Plant Domestication Dr. Duncan Vaughan

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1 Plant Domestication 1 Formerly National Institute of Agrobiological Sciences, Tsukuba, Japan Overview of the seminar Nature of plant domestication Why plants were domesticated Where and when plants were first domesticated The basic genetics of plant domestication The causes of genetic variation How genetic variation is conserved Current trends 2 The crops that feed the world Species in 160 plant families have been domesticated Annual production of major food crops for (metric tons) Maize 885,289,935 Wheat 701,395,334 Rice 722,599,583 Potato 373,158,351 Cassava 256,404,044 Soybean 262,037,569 Source: Wikipedia 1

2 What is plant domestication? Domestication is a unique kind of biological evolution Crop domestication is a co evolutionary process Wild species changing morphologically and physiologically Wild species require humans for survival Humans require the domesticated species for sustenance 4 Why were plants domesticated? Agriculture is a natural evolution of gathering certain plants Agriculture was a discovery Agriculture was the result of increasing human population Agriculture was a response to changing climates and environments 5 Rice has hard cover for its grain Zizania (below) lacks genetic architecture for domestication Wild soybean population (above) Domesticated soybean (below) 6 2

3 Areas where major plants were domesticated (earliest domestication dates in blue) Nikolai Vavilov 10,000 BP 4500 BP 4500 BP >4000 BP 13,000 BP 8500 BP 9000 BP 7000 BP 10,000 BP 7 Dates based on Purugganan and Fuller, 2009 Photo of Nikolai Vavilov from Wikipedia Crop complexes Crop Wild relative Weedy relative 8 Panicles from a rice/wild rice hybrid swarm Cultivated rice Gene flow Weedy rice Crop genepools Genepool 3 Hybrids with GP1 lethal or completely sterile Genepool 2 Species with some fertility with GP1 Genepool 1 Biological Species Cultivated and spontaneous races Gene transfer possible but difficult 9 Gene transfer requiring radical techniques 3

4 Changes that may result from domestication 1. Reduced fertility 2. Loss of survival characteristics Reduction or loss of toxic or bitter compounds 4. Loss of protective defense structures 5. Loss of seed dormancy 6. Simultaneous maturity Changes that may result from domestication (2) 7. Change in life span 8. Changes in the shape of the harvested organ 9. Change in breeding system 10. Increase in size X8 Azuki bean X5 Rice bean X5 Mung bean 11 X5 Black gram The domestication syndrome Important traits that distinguish a domesticate from its wild progenitor Azuki bean genome and main locations of domestication related genes Modern rice variety with short stature and erect leaves 12 4

5 Genetic bottleneck of domestication Genetic diversity in wild progenitor Domestication bottleneck Reduced genetic diversity in domesticated crop 13 Allelic reduction around target domestication gene Selective sweep: Results in significant reduction in the nucleotide diversity in localized regions of the genome 14 Stages in plant domestication Stage 1 Wild Cultivated Stage 2 Increased fixation of domestication genes Stage 3 Varietal diversification Stage 4 Deliberate breeding 15 Based on Meyer and Purugganan,

6 Genetics of domestication Whole genome changes Changes at the chromosome level Changes at the gene level Changes at the nucleotide level 16 Domestication target 1 Whole genome changes polyploidy Autopolyploidy Species A Allopolyploidy X 17 Species B Domestication target 2 Mutations at the chromosome level Genome duplication (polyploidy), deletions, translocations 18 Based on Olsen and Wendel,

7 Domestication target 3 Mutations at the gene level Deletion Gene multiplication Retrotransposon insertion 19 Based on Olsen and Wendel, 2013 Domestication target 4 Mutations within the gene Nucleotide scale DNA CAT GGC ATA CAA GCT AAC Amino Acids His Gly lle Gln Ala Asn TAT GGC ATA CAA GCT AAC Tyr Thr Ser * Amino acid Deletion ( ) causing frame shift replacement and premature stop (*) 20 Based on Olsen and Wendel, 2013 Why is there so much variation in crops? Human selection Different growing ecologies 21 7

8 Safe guarding crop diversity Genebank Genebanks Seed store Ex situ conservation In situ conservation On farm conservation Wild rice 22 The future of domestication Overcoming yield plateaus Genomics and bioinformatics Gene discovery and analysis G.M. Revolution Gene Revolution 23 References for further details Meyer, R.S. and M. D. Purugganan Evolution of crop species: genetics of domestication and diversification. Nature Reviews Genetics 14: Meyer, R.S., A.E. DuVal and H.R. Jensen Patterns and processes in crop domestication: an historical review and quantitative analysis of 203 global food crops. New Phytologist 196:20 48 Olsen, K.M. and J.F. Wendel A Bountiful Harvest: Genomic insights into crop domestication phenotypes. Annual Review of Plant Biology 64:47 70 Purugganan, M.D. and D.Q. Fuller The nature of selection during plant domestication. Nature 457: Annals of Botany Special Issue Volume 100 no. 5 October 2007; this is an open access volume with papers covering many crop domestication topics and crops 24 8

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