* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download Realistic population and molecular genetic tools for genetic
Genetic code wikipedia , lookup
Quantitative trait locus wikipedia , lookup
Biodiversity wikipedia , lookup
Genetic studies on Bulgarians wikipedia , lookup
Pharmacogenomics wikipedia , lookup
Medical genetics wikipedia , lookup
Designer baby wikipedia , lookup
Behavioural genetics wikipedia , lookup
Heritability of IQ wikipedia , lookup
Polymorphism (biology) wikipedia , lookup
Genetics and archaeogenetics of South Asia wikipedia , lookup
Public health genomics wikipedia , lookup
History of genetic engineering wikipedia , lookup
Genetic testing wikipedia , lookup
Hybrid (biology) wikipedia , lookup
Genetic engineering wikipedia , lookup
Genome (book) wikipedia , lookup
Koinophilia wikipedia , lookup
Genetic drift wikipedia , lookup
Population genetics wikipedia , lookup
Realistic population and molecular genetic tools for genetic assessment (a simple minded, but pragmatic view!) Brian Ford-Lloyd What will I talk about? 1. Definitions 2. Molecular and Popgen Background 3. The CWR list 4. Easy guides to erosion 5. Genetic pollution 6. Application of methodologies 7. CBD targets 8. When to do Molpopgen? 1. Definitions • Genetic erosion – a permanent reduction in richness or evenness of common localized alleles – or the loss of combinations of alleles over time in a defined area ( after Guarino) • Genetic pollution – gene flow from transgenic (or nontransgenic ?) crops to natural populations 2. Some background • sampling variation or drift causes loss of genetic variation in small populations • effective size, Ne, not actual size N, determines the rate of this loss • in natural populations Ne is less than N • difficult to obtain an estimate of the ratio Ne/N An example of Ne /N • Papaver dubium: – 50% of all seed set from 2% of plants – This gives a ratio of Ne /N of 0.07 – Papaver plants set 75% of seed by selfpollination – Ratio reduced to 0.024 Minimum viable population (MVP) • ‘The minimum size of a population which will allow us to reduce the loss of genetical variation and heterozygosity by the inbreeding caused by drift to an acceptable level’ • (there are several other definitions) wild Beta Ne? In situ conservation • for species like P. dubium a population size of N = 5000 is reasonably safe • populations of herbaceous CWR such as wild wheat, in which the density of plants is often around 10 per m2, occupy only about 500 m2 of ground • for a tropical forest dipterocarp (density can be as low as only 2 per km2), a population of this size would require a reserve of 2500 km2!!! Important information at the gene level • Effective population size – Level of heterozygosity – Inbreeding • Change in allele frequency • Genetic diversity • Allele richness • Gene flow • Genetic drift – genetic erosion • Natural selection – erosion and pollution • Migration – pollution (erosion) or replenishment Molecular markers/DNA profiling • • • • • • Arbitrarily primed markers (RAPD/ISSR) -? AFLPs -? SNPs/DNA sequence -? EST based markers -? isozymes/allozymes SSRs (microsatellites) – Yes because they are co-dominant, but..... Are there primers available for species on the CWR list? • Out of 160 random CWR taxa (genera) surveyed: • 29% had SSR primers available in the published literature CWR genera with SSR primers: Acer Aegilops Albizia Allium Arachis Armeniaca Asparagus Avena Begonia Cannabis Castanea Citrullus Corylus Cynodon Dianthus Diplotaxis Elymus Eruca Eryngium Festuca Ficus Fragaria Geum Gossypium Iris Lactuca Lolium Lupinus Malus Nigritella Olea Pelargonium Pinus Plantago Prangos Prunus Pterocarya Ribes Rosa Salix Sinapis Sophora Sorbus Taraxacum Tripolium Vicia Vitis Zostera CWR genera without primers: Abutilon Achillea Aconitum Agave Agrostis Alternanthera Amygdalus Anthericum Apium Aquilegia Artemisia Atriplex Atropa Axonopus Berberis Bituminaria Broussonetia Calliandra Capparis Carum Ceratonia Chamaecytisus Chamaemelum Chrysanthemoides Cichorium Cleome Colocasia Consolida Convallaria Cordia Corynephorus Crocus Cryptotaenia Cynara Cyperus Dalbergia Daucus Digitalis Drosophyllum Elaeagnus Epimedium Fagopyrum Flaveria Furcraea Galega Halimodendron Hedera Helleborus Hippocrepis Hydrocotyle Iberis Imperata Isatis Juglans Juncus Laurus Lavandula Lens Leucaena Limodorum Linum Lotus Ludwigia Maclura Matteuccia Melissa Mentha Mercurialis Monochoria Myrrhis Narcissus Nasturtium Nigella Onobrychis Ornithopus Osmunda Papaver Parietaria Phacelia Phalaris Phleum Phoenix Phyla Poa Polemonium Portulaca Ranunculus Rhododendron Rubus Rumex Sagittaria Salvia Sambucus Santolina Scilla Securigera Sesleria Silphium Stachys Syringa Tetragonia Thymus Trapa Trigonella Tulipa Vaccinium Valerianella Vallisneria Verbena Vincetoxicum Viola Vulpia Xanthium 3. The CWR list • The CWR list has around 20,000 species • In theory we could undertake detailed genetic assessment of genetic erosion/pollution on over 6000 taxa using SSRs • If we wanted to, and had the resources • and....... A huge task! The key issues might be: • How can we assess the majority of our CWR species simply and easily? – and minimise genetic erosion/pollution – and maximise genetic diversity in in situ conservation • How do we prioritise the taxa for molecular population genetic intensive study? – (workshop 2?) 4. Simple and easy guides? • Information on breeding system – around 80% of diversity is within populations of outbreeders – most diversity is among populations of inbreeders Further simple guides: • Effective and actual population sizes are not the same • But, actual population size can be a rough guide • Will give us an idea about erosion if actual population is getting smaller Resampling? • If populations are staying the same size, then molecular population genetic analysis may be needed only once • If population size is decreasing, then may need resampling - when? how often? Other simple guides: • Taxonomic diversity – assuming diversity is spread across taxa, ensuring that subspecific taxa are conserved should ensure that diversity is conserved • Ecogeographic diversity – populations that have different adaptive norms will be genetically diverse • Red data listing – what genetic information is revealed? 5. Genetic pollution • “It is clear that spontaneous hybridisation and introgression of genes from domesticated plants into wild relatives is a common characteristic of domesticated plants” – Ellstrand, 1999 conventional or transgenic Genetic pollution: • The Gene Pool Concept will provide an indicator of the CWR species that are vulnerable, but • 22 out of 25 of the World’s most important crops have evidence of natural hybridisation with one or more wild relative • This could extrapolate to over 18,000 (90%) of our CWR species wheat rice maize soybean barley sorghum millet cotton rape beans sunflower potato sugarcane cassava oats coconut coffee cowpea rye oil palm sweet potato olive grape Can genetic pollution affect genetic diversity? Data not involving transgenes • gene flow can cause change in genetic diversity – in 12 different studies, diversity in introgressed populations was greater • can gene flow cause extinction? – more data are needed – it is ‘speculated’ that hybridisation may have caused extinction of CWR of Capsicum, date palm, hemp, maize, sweet pea 6. How to apply assessment methodologies? • Other prioritisations first, then • are any subspecific taxa seriously threatened? • are any major habitats/regions threatened? • are most populations’ sizes declining (outbreeding species) ? • are some populations’ sizes declining (inbreeding species) ? • do sampled populations contain significant genetic diversity? – if yes, then only re-sample if change in population size Monitoring genetic pollution? • Bottom line - measure gene flow – need FST and molecular markers • Could assess: – occurrence of hybrids and hybrid derivatives (morphological) – fitness of hybrids/hybrid derivatives – spread of hybrids/hybrid derivatives • Must be over large timescale, large geographical area, large sample size 7. CBD 2010 targets and WS5 CWR list & Euro+Med A: Focal area B: Indicator for immediate testing C: Possible indicators (require further development) Status and trends of the components of biological diversity Threats to biodiversity Trends in abundance and distribution of selected species Trends in genetic diversity of .... cultivated plants... Number and cost of alien invasions 8. When to do molecular population genetics? Red Data Listing? • if most populations’ sizes are declining (outbreeding species) ? • if some populations’ sizes are declining (inbreeding species) ? – and/or because any one major habitat/region is threatened – and/or because any subspecific taxon is seriously threatened • then sample and do molpopgen to establish whether populations in protected areas are adequate, or which populations to protect A realistic message? • Don’t - plan to do molpopgen first • Do - molpopgen last or even not at all – when other guides have been examined – when other assessments have been done • Do - use molpopgen as last resort to: – select best populations for in situ conservation – monitor populations or critical situations • Don’t - use molpopgen to prioritise CWR list!