Genomics and DNA Barcoding approaches in plant breeding ... · Plant Genomes – Total Size Human...

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

The problem

• Population increase

The problem • Climate change

– Water (drought or flooding)

– Less land

– Less inputs

The problem

• Increased demands

The Solution Plant Breeding

We need another Green Revolution

Norman Borlauge 1960 High Yielding Variety (HYV) semi-dwarf

Genomics

From Mendel to Genomics

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

Sequenced Genomes

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

Plant Genomes – Total Size

Human Cotton Sugarcane

3,300Mbp 2,500Mbp 930Mbp

x2 x4 x8-12

Wheat

17,000

x6

Tomato breeding

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)

Methylation Studies

Salt tolerance Over-expression of GSTs

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!

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

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

Leguminous crops

Fava Santorinis

Fava Santorinis

Other “Fava” species

Fava Santorinis

Prespes beans

Bean varieties

Lentils Eglouvis

Lentil varieties

Olive varieties

Olive varieties

Olive oil

Oil authentication

Olive oil

Cherries – Tragana Edessis

Identification of Cherry varieties and rootstocks

Traceability of Tragana Edessis Cherries in commercial products

Medicinal Plants Sideritis species “tsai tou vounou - Mountain Tea”

Madesis et al 2014 in Press

ITS2

Mediterranean Pine species

Feta cheese

Greek Feta Cheese

Goat + sheep milk Goat milk up to 30%

Authentication of Greek feta cheese

Greek feta

New varieties development Cultivation Processing

Agricultural Production

Genetics and Genomics technologies are invaluable sources

teosinde Maize Breeding

Plant Breeding - Genomics

Einkorn Emmer spelt AA AABB AABBDD Aegilops tauschii

Triticum aestivum ΑΑΒΒDD Wheat

Plant Breeding - Genomics

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

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

Acknowledgments Antonios Makris Anagnostis Argyriou Theodora Farmaki Zoi Hilioti Kostas Stamatopoulos Kostas Pasentsis Fotini Kopani Athanasios Tsaftaris

www.inab.certh.gr inab@certh.gr

pmadesis@certh.gr