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Domestication, Diversity and Molecular Cytogenetics Pat Heslop-Harrison

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Domestication, Diversity and Molecular Cytogenetics Pat Heslop-Harrison

  1. 1. Pat Heslop-Harrison Talk 2: Genome evolution: perspectives from billions of years to plant breeding timescales, from the base pair to trillions of bases, and from the cell to the planet and beyond phh4@le.ac.uk www.molcyt.com pw/user: ‘visitor’ Social media: pathh1 Twitter/YouTube PAU, Ludhiana 21 – 2 – 12
  2. 2. Brassica Wheat Banana Others Crocus Panicum Drosophila Arachis Medicago
  3. 3. Genomics & Genome organization in chromosomes Hybrids/polyploids Biodiversity Systems biology Introgression and breeding Socio-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 wild 02/03/2012 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 fungi 7
  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/unpleasant 8 ¡ 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 and 9 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 toxic All 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 Egg 02/03/2012 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 § Quality 23
  21. 21. 4 3.5 Maize 3 Rice 2.5 Wheat 2 Human 1.5 Area 1 0.5 0 1961 1970 1980 1990 2000 2007
  22. 22. 4 GM 3.5 maize Maize 3 Genetics Rice 2.5 Agronomy Wheat 2 Human 1.5 Area 1 0.5 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 cultivars 31
  25. 25. ¡ Cross the best with the best and hope for something better
  26. 26. lLandraces 33
  27. 27. lLandraces lWild and cultivated relatives 34
  28. 28. 35
  29. 29. Inheritance of Chromosome 5D Aegilops ventricosa × Triticum persicum Ac.1510 DDNN 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 standing Lodging in cereals Crop 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 of chromosome regions from radish (Raphanus sativus) carrying the fertility restorer Rfk1 gene and transfer to spring turnip rape (Brassica rapa) Tarja Niemelä, Mervi Seppänen, Farah Badakshi,Veli-Matti Rokka and J.S.(Pat) Heslop-Harrison Chromosome Research (subject to minor revision Feb 2012)
  36. 36. Cell fusion hybrid of two 4x tetraploid tobacco species Patel, Badakshi, HH, Davey et al 2011 Annals 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 genepool Benefits to all stakeholders: Breeders, Farmers, Processors, Retailers, Consumers, Citizens in developed and developing countries and 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 breeders 53
  42. 42. ¡ The additions to the FAO list of crops since 1961 § Triticale § Kiwi fruit § Jojoba + two split categories: popcorn, feed legumes 54
  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 Food Rice 400 Mb 24 2 3x endosperm Wheat 17,000 Mbp 42 6 3x endosperm Maize 950 Mbp 10 4 (palaeo-tetraploid) 3x endosperm Rapeseed B. 1125 Mbp 38 4 Cotyledon oil/protein napus Sugar beet 758 Mbp 18 2 Modified root Cassava 770 Mbp 36 2 Tuber Soybean 1,100 Mbp 40 4 Seed cotyledon Oil palm 3,400 Mbp 32 2 Fruit mesocarp Banana 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 crops 2: Species, crops and domestication 3: Diversity sources: mutations and germplasm 4: Genome & chromosome organization 5: Markers, mapping and QTL analysis 6: DNA markers from genomics 7: Markers for biodiversity 8: Superdomestication and breeding 9: Agriculture, food and Millennium Dvlpmnt Goals 10: PCR for genes and diversity
  52. 52. • Targeted breeding and transgenic strategies • Increase in high value niche crops 66
  53. 53. ¡ Technology underpins developments § Complexity § Direction § Safety ¡ Germplasm collection and diversity ¡ Statistical methods ¡ Screening 67
  54. 54. ¡ Genes, gene combinations and species with limited exploitation in agriculture ¡ Present in non-domesticated species, unimproved cultigens and crops with different characteristics 68
  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 world's 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-Harrison Talk 2: Genome evolution: perspectives from billions of years to plant breeding timescales, from the base pair to trillions of bases, and from the cell to the planet and beyond phh4@le.ac.uk www.molcyt.com pw/user: ‘visitor’ Social media: pathh1 Twitter/YouTube PAU, Ludhiana 21 – 2 – 12

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