Pat Heslop-HarrisonTalk 2: Genome evolution: perspectives from billionsof years to plant breeding timescales, from the bas...
BrassicaWheatBananaOthersCrocusPanicumDrosophilaArachisMedicago
Genomics & Genome  organization in  chromosomesHybrids/polyploidsBiodiversitySystems biologyIntrogression and  breedingSoc...
l Those where people control their             reproduction and nutrition             lMany alternatives                  ...
l Those where people control their             reproduction and nutrition                          What about             ...
¡ 350,000 plants¡ 4,629 mammals¡ 9,200 birds¡ 10,000,000 insects¡ 500,000 fungi7
¡   Animals and plants        § Not ‘fussy’ for diet, soil, climate        § Control reproduction          ▪ Fast and fert...
¡ 350,000 plants¡ 4,629 mammals¡ 9,200 birds¡ 10,000,000 insects¡ 500,000 fungi¡ But only 200 plants, 15    mammals, 5 bir...
¡    Spread of these few species¡    Little change since early agriculture¡    Repeated domestication of these species    ...
¡   New uses and demands – biofuels, animal    feed, medicinal/neutraceutical,    water/climate, food changes¡   Knowledge...
12
About 10,000 years before                      present                 Plants and animals                   In context:   ...
Genetic:¡ No seed dormancy¡ Determinate and synchronized growth¡ Gigantism in the harvested parts¡ No seed dispersal      ...
¡   Technology:¡   Tilling, planting, watering, feeding,    weeding, disease control, ‘growing’,    harvesting, threshing,...
¡   Human: a tiny part of history¡   Many animals plan ahead: store food, make    nests, post guards/lookouts, plan battle...
¡   And its worse ...¡   If you put goats on an island, after 10 years you    will only have goat-proof plants left!¡   Hu...
Population increase              Population increase                   Chicken                       ↑                    ...
(Not Archaeology and Anthropology!)  Hunter-gatherer no longer sustainable           Over-exploitation?    Habitat destruc...
¡ Habitat destruction¡ Climate change (abiotic stresses)¡ Diseases (biotic stresses)¡ Changes in what people want¡ Blindne...
¡   Will not be displaced     ¡   Continue to need 1 to 1.5% year-on-year         productivity increase     ¡   Increased ...
43.5                                             Maize 3                                              Rice2.5             ...
4                                                GM3.5                                                maize          Maize...
From Ian Mackay, NIAB, UK. 2009. Re-analyses of historical series of variety trials:lessons from the past and opportunitie...
lOther people’s cultivars31
¡   Cross the best with the best and hope for    something better
lLandraces33
lLandraceslWild and cultivated relatives34
35
Inheritance of Chromosome 5DAegilops ventricosa       × Triticum persicum Ac.1510DDNN                        AABB         ...
¡   Eyespot (fungus    Pseudocercosporella)    resistance from Aegilops    ventricosa introduced to    wheat by chromosome...
Crop standingLodging in cerealsCrop fallen
Susanne Barth, Ulrike Anhalt, Celine Tomaszewski
n   Formidable    genetic and    environmental    interactions       Anhalt, Barth, HH       Euphytica 2009       Theor Ap...
Anhalt UCM, Heslop-Harrison JS, Piepho HP, Byrne S, Barth S. 2009. Quantitative trait loci
Size and location ofchromosome regionsfrom radish (Raphanussativus) carrying thefertility restorer Rfk1gene and transfer t...
Cell fusionhybrid of two4x tetraploidtobaccospeciesPatel, Badakshi, HH,Davey et al 2011Annals of Botany
¡   How many genes are there?¡   1990s: perhaps 100,000¡   2000: 25,000¡   How does this give the range of functions and  ...
¡ Increased sustainability¡ Increased value¡ Uses genes outside the     conventional genepoolBenefits to all stakeholders:...
United Nations       Millennium Development Goals- MDGs• Goal 1 – Eradicate extreme  poverty and hunger•    Goal 2 – Achie...
¡   Cross the best with the best and hope for    something better¡   Decide what is wanted and then plan how to get it¡   ...
¡ Optimistic for improved crops from novel  germplasm¡ Benefits for people of developed and  developing countries¡ Major r...
¡ The additions to the FAO list of      crops since 1961      § Triticale      § Kiwi fruit      § Jojoba        + two spl...
¡ The additions to the FAO list      § Triticale (Genome engineering)      § Kiwi fruit (High value niche)      § Jojoba (...
•   Food (people)•   Feed (animals)•   Fuel (biomass and liquid)•   Flowers (ornamental and horticulture)•   Fibres & chem...
¡ Separate into increases in inputs  (resources, labour and capital) and  technical progress¡ 90% of the growth in US outp...
Crop               Genome size        2n     Ploidy                   FoodRice               400 Mb             24     2  ...
¡   Sequences¡   Genes / motifs¡   Repetitive DNA¡   Chromosomes                      ¡   Mutation¡   Chromosome sets     ...
¡   Farmers and agriculture underpin the well-being of the world’s    population. Agriculture is changing continuously: ev...
¡   It is interesting to contemplate … many    plants of many kinds … and to reflect    that these elaborately constructed...
¡   There is grandeur in this view of life, with its    several powers ... whilst this planet has gone    circling on acco...
1: Genes, genomes and genomics in crops2: Species, crops and domestication3: Diversity sources: mutations and germplasm4: ...
• Targeted breeding and transgenic  strategies• Increase in high value niche crops66
¡    Technology underpins developments     § Complexity     § Direction     § Safety¡    Germplasm collection and diversit...
¡    Genes, gene combinations and species with     limited exploitation in agriculture¡    Present in non-domesticated spe...
¡   Make more money - OUTPUT¡   Sell more for the same per unit¡   Sell the same units for more¡   Sell different (produce...
¡   There aren’t any!¡   Crops come from anywhere¡   They might be grown anywhere¡   Polyploids and diploids (big genomes-...
¡   40% of the worlds protein needs are derived    from atmospheric nitrogen fixed by the    Haber-Bosch process and its s...
¡   Farm    § Not wild-collected    § Mostly kept land in production      ▪ No slash/burn      ▪ Erosion control      ▪ In...
¡   Over the last 150 years,¡   1.5% reduction in production costs per year¡   similar across cereals, fruits, milk, meat ...
Pat Heslop-HarrisonTalk 2: Genome evolution: perspectives from billionsof years to plant breeding timescales, from the bas...
Domestication, Diversity and Molecular Cytogenetics Pat Heslop-Harrison
Domestication, Diversity and Molecular Cytogenetics Pat Heslop-Harrison
Domestication, Diversity and Molecular Cytogenetics Pat Heslop-Harrison
Domestication, Diversity and Molecular Cytogenetics Pat Heslop-Harrison
Domestication, Diversity and Molecular Cytogenetics Pat Heslop-Harrison
Domestication, Diversity and Molecular Cytogenetics Pat Heslop-Harrison
Domestication, Diversity and Molecular Cytogenetics Pat Heslop-Harrison
Domestication, Diversity and Molecular Cytogenetics Pat Heslop-Harrison
Domestication, Diversity and Molecular Cytogenetics Pat Heslop-Harrison
Domestication, Diversity and Molecular Cytogenetics Pat Heslop-Harrison
Domestication, Diversity and Molecular Cytogenetics Pat Heslop-Harrison
Domestication, Diversity and Molecular Cytogenetics Pat Heslop-Harrison
Domestication, Diversity and Molecular Cytogenetics Pat Heslop-Harrison
Domestication, Diversity and Molecular Cytogenetics Pat Heslop-Harrison
Domestication, Diversity and Molecular Cytogenetics Pat Heslop-Harrison
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Domestication, Diversity and Molecular Cytogenetics Pat Heslop-Harrison

  1. 1. Pat Heslop-HarrisonTalk 2: Genome evolution: perspectives from billionsof years to plant breeding timescales, from the basepair to trillions of bases, and from the cell to the planetand beyondphh4@le.ac.ukwww.molcyt.com pw/user: ‘visitor’Social media: pathh1 Twitter/YouTubePAU, Ludhiana 21 – 2 – 12
  2. 2. BrassicaWheatBananaOthersCrocusPanicumDrosophilaArachisMedicago
  3. 3. Genomics & Genome organization in chromosomesHybrids/polyploidsBiodiversitySystems biologyIntrogression and breedingSocio-economics and applications
  4. 4. l Those where people control their reproduction and nutrition lMany alternatives People control their access to space People have selected the variety They are different from wild species They would die out in the wild02/03/2012 Species useful to humans 5
  5. 5. l Those where people control their reproduction and nutrition What about Weeds Commensuals Diseases ?02/03/2012 6
  6. 6. ¡ 350,000 plants¡ 4,629 mammals¡ 9,200 birds¡ 10,000,000 insects¡ 500,000 fungi7
  7. 7. ¡ Animals and plants § Not ‘fussy’ for diet, soil, climate § Control reproduction ▪ Fast and fertile § Fast growing § Doesn’t die § Thrives in monoculture § Not aggressive/unpleasant8 ¡ Are there many candidate species?
  8. 8. ¡ 350,000 plants¡ 4,629 mammals¡ 9,200 birds¡ 10,000,000 insects¡ 500,000 fungi¡ But only 200 plants, 15 mammals, 5 birds, c. 5 fungi and9 2 insects are domesticated
  9. 9. ¡ Spread of these few species¡ Little change since early agriculture¡ Repeated domestication of these species (sometimes)¡ Lack of new species even with attempts with species known to be valuable¡ Some groups of good candidates with no domestication eg ferns, sub-Saharan mammals ...10 § Two ferns are invasive problem
  10. 10. ¡ New uses and demands – biofuels, animal feed, medicinal/neutraceutical, water/climate, food changes¡ Knowledge why species aren’t suitable for domestication or were not useful¡ Better understanding of genetics and selection¡ Sustainability of production¡ Reliability of production
  11. 11. 12
  12. 12. About 10,000 years before present Plants and animals In context: Humans 6,000,000 years since divergence from apes or 50,000 years since recognizably ‘modern’02/03/2012 Worldwide! 13
  13. 13. Genetic:¡ No seed dormancy¡ Determinate and synchronized growth¡ Gigantism in the harvested parts¡ No seed dispersal (after Hammer)¡ Increased harvest index¡ Sweetness no bitterness¡ Productivity high¡ Not toxicAll still a challenge today – and many improvements are still coming
  14. 14. ¡ Technology:¡ Tilling, planting, watering, feeding, weeding, disease control, ‘growing’, harvesting, threshing, storing, packaging, transporting, propagating, fields, cooking and preparation¡ All still a challenge today – with many changes and opportunities – worldwide
  15. 15. ¡ Human: a tiny part of history¡ Many animals plan ahead: store food, make nests, post guards/lookouts, plan battle strategies, broker marriages, build sanitation systems/toilets ... But only two farm¡ Ants: clearing weeds, farming insects and fungi, feeding them, maintaining fungal cultures ...
  16. 16. ¡ And its worse ...¡ If you put goats on an island, after 10 years you will only have goat-proof plants left!¡ Humans too have strong tendency to overexploitation § Dodo § Cape Cod
  17. 17. Population increase Population increase Chicken ↑ Farming Competitive Advantage ↓ Farming Egg02/03/2012 19
  18. 18. (Not Archaeology and Anthropology!) Hunter-gatherer no longer sustainable Over-exploitation? Habitat destruction/extinction? Population growth? Climate change? Food stability? Diet change? sf (Is farming reaching its end now?)02/03/2012 20
  19. 19. ¡ Habitat destruction¡ Climate change (abiotic stresses)¡ Diseases (biotic stresses)¡ Changes in what people want¡ Blindness to what is happening¡ Unwillingness to change
  20. 20. ¡ 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 § Quality23
  21. 21. 43.5 Maize 3 Rice2.5 Wheat 2 Human1.5 Area 10.5 0 1961 1970 1980 1990 2000 2007
  22. 22. 4 GM3.5 maize Maize 3 Genetics Rice2.5 Agronomy Wheat 2 Human1.5 Area 10.5 0 1961 1970 1980 1990 2000 2007
  23. 23. From Ian Mackay, NIAB, UK. 2009. Re-analyses of historical series of variety trials:lessons from the past and opportunities for the future. SCRI website.
  24. 24. lOther people’s cultivars31
  25. 25. ¡ Cross the best with the best and hope for something better
  26. 26. lLandraces33
  27. 27. lLandraceslWild and cultivated relatives34
  28. 28. 35
  29. 29. Inheritance of Chromosome 5DAegilops ventricosa × Triticum persicum Ac.1510DDNN AABB ABDN AABBDDNN × Marne AABBDD VPM1 × Hobbit Dwarf A CWW1176-4 × Virtue Rendezvous × {Kraka × (Huntsman × Fruhgold)} dpTa1 pSc119.2 Piko 96ST61 Genomic Ae.ventricosa
  30. 30. ¡ 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 resistances
  31. 31. Crop standingLodging in cerealsCrop fallen
  32. 32. Susanne Barth, Ulrike Anhalt, Celine Tomaszewski
  33. 33. n Formidable genetic and environmental interactions Anhalt, Barth, HH Euphytica 2009 Theor App Gen 2008
  34. 34. Anhalt UCM, Heslop-Harrison JS, Piepho HP, Byrne S, Barth S. 2009. Quantitative trait loci
  35. 35. Size and location ofchromosome regionsfrom radish (Raphanussativus) carrying thefertility restorer Rfk1gene and transfer tospring turnip rape(Brassica rapa)Tarja Niemelä, MerviSeppänen, FarahBadakshi,Veli-MattiRokka and J.S.(Pat)Heslop-HarrisonChromosomeResearch (subject tominor revision Feb2012)
  36. 36. Cell fusionhybrid of two4x tetraploidtobaccospeciesPatel, Badakshi, HH,Davey et al 2011Annals of Botany
  37. 37. ¡ How many genes are there?¡ 1990s: perhaps 100,000¡ 2000: 25,000¡ How does this give the range of functions and control? Najl Valeyev
  38. 38. ¡ Increased sustainability¡ Increased value¡ Uses genes outside the conventional genepoolBenefits to all stakeholders:Breeders, Farmers, Processors,Retailers, Consumers, Citizensin developed and developing countriesand to all members of society.50
  39. 39. 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 partnership for development
  40. 40. ¡ Cross the best with the best and hope for something better¡ Decide what is wanted and then plan how to get it¡ - variety crosses¡ - mutations¡ - hybrids (sexual or cell-fusion)¡ - genepool¡ - transformation
  41. 41. ¡ 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-national breeders53
  42. 42. ¡ The additions to the FAO list of crops since 1961 § Triticale § Kiwi fruit § Jojoba + two split categories: popcorn, feed legumes54
  43. 43. ¡ The additions to the FAO list § Triticale (Genome engineering) § Kiwi fruit (High value niche) § Jojoba (New product) § Popcorn is split (High value)55
  44. 44. • 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
  45. 45. ¡ 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
  46. 46. 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
  47. 47. ¡ Sequences¡ Genes / motifs¡ Repetitive DNA¡ Chromosomes ¡ Mutation¡ Chromosome sets ¡ Rearrangement (‘Genomes’) ¡ Duplication¡ Genotypes/CVs ¡ Deletion¡ Species ¡ Homogenization¡ Genera and above ¡ Crops / wild species ¡ Selection ¡ Speciation
  48. 48. ¡ Farmers and agriculture underpin the well-being of the world’s population. Agriculture is changing continuously: every year for the last 10,000 years, farmers have improved their weed control and water management, and each decade, farmers have won and lost battles with pests and diseases, and adopted new varieties of their crops. Over a longer timescale of 50 to 100 years, they introduce new species to cultivation and the food supply, even if the exchanges of old-world and new-world crops in the 16th and 17th centuries – including maize and potato from tropical America with wheat from the middle-east and sugar cane from southeast Asia – are unlikely to be repeated. ‘Novelty’ in crops can come from finding and exploiting new diversity in existing major crops or from improving and introducing species not previously used on a significant scale. The exploitation of new diversity is important to the livelihood of subsistence farmers and commercial growers. Modern genetics, mutation and molecular methods, and plant breeding can benefit producers, consumers and the environment.
  49. 49. ¡ It is interesting to contemplate … many plants of many kinds … and to reflect that these elaborately constructed forms, so different from each other …
  50. 50. ¡ There is grandeur in this view of life, with its several powers ... whilst this planet has gone circling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved.
  51. 51. 1: Genes, genomes and genomics in crops2: Species, crops and domestication3: Diversity sources: mutations and germplasm4: Genome & chromosome organization5: Markers, mapping and QTL analysis6: DNA markers from genomics7: Markers for biodiversity8: Superdomestication and breeding9: Agriculture, food and Millennium Dvlpmnt Goals10: PCR for genes and diversity
  52. 52. • Targeted breeding and transgenic strategies• Increase in high value niche crops66
  53. 53. ¡ Technology underpins developments § Complexity § Direction § Safety¡ Germplasm collection and diversity¡ Statistical methods¡ Screening67
  54. 54. ¡ Genes, gene combinations and species with limited exploitation in agriculture¡ Present in non-domesticated species, unimproved cultigens and crops with different characteristics68
  55. 55. ¡ Make more money - OUTPUT¡ Sell more for the same per unit¡ Sell the same units for more¡ Sell different (produce or service)¡ Spend less money - INPUT¡ Less inputs¡ Less labour¡ Less capital (land and equipment)
  56. 56. ¡ 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
  57. 57. ¡ 40% 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
  58. 58. ¡ Farm § Not wild-collected § Mostly kept land in production ▪ No slash/burn ▪ Erosion control ▪ Intelligent irrigation
  59. 59. ¡ 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
  60. 60. Pat Heslop-HarrisonTalk 2: Genome evolution: perspectives from billionsof years to plant breeding timescales, from the basepair to trillions of bases, and from the cell to the planetand beyondphh4@le.ac.ukwww.molcyt.com pw/user: ‘visitor’Social media: pathh1 Twitter/YouTubePAU, Ludhiana 21 – 2 – 12

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