1. DNA Fingerprinting for Varietal
Identification
December 30, 2020
Dr. Rajendra Prasad Central Agricultural University, Pusa
Ahmed Aquib
B.Tech. Biotechnology, VII-Sem
Under the Guidance of Dr. Rajeev Kumar and Dr. K.L. Bhutiya
3. Varietal Identification
● Protecting Plant Breeder’s Right
○ Unique Genetic Fingerprints (DUS Test)
○ Characterization of Essentially Derived Varieties (EDV)
● Guaranteeing the Authenticity of Crop being Purchased
○ To Farmers and Consumers
Smith, J. S. C., and O. S. Smith. "Fingerprinting crop varieties." Advances in agronomy. Vol. 47. Academic Press, 1992. 85-140.
4. DNA Profiles / Fingerprints
● Traditionally, varietal identification relied heavily on morphological
differences.
● DNA fingerprinting, is regarded as a more objective and, ostensibly, less
error-prone method of identifying plant varieties
○ high degree of non-tissue specific polymorphism,
○ minimal influence of environment and,
○ simple inheritance pattern.
https://cas.cgiar.org/spia/publications/dna-fingerprinting-crop-varietal-identification-fit-purpose-
protocols-their-costs
5. Molecular Markers
90s
AFLP, RAPD and
Adaptations
SSR (Simple Sequence
Repeats)
Highly Polymorphic,
Reproducible, Multiallelic,
Co-dominant
…
SNP (Single Nucleotide
Repeats)
Today
https://www.seedtest.org/upload/cms/user/AM2015-June15-0845-1b-Vieriria.pdf
6. SSR Markers
AGTCTAGCTnnnnnnnnTATATATATATATAnnnnnnnGCTAGCTAGA
SSR Markers
Primer 1
Primer 2Microsatellite Region
Insertion Range With
High Preservability
(SSR Primer)
Simple Repeat Base Sequence Range
(SSR)
Insertion Range With
High Preservability
(SSR Primer)
Variety A ⚪⚪⚪⚪⚪⚪⚪ ▉ ▉ ▉ ▉ (4 Times) . . . . . . . . . . . . ⚪⚪⚪⚪⚪⚪⚪
Variety B ⚪⚪⚪⚪⚪⚪⚪ ▉ ▉ ▉ ▉ ▉ ▉ ▉ ▉ ▉ (9 Times) ⚪⚪⚪⚪⚪⚪⚪
Variety C ⚪⚪⚪⚪⚪⚪⚪ ▉ ▉ ▉ ▉ ▉ ▉ (6 Times). . . . . . . ⚪⚪⚪⚪⚪⚪⚪
8. Rationale for
Choosing a
Combination of
Primers
❏ N = no. of varieties
❏ pi
= frequency of the
pattern being present in
a population
❏ k = no. of primers
Tessier, Cécile, et al. "Optimization of the choice of molecular markers for varietal identification in Vitis vinifera L." Theoretical
and Applied Genetics 98.1 (1999): 171-177.