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Genetic variations in plants thatGenetic variations in plants thathave been produced by plant tissuehave been produced by plant tissueculture and can be detected asculture and can be detected as

genetic or phenotypic traits.genetic or phenotypic traits.

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Basic Features ofBasic Features of SomaclonalSomaclonal

VariationsVariations

VariationsVariations forfor KaryotypeKaryotype,, isozymeisozyme characteristicscharacteristics andandmorphologymorphology inin somaclonessomaclones maymay alsoalso bebe observedobserved..

CallicloneCalliclone (clones(clones ofof callus),callus), mericlonemericlone (clones(clones ofofmeristemmeristem)) andand protocloneprotoclone (clones(clones ofof Protoplast)Protoplast) ..

GenerallyGenerally heritableheritable mutationmutation persistpersist inin plantplant

populationpopulation eveneven afterafter plantationplantation intointo thethe fieldfield

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Mechanism of SomaclonalMechanism of Somaclonal

VariationsVariations1. Genetic (Heritable Variations)

Pre-existing variations in the somatic cells of

explant

Caused by mutations and other DNA changes

Occur at high frequency

2. Epigenetic (Non-heritable Variations)

Variations generated during tissue culture

Caused by temporary phenotypic changes

Occur at low frequency

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Callus Tissue

Organogenesis

Regenerated plants Hardening and Selfing

Somaclonal Variants

Steps involved in induction and selection ofSomaclonal Variations

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Causes of Somaclonal

Variations

Physiological

Cause

Genetic Cause

Biochemical

Cause

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Physiological CausePhysiological Cause

Exposure of culture to plant growthExposure of culture to plant growth

regulators.regulators.

Culture conditionsCulture conditions--genotype andgenotype andexplant,durationexplant,duration of cell culture.of cell culture.

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Physiological CausePhysiological Cause

Variation in chromosomeVariation in chromosome--preexistingpreexisting

chromosome variationchromosome variation

Nuclear fragmentationNuclear fragmentation

AbnormalitiesAbnormalities occuringoccuring in mitotic processin mitotic process

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Genetic CauseGenetic Cause

1.1. Change in chromosome numberChange in chromosome number Euploidy: Changes chromosome SetsEuploidy: Changes chromosome Sets

Aneuploidy: Changes in parts of chromosome SetsAneuploidy: Changes in parts of chromosome Sets

Polyploidy: Organisms with more than two chromosomePolyploidy: Organisms with more than two chromosomesetssets

Monoploidy: Organism with one chromasomes setMonoploidy: Organism with one chromasomes set

2.2. Change in chromosome structureChange in chromosome structure DeletionDeletion

InversionInversion

DuplicationDuplication

TranslocationTranslocation

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3.3. Gene MutationGene Mutation TansitionTansition

TransversionTransversion

InsertionInsertion

DeletionDeletion

4.4. Plasmagene MutationPlasmagene Mutation

5.5. Transposable element activationTransposable element activation

Genetic CauseGenetic Cause

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6.6. DNA sequenceDNA sequence

Change in DNAChange in DNA Detection of altered fragment size by using Restriction enzymeDetection of altered fragment size by using Restriction enzyme

Change in ProteinChange in Protein Loss or gain in protein bandLoss or gain in protein band

Alteration in level of specific proteinAlteration in level of specific protein

Methylation ofDNAMethylation ofDNA Methylation inactivates transcription process.Methylation inactivates transcription process.

Genetic CauseGenetic Cause

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Biochemical CauseBiochemical Cause

Lack of photosynthetic ability due to alterationLack of photosynthetic ability due to alterationin carbon metabolismin carbon metabolism

Biosynthesis of starch via carotenoid pathwayBiosynthesis of starch via carotenoid pathway

Nitrogen metabolismNitrogen metabolism

Antibiotic resistance.Antibiotic resistance.

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Detection and Isolation of SomaclonalDetection and Isolation of Somaclonal

VariantsVariants

1.1. Analysis of morphological charactersAnalysis of morphological characters Qualitative characters: Plant height, maturity date,Qualitative characters: Plant height, maturity date,

flowering date and leaf sizeflowering date and leaf size

Quantitative characters: yield of flower, seeds and waxQuantitative characters: yield of flower, seeds and wax

contents in different plant partscontents in different plant parts

2.2. Variant detection by cytological StudiesVariant detection by cytological Studies Staining of meristematic tissues like root tip, leaf tip withStaining of meristematic tissues like root tip, leaf tip with

feulgen and acetocarmine provide the number andfeulgen and acetocarmine provide the number andmorphology of chromosomes.morphology of chromosomes.

3.3. Variant detection by DNA contentsVariant detection by DNA contents Cytophotometer detection of feulgen stained nuclei canCytophotometer detection of feulgen stained nuclei can

be used to measure the DNA contentsbe used to measure the DNA contents

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4.4. Variant detection by gel electrophoresisVariant detection by gel electrophoresis Change in concentration of enzymes, proteins andChange in concentration of enzymes, proteins and

chemical products like pigments, alkaloids and aminochemical products like pigments, alkaloids and amino

acids can be detected by theiracids can be detected by their electrophoreticelectrophoretic patternpattern

5.5. Detection of disease resistance variantDetection of disease resistance variant Pathogen or toxin responsible for disease resistance canPathogen or toxin responsible for disease resistance can

be used as selection agent during culture.be used as selection agent during culture.

6.6. Detection of herbicide resistance variantDetection of herbicide resistance variant Plantlets generated by the addition of herbicide to the cellPlantlets generated by the addition of herbicide to the cell

culture system can be used as herbicide resistance plant.culture system can be used as herbicide resistance plant.

Detection and Isolation of SomaclonalDetection and Isolation of Somaclonal

VariantsVariants

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7.7. Detection of environmental stress tolerantDetection of environmental stress tolerant

variantvariant

Selection of high salt tolerant cell lines in tobaccoSelection of high salt tolerant cell lines in tobacco Selection of waterSelection of water--logging and drought resistance celllogging and drought resistance cell

lines in tomatolines in tomato

Selection of temperature stress tolerant in cell lines in pear.Selection of temperature stress tolerant in cell lines in pear.

Selection of mineral toxicities tolerant in sorghum plantSelection of mineral toxicities tolerant in sorghum plant

(mainly for aluminium toxicity)(mainly for aluminium toxicity)

Detection and Isolation of SomaclonalDetection and Isolation of Somaclonal

VariantsVariants

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Advantages of Somaclonal VariationsAdvantages of Somaclonal Variations

Help in crop improvementHelp in crop improvement

Creation of additional genetic variationsCreation of additional genetic variations

Increased and improved production ofIncreased and improved production ofsecondary metabolitessecondary metabolites

Selection of plants resistant to variousSelection of plants resistant to various

toxins, herbicides, high salt concentrationtoxins, herbicides, high salt concentrationand mineral toxicityand mineral toxicity

Suitable for breeding of tree speciesSuitable for breeding of tree species

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Disadvantages of SomaclonalDisadvantages of Somaclonal

VariationsVariations

AA seriousserious disadvantagedisadvantage occursoccurs inin operationsoperations whichwhich requirerequireclonalclonal uniformity,uniformity, asas inin thethe horticulturehorticulture andand forestryforestryindustriesindustries wherewhere tissuetissue cultureculture isis employedemployed forfor rapidrapid

propagationpropagation ofof eliteelite genotypesgenotypes SometimeSometime leadsleads toto undesirableundesirable resultsresults

SelectedSelected variantsvariants areare randomrandom andand geneticallygenetically unstableunstable

RequireRequire extensiveextensive andand extendedextended fieldfield trialstrials

NotNot suitablesuitable forfor complexcomplex agronomicagronomic traitstraits likelike yield,yield, qualityquality

etcetc.. MayMay developdevelop variantsvariants withwith pleiotropicpleiotropic effectseffects whichwhich areare notnot

truetrue..