Methods of Domestication PDF

Farming in ancient Egypt BIOB38: Plants and Society 1-2. Origin of agriculture 3-6. Plant domestication 7-10. Green Revolution & its legacy 11-14. Plants that feed the world 15-16. Plants that please the palate 17-18. Plants that heal the sick 19-20. Plants that hook the mind and...

Farming in ancient Egypt BIOB38: Plants and Society 1-2. Origin of agriculture 3-6. Plant domestication 7-10. Green Revolution & its legacy 11-14. Plants that feed the world 15-16. Plants that please the palate 17-18. Plants that heal the sick 19-20. Plants that hook the mind and body 21-22. Plants the world thirsts after 23-24. Plants of warmth and strength Plant domestication 3-4. Altered plant traits 5-6. Methods of domestication Methods of domestication 1. Introduction and historical overview 2. Selective breeding, aka mass selection 3. Hybrid breeding 4. Mutation breeding 5. Backcross breeding 6. Genetic modification GM Selected milestones in plant breeding 11000 BP Beginning of plant domestication, Fertile Crescent Pre-science 1694 Plant crossing → obtain new plant types 1761-1766 Discovery: hybrid offspring has traits from both parents 1866 Mendel: experiments in plant inheritance Renaissance to 1900 Mendel’s laws of heredity rediscovered pre-DNA discovery 1920 Discovery of hybrid vigor science 1944 DNA is hereditary 1953 Description of DNA structure Post-DNA 1972 Discovery: Recombinant DNA technology discovery science 1. Introduction and historical overview Selective breeding, aka mass selection 11000 BP Beginning of plant domestication, Fertile Crescent 1694 Plant crossing → obtain new plant types 1761-1766 Discovery: hybrid offspring has traits from both parents 1866 Mendel: experiments in plant inheritance 1900 Mendel’s laws of heredity rediscovered 1920 Discovery of hybrid vigor 1944 Discovery: DNA is hereditary 1953 Description of DNA structure 1972 Discovery: Recombinant DNA technology 1. Introduction and historical overview Methods of domestication 1. Introduction and historical overview 2. Selective breeding, aka mass selection 3. Hybrid breeding 4. Mutation breeding 5. Backcross breeding 6. Genetic modification A few mutants in a sea of wild type Pre-existing var. of traits Heritability of traits More/better/easier food 2. Selective breeding, aka mass selection Mass selection in a nutshell 1 2 3 4 2. Selective breeding, aka mass selection Reduced seed dispersal Unconscious 2. Selective breeding, aka mass selection Dominance of photo-neutral mutants Summer-dry seeds in a winter-cold climate Seeds sown Yield Yield 3 2 1 Conscious or unconscious? Wheat, barley 2. Selective breeding, aka mass selection Increase in seed size Barley (also for wheat) Rice Bean late late mid early early Fertile Crescent China India Conscious or unconscious? Modified from Fuller. 2007. Annals of Botany 100: 903-924 2. Selective breeding, aka mass selection Sunflower effect Sunflower, corn, beans Conscious or unconscious? Harlan. 1995. The Living Fields. Cambridge University Press. Pg. 199. 5. More compact growth habit Selective breeding, mass selection Needs variable population Recurrent rounds of selection Based on phenotype and functional difference Genetically speaking: fishing in the dark… On the side of the domesticating farmer: Mostly unconscious 2. Selective breeding, aka mass selection Result of selective breeding Vast majority of all crops today! 2. Selective breeding, aka mass selection Methods of domestication 1. Introduction and historical overview 2. Selective breeding, aka mass selection 3. Hybrid breeding 4. Mutation breeding 5. Backcross breeding 6. Genetic modification Selective breeding, aka mass selection 11000 BP Beginning of plant domestication, Fertile Crescent 1694 Plant crossing → obtain new plant types 1761-1766 Discovery: hybrid offspring has traits from both parents 1866 Mendel: experiments in plant inheritance 1900 Mendel’s laws of heredity rediscovered 1920 Discovery of hybrid vigor 1944 Discovery: DNA is hereditary 1953 Description of DNA structure 1972 Discovery: Recombinant DNA technology 3. Hybrid breeding Btw species cross: hybrid offspring are intermediate Nicotiana rustica N. paniculata X J.G. Koelreuter in 1761-1766 Phenotypically intermediate offspring 3. Hybrid breeding Mendel’s rules of inheritance vs. plant breeding Genetics puts plant breeding on a scientific basis Key: segregation → different traits can produce new combinations of organisms Science of genetics: profound effect on breeding, agriculture Especially for hybrid breeding (corn) 3. Hybrid breeding  Fitness Hybrid breeding or heterosis Horse Donkey Btw and within species crosses Mule 3. Hybrid breeding “MOST IMPORTANT” hybrid breeding BTW. species Einkorn wheat1 x goatgrass2 = emmer and durum wheats3 (pre-agricultural times) x = 3 1 2 Emmer and durum wheats3 x goatgrass4 = bread wheats5 (in early fields of the Fertile Crescent) x = More in: Plants that feed the world 3 4 5 3. Hybrid breeding “MOST IMPORTANT” cross between tree species Different compatible species of Malus Diversification Hybridization Spengler. 2020. Trends in Plant Science 3. Hybrid breeding “MOST IMPORTANT” hybrid breeding WITHIN a species Hybrid breeding in corn Hybrid offspring Making use of heterosis = hybrid Parent 2 vigor Parent 1 Phenomenon where progeny of diverse varieties of a species (or crosses between species) exhibit greater biomass, speed of development, and fertility than either parent 3. Hybrid breeding Corn sexual reproduction 101 M Monoecious Wind species pollinated M F M Stigma F 3. Hybrid breeding Heterosis or hybrid vigor in corn Parental lines produced 20 bushels of corn, hybrids 80! 1908: US plant breeder was the first to interbreed two lines of corn with different characteristics (i.e. hybrid crossing) 1920: first commercial hybrid corn was available in the US From 1940s until today (US, CA etc.): ONLY hybrid corn is grown commercially Hybrid breeding in corn is big (agro-) business! 3. Hybrid breeding Hybrid breeding in corn, simplified key steps (idea) 1. Pick good candidates 2. Self good candidates to turn them from likely heterozygous to homozygous Hybrid offspring 3. Screen selfed offspring, keep good for Parent 2 further selfing, discard bad Parent 1 4. Cross the homozygous candidates to create hybrid offspring seeds (goal of the hybrid breeding program) 5. Go through these steps at a massive scale to produce seed to sell to farmers 3. Hybrid breeding 1. Pick good candidates Choose useful target traits (genes) Strong stalk Good N uptake Large roots High starch content Big ears Hardiness Pop-ability of seeds … (1000s of traits/genes) Outcrossed species: recombination at work → an individuum = never good at all traits! → pick two key target traits 3. Hybrid breeding Pick one candidate for one trait and another for another Individual 1 Individual 2 A Alleles x x A Strong stalk gene Good N uptake gene 3. Hybrid breeding Outcrossed species: recombination btw parents… → individuals = probably heterozygous at target loci Individual 1 Individual 2 Ax xx xx Ax Axxx xxAx Strong stalk Good nitrogen uptake 3. Hybrid breeding Hybrid breeding in corn, simplified key steps (idea) 1. Pick good candidates 2. Self good candidates to turn them from likely heterozygous to homozygous 3. Screen selfed offspring, keep good for Hybrid offspring further selfing, discard bad Parent 2 Parent 1 4. Cross the homozygous candidates to create hybrid offspring seeds (goal of the hybrid breeding program) 5. Go through these steps at a massive scale to produce seed to sell to farmers 3. Hybrid breeding Heterozygous plants produce different classes of zygotes Strong stalk Good N uptake Axxx AAxx xxAx xxAA Possible Ax xA zygotes xx Ax xx xA How to get just good zygotes? Create selfed lines! 3. Hybrid breeding Self good candidates Axxx Egg M self Ax xx Pollen F Offspring Ax AAxx Axxx carrying alleles for strong stalks Possible Ax Offspring zygotes xx xx Axxx xxxx lacking alleles for strong stalks Need to eliminate offspring with bad alleles 3. Hybrid breeding Hybrid breeding in corn, the simplified key steps 1. Pick good candidates 2. Self good candidates to turn them from likely heterozygous to homozygous Hybrid offspring 3. Screen selfed offspring, keep good for Parent 2 Parent 1 further selfing, discard bad 4. Cross the homozygous candidates to create hybrid offspring seeds (goal of the hybrid breeding program) 5. Go through these steps at a massive scale to produce seed to sell to farmers 3. Hybrid breeding 3. Screen selfed offspring, keep good, discard bad ones Optimizing for a strong stalk Axxx Egg M Ax xx self Pollen F Ax AAxx Axxx X Possible Ax xx Axxx xxxx zygotes xx Strong stalk? → continue selfing Weak stalk? → discard X 3. Hybrid breeding 3. Screen selfed offspring, keep good, discard bad ones Optimizing for a high N content xxAx Egg M xA xx self Pollen F xA xxAA xxAx X Possible xA xx xxAx xxxx zygotes xx High N content? → continue selfing Low N? → discard X 3. Hybrid breeding Several rounds of selfing: bad alleles gone M Egg M Egg Ax xA F Pollen Pollen F Ax AAxx xA xxAA Several years! AAxx xxAA Multiple rounds of selfing & screening → homozygous individuals 3. Hybrid breeding Hybrid breeding in corn, the simplified key steps 1. Pick good candidates 2. Self good candidates to turn them from likely heterozygous to homozygous Hybrid offspring 3. Screen selfed offspring, keep good for Parent 2 further selfing, discard bad Parent 1 4. Cross the homozygous candidates to create hybrid offspring seeds (goal of the hybrid breeding program) 5. Go through these steps at a massive scale to produce seed to sell to farmers 3. Hybrid breeding Step 4: create hybrid Detassel one Collect pollen from parent, use as F other parent, use as M Egg Sell these M Ax superior M Pollen seeds to F farmers xA AxAx F AAxx X xxAA Cross inbred lines All seeds grow into plants with strong stalks and good N uptake 100% HYBRID VIGOR (HETEROSIS) AxAx 3. Hybrid breeding Hybrid breeding in corn, simplified key steps (idea) 1. Pick good candidates 2. Self good candidates to turn them from likely heterozygous to homozygous Hybrid offspring 3. Screen selfed offspring, keep good for Parent 2 further selfing, discard bad Parent 1 4. Cross the homozygous candidates to create hybrid offspring seeds (goal of the of hybrid breeding program) 5. Go through these steps at a massive scale to produce seed to sell to farmers 3. Hybrid breeding Hybrid corn breeding: key for increase in corn yields Hybrid offspring Parent 2 Parent 1 100% AxAx 3. Hybrid breeding Hybrid breeding in corn: the reality for agrobusinesses Dozens or hundreds of genes involved Very time-consuming and involved process Year 1: start with hundreds potential parents Years 2 to 4: self to create homozygous lines, only self promising candidates among offspring Years 5 to 10: hundreds of hybrids are tested for growth characteristics and quality Years 11: Final hybrid cross btw fully inbred and tested parent lines → seed of a few hybrids is good enough for marketing Need to produce uniformly high-performing seeds on mass scale Modified from Chrispeels and Sadava. 1994. Plants, Genes and Agriculture 3. Hybrid breeding Hybrids: farmers need to buy seed each year Open pollination on farmer’s field Possible zygotes AA Ax xA xx Continued use of own 100% seeds in years after the AxAx purchase of hybrid seeds AA AAAA AAAx AxAA AAAa % high yield traits Keep some seeds Ax AAAx AAxx AxAa Axxx for new crop (AxAx) Harvest xA AxAA AxAx xxAA xxAa Year Sell most xx AxAx Axxx xxAx xxxx seeds for profit Productive hybrid AxAx Farmers: dependent on agrobusinesses 3. Hybrid breeding Food production via hybrid seeds: big business Farmers need to produce big enough surplus to be able to afford to buy hybrid seed every year to maintain a uniformly large yield Difficult for small farmers Difficult for farmers in developing countries 3. Hybrid breeding Hybrid breeding in rice The hybrid generation of a rice cross between two genetically diverse parents Productivity (yield/unit/time): 15-20% higher in hybrids 3. Hybrid breeding Heterosis in rice: within and btw species Indica x Japonica Indica x Javanica Relative yield Japonica x jJavanica Indica x Indica More about Japonica x Japonica rice in ‘Plants that feed the world’ 3. Hybrid breeding Hybrid breeding Pros and cons + Reproducible + Predictable - Only possible in crossable species - Only possible with dominant traits - Very slow process - Breeding program needs to start anew after each season 3. Hybrid breeding Methods of domestication 1. Introduction and historical overview 2. Selective breeding, aka mass selection 3. Hybrid breeding 4. Mutation breeding 5. Backcross breeding 6. Genetic modification Selected milestones in plant breeding 11000 BP Beginning of plant domestication, Fertile Crescent Pre-science 1694 Plant crossing → obtain new plant types 1761-1766 Discovery: hybrid offspring has traits from both parents 1866 Mendel: experiments in plant inheritance Renaissance 1900 Mendel’s laws of heredity rediscovered to pre-DNA 1920 Discovery of hybrid vigor discovery science 1944 DNA is hereditary 1953 Description of DNA structure Post-DNA 1972 Discovery: Recombinant DNA technology discovery science 4. Mutation breeding 4. Mutation breeding Chemical mutagens or physical radiation: generate mutants with hopefully desirable traits May involve any trait, e.g. from minute to drastic morphological changes Most mutations: harmful or even lethal, only rarely advantageous 4. Mutation breeding Techniques for inducing mutations Physical: ionizing radiation UV, X, gamma rays Chemical: compounds interacting with DNA (mutagens) Chemical mutagens: more effective than physical ones, also easier to fine-tune 4. Mutation breeding Ionizing radiation to search for promising mutations 4. Mutation breeding Only some mutations are heritable Sexually reproducing crop plants M F Gametes Seeds Anywhere else in the plant body? Not heritable, thus not useful 4. Mutation breeding Most mutations are recessive → hard to work with Mutations mostly happen just in one DNA strand Dominant mutations easier to detect 4. Mutation breeding Example of cultivar developed through mutagenesis Low seeded Kinnow orange 4. Mutation breeding Mutation breeding Pros (+) and cons (-) + Applied to single cells or whole organisms + Screen very large populations (of individuals & cells) + If introduced to germline → stable trait - Non-heritability of many mutations (outside germline) - Requires dominant mutation (or double recessive mutation); most mutations are recessive and single - Unpredictability of mutations 4. Mutation breeding Methods of domestication 1. Introduction and historical overview 2. Selective breeding, aka mass selection 3. Hybrid breeding 4. Mutation breeding 5. Backcross breeding 6. Genetic modification Selected milestones in plant breeding 11000 BP Beginning of plant domestication, Fertile Crescent Pre-science 1694 Plant crossing → obtain new plant types 1761-1766 Discovery: hybrid offspring has traits from both parents 1866 Mendel: experiments in plant inheritance Renaissance 1900 Mendel’s laws of heredity rediscovered to pre-DNA 1920 Discovery of hybrid vigor discovery science 1944 DNA is hereditary 1953 Description of DNA structure Post-DNA 1972 Discovery: Recombinant DNA technology discovery science 5. Backcross breeding Backcross breeding Transfer a desired trait from donor parent into the favored genetic background of the target cultivar Applications Improvement of established cultivars Introgression of genes from wild relatives 5. Backcross breeding Example: flax seed Elite flax seed cultivar, but Wild type flax seed, low susceptible to rust productivity, but rust resistant Transfer gene for rust resistance into elite cultivar, but otherwise do not change elite cultivar 5. Backcross breeding  Basically good cultivar (GC) 50% GC Plant with desired trait, but otherwise crappy 75% GC cultivar 87.5% GC 93.75% GC 96.875% GC 98.375% GC … 99.999% GC 5. Backcross breeding Backcross breeding Pros and cons + Reproducible + Predictable + Fully inheritable trait - Only possible in crossable species - Slow process (multiple generations needed) 5. Backcross breeding Methods of domestication 1. Introduction and historical overview 2. Selective breeding, aka mass selection 3. Hybrid breeding 4. Mutation breeding 5. Backcross breeding 6. Genetic modification Selected milestones in plant breeding 11000 BP Beginning of plant domestication, Fertile Crescent Pre-science 1694 Plant crossing → obtain new plant types 1761-1766 Discovery: hybrid offspring has traits from both parents 1866 Mendel: experiments in plant inheritance Renaissance 1900 Mendel’s laws of heredity rediscovered to pre-DNA 1920 Discovery of hybrid vigor discovery science 1944 DNA is hereditary 1953 Description of DNA structure Post-DNA 1972 Discovery: Recombinant DNA technology discovery science 5. Backcross breeding Recombinant DNA technology GM A. Recombinant DNA technology using vector plasmids B. Basic biology of Agrobacterium tumefaciens C. Use of A. tumefaciens for recombinant DNA technology D. Most common uses of the technology 6. Genetic modification Recombinant DNA technology Regardless of relatedness btw donor and recipient → source of novel traits New plant variety can be produced relatively quickly Genetic modification GM Recombinant DNA tech Herbicide Herbicide resistant susceptible crop plant crop plant Herbicide tolerance: crops can be sprayed with a herbicide → kills weeds but not the crop 6. Genetic modification Recombinant DNA technology DNA from one organism put into (recombined) with DNA from another organism → recombinant DNA Herbicide resistance gene 6. Genetic modification Recombinant DNA technology DNA from one organism put into (recombined) with DNA from another organism → recombinant DNA Basic necessary tools/units: DNA donor (specific gene) Herbicide resistance gene 6. Genetic modification Recombinant DNA technology DNA from one organism put into (recombined) with DNA from another organism → recombinant DNA Basic necessary tools/units: Herbicide DNA donor (specific gene) tolerance gene DNA recipient (e.g. crop plant) Herbicide susceptible crop plant 6. Genetic modification Recombinant DNA technology DNA from one organism put into (recombined) with DNA from another organism → recombinant DNA Basic necessary tools/units: Herbicide DNA donor (specific gene) tolerance gene DNA recipient (e.g. crop plant) Herbicide susceptible Method to transfer & insert donor DNA: crop plant plasmid DNA of Agrobacterium tumefaciens 6. Genetic modification Recombinant DNA technology GM A. Recombinant DNA technology using vector plasmids B. Basic biology of Agrobacterium tumefaciens C. Use of A. tumefaciens for recombinant DNA technology D. Most common uses of the technology 6. Genetic modification Agrobacterium tumefaciens: some basic biology Crown gall bacterium Free-living soil bacterium tume-faciens: ‘cancer-making’ Infects roots of certain plants Causes plant to grow a cankerous structure Bacterium lives inside canker as a parasite Understanding the biology: vital for recombinant DNA technique! 6. Genetic modification Two types of DNA Longer bacterial DNA Shorter, tumor-inducing plasmid DNA 6. Genetic modification Infection of plant by A. tumefaciens 6. Genetic modification Recombinant DNA technology GM A. Recombinant DNA technology using vector plasmids B. Basic biology of Agrobacterium tumefaciens C. Use of A. tumefaciens for recombinant DNA technology D. Most common uses of the technology 6. Genetic modification Agrobacterium tumefaciens: key characteristics Ability to invade plant tissue Ability to move plasmid DNA into plant cells Plasmid DNA inserts genes to plant DNA to force plant to do grow tumor Recombinant DNA technology (1970ies): Uses this basic mechanism, but inserts not tumor genes, but genes of interest 6. Genetic modification Choose target gene in a donor organism Donor DNA Herbicide tolerance gene Target gene Target gene: herbicide tolerance: crops can be sprayed with a herbicide → kills weeds but not the crop 6. Genetic modification Isolate donor gene from donor DNA with restriction enzyme Herbicide Donor DNA tolerance gene Target gene 6. Genetic modification Bring in A. tumefaciens with its plasmid DNA 6. Genetic modification Insert target gene into plasmid 6. Genetic modification Result: transformed (recombinant) plasmid DNA 6. Genetic modification Insert recombinant plasmid into A. tumefaciens 6. Genetic modification Allow A. tumefaciens to multiply 6. Genetic modification Bring in recipient, to-be-transformed organism Herbicide susceptible crop plant 6. Genetic modification Create a tissue culture from recipient root cells Herbicide susceptible crop plant 6. Genetic modification Dissociate tissue and suspend cells in liquid culture Herbicide susceptible crop plant 6. Genetic modification Innoculate cell culture with recombined A. tumefaciens Herbicide susceptible crop plant 6. Genetic modification Add herbicide: surviving plant cells are transformed Herbicide susceptible crop plant 6. Genetic modification Grow plant embryo from a recombined cell Herbicide susceptible crop plant 6. Genetic modification Grow embryo into plant Herbicide susceptible crop plant 6. Genetic modification Plant: genetically modified to resist herbicide Herbicide susceptible crop plant Herbicide resistant crop plant 6. Genetic modification Recombinant DNA technology GM A. Recombinant DNA technology using vector plasmids B. Basic biology of Agrobacterium tumefaciens C. Use of A. tumefaciens for recombinant DNA technology D. Most common uses of technology 6. Genetic modification Most common use of A. tum. recombinant technology Herbicide tolerance HT: crops can be sprayed with a herbicide → kills weeds but not the crop Systemic toxicity to insect pests: plant tissue produces its own natural pesticide (Bt) More in ‘The Green Revolution’ 6. Genetic modification HT soy (corn, cotton) 6. Genetic modification Use of Bt and HT crops 6. Genetic modification Vitamin A deficiency in the world Goal: GM ‘Golden rice’ to deal with Vit A deficiency Vit. A deficiency Blindness in children Source: World Health Organization 6. Genetic modification Problems with Golden Rice Low acceptance of GM rice With low-fat diets of poor people, vit A not taken up 6. Genetic modification Larger issue… 6. Genetic modification BIOB38: Plants and Society 1-2. Origin of agriculture 3-6. Plant domestication 7-10. Green Revolution & its legacy 11-14. Plants that feed the world 15-16. Plants that please the palate 17-18. Plants that heal the sick 19-20. Plants that hook the mind and body 21-22. Plants the world thirsts after 23-24. Plants of warmth and strength