
Hyrcana 100
Mairei 100
Santai and ``castellata´´ 100
Smithii 100
Metlesicii 100
Juncinella 101
Ibizensis 101
Judaica 101
5.3.2.4 Tetraploid D. glomerata Forms 101
5.3.2.5 Origin of Tetraploids 101
5.3.2.6 The Tetraploid Subspecies 102
Glomerata 102
Slovenica 102
Hispanica 102
Marina 103
Oceanica 103
Hylodes 104
5.3.2.7 Hexaploid D. glomerata 104
5.3.3 Climatic Races 104
5.3.4 Edaphic Adaptation 104
5.3.5 Genome Size 105
5.4 Genetic Resources 105
5.4.1 Primary Gene Pool 105
5.4.2 Secondary Gene Pool 105
5.4.3 Tertiary Gene Pool 105
5.4.4 Quaternary Gene Pool 106
5.4.5 Conservation Recommendations 106
5.4.6 Genomics Resources 106
5.4.7 Karyotype 106
5.4.8 Inheritance 107
5.4.9 Role in Crop Improvement Through Traditional and Advanced Tools 107
5.4.10 The Future Improvement of Dactylis Using Wild Relatives 107
References 107
Chapter 6: Dichanthium 110
6.1 Introduction 110
6.2 Taxonomy and Distribution 110
6.3 Cytology and Hybridization 117
6.3.1 Cytological Characters 117
6.3.2 Ploidy Cycles in Dichanthium 118
6.3.3 Hybridization 118
6.4 Embryology 119
6.5 Nature and Inheritance of Apomixis in Dichanthium 120
6.5.1 Bothriochloa-Dichanthium-Capillipedium Agamic Complex 121
6.6 Breeding and Genomics 121
6.6.1 Germplasm Collections 121
6.6.2 Development of Cultivars 122
6.6.3 Genomics 123
6.6.3.1 DNA Extraction Methodology 123
6.6.3.2 Protein or Isozyme Markers 123
6.6.3.3 DNA Markers 123
6.6.3.4 Phylogenetic Studies 124
6.6.4 Biotechnological Studies in Dichanthium 126
6.7 Primary Productivity and Biomass Production 126
6.7.1 Various Factors Affecting Productivity and Biomass Production in Dichanthium 128
6.7.1.1 Biotic Factors 128
Grazing and Herbage Removal 128
Diseases and Pests 128
6.7.1.2 Abiotic Factors 129
Seasonal Burning 129
Factors affecting Seed Germination 129
Seed Dormancy 129
Salinity 129
Soil Moisture 129
Shade 129
6.8 Conclusion 130
References 130
Chapter 7: Eleusine 134
7.1 Introduction 134
7.2 Taxonomy and Species Characterization 134
7.2.1 E. coracana 135
7.2.1.1 E. coracana subsp. coracana 138
7.2.1.2 E. coracana subsp. africana 138
7.2.2 E. floccifolia 139
7.2.3 E. indica 139
7.2.4 E. intermedia 139
7.2.5 E. jaegeri 139
7.2.6 E. kigeziensis 139
7.2.7 E. multiflora 140
7.2.8 E. tristachya 141
7.2.9 Species of Uncertain Status or Now Placed in Other Genera 141
7.3 Morphological, Classical Genetic and Cytogenetic Studies in the Genus Eleusine 141
7.3.1 FISH and GISH Analyses 142
7.3.2 Genome Size 143
7.4 Evolution of the Genus Eleusine: Molecular Evidence 143
7.4.1 Eleusine Evolution: The DNA Data 143
7.4.2 Phylogenetic Placement of Eleusine Among Other Grasses 145
7.5 The Origin of Finger Millet: Current Understanding 145
7.6 Genome Analysis in Eleusine: Molecular Tools and Genomic Resources 146
7.6.1 Molecular Tools: SSRs, AFLPs, ESTs, and Others 146
7.6.2 The Genetic Map of E. coracana and Comparative Genomics 147
7.6.3 Genetic Diversity and Structure of Populations 148
7.7 Conservation of Genetic Resources 148
7.8 Problems and Limitations of the Eleusine Species 149
7.8.1 Diseases and Pests 149
7.8.2 E. indica: An ``Intractable´´ Weed 150
7.9 Future Prospects and Recommendations 151
References 152
Chapter 8: Eragrostis 155
8.1 Introduction 155
8.2 Basic Botany of the Species 155
8.2.1 Taxonomic Position 155
8.2.2 Morphology of Eragrostis 156
8.2.3 Cytology and Karyotype 157
8.2.4 Agricultural Status 159
8.3 Conservation Initiatives 159
8.4 Role in Elucidation of Origin and Evolution of Allied Crop Plants 160
8.5 Crop Improvement Through Traditional and Advanced Tools 162
8.5.1 Forage Crop Improvement 162
8.5.1.1 Traditional Tools 162
8.5.1.2 Advanced Tools 163
8.5.2 Improvement in Cultivated E. tef Utilizing Its Wild Relatives 164
8.5.2.1 Traditional Tools 164
8.5.2.2 Advanced Tools 164
8.6 Genomics Resources Developed 165
8.7 Scope for Domestication and Commercialization 165
8.8 Some Dark Sides 166
8.8.1 The Invasive Nature of Some Eragrostis Species 166
8.9 Recommendations for Future Actions 167
References 167
Chapter 9: Festuca 172
9.1 Basic Botany of the Species 172
9.2 Conservation Initiatives 174
9.3 Role in Elucidation of Origin and Evolution of Allied Crop Plants 175
9.4 Role in Development of Cytogenetic Stocks and Their Utility 175
9.5 Role in Classical and Molecular Genetic Study 176
9.6 Role in Crop Improvement Through Traditional and Advanced Tools 177
9.7 Genomics Resources Developed 179
9.8 Scope for Domestication and Commercialization 179
9.9 Some Dark Sides and Their Addressing 179
9.10 Recommendations for Future Actions 179
References 180
Chapter 10: Lolium 184
10.1 Introduction 184
10.2 Basic Botany of the Species 185
10.3 Genetic Resources 186
10.4 Genetic Diversity of L. temulentum, L. rigidum, and L. persicum 187
10.5 The Classical and Molecular Genetic Studies of L. temulentum and Other Lolium species 187
10.6 Introgression Studies and Genetic Transformation of L. temulentum 188
10.7 Genomics Resources: ESTs and SSR Markers 188
10.8 Endophytic Fungi 189
10.9 Conclusion 190
References 190
Chapter 11: Panicum 193
11.1 Introduction 193
11.2 Botany 193
11.3 Allied Crops 196
11.4 Distribution 196
11.5 Conservation Initiatives 198
11.6 Cytology and Karyotype 198
11.7 Origin of the Genera and Molecular Phylogeny 198
11.8 Cytogenetics 199
11.9 Ploidy Level and Apomixis-Related Gene Region 203
11.10 Molecular Markers 204
11.11 Crop Improvement 205
11.12 Genomics 208
11.13 Invasive Species 209
11.14 Economic Advantages 209
11.15 Recommendations for Future Resource Utilization 210
References 211
Chapter 12: Paspalum 215
12.1 Introduction 215
12.2 Taxonomy 216
12.3 Sexual Species of Paspalum 216
12.4 Paspalum as a Model for Apomixis 217
12.5 Subgenus Anachyris Chase 219
12.6 Subgenus Paspalum 220
12.6.1 Informal Group Dilatata Chase 220
12.6.1.1 P. dilatatum Poir.: Dallisgrass 221
12.6.1.2 P. pauciciliatum (Parodi) Herter: Prostrate Dallisgrass 223
12.6.1.3 P. urvillei Steud.: Vasey Grass 223
12.6.1.4 P. dasypleurum Kunze ex E. Desv 223
12.6.2 Informal Group Livida Chase 224
12.6.2.1 P. denticulatum Trin.: Longtom Paspalum 224
12.6.3 Informal Group Virgata Chase 224
12.6.3.1 P. conspersum Schrad.: Scattered Paspalum 224
12.6.3.2 P. rufum Nees ex. Steud 224
12.6.3.3 P. virgatum L.: Talquezal 224
12.6.4 Informal Group Quadrifaria Barreto 224
12.6.4.1 P. coryphaeum Trin.: Emperor Crowngrass 225
12.6.4.2 P. exaltatum J. Presl 225
12.6.4.3 P. haumanii Parodi 225
12.6.4.4 P. intermedium Monro ex Morong and Britton: Intermediate Paspalum 225
12.6.4.5 P. quadrifarium Lamk.: Tussock Paspalum 225
12.6.5 Informal Group Paniculata Chase 225
12.6.5.1 P. juergensii Hack 225
12.6.5.2 P. paniculatum L.: Arrocillo 225
12.6.6 Informal Group Notata Chase 226
12.6.6.1 P. notatum Flügge: Bahiagrass 226
12.6.6.2 P. subciliatum Chase 227
12.6.7 Informal Group Disticha Chase 228
12.6.7.1 P. vaginatum Swartz: Seashore Paspalum 228
12.6.7.2 P. distichum L.: Knot Grass 228
12.6.8 Informal Group Plicatula Chase 228
12.6.8.1 P. atratum Swallen: Atra Paspalum, Capim-pojuca, Pasto Pojuca 229
12.6.8.2 P. plicatulum Michx.: Brownseed Paspalum 229
12.6.8.3 P. guenoarum Arechav.: Pasto Rojo 229
12.6.8.4 P. glaucescens Hackel 230
12.6.8.5 P. nicorae Parodi: Brunswick Grass 230
12.6.8.6 P. compressifolium Swallen 230
12.6.8.7 Other Species in the Plicatula Group 230
12.6.8.8 P. scrobiculatum L.: Kodo Millet 230
12.6.9 Recommendations for Further Action 230
References 231
Chapter 13: Pennisetum 235
13.1 Structure and Evolutionary Relationships Within Pennisetum Complex of Species 235
13.1.1 Systematic Considerations of the Genus 235
13.1.2 Chromosome Evolution 235
13.1.2.1 Species with x = 7 Basic Chromosome Number 239
13.1.2.2 Species with x = 5, 8, or 9 as Basic Chromosome Number 241
13.1.2.3 Phylogeny and Dysploidy 242
13.1.2.4 B-Chromosomes 245
Behavior of B-Chromosomes in Confrontations Between ``Wild and Domesticated´´ Genomes 245
The Effect of B-Chromosomes 247
13.1.3 Domestication Process Hallmarks in the Genus Pennisetum 248
13.1.3.1 Where, When, and How Pearl Millet (P. glaucum) Was Domesticated? 248
Origin of Pearl Millet 248
Center or Non-Center Domestication of Pearl Millet? 248
The Beginning of Agriculture in Africa and Pearl Millet Domestication 249
Contribution of the Genetic Tools in Order to Enlighten the History of Pearl Millet Domestication 251
Dynamics of Spontaneous Wild-Weed-Pearl Millet Complex 253
Conclusion 256
13.1.3.2 Evolutionary Genomics and the Wealth of Wild Relatives for Deciphering the Genetic Basis of Quantitative Traits in Pea 256
The Genetic Basis of Pearl Millet Domestication 256
Genetic Dissection of Domestication Syndrome Traits 257
Traits of the Spikelet Structure Displayed a Monogenic or Digenic Inheritance 258
Some Insights in the QTL Dissection of Other Domestication Syndrome Traits 258
Spike Morphology 258
Plant Architecture 260
Flowering 261
Concluding Remarks on the Wealth of Wild Relatives for Unraveling the Evolutionary Mechanisms Underlying the Domestication Proc 261
Transgressive Phenotypes Resulting from Wild QTL Effects: An Evolutionary Fancy and Basis for New Genetic Resources Enhancement 261
Transgressions and Genetic Resource 261
13.2 Enhancement of Genetic Resources Using Genes from Wild Pennisetum Relatives 263
13.2.1 Wild Pennisetum Species as Sources of Major Genes of Agronomic Interest (GAI) 263
13.2.1.1 Apomixis 263
Male Sterility When Natural Reproductive Barriers Turn to be Source of GAI 264
Genes Involved in Tolerance to Biotic and Abiotic Stress 264
13.2.2 Wide Use of Wild Pennisetum Species 264
13.2.2.1 Breeding for Fodder 264
13.2.2.2 Miscellaneous Uses of Wild Relatives 265
BioEnergy 265
Hedge Vegetative Barriers for Monitoring Soil Erosion in Fields 265
Push-Pull 265
13.2.2.3 Pre-breeding Strategies 265
13.3 Conclusion and Future Scope of Research 266
References 267
Databases 273
Chapter 14: Phleum 274
14.1 Introduction 274
14.2 Agricultural Status 274
14.3 Morphology and Flowering Behavior 274
14.4 Taxonomy 275
14.4.1 Section Phleum 275
14.4.1.1 P. alpinum L. 275
14.4.1.2 P. pratense L. 275
14.4.1.3 Phleum echinatum Host. 275
14.4.2 Section Chilochloa (Beauv.) Dum. 275
14.4.2.1 P. phleoides (L.) Karsten, 275
14.4.2.2 P. hirsutum Honckeny 275
14.4.2.3 P. arenarium L. 276
14.4.2.4 P. montanum C Koch 276
14.4.2.5 P. paniculatum Hudson 276
14.4.2.6 P. himalaicum Mez. 276
14.4.2.7 P. iranicum Bornm. et Gauba 277
14.4.3 Section Achnodon (Nees) Griseb. 277
14.4.3.1 P. subulatum (Savi) Asch. et Graelon. 277
14.4.3.2 P. boissieri Bornm. 277
14.4.3.3 P. exaratum Hochst. 277
14.4.4 Section Maillea (Parl.) Horn af Rantzien 277
14.4.5 Cytology and Karyotype 277
14.4.6 Genome Size 277
14.4.7 Genomic Formula 278
14.4.7.1 P. alpinum 278
14.4.7.2 P. pratense 278
14.4.7.3 P. echinatum 278
14.4.7.4 Other Sections 278
14.5 Distribution in Relation to Historical Glaciations and Migrations 278
14.5.1 Phleum alpinum 280
14.5.1.1 Diploid Phleum alpinum 280
Subsp. rhaeticum RR 280
Form ``commutatum´´ 281
Hybrids Between rhaeticum and ``commutatum´´ 281
14.5.1.2 Tetraploid Phleum alpinum 281
Tetraploid Euro-American P. alpinum RRXX 281
Tetraploid Hybrids Between rhaeticum and ``commutatum´´ RRCC, CCRR 281
14.5.2 P. pratense 282
14.5.2.1 Diploid subsp. bertolonii 282
14.5.2.2 Tetraploid P. pratense 283
14.5.2.3 Hexaploid P. pratense 283
14.5.2.4 Octoploid P. pratense 283
14.5.3 P. echinatum 283
14.5.4 Migration History in Relation to Glaciation Events 284
14.5.5 Gene Exchange Between Genomes and Inheritance 285
14.6 Wild Relatives as Genetic Resources for Phleum pratense 286
14.6.1 Primary Gene Pool 286
14.6.2 Secondary Gene Pool 286
14.6.3 Tertiary Gene Pool 286
14.6.4 Quaternary Gene Pool 287
14.6.5 The Conservation of Genetic Resources 287
14.6.6 Germplasm Banks 287
14.6.7 Development of Core Collections 287
14.6.8 Endophytic Fungi 288
14.7 Cytological, Genomic and Molecular Resources in Phleum 288
14.8 Recommendations for Future Actions 288
References 289
Chapter 15: Setaria 292
15.1 Introduction 292
15.2 The Complex of Species of Foxtail Millet 293
15.2.1 A Brief Glance 293
15.2.2 Taxonomy 294
15.2.3 Phylogeny 295
15.3 Genetics Attributes 296
15.3.1 Cytogenetics and Karyotypes 296
15.3.2 Mating System 296
15.3.3 Interspecific Hybridization 297
15.3.3.1 Hand Crossing 297
15.3.3.2 Spontaneous Crosses 298
15.4 Phenotypic Variations 298
15.4.1 Morphological Variants 298
15.4.2 Physiological Variants 299
15.4.3 Geographic Variants 300
15.4.4 Domesticated Foxtail Millet Variants 300
15.4.5 Plasticity of Weedy Setaria 300
15.5 Biology and Habitat of the Wild Setaria 301
15.5.1 Habitat and Distribution 301
15.5.2 Population Genetic Structure 301
15.6 Role of Wild Setaria in Elucidation of Origin and Evolution of Foxtail Millet 302
15.6.1 Analysis of the Domesticated Traits 302
15.6.1.1 Seed Shedding 302
15.6.1.2 Inflorescence Architecture 302
15.6.1.3 Tillering 303
15.6.1.4 Germination 303
15.6.1.5 Grain Size 303
15.6.1.6 Grain Quality 304
15.6.1.7 Miscellaneous 304
15.6.2 Application of Morphotaxonomy, Chemotaxonomy, Biochemical and Molecular Markers 304
15.7 Role of Wild Setaria in Molecular Genetic Studies 305
15.7.1 Development of Cytogenetic Stocks and Genetic Maps 305
15.7.2 Genes and Genome Sequencing 305
15.8 Methods for Hybridization and Introgression of Traits from Wild Setaria 305
15.8.1 Hybridization 305
15.8.2 Introgression 306
15.9 Role in Crop Improvement 306
15.9.1 Male Sterility 306
15.9.2 Tetraploidy 306
15.9.3 Herbicide Resistance 306
15.9.3.1 Triazine Resistance 307
15.9.3.2 Trifluralin Resistance 307
15.9.3.3 Sethoxydim Resistance 307
15.9.3.4 Other Sources of Resistance 308
15.9.4 Other Desirable Agricultural Traits 308
15.10 Conclusion 308
References 309
Chapter 16: Zoysia 314
16.1 Basic Botany of the Species and Conservation Initiatives 314
16.2 Salt Tolerance Mechanisms and Phylogenetic Relationships 316
16.3 Classical and Molecular Genetic Studies 317
16.4 Crop Improvement Using Traditional and Advanced Tools 319
16.5 Controlling Weeds in Zoysia Grass 322
16.6 Recommendations for Future Actions 324
References 324
Index 327