BS2081    Ecology and Biodiversity                 Pat Heslop-Harrison          University of Leicester, UK               ...
Flip – teaching : Wiki “Flip teaching is a form of blended   learning which encompasses any use of technology to   leverag...
Biodiversity   What is biodiversity?20/02/2013                  3
Rio de Janeiro Conference in June 1992Defined biological diversity as “the variability among living organisms from all s...
Biodiversity   Agriculture brings in new   species and new genotypes   „Biodiversity‟ includes   weeds, pests, vectors, ...
Domesticated species    What are domesticated    species?20/02/2013                   6
What are domesticated species?Those where people control theirreproduction and nutritionMany alternatives  – People cont...
Domesticated species     What?     Mammals     Plants     Other species           –Fungi, Insects           –Fish, Moll...
Are there many candidates?380,000 plants4,629 mammals9,200 birds10,000,000 insectsBut only 200 plants, 15 mammals, 5 ...
10
11
12
13
14
How? The biological changes (others think of the anthropology)Animals and plants  – Not „fussy‟ for diet, soil, climate  ...
The first steps to domesticationBeing worthwhile to grow  – Can propagate: Seeds germinate, eggs hatch,    young produced...
Suite ofplant domestication traitsSeed dispersal – no!Seed dormancy – yes then no!Large harvested parts  – Gigantism  –...
ExamplesWheatTomatoCattlePigshttp://www.els.net/WileyCDA/                                18
Tinyurl.com/domesthttp://www.le.ac.uk/biology/phh4/p ublic/PHH_AltmanHasegawa_ch001. pdf                                ...
20
S. Banga – Punjab Agricultural Universityfirst determinate / terminal floweringBrassica juncea / B. napus lines Feb 2012  ...
22
23
When did domestication start?    About 8,000 years before            present         Plants and animals              In co...
Why did domestication start?   (Not Archaeology and Anthropology!) Hunter-gatherer no longer sustainable          Over-exp...
Where?After Diamond 2002
Domesticated species    What?    How?    When?    Why?    Where?20/02/2013          27
28
NASA    The Blue MarbleApollo 17 7 Dec 1972
Ecosystems anchor slide               Largely                 –   Self-organizing                 –   Self-maintained     ...
EcosystemsLiving components  – Plants and cyanobacteria (primary producers)  – Bacteria, fungi, animalsInteracting with ...
Rainfall           Distribution                mm/yr                          32
EcosystemsRecognizing  – Inputs  – Outputs  – Networks / webs of organisms  – Cycles  – Scales  – Functions              ...
Inputs  –   Light  –   Heat  –   Water  –   Gasses  –   Nutrients                  34
50% of the worlds protein needs are derived from atmospheric nitrogen fixed by the Haber-Bosch process and its successors...
Outputs     – Light     – Heat   – Water   – Gasses– Nutrients               36
OutputsEcosystemServicesWater, gasses,nutrients”nature‟s services, like flood control, waterfiltration, waste assimilation...
Dynamic processes: turn-over                                    Outputs                               – Limestone         ...
Inputs - Biotic  – Diseases  – New organisms    • Aliens/invasives  – New genes and    genotypes of    existing    organis...
Outputs              – Light              – Heat– Ecosystem services   – Chemical energy – Long term storage        Requir...
Biotic Inputs  – New genes  – New species       • Diseases       • Alien speciesAbiotic inputs  –   Irrigation  –   „Salt...
Water hyacinth – Eichornia: an invasive alienplant from South America, fills water courses (asurface habitat not used by a...
Argenome mexicana: a goat-proof plant from Mexcio introduced and successful in Africa   43
44
Occasional ‘extreme inputs’:Limiting composition of ecosystemsmore than ‘mean input’ - Robustness   45
46
47
Anhalt, Barth, HHEuphytica 2009 Theor App Gen
Light in ecosystems  Heat                           Information  Energy                 Quantity Quality Direction Periodi...
Threats to sustainability: no different for 10,000 yearsHabitat destructionClimate change (abiotic stresses)Diseases (b...
51
How to exploit models Increased sustainability Increased value Genetic improvement Robustness („food security‟) Benefi...
50 years of plant breeding progress 4                                        GM maize                                     ...
UK Wheat 1948-2007           52,909 data points, 308 varietiesFrom Ian Mackay, NIAB, UK. 2009. Re-analyses of historical s...
Conventional BreedingCross the best with the best and hope for something better SuperdomesticationDecide what is wanted ...
Economic growthSeparate into increases in inputs (resources, labour and capital) and technical progress90% of the growth...
Market Demand “MORE”Food production volume – No possibility of market collapse – Only slow market increase – Reduced post...
InputsBetter genetically  – Harvest more  – Stress resistant (Disease = biotic and    environment – abiotic)Higher  – We...
Needs from Stochastic Models of Ecosystems  Outputs                      Inputs Ecosystem                           –   Li...
The major crops     Will not be displaced     Continue to need 1 to 1.5% year-on-      year productivity increase     I...
Where do thesegenes come from?                   63
Other cultivarsLandracesWild and cultivated relativesOther speciesMutation breedingSynthetic biology64
Conventional BreedingCross the best with the best and hope for something better SuperdomesticationDecide what is wanted ...
Exploiting novel germplasmOptimistic for improved crops from novel germplasmBenefits for people of developed and develop...
United Nations Millennium Development Goals-MDGs  • Goal 1 – Eradicate extreme    poverty and hunger  •      Goal 2 – Achi...
50 years of plant breeding progress
50 years of plant breeding progress 43.5                                             Maize 3                              ...
50 years of plant breeding progress                                              GM 4                                     ...
Why exploit novel germplasm? Increased sustainability Increased value Uses genes outside the  conventional genepool Ben...
Conventional BreedingCross the best with the best and hope for something better
New crops     The additions to the FAO list      – Triticale (Genome engineering)      – Kiwi fruit (High value niche)   ...
Farming – the seven Fs •   Food (people) •   Feed (animals) •   Fuel (biomass and liquid) •   Flowers (ornamental and hort...
Nothing special about crop genomes?Crop            Genome size      2n    Ploidy                  FoodRice            400 ...
Lolium Biomass productionSusanne Barth, Ulrike Anhalt, Celine Tomaszewski
Size andlocation ofchromosomeregions fromradish(Raphanussativus)carrying thefertilityrestorerRfk1 geneand transferto sprin...
Chromosomeand genomeengineeringCell fusionhybrid oftwo4x tetraploidtobaccospecies
Nicotianahybrid4x + 4xcell fusionsEach of 4chromosomesets hasdistinctiverepetitiveDNA whenprobed withgenomic DNAPatel et a...
Exploiting novel germplasmSuperdomestication• Targeted breeding and  transgenic strategies• Increase in high value niche  ...
Market Demand “MORE”Food production volume  –   No possibility of market collapse  –   Only slow market increase  –   Red...
Market demand “MORE” Food (people) Feed (animals)  - Major driver of volumeEnormous increase in pigs and poultryIncrease...
InputsBetter genetically  – Harvest more  – Stress resistant (Disease = biotic and    environment – abiotic)Higher  – We...
Better stress resistance:  – From the genepool  – From engineering genes  – Existing crops will be the major food    sour...
90
91
92
93
94
95
96
97
Inheritance of Chromosome 5DAegilops ventricosa               × Triticum persicum Ac.1510DDNN                    AABB     ...
Eyespot (fungus Pseudocercosporella) resistance from Aegilops ventricosa introduced to wheat by chromosome engineeringMa...
Crop standingLodging in cerealsCrop fallen
Rules for successfuldomesticationThere aren‟t any!Crops come from anywhereThey might be grown anywherePolyploids and d...
55% of the worlds protein needs are derived from atmospheric nitrogen fixed by the Haber-Bosch process and its successors...
What have farmers done?Over the last 150 years, 1.5% reduction in production costs per  year similar across cereals, fr...
What have farmers done? Over the last 4500 years: Long-term „effort‟ reduction: 4500 years ago, getting food was full-t...
Do we need change?Do we need faster change?              Crop varieties              -High yield              -High qualit...
Genomics …The genepool has the diversity to address these challenges …New methods to exploit and characterize let use ma...
108
http://blog.ecoagriculture.org/2012/02/29/pac                                          109
110
Bs2081 Heslop-Harrison Summary Lecture Ecology and Biodiversity - Agricultural Systems
Bs2081 Heslop-Harrison Summary Lecture Ecology and Biodiversity - Agricultural Systems
Bs2081 Heslop-Harrison Summary Lecture Ecology and Biodiversity - Agricultural Systems
Bs2081 Heslop-Harrison Summary Lecture Ecology and Biodiversity - Agricultural Systems
Bs2081 Heslop-Harrison Summary Lecture Ecology and Biodiversity - Agricultural Systems
Bs2081 Heslop-Harrison Summary Lecture Ecology and Biodiversity - Agricultural Systems
Bs2081 Heslop-Harrison Summary Lecture Ecology and Biodiversity - Agricultural Systems
Bs2081 Heslop-Harrison Summary Lecture Ecology and Biodiversity - Agricultural Systems
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Bs2081 Heslop-Harrison Summary Lecture Ecology and Biodiversity - Agricultural Systems

  1. 1. BS2081 Ecology and Biodiversity Pat Heslop-Harrison University of Leicester, UK phh4@le.ac.uk www.molcyt.com UserID/PW „visitor‟ Twitter: pathh1 – cytogenomics.wordpress.com20/02/2013 1
  2. 2. Flip – teaching : Wiki “Flip teaching is a form of blended learning which encompasses any use of technology to leverage the learning in a classroom, so a teacher can spend more time interacting with students instead of lecturing. This is most commonly being done using teacher-created videos that students view outside of class time.” 2
  3. 3. Biodiversity What is biodiversity?20/02/2013 3
  4. 4. Rio de Janeiro Conference in June 1992Defined biological diversity as “the variability among living organisms from all sources including, among other things, terrestrial, marine, and other aquatic ecosystems and the ecological complexes of which they are part: this includes diversity within species, between species and of ecosystems.” 4
  5. 5. Biodiversity Agriculture brings in new species and new genotypes „Biodiversity‟ includes weeds, pests, vectors, predators20/02/2013 5
  6. 6. Domesticated species What are domesticated species?20/02/2013 6
  7. 7. What are domesticated species?Those where people control theirreproduction and nutritionMany alternatives – People control their access to nutrition/space – People have selected the variety – They are different from wild species – They would die out in the wild – Species useful to humans – Those with molecular signatures of selection/bottlenecks 20/02/2013 7
  8. 8. Domesticated species What? Mammals Plants Other species –Fungi, Insects –Fish, Molluscs20/02/2013 –Birds 8
  9. 9. Are there many candidates?380,000 plants4,629 mammals9,200 birds10,000,000 insectsBut only 200 plants, 15 mammals, 5 birds and 2 insects are domesticated! 9
  10. 10. 10
  11. 11. 11
  12. 12. 12
  13. 13. 13
  14. 14. 14
  15. 15. How? The biological changes (others think of the anthropology)Animals and plants – Not „fussy‟ for diet, soil, climate – Control reproduction • Fast and fertile – Fast growing – Doesn‟t die – Thrives in monoculture – Not aggressive/unpleasant 15
  16. 16. The first steps to domesticationBeing worthwhile to grow – Can propagate: Seeds germinate, eggs hatch, young produced – Can harvest: Seeds not dispersed/can catch, doesn‟t rot, don‟t die – Reasonably persistent (but the odd extinction does not matter) – Determinate growth / uniform ripening – Large yield - seed/fruits/meat/milk 16
  17. 17. Suite ofplant domestication traitsSeed dispersal – no!Seed dormancy – yes then no!Large harvested parts – Gigantism – High proportion usefulDeterminate/synchronized growthEdible and tasty 17
  18. 18. ExamplesWheatTomatoCattlePigshttp://www.els.net/WileyCDA/ 18
  19. 19. Tinyurl.com/domesthttp://www.le.ac.uk/biology/phh4/p ublic/PHH_AltmanHasegawa_ch001. pdf 19
  20. 20. 20
  21. 21. S. Banga – Punjab Agricultural Universityfirst determinate / terminal floweringBrassica juncea / B. napus lines Feb 2012 21
  22. 22. 22
  23. 23. 23
  24. 24. When did domestication start? About 8,000 years before present Plants and animals In context: Humans 6,000,000 years since divergence from apes or 50,000 years since recognizably20/02/2013 „modern‟ 24
  25. 25. Why did domestication start? (Not Archaeology and Anthropology!) Hunter-gatherer no longer sustainable Over-exploitation? Habitat destruction/extinction? Population growth? Climate change? Food stability? Diet change? sf20/02/2013 25
  26. 26. Where?After Diamond 2002
  27. 27. Domesticated species What? How? When? Why? Where?20/02/2013 27
  28. 28. 28
  29. 29. NASA The Blue MarbleApollo 17 7 Dec 1972
  30. 30. Ecosystems anchor slide Largely – Self-organizing – Self-maintained – Cycling – Defined scope – cf Household – Aircraft – 30
  31. 31. EcosystemsLiving components – Plants and cyanobacteria (primary producers) – Bacteria, fungi, animalsInteracting with abiotic components – Light – Water – Wind, soil, nutrients, toxins, gasses ...Recognizable homogeneity in one ecosystem 31
  32. 32. Rainfall Distribution mm/yr 32
  33. 33. EcosystemsRecognizing – Inputs – Outputs – Networks / webs of organisms – Cycles – Scales – Functions 33
  34. 34. Inputs – Light – Heat – Water – Gasses – Nutrients 34
  35. 35. 50% of the worlds protein needs are derived from atmospheric nitrogen fixed by the Haber-Bosch process and its successors.Global consumption of fertilizer (chemically fixed nitrogen) 80 million tonnes<<200 million tonnes fixed naturally
  36. 36. Outputs – Light – Heat – Water – Gasses– Nutrients 36
  37. 37. OutputsEcosystemServicesWater, gasses,nutrients”nature‟s services, like flood control, waterfiltration, waste assimilation” 37
  38. 38. Dynamic processes: turn-over Outputs – Limestone 38– Made by marine organisms, formation and stability affected by pH and temperature
  39. 39. Inputs - Biotic – Diseases – New organisms • Aliens/invasives – New genes and genotypes of existing organisms 39
  40. 40. Outputs – Light – Heat– Ecosystem services – Chemical energy – Long term storage Required and valued 40
  41. 41. Biotic Inputs – New genes – New species • Diseases • Alien speciesAbiotic inputs – Irrigation – „Salt‟ (NaCl) – Nitrogen – Phosphorous 41
  42. 42. Water hyacinth – Eichornia: an invasive alienplant from South America, fills water courses (asurface habitat not used by any native species)in Asia and Africa 42
  43. 43. Argenome mexicana: a goat-proof plant from Mexcio introduced and successful in Africa 43
  44. 44. 44
  45. 45. Occasional ‘extreme inputs’:Limiting composition of ecosystemsmore than ‘mean input’ - Robustness 45
  46. 46. 46
  47. 47. 47
  48. 48. Anhalt, Barth, HHEuphytica 2009 Theor App Gen
  49. 49. Light in ecosystems Heat Information Energy Quantity Quality Direction PeriodicityPhotosynthesis Control of development
  50. 50. Threats to sustainability: no different for 10,000 yearsHabitat destructionClimate change (abiotic stresses)Diseases (biotic stresses)Changes in what people wantMORE outputs neededMORE stability in outputs from less stable inputs / poorer environments
  51. 51. 51
  52. 52. How to exploit models Increased sustainability Increased value Genetic improvement Robustness („food security‟) Benefits to all stakeholders: Breeders, Farmers, Processors, Retailers, Consumers, Citizens 53
  53. 53. 50 years of plant breeding progress 4 GM maize Maize Genetics3.5 3 Rice2.5 Agronomy Wheat 2 Human1.5 Area 10.5 0 1961 1970 1980 1990 2000 2007
  54. 54. UK Wheat 1948-2007 52,909 data points, 308 varietiesFrom Ian Mackay, NIAB, UK. 2009. Re-analyses of historical series ofvariety trials: lessons from the past and opportunities for the future. SCRI
  55. 55. Conventional BreedingCross the best with the best and hope for something better SuperdomesticationDecide what is wanted and then plan how to get it – Variety crosses – Mutations – Hybrids (sexual or cell-fusion) – Genepool – Transformation
  56. 56. Economic growthSeparate into increases in inputs (resources, labour and capital) and technical progress90% of the growth in US output per worker is attributable to technical progress Robert Solow – Economist
  57. 57. Market Demand “MORE”Food production volume – No possibility of market collapse – Only slow market increase – Reduced post-harvest loss – Some crops gain/hit by global trends
  58. 58. InputsBetter genetically – Harvest more – Stress resistant (Disease = biotic and environment – abiotic)Higher – Weed control improving for 8000 yearsLower – Production loss less than cost decrease – Better agronomy (cropping cycles etc.)
  59. 59. Needs from Stochastic Models of Ecosystems Outputs Inputs Ecosystem – Light services – Heat – Chemical – Water energy – Gasses– Long term – Nutrients storage 61
  60. 60. The major crops Will not be displaced Continue to need 1 to 1.5% year-on- year productivity increase Increased sustainability essential Major breeding targets – Post-harvest losses – Water use – Disease resistance – Quality62
  61. 61. Where do thesegenes come from? 63
  62. 62. Other cultivarsLandracesWild and cultivated relativesOther speciesMutation breedingSynthetic biology64
  63. 63. Conventional BreedingCross the best with the best and hope for something better SuperdomesticationDecide what is wanted and then plan how to get it - variety crosses - mutations - hybrids (sexual or cell-fusion) - genepool - transformation
  64. 64. Exploiting novel germplasmOptimistic for improved crops from novel germplasmBenefits for people of developed and developing countriesMajor role for national and international governmental breedingMajor role for private-sector local, national and multi-national66
  65. 65. United Nations Millennium Development Goals-MDGs • Goal 1 – Eradicate extreme poverty and hunger • Goal 2 – Achieve universal primary education • Goal 3 – Promote gender equity and empower women • Goal 4 – Reduce child mortality • Goal 5 – Improve maternal health • Goal 6- Combat HIV/AIDS, malaria and other diseases • Goal 7 - Ensure environmental sustainability • Goal 8 - Develop a global
  66. 66. 50 years of plant breeding progress
  67. 67. 50 years of plant breeding progress 43.5 Maize 3 Rice2.5 Wheat 2 Human1.5 Area 10.5 0 1961 1970 1980 1990 2000 2007
  68. 68. 50 years of plant breeding progress GM 4 maize Maize Genetics3.5 3 Rice2.5 Agronomy Wheat 2 Human1.5 Area 10.5 0 1961 1970 1980 1990 2000 2007
  69. 69. Why exploit novel germplasm? Increased sustainability Increased value Uses genes outside the conventional genepool Benefits to all stakeholders: Breeders, Farmers, Processors, Retailers, Consumers, Citizens in developed and developing countries and to all members of society. 74
  70. 70. Conventional BreedingCross the best with the best and hope for something better
  71. 71. New crops The additions to the FAO list – Triticale (Genome engineering) – Kiwi fruit (High value niche) – Jojoba (New product) – Popcorn is split (High value)76
  72. 72. Farming – the seven Fs • Food (people) • Feed (animals) • Fuel (biomass and liquid) • Flowers (ornamental and horticulture) • Fibres & chemicals • Construction (timber) • Products (wood, „plastics‟) • Fibres (paper, clothing) • Fun – Recreational/Environmental • Golf courses, horses, walking etc. • Environmental - Water catchments, Biodiversity, Buffers, Carbon capture, Security • Pharmaceuticals
  73. 73. Nothing special about crop genomes?Crop Genome size 2n Ploidy FoodRice 400 Mb 24 2 3x endospermWheat 17,000 Mbp 42 6 3x endospermMaize 950 Mbp 10 4 (palaeo-tetraploid) 3x endospermRapeseed B. 1125 Mbp 38 4 Cotyledon oil/proteinnapusSugar beet 758 Mbp 18 2 Modified rootCassava 770 Mbp 36 2 TuberSoybean 1,100 Mbp 40 4 Seed cotyledonOil palm 3,400 Mbp 32 2 Fruit mesocarpBanana 500 Mbp 33 3 Fruit mesocarp Heslop-Harrison & Schwarzacher 2012. Genetics and genomics of crop domestication. In Altman & Hasegawa Plant Biotech & Agriculture. 10.1016/B978- 0-12-381466-1.00001-8 Tinyurl.com/domest
  74. 74. Lolium Biomass productionSusanne Barth, Ulrike Anhalt, Celine Tomaszewski
  75. 75. Size andlocation ofchromosomeregions fromradish(Raphanussativus)carrying thefertilityrestorerRfk1 geneand transferto springturnip rape(Brassicarapa)
  76. 76. Chromosomeand genomeengineeringCell fusionhybrid oftwo4x tetraploidtobaccospecies
  77. 77. Nicotianahybrid4x + 4xcell fusionsEach of 4chromosomesets hasdistinctiverepetitiveDNA whenprobed withgenomic DNAPatel et alAnn Bot 2011
  78. 78. Exploiting novel germplasmSuperdomestication• Targeted breeding and transgenic strategies• Increase in high value niche crops84
  79. 79. Market Demand “MORE”Food production volume – No possibility of market collapse – Only slow market increase – Reduced post-harvest loss – Some crops gain/hit by global trends
  80. 80. Market demand “MORE” Food (people) Feed (animals) - Major driver of volumeEnormous increase in pigs and poultryIncreases in farmed fishSmaller changes in cattle… animals with the same diet as us are increasing… to feed a person meat means the farmer sells 2½ to 11 times more grain than in the person eats the grain
  81. 81. InputsBetter genetically – Harvest more – Stress resistant (Disease = biotic and environment – abiotic)Higher – Weed control improving for 8000 yearsLower – Production loss less than cost decrease – Better agronomy (cropping cycles etc.)
  82. 82. Better stress resistance: – From the genepool – From engineering genes – Existing crops will be the major food sourcesNew crops – Some will become important – Many niche crops will make money
  83. 83. 90
  84. 84. 91
  85. 85. 92
  86. 86. 93
  87. 87. 94
  88. 88. 95
  89. 89. 96
  90. 90. 97
  91. 91. Inheritance of Chromosome 5DAegilops ventricosa × Triticum persicum Ac.1510DDNN AABB ABDN AABBDDNN × Marne AABBDD VPM1×Hobbit Dwarf A × CWW1176-4Virtue Rendezvous {Kraka × (Huntsman × × Fruhgold)} dpTa1 pSc119.2 Genomic Ae.ventricosa Piko 96ST61
  92. 92. Eyespot (fungus Pseudocercosporella) resistance from Aegilops ventricosa introduced to wheat by chromosome engineeringMany diseases where all varieties are highly susceptibleAlien variation can be found and used7Host and non-host
  93. 93. Crop standingLodging in cerealsCrop fallen
  94. 94. Rules for successfuldomesticationThere aren‟t any!Crops come from anywhereThey might be grown anywherePolyploids and diploids (big genomes- small genomes, many chromosomes- few chromosomes)Seeds, stems, tubers, fruits, leaves
  95. 95. 55% of the worlds protein needs are derived from atmospheric nitrogen fixed by the Haber-Bosch process and its successors.Global consumption of fertilizer (chemically fixed nitrogen) 80 million tonnes<<200 million tonnes fixed naturally
  96. 96. What have farmers done?Over the last 150 years, 1.5% reduction in production costs per year similar across cereals, fruits, milk, meat … coal, iron With increased quality and security Remarkable total of 10-fold reduction in costs
  97. 97. What have farmers done? Over the last 4500 years: Long-term „effort‟ reduction: 4500 years ago, getting food was full-time job for everyone = 365*12 = 4380 hr/yr/person (Minimal towns, few wars, few monuments, few records: all these need time-out from farming!) Now: In Europe and North America, 2% of the population are farmers = 0.02*8*300 = 48 hr/yr/person spent farming 0.1% per year cumulative reduction
  98. 98. Do we need change?Do we need faster change? Crop varieties -High yield -High quality and safe -Easy to grow agronomically -Disease resistant -Insect/nematode resistant -Efficient water use -Secure, stable production -Environmentally friendly -Not invasive
  99. 99. Genomics …The genepool has the diversity to address these challenges …New methods to exploit and characterize let use make better and sustainable use of the genepool
  100. 100. 108
  101. 101. http://blog.ecoagriculture.org/2012/02/29/pac 109
  102. 102. 110

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