GENETIC DIVERSITY

Ngon T.TRUONG

Molecular Biology Laboratory

Content:
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Introduction
1. Mechanism of Genetic Diversity (GD)
2. Where is GD ?
3. Methods & Indexes for identifying GD
4. Genetic diversity-measures
5. Risks causing Genetic erosion
6. Methods for enhancing & maitaining GD
7. BioPro : tool for analyzing genetic diversity
Conclusion

Introduction: Biodiversity
World wildlife fund (1998) defines :

- all living organism on the planet

- genes they contain

- ecosystems they reside in

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Definition
Species

Biodiversity
Genetic

Ecology

Genetic Diversity
 GD refers to the variation at the level of individual
genes (polymorphism), and provides a mechanism for
population to adapt to their ever-changing environment.
 The more variation, the better the chance that at least
some of the individuals will have an allelic variant being
suited for the new environment.

Fig. 1. Genetic Diversity in human being

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Fig. 3. Genetic Diversity in mungbean seeds
(Vigna sp.)


Fig. 4. Genetic Diversity in hot pepper fruits
(Capsicum sp.)

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Why?
Genes

Chromosomes

Adaptation

Changed

Evolution

Centers of origin

Where?
Diversity

How importance?

How?
Mechanism

Mechanism of Genetic Diversity
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Jumping Gene : Barbara Mc Clintock, 1951 (video.)
Recombination : meiosis
Variations :
gene mutation : deletion, insertion (animation)
chromosomes variation:
- in number : euploidy, aneuploidy
- in morphological : translocation, inversion

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Crossing over
(Meiosis)

Duplication

Deletion

Inversion

Reciprocal
Translocation
Ring
Chromosome

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Effects of genetic variation

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Vavilov, 1951

1/. Benefits :
- Medicine : providing medicinal plants
- Agriculture : enhancing soil fertility, controlling epidemy,
providing food safety ....
- Environment : limiting pollution
2/. Importance :
 varieties, species adapted for ecological conditions
 valuable genes as parental material source to make
cross

Methods for identifying GD

P= G+E
PHENOTYPE
GENOTYPE
Traits:
Qualitative
Quantitative

ENVIRONMENT

DNA


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Genetic Diversity – measures
Source: Lee’s course

5 basic methods to determine which alleles are
present at a given locus. All techniques use
electrophoresis

 Protein electrophoresis – indirect, but commonly done
 Restriction Fragment Length Polymorphism (RFLP)
 Random Amplification of Polymorphic DNA (RAPD’s)
 Simple Sequence Repeat (SSR) polymorphisms
 DNA sequencing (fingerprinting)

Polymorphic bands by RAPD marker
Source: Ngon & Nelson 2001
M1.....

5

10 . . . . .

15

21

Polymorphic band by SSR marker


Source : Ngon & Nelson 2001
M 1. ...

5

10 . . .

15

20

M

ABI systems

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Diversity indices
 Shannon
 Simpson
 McIntosh
 Brillouin
 Gleason
 Margalet
 Menhinick
 Standard deviation (SD)

Keywords & formulas

Richness : number of species/1 area unit
Abundance : number of individual in certain species

Shannon

H    p i ln p i

Simpson

D  1

S

i 1

 pi
S

2

i1

Similarity indices
Simple Matching Coefficient
Jaccard index
Sorensen index
Ochiai,Kendall, Morisita, Horn indexes....
Pearson correlation index
Similarity percentage : Whittaker
Similarity index : Bray Curtis

Genetic distance: Euclide, D2 Mahalanobis....

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Risks causing Genetic erosion :
Putting genetic resource in unapproriate ecological
conditions, and living environment;
 Changing in cropping system;
 Destroying living environment;
 Market pressure;
 Natural calamity, or catastrophe by human;
 Setting up unapproriate agricultural policy.

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Methods for enhancing genetic diversity:
 genetic resource : introduce, making cross, mutation,
wild species, transgenics.
 cropping system: rotation, intercrop, overlapping crop
....
 ecological systems :
crops + fish feeding
crops + shrimp feeding
crops + living organism feeding in flooding regions ...

BioPro software : tool for analyzing biodiversity
Analyse descriptor parameters : mean, variance, SD .etc...
Analyze biodiversity indexes : Shannon, Simpson, .etc...
Analyse genetic diversity, species diversity.

Cluster analysis (CA)
Principal Component Analysis (PCA)
Correspondence Analysis
Can interface with other softwares EXCEL,ACCESS....

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Summaries:
Why?

Living Organisms

Adaptation

Evolution

to occur? Genes : jumping; mutation

Variation in chromosomes: number; morphology

How

to identify? Phenotype evaluation

Genotype analysis: Protein, DNA markers

to analyse?

Softwares : common; professional (Biopro)


Definition of genetic variations
A gene mutation is a situation where a new allele arises
through a change in the DNA code

A chromosome variation is a situation where a segment of
chromosome, a whole chromosome, or a set of chromosomes
changes
Transposable elements are DNA sequences which have the
capacity to move about the genome.

References

1. Heal, G. et al. Genetic Diversity and Interdependent Crop Choices in Agriculture. In:
Genetic diversity in Agriculture.
2. />3. Brown, T., T. Hodgkin. 2003. Maintaining Plant Genetic Diversity in
Agroecosystems. IPGRI’s report.
4. Hawtin, G. 2002. Biotechnolgy in the maintenance and use of Crop Genetic
Diversity. IPGRI.
5. Fedoroff, N. 2001. How jumping genes were discovered. .
6. NBII homepage. Biodiversity-Genetic Diversity.
7. Sivaprakash, K.R. et al. 2004. Genetic diversity of black gram (Vigna mungo)
landraces as evaluated by AFLP markers. Current Science, vol.86.
8. Baranek, M. et al. 2002. Evaluation of Genetic Diversity in 19 Glycine max (L.)
Merr. Accessions included in the Czech National Collection of Soybean Genotypes.
Czech J. Genet. Plant Breed. 38: 69-74.
9. Falco, S.D., and C. Perrings. 2003. Crop Genetic Diversity, Productivity and Stability
of Agroecosystems. A theoretical and Empirical investigation. Scottish Journ. of
Political Economy. Vol. 50 N.2.
10. Brown-Guerdira, G.L., J.A. Thompson, R.L. Nelson, and M.L. Warburton. 2000.

Evaluation of Genetic Diversity of Soybean Introductions and North American
Ancestor Using RAPD and SSR markers.

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THANK YOU VERY MUCH !!

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