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Genomics and DNA Barcoding approaches in plant breeding, species identification,
food authentication and adulteration traceability
Panagiotis Madesis Researcher C
Institute of Applied Biosciences CERTH, Thessaloniki
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The problem
• Population increase
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The problem • Climate change
– Water (drought or flooding)
– Less land
– Less inputs
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The problem
• Increased demands
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The Solution Plant Breeding
We need another Green Revolution
Norman Borlauge 1960 High Yielding Variety (HYV) semi-dwarf
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Genomics
From Mendel to Genomics
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Genomics The next Green Revolution ?
• Bacteriophage fX174, was the first genome to be sequenced, a viral genome with only 5,368 base pairs (bp).
• In 2000 the first plant genome was
announced Arabidopsis thaliana
(115.4 megabases of the 125-megabase
genome, 25,498 genes found
• In 2007 the first Human genome is announced 14.8 billion bp, 26,588 genes
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Sequenced Genomes
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Sequencing of crop-plant genomes
– Importance as crop
• Largest food source for poor
• Feeds half of world’s population (3 billion)
– Demand likely to increase dramatically
– 80% of daily calories in Asia come from rice
– In Asia alone, demand will increase by at least 35%.
– 1000 varieties have been sequenced
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Plant Genomes – Total Size
Human Cotton Sugarcane
3,300Mbp 2,500Mbp 930Mbp
x2 x4 x8-12
Wheat
17,000
x6
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Tomato breeding
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Genotyping and Phenotyping of Vitis vinifera
• 450 samples, ~300 varieties
• SSR analysis, RNA-Sequencing of elite cultivars
• Partner of the EU Vitis Database
Aidani Agiorgitiko Vidiano Vertzami
GrapeNet (COST action FA1003)
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Methylation Studies
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Salt tolerance Over-expression of GSTs
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Species identification, food authentication and adulteration
traceability
• 6300 plant taxa (species and subspecies)
• ~ 1000 endemic taxa
• 45 PDO related to plants http://ec.europa.eu/agriculture/quality/door/
Identification and authentication of Greek biodiversity: a major objective!
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EU categories of quality agricultural products and foodstuffs
• Protected Designation of Origin (PDO),
• Protected Geographical Indication (PGI),
• Traditional Speciality Guaranteed (TSG)
• Mountain products
• Island products
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Plant Genetic Resources and landraces
• Important for local society: adapted to the local conditions, important nutritional and economical value
• Important for breeding : source of invaluable genes for the development of new varieties
• Genetic erosion: more than 90% of wheat and vegetable varieties have been lost in the last 50 years
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Leguminous crops
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Fava Santorinis
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Fava Santorinis
Other “Fava” species
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Fava Santorinis
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Prespes beans
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Bean varieties
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Lentils Eglouvis
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Lentil varieties
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Olive varieties
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Olive varieties
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Olive oil
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Oil authentication
Olive oil
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Cherries – Tragana Edessis
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Identification of Cherry varieties and rootstocks
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Traceability of Tragana Edessis Cherries in commercial products
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Medicinal Plants Sideritis species “tsai tou vounou - Mountain Tea”
Madesis et al 2014 in Press
ITS2
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Mediterranean Pine species
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Feta cheese
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Greek Feta Cheese
Goat + sheep milk Goat milk up to 30%
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Authentication of Greek feta cheese
Greek feta
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New varieties development Cultivation Processing
Agricultural Production
Genetics and Genomics technologies are invaluable sources
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teosinde Maize Breeding
Plant Breeding - Genomics
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Einkorn Emmer spelt AA AABB AABBDD Aegilops tauschii
Triticum aestivum ΑΑΒΒDD Wheat
Plant Breeding - Genomics
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defense and adaptation in the agri-bio + food domain
catalysts
information sciences big data
core facilities tissue banks
technology transfer & incubator workshops & training
agri-bio/food health
Institute of Applied Biosciences
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Conclusions
• Genomics could be the next green revolution being a valuable tool in plant breeding
• Barcoding plants for species identification “plant molecular forensics”
• Identification and authentication of plants and food products
• Valuable tool for innovative crop and food production
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Acknowledgments Antonios Makris Anagnostis Argyriou Theodora Farmaki Zoi Hilioti Kostas Stamatopoulos Kostas Pasentsis Fotini Kopani Athanasios Tsaftaris