STOG conference Matt Ordidge

DNA Fingerprinting for Fruit Identification Dr Matthew Ordidge Scientific Curator, National Fruit Collections, Brogdale

www.reading.ac.uk

• Introduction to DNA Fingerprinting

• Summary of Fruit Identification by DNA Fingerprinting

• Introduction to DNA Fingerprinting “We were getting extraordinarily variable patterns of DNA, including from our technician and her mother and father, as well as from non human samples. My first reaction to the results was ‘this is too complicated’, and then the penny dropped and I realised we had genetic fingerprinting” Professor Sir Alec Jeffreys, University of Leicester From The Gene Genius, University of Leicester 2004

DNA Fingerprinting

Credit: Anita Corbin and John O'Grady, Copyright British Council 1989

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Jeffreys AJ, Wilson V, Thein SL. Hypervariable 'minisatellite' regions in human DNA. Nature 314: 67-73 (1985) Jeffreys AJ, Wilson V, Thein SL. Individual-specific 'fingerprints' of human DNA. Nature 316: 76-9 (1985)

DNA Fingerprinting • DNA

From Nature Education 2013

DNA Fingerprinting • Polymorphism – Minisatellites (10-15 base pair repeats) – Microsatellites (2-4 base pair repeats)

From DNA Fragment Analysis by Capillary Electrophoresis, Life Technologies

DNA Fingerprinting • Restriction fragment length polymorphism

From Nybom et al. Investigative Genetics 2014, 5:1

DNA Fingerprinting • Polymerase Chain Reaction (PCR)

From National Human Genome Research Institute

DNA Fingerprinting • Random amplified polymorphic DNA

From Nybom et al. Investigative Genetics 2014, 5:1

DNA Fingerprinting • Polymorphism – Minisatellites (10-15 base pair repeats) – Microsatellites (2-4 base pair repeats)

From DNA Fragment Analysis by Capillary Electrophoresis, Life Technologies

DNA Fingerprinting • PCR based single locus methods

From Nybom et al. Investigative Genetics 2014, 5:1

DNA Fingerprinting • Capillary electrophoresis – Labelled primer

From DNA Fragment Analysis by Capillary Electrophoresis, Life Technologies

DNA Fingerprinting • Capillary electrophoresis

From DNA Fragment Analysis by Capillary Electrophoresis, Life Technologies

• Introduction to DNA Fingerprinting

• Summary of Fruit Identification by DNA Fingerprinting

National Fruit Collection • Owned by Defra

• Maintained as a field genebank • Approx. 4,000 varieties of tree fruit and bush fruit – Two trees of each accession

Characterisation

Characterisation • Morphological characterisation

Characterisation • Morphological characterisation

• Verification – Against published descriptions

Reproduced from: Beach, 1905

Characterisation • Morphological characterisation

• Verification – Against published descriptions – Using genetic fingerprinting

Characterisation • Morphological characterisation

• Verification – Against published descriptions – Using genetic fingerprinting • Using agreed standards Marker CH01d08 CH03g07 CH01f07a CH04e03 CH02b10 CH01d09 GD96 CH03d12 CH05c06 EMPc11 EMPc117 GD147 CH_Vf1 CH04c07 CH05a02 GD142 NZ05g8

Dyea EMR Npig F V P P V N F F N V P N F F F F

Multi-plexb L L L L M M M M S S S S -

Priority groupc 1a 1a 1a 3 2 2 2 3 1b 1b 1b 3 4 4 4 4 4

Size Range 239-321 198-264 175-214 180-205 112-160 122-172 139-195 84-162 83-119 123-171 82-142 112-164 130-164 79-151 (103-125) (141-186) (98-116)

LG 15 3 10 5 2 12 17 6 16 11 7 13 1 14 8 9 4

No of allelesd (11)16 (10)28 (11)23 (4)11 (10)19 (7)21 (6)19 (6)20 (8)17 (9)14 (9)22 (6)14 (9)14 (7)27 (11) (8) (5)

From Evans KM, Fernández-Fernández F, Govan C. 2009. Acta Horticulturae 814:103-106.

Characterisation • Morphological characterisation

• Verification – Against published descriptions – Using genetic fingerprinting

Characterisation • Morphological characterisation

• Verification – Against published descriptions – Using genetic fingerprinting

Characterisation • Morphological characterisation

• Verification – Against published descriptions – Using genetic fingerprinting

Characterisation • Morphological characterisation

• Verification – Against published descriptions – Using genetic fingerprinting

Further Characterisation • Markers available for – Apple – Cherry – Cobnut…