![Page 1: Use of SNP-DNA analysis in authenticating Basmati rice](https://reader035.vdocuments.us/reader035/viewer/2022062802/56814483550346895db11ae3/html5/thumbnails/1.jpg)
Use of SNP-DNA analysis in authenticating Basmati
rice
![Page 2: Use of SNP-DNA analysis in authenticating Basmati rice](https://reader035.vdocuments.us/reader035/viewer/2022062802/56814483550346895db11ae3/html5/thumbnails/2.jpg)
• DNA based authentication of basmati rice • Background to Single nucleotide
polymorphisms (SNPs)• Introduction to SNP genotyping using
MALDI-ToF MS • Authentication of basmati rice using
MALDI-ToF MS-based SNP genotyping• Launching a commercial genotyping service
Summary
![Page 3: Use of SNP-DNA analysis in authenticating Basmati rice](https://reader035.vdocuments.us/reader035/viewer/2022062802/56814483550346895db11ae3/html5/thumbnails/3.jpg)
Authentication of basmati rice
by DNA genotyping • Micro-satellite markers
• Single nucleotide polymorphisms
![Page 4: Use of SNP-DNA analysis in authenticating Basmati rice](https://reader035.vdocuments.us/reader035/viewer/2022062802/56814483550346895db11ae3/html5/thumbnails/4.jpg)
TCGAAATGCATGCGCATGATTVariety 1
TCGAAATGCATGCGCGTGATTVariety 2
Single nucleotide differences exist betweenindividuals, plant and animal varieties
and bacterial strains
Single nucleotide polymorphisms
![Page 5: Use of SNP-DNA analysis in authenticating Basmati rice](https://reader035.vdocuments.us/reader035/viewer/2022062802/56814483550346895db11ae3/html5/thumbnails/5.jpg)
Authentication using SNPs
• PCR based SNP genotyping
• MALDI-ToF MS based SNP genotyping
Single nucleotide polymorphisms
![Page 6: Use of SNP-DNA analysis in authenticating Basmati rice](https://reader035.vdocuments.us/reader035/viewer/2022062802/56814483550346895db11ae3/html5/thumbnails/6.jpg)
Once a SNP is identified, 3 primers are required to enable genotyping including:-
- Two PCR primers to amplify the region around the SNP
5’ 3’
- One Extension primer which anneals directly adjacent to the SNP.
5’ 3’
Assaying SNPs by MALDI-ToF MS
![Page 7: Use of SNP-DNA analysis in authenticating Basmati rice](https://reader035.vdocuments.us/reader035/viewer/2022062802/56814483550346895db11ae3/html5/thumbnails/7.jpg)
TCGAAATGCATGCGCATGATT TCGAAATGCATGCGCGTGATT
TCGAAATGCATGCGCATGATT TCGAAATGCATGCGCGTGATTTTACGTACGCG TTACGTACGCG
TCGAAATGCATGCGCATGATT TCGAAATGCATGCGCGTGATTTTACGTACGCGT TTACGTACGCGC
+polymerase+ddNTP’s
Anneal primer
Analyse extension products by MALDI-TOF MS
Assaying SNPs by MALDI-ToF MS
![Page 8: Use of SNP-DNA analysis in authenticating Basmati rice](https://reader035.vdocuments.us/reader035/viewer/2022062802/56814483550346895db11ae3/html5/thumbnails/8.jpg)
MALDI-TOF Mass Spectrometry
Samples mixed with a matrix in great excess and spotted onto a MALDI plate and loaded into the Mass Spectrometer.
Sample spot is subjected to repeated pulses of a nitrogen laser at 337nm in a vacuum which vaporises and ionises sample. Matrix absorbs the majority of incident laser energy, preventing degradation or fragmentation of the sample, and allows the vaporisation and ionisation of some of the substrate.
Delayed application of an electric field causes ions to enter flight tube and accelerate towards detector. Delayed Extraction applies high voltage electric pulse after predetermined time delay to minimise energy spread of ions. All ions gain same kinetic energy, so larger ions take longer to reach detector. This variation in Time of Flight allows the separation of ions on the basis of size.
![Page 9: Use of SNP-DNA analysis in authenticating Basmati rice](https://reader035.vdocuments.us/reader035/viewer/2022062802/56814483550346895db11ae3/html5/thumbnails/9.jpg)
Assaying SNPs by MALDI-ToF MS
0
20
40
60
80
100
120
4300 4400 4500 4600 4700 4800 4900 5000
C = 273 Da
T = 288 Da
A = 297 Da
G = 313 Da
Difference in peak size reveals the SNP
allele for that rice variety
Unextended SNP primer
Extended SNP primer
![Page 10: Use of SNP-DNA analysis in authenticating Basmati rice](https://reader035.vdocuments.us/reader035/viewer/2022062802/56814483550346895db11ae3/html5/thumbnails/10.jpg)
Multiplexing SNP assays
![Page 11: Use of SNP-DNA analysis in authenticating Basmati rice](https://reader035.vdocuments.us/reader035/viewer/2022062802/56814483550346895db11ae3/html5/thumbnails/11.jpg)
Quantitative SNP assays
![Page 12: Use of SNP-DNA analysis in authenticating Basmati rice](https://reader035.vdocuments.us/reader035/viewer/2022062802/56814483550346895db11ae3/html5/thumbnails/12.jpg)
MALDI-TOF-based DNA authentication of basmati
rice
Sponsored by the FSA
![Page 13: Use of SNP-DNA analysis in authenticating Basmati rice](https://reader035.vdocuments.us/reader035/viewer/2022062802/56814483550346895db11ae3/html5/thumbnails/13.jpg)
• Completing a SNP database for the main commercial varieties and their adulterants.
• Assessing the reproducibility of the protocols to determine the uncertainty of the method.
• Performing a limited survey of Basmati Products being sold in UK supermarkets.
• Developing a Standard Operating Procedure
FSA sponsored work includes:-
![Page 14: Use of SNP-DNA analysis in authenticating Basmati rice](https://reader035.vdocuments.us/reader035/viewer/2022062802/56814483550346895db11ae3/html5/thumbnails/14.jpg)
Basmati rice varieties
Traditional breeds
Basmati 386Basmati 370DehradunRanbir BasmatiTaraori (HBC-19)
HybridBasmati 385Super BasmatiPusa BasmatiKasturiBasmati 198
Common AdulterantsPusa 169SabarmatiPR 106Kali-muchLakraSaket 4ParimalSherbati
Terricot
![Page 15: Use of SNP-DNA analysis in authenticating Basmati rice](https://reader035.vdocuments.us/reader035/viewer/2022062802/56814483550346895db11ae3/html5/thumbnails/15.jpg)
RICE VARIETY Basmati 370 Derhadun Kernal PK370 l Pak 385 Pusa 1 Sherbati Super TaraoriLINEAGE Pure Bred Pure Bred Pure Bred Pure Bred Hybrid Hybrid Non-Bas Hybrid Pure Bred
ory-122-1 GA GG AA GG GG AA GG GG GA
ory-58-2 AA AA AA AA TT AA TT AA AA
ory-262 GG GG GG GG GG GG CC GG GG
ory-S0186 TT TT TT TT TT CC CC TT TT
ory-S0157 GG GG GG GG GG CG CC GG GG
ory-S0153 GG GG GG GG GG GG CC GG GG
ory-462 GA GA GA Ga GA GA GA GA GAory-592 GG GG AA GG GG AA GG GG AA
ory-599 TC TC TC TC CC CC CC TC TCory-624-1 GG GG GG GG CC GG GC GG GG
ory-668 AG AA AA GA GG GG GG AA AA
Assembling a SNP database for Basmati varieties and adulterants
![Page 16: Use of SNP-DNA analysis in authenticating Basmati rice](https://reader035.vdocuments.us/reader035/viewer/2022062802/56814483550346895db11ae3/html5/thumbnails/16.jpg)
Assessing reproducibility
![Page 17: Use of SNP-DNA analysis in authenticating Basmati rice](https://reader035.vdocuments.us/reader035/viewer/2022062802/56814483550346895db11ae3/html5/thumbnails/17.jpg)
Examples of survey work
![Page 18: Use of SNP-DNA analysis in authenticating Basmati rice](https://reader035.vdocuments.us/reader035/viewer/2022062802/56814483550346895db11ae3/html5/thumbnails/18.jpg)
SNP Genotyping using primer I
0
20
40
60
80
100
120
4300 4400 4500 4600 4700 4800 4900 5000
Primer Primer + TPrimer + C
Tilda basmatiRice
ASDA basmatirice
![Page 19: Use of SNP-DNA analysis in authenticating Basmati rice](https://reader035.vdocuments.us/reader035/viewer/2022062802/56814483550346895db11ae3/html5/thumbnails/19.jpg)
SNP Genotyping using 11 primers
Tilda D6 Asda D5 Kernal (a1)A AA AA AAB AA AA AAC GG GG GGD TT CC TTE GG CC GGF GG GG GGG GA GA GAH AA AA AAI TC CC TCJ GG GG GGK AA GG AA
Tilda basmati rice behaves like traditional variety Kernal
Asda basmati rice is most like the basmati hybrid Pusa
![Page 20: Use of SNP-DNA analysis in authenticating Basmati rice](https://reader035.vdocuments.us/reader035/viewer/2022062802/56814483550346895db11ae3/html5/thumbnails/20.jpg)
MALDI-ToF MS based genotyping represents an effective analytical
approach to assess:-
• Product authentication using a diagnostic panel of multiplexed SNP markers based on an expanded database.
• Product adulteration, exploiting the techniques ability to quantitate SNPs in the 5-100% range.
Summary
![Page 21: Use of SNP-DNA analysis in authenticating Basmati rice](https://reader035.vdocuments.us/reader035/viewer/2022062802/56814483550346895db11ae3/html5/thumbnails/21.jpg)
Marker Super Thai 2003ory-122-1 GG GG GGory-58-2 AA AA ATory-262 GG GG CGory-S0186 TT TT CTory-S0157 GG GG CGory-S0153 GG CC GGory-462 AG AG AGory-592 GG AA GGory-599 CT CT CC ory-624-1 GG GG CGory-668 AA AA AG
SNP analysis as a QC tool
![Page 22: Use of SNP-DNA analysis in authenticating Basmati rice](https://reader035.vdocuments.us/reader035/viewer/2022062802/56814483550346895db11ae3/html5/thumbnails/22.jpg)
S+T 2003GG GGAA ATGG CGTT CTGG CGGC GGAG AGGA GGCT CC GG CGAA AG
SNP analysis as a QC tool
SNP markers revealed that results with the 2003 crop
could NOT have arisen from mixing
Super Basmati (S) with Thai (T) rice
![Page 23: Use of SNP-DNA analysis in authenticating Basmati rice](https://reader035.vdocuments.us/reader035/viewer/2022062802/56814483550346895db11ae3/html5/thumbnails/23.jpg)
Applying cutting-edge DNA technology to provide analytical services
for product authentication to the food industry.
http://Authentigene.comhttp://Authentigene.info
THE gold standard
Providing a commercial genotyping service
![Page 24: Use of SNP-DNA analysis in authenticating Basmati rice](https://reader035.vdocuments.us/reader035/viewer/2022062802/56814483550346895db11ae3/html5/thumbnails/24.jpg)
The Authentigene team
Prof. David Archer Prof. Malcolm Bennett Prof. Ian ConnertonDr. Sean May Prof. Gregory Tucker