1. Somaclonal Variations

2. New variety production (somaclonal variation)

5. Tuberosum cultivar and new andigenum introduction

6. Somaclonal Variation
Somaclonal variation is a general phenomenon of all plant regeneration systems that involve a callus phase
There are two general types:
Heritable, genetic changes (alter the DNA)
•Stable, but non-heritable changes (alter gene expression, epigenetic)
With or without mutagen 6

7. Somaclonal/Mutation Breeding
Advantages:
Screen very high populations (cell based)
Can apply selection to single cells
Disadvantages:
Many mutations are non-heritable
Requires dominant mutation (or double recessive mutation); most mutations are recessive
Can avoid this constraint by not applying selection pressure in culture, but you lose the advantage of high through-put screening –have to grow out all regenerated plants, produce seed, and evaluate the M2 7

8. Targets for Somaclonal Variation
Herbicide resistance and tolerance
Specific amino acid accumulators
Screen for specific amino acid production
e.g.Lysine in cereals
Abiotic stress tolerance
Add or subject cultures to selection agent– e.g.: salt, temperature stress
Disease resistance
Add toxin or culture filtrate to growth media 8

9. 9

10. Somaclonal Variation
Genetic variations in plants that have been produced by plant tissue culture and can be detected as genetic or phenotypic traits.

11. In vitro plant regeneration
In vitro plant regeneration. The choice of different tissue types and culture conditions including plant growth regulators (PGRs), nutrients, light/dark, and temperature, and the occurrence of extensive cell division before organogenesis or somatic embryogenesis may affect the regeneration of variant plants. Chromatin modifiers (in green) referred to in the text as well as interacting genes (in black) or putative targets with a potential role during cell fate switch/cell division and differentiation of plant cells cultured in vitro are represented. Although many key regulators have been identified, it is still not well understood how they function at the molecular level. For a detailed overview of the genes taking part in these plant developmental processes refer to Desvoyes et al. (2010). Abbreviations: BRM, BRAHMA; PKL, PICKLE; PKR2, PICKLE RELATED 2; SWN, SWINGER; SYD, SPLAYED.

13. Visual observations regarding somaclonal variation

14. Basic Features of Somaclonal Variations
Variations for Karyotype, isozyme characteristics and morphology in somaclones may also observed.
Calliclone (clones of callus), mericlone (clones of meristem) and protoclone (clones of Protoplast) produced.
Generally heritable mutation and persist in plant population even after plantation into the field

15. Mechanism of Somaclonal Variations
Genetic (Heritable Variations)
Pre-existing variations in the somatic cells of explant
Caused by mutations and other DNA changes
Occur at high frequency
Epigenetic (Non-heritable Variations)
Variations generated during tissue culture
Caused by temporary phenotypic changes
Occur at low frequency

16. Steps involved in induction and selection of Somaclonal Variations
Callus Tissue
Somaclonal
Variants
Organogenesis
Hardening and
Selfing
Regenerated plants
Steps involved in induction and selection of Somaclonal Variations

17. Causes of Somaclonal Variations
Physiological Cause
Biochemical Cause
Genetic Cause

18. Physiological Cause Exposure of culture to plant growth regulators.
Culture conditions

19. Genetic Cause Change in chromosome number
Euploidy: Changes chromosome Sets
Aneuploidy: Changes in parts of chromosome Sets
Polyploidy: Organisms with more than two chromosome sets
Monoploidy: Organism with one chromasomes set
Change in chromosome structure
Deletion
Inversion
Duplication
Translocation

20. Genetic Cause 3. Gene Mutation
Tansition DNA substitution mutations are of two types. Transitions are interchanges of two-ring purines (A G) or of one-ring pyrimidines (C T): they therefore involve bases of similar shape.
Transversion Transversions are interchanges of purine for pyrimidine bases, which therefore involve exchange of one-ring and two-ring structures.
Insertion
Deletion
4. Plasmagene Mutation a self-replicating genetic particle postulated to be in the cytoplasm of a cell, as in mitochondria.
5. Transposable element activation

22. Transposable element activation
Under most circumstances this process is highly efficient, and the vast majority of transposons are inactive. Nevertheless, transposons are activated by a variety of conditions likely to be encountered by natural populations, and even closely related species can have dramatic differences in transposon copy number. Transposon silencing has proved to be closely related to other epigenetic phenomena, and transposons are known to contribute directly and indirectly to regulation of host genes. Together, these observations suggest that naturally occurring changes in transposon activity may have had an important impact on the causes and consequences of epigenetic silencing in plants.

23. Genetic Cause 6. DNA sequence Change in DNA Change in Protein
Detection of altered fragment size by using Restriction enzyme
Change in Protein
Loss or gain in protein band
Alteration in level of specific protein
Methylation of DNA
Methylation inactivates transcription process.

24. Biochemical Cause
Lack of photosynthetic ability due to alteration in carbon metabolism
Biosynthesis of starch via carotenoid pathway
Nitrogen metabolism
Antibiotic resistance.

25. Detection and Isolation of Somaclonal Variants
Analysis of morphological characters
Qualitative characters: Plant height, maturity date, flowering date and leaf size
Quantitative characters: yield of flower, seeds and wax contents in different plant parts
Variant detection by cytological Studies
Staining of meristematic tissues like root tip, leaf tip with feulgen and acetocarmine provide the number and morphology of chromosomes.
Variant detection by DNA contents
Cytophotometer detection of feulgen stained nuclei can be used to measure the DNA contents

26. 4. Variant detection by gel electrophoresis
Change in concentration of enzymes, proteins and chemical products like pigments, alkaloids and amino acids can be detected by their electrophoretic pattern
5. Detection of disease resistance variant
Pathogen or toxin responsible for disease resistance can be used as selection agent during culture.
6. Detection of herbicide resistance variant
Plantlets generated by the addition of herbicide to the cell culture system can be used as herbicide resistance plant.

27. Detection and Isolation of Somaclonal Variants
7. Detection of environmental stress tolerant variant
Selection of high salt tolerant cell lines in tobacco
Selection of water-logging and drought resistance cell lines in tomato
Selection of temperature stress tolerant in cell lines in pear.
Selection of mineral toxicities tolerant in sorghum plant (mainly for aluminium toxicity)

28. Advantages of Somaclonal Variations
Help in crop improvement
Creation of additional genetic variations
Increased and improved production of secondary metabolites
Selection of plants resistant to various toxins, herbicides, high salt concentration and mineral toxicity
Suitable for breeding of tree species

29. Disadvantages of Somaclonal Variations
A serious disadvantage occurs in operations which require clonal uniformity, as in the horticulture and forestry industries where tissue culture is employed for rapid propagation of elite genotypes
Sometime leads to undesirable results
Selected variants are random and genetically unstable
Require extensive and extended field trials
Not suitable for complex agronomic traits like yield, quality etc.
May develop variants with pleiotropic effects which are not true.