Plant tissue culture or micropropagation technique is the rapid method to multiply newly released cultivar in limited time. Crop improvement by conventional method in vegetatively propagated crops like sugarcane is very difficult due to its narrow genetic base and other limitations. Somaclonal variations are easily achieved in asexually propagated crops like sugarcane and banana. Tissue culture derived variations are known as somaclonal variation. These variations play an important role in crop improvement program. Genetic variations are heritable in next generation and important for crop improvement, epigenetic changes are temporary ultimately reversible. Mutation breeding is also very advantageous for improving a cultivar. Somaclonal variants of sugarcane are available for several traits like drought, salt tolerance, red rot, eye spot disease, quality and quantity trait. Molecular marker techniques like RFLP, RAPD, AFLP and SSR etc. are regularly used preferentially over traditional phenotypic or cytological methods.

1. GERF Bulletin of Biosciences
June2015, 6(1):5-10
Abstract
Introduction
*Corresponding author: jyotigenpro@gmail.com
Key words: Somaclonal variation, crop improvement, plant tissue culture, sugarcane, conventional breeding
© Malhotra et al., 2015; licensee Green Earth Research Foundation. This article distributed under terms of Creative Commons Attribution
License (http://creativecommons.org/licenses/by/4.0). Which permits unrestricted use, distribution, and reproduction in any medium, provided
the original author and source are credited.
Review Article Open Access
www.gerfbb.com
ISSN:2229-6433
Received: 31 December 2014 Accepted: 18 June 2015 Published online: 27 July2015
Somaclonal Variation:Anew dimensionforsugarcane improvement
Jyoti Rastogi*1
, Siddhant1
, Parvesh Bubber2
and Brij Lal Sharma1
1
Center for Sugarcane Biotechnology,
Sugarcane Research Institute (UPCSR), Shahjahanpur- 242001, India
2
BiochemistryDiscipline, School ofSciences, IGNOU, New Delhi-110068, India
Plant tissue culture or micropropagation technique is the rapid method to multiply newly released cultivar in limited
time. Crop improvement by conventional method in vegetativelypropagated crops like sugarcane is very difficultdue to
its narrow genetic base and other limitations. Somaclonal variations are easily achieved in asexually propagated crops
like sugarcane and banana. Tissue culture derived variations are known as somaclonal variation. These variations play
an important role in crop improvement program. Genetic variations are heritable in next generation and important for
cropimprovement, epigenetic changes are temporaryultimately reversible. Mutationbreeding is alsoveryadvantageous
for improvinga cultivar. Somaclonal variantsof sugarcane are available for several traitslike drought, salt tolerance, red
rot, eye spot disease, qualityand quantitytrait. Molecular marker techniqueslike RFLP, RAPD,AFLPand SSR etc. are
regularly usedpreferentially over traditional phenotypic or cytological methods.
Sugarcane (Saccharum species complex), being the most
valuable commercial crop ofthe world. It is the major source
of sugar in the world and recently to produce ethanol, a
high energy rich biofuel. The crop improvement in many
crops like sugarcane is very difficult and time taking
because it has a complex poly-aneuploid, large genome size
and long breeding cycle. With the advancement of
biotechnological tools for the genetic improvement of many
economically important crops like have been highlighting
by different researchers in past years. In the past decade
considerable progress has been made in understanding and
manipulating the sugarcane genome using various biotech-
nological and cell biological approaches. Notable among
them are the crop improvement through somaclonal
variation, creation of transgenic plants with improved
agronomic or other important traits, advances in genomics
and molecular markers, and progress in understanding the
molecular aspects of sucrose transport and accumulation. It
is anticipated that the rapid advancements in emerging
biotechnology innovations would play a significant role in
the future sugarcane crop improvement programs and offer
many new opportunities to develop it as a new generation
industrial crop. Plant tissue culture gave an excellent
opportunity for the creation of genetic variability of clones

2. www.gerfbb.com
GERF Bulletin of Biosciences 2015, 6(1):5-10 6
with desired character in sugarcane (1,2,3). Somaclonal
variations are important tool to overcome the constrains of
conventional breeding (4). The accumulation of genetic
variability is an important aspect in plant breeding. Genetic
variability has been easily discernible in in vitro regener-
ated somaclonal variants.
In vitro regenerated variants are known as Somaclonal
variation or sub-clonal variation (5,6,7) mainlydepends on
various modes of plant regeneration . Somaclonal variants
have been available in manyhorticultural traits, ornamental
plants and recently the selection of new variants of many
crops like sugarcane for disease resistance (8,9,10) and
various agronomic characters like yield and quality(4). The
occurrence ofphenotypic instabilityis a major problem, when
our objective to produce the true copies of original plant
(11). The occurrence ofsomaclonal variation in tissue culture
culture derived plants is an alternative method to sort out
manybarriers of traditional breeding program. Sugarcane is
a good candidate for such type of studies due to its complex
polyploidy. The use ofvariation was first established through
the recovery of disease resistant plants in potato (resistance
against late blight and earlyblight) and sugarcane (resistance
against eye-spot disease, Fiji disease and downy mildew).
Somaclonal variation may be of two types 1- genetic
variations (may be occurred in somatic cells of the mother
plant), 2- epigenetic (may be occurred during in vitro tissue
culture practices).
Types of variations
Genetic variation
The variation occurs due to mutations or other changes
in the DNA of the tissue are known as genetic variation.
These are heritable in next generation and important for crop
improvement. Genetic changes behave as Mendelian traits
in crosses.
Epigenetic variation
Epigenetic changes are temporary ultimately reversible
(plants ‘revert’ to normal phenotype) also known as
developmental variation. These are non-heritable phenotypic
variation. There are several factors like explants source, age
of the donar plant, genotype, number of sub-culture
passaging, in vitro culture environment, concentration of
plant growth regulators, medium composition etc are the
components that might be induce variability in vitro
(12).Tissue culture system itself acts as a mutagenic system
because cells experience traumatic experiences from isolation
and may re-programme during plant regeneration.
Reprogramming or restructuring of events can create a wide
range of epigenetic variation in newly regenerated plants
(13).
Physiological variation
These variations are temporary in response to stimulus
and disappear when it is removed.
Need of improved varieties and limitations of
conventional approaches
Plant breeders have exploited the germplasm resource to
develop new cultivars with desirable traits viz., high yield,
diseases resistance and tolerance to many abiotic stresses
(14). However enormityof growing world population, crisis
of arable land and continual demand for newer improved
cultivars by using available natural and induced genetic
diversity. Conventional breeding takes approx 8-10 years to
develop and commercialize a newselected sugarcane cultivar
(15, 9).Another major problem of sugarcane growers its slow
multiplication rate cannot fulfill the need of colossal demand
ofnewlyreleased cultivar. In vitromultiplication and mutation
breeding is an alternative method to broaden the area of
novel cultivar. Due to limited availability of seed cane of a
new variety at the time of its release, it further takes several
years to cover the desired area for commercial cultivation,
by the time the varietystarts deteriorating due to biotic and
abiotic stresses. Tissue culture derived variations could be
veryuseful in sugarcane crop improvement program for the
development of new trait.
Potential role of somaclonal variation
Somaclonal variants of various agriculturallyimportant
traits have been studied also in sugarcane. The first in vitro
screened somaclone of commercial sugarcane for resistant
to Fiji disease reported by Heinz, 1973 (16). Somaclonal
variations are highly useful in plant breeding program.
Somaclonal variations are easily achieved in vegetatively
propagated crops like sugarcane. The potential role ofnatural
or induced genetic variation is a very essential component
ofcrop improvement program. Induced mutations have been
used in the improvement of major crops such as sugarcane
wheat, rice, barley, cotton, peanuts and beans, which are
seed propagated. Mutation breeding is very advantageous
for the vegetatively propagated plants like sugarcane, by
which a single or few characters of an excellent cultivar can
be change. The crop improvement through somaclonal
variation was first reported byHeinz and Mee 1971 (17).

3. www.gerfbb.com
7 GERF Bulletin of Biosciences 2015, 6(1):5-10
Table1:Crop improvement through somaclonal variation in many crops included sugarcane
Crop Trait
Sugarcane Diseases (Eye spot, Red rot, Fiji virus, Downy miledew, Leaf scald resistant),
drought & salt tolerance, improvement of qualitative and quantitative traits viz.,
sugar content, sugar recovery and cane yield.
Rice Plant height, heading date, seed fertility, grain number and weight
Wheat Plant and ear morphology, awns, grain weight and yield, gliadin proteins, amylase
Maize T toxin resistance, male fertility
Potato Tuber shape, maturity date, plant morphology, photoperiod, leaf colour, vigour,
height, skin colour, Resistance to early and late blight
Tomato Leaf morphology, branching habit, fruit colour, pedicel, male fertility and growth
Studies on Somaclonalvariation in sugarcane
Somaclonal variations has been usually reported bymany
researchers in tissue culture raised plants of sugarcane (18,
19). Variations in morphology, chromosome number and
enzymatic pattern in sugarcane plants derived from callus
have been reported (17, 20, 21). These make up a basic
constraint for a breeding program because the more variable
the genetic resources used, the more opportunities to select
superior genotype. In sugarcane somaclonal variation have
been exloited for the improvement of many economically
important traits like salt tolerant, eye spot and red rot
resistant. Patade et al (22) studied the effects of salt and
drought stresses on irradiated cells of sugarcane and
obtained plants tolerant to higher salt stress. Gandonou et
al (23) deliberate the effects of salt stress by exposing the
callus to a single level of 68 mM NaCl, and observed that
physiological and biochemical indicators could playa crucial
role in salt tolerance. Salt (NaCl) tolerent sugarcane cultivar
CP65-357 developed from callus culture (24). Wagih et al
(25) developed eight drought tolerant variants from
embryogenic callus of sugarcane (Saccharum hybrids) and
grown in a greenhouse for further testing under water stress.
They found improved tolerance to drought in amongst the
somaclonal variants for different areas of tropics and sub-
tropics. Four salt tolerant somaclonal variants were
developed from embryogenic calli of sugarcane variety
CP48-103 (26). Clonal variation in combination with in vitro
mutagenesis and selection has been applied for the isolation
Detection ofSomaclonal variants
Somaclonal variations can be detected easily by
morphological characteristics, such as cane height, leaf
morphology, bud shape, number of milable cane, sugar
concentration etc. (31). Chromosomal abbreviation and ploidy
changes are highlighted by cytogenetic analysis, including
chromosome counting under microscope / flow cytometry.
Proteins and isozymes also have been used as markers for
recognizing somaclonal variants in many fruit species but
theyare limited in their sensitivity. Cytological evaluation is
not often used and can be complicated to detect in numerous
crops.
With the advancement of molecular marker techniques
like RFLP, RAPD, AFLP and SSR etc. are regularly used
preferentially over traditional phenotypic or cytological
methods. Restriction Fragment Length Polymorphism (41)
analysis is one of the first techniques widely used to detect
variation. Later, PCR-based techniques, RandomAmplified
Polymorphic DNA(RAPD), ArbitrarilyPrimed Polymerase
Chain Reaction (AP-PCR), Amplified Fragment Length
Polymorphism (AFLP), Simple sequence repeat (SSR) are
most extensively used molecular techniques throughout the
world. Among these PCR based techniques, the RAPD is
faster, inexpensive, simple, less timeconsuming, most reliable
and frequently used to detect genetic variability at DNA
level (11, 42) in sugarcane and other crops. As in typical
PCR, where a pair of reverse and forward primer is used, in
RAPD only single primer amplify the unknown site in the
target genome.
Oropeza et al (43) identified somaclonal variants of
sugarcane resistant to sugarcane mosaic virus through
RAPD marker. The somaclones AT 626 and BT 627 were
selected bytheir resistant to SCMV and analyzed byRAPD.
Genetic changes have been detected with the help of RAPD
marker in sugarcane during tissue culture. Simple Sequence
Repeat (ISSR) technique is a new technique based on the
amplification of regions between microsatellites. It is using
to check genetic instability at early stages in in vitro.

4. GERF Bulletin of Biosciences 2015, 6(1):5-10 8
www.gerfbb.com
Advantages
 Somaclonal variations occur in high frequencies.
 Some changes can be novel and may not be
achieved by conventional breeding.
 In vitro screening reduces the time to isolation a
somaclone with desirable trait.
 Sometimes new desirable characters may be
occurredwhich werenot availablein thegermplasm.
 It is a cheaper than other genetic engineering
methods
Limitations
 These variations are not stable after selfing or
crossing.
 The variations are unpredictable in nature and
uncontrollable.
 Selected cell lines often reduced their regeneration
potential.
 Many selected clones show undesirable features
like reduced fertility, growth and even overall
performance.
Strategies to overcome the constraints
1. The breeding objective should be simple and
improve onecharacter at a time. If we required more
than one trait, stepwise improvement must be
possible.
2. An easy and efficient screening technique should
be needed to select a desired trait in somaclonal
variants.
3. Molecular markers and in vitro selection techniques
for various diseases are very helpful in the
identification of valuable variants.
4. A comparative study of plants produced through
somaclonal variation and conventionally
propagated should be tested in field trials before
cultivation.
Conclusion
With a continued cultivation of a sugarcane variety for
over 15-20 years, tremendous deterioration occurs in variety
leading in significant losses in cane yield and sugar recovery.
Loss of resistance against major diseases and pests in old
elite varieties are the main reasons of deterioration. If the old
existing varieties are improved using biotechnological tools
such as somaclonal variation, the cane and sugar
productivitywill be increase significantly. It is more efficient
and feasible technology for wider adoption in the field of
sugarcane improvement through biotechnological tools.
References
1. Nwauzoma,ABand Jaja ET.Areviewofsomaclonal
variation in plantain (Musa spp): mechanisms and
applications. Journal ofApplied Biosciences. 2013;
67: 5252–5260.
2. Heinz DJ and Mee GWP. Plant differentiation from
callus tissue of Saccharum spp. Crop Sci. 1969; 9:
346–348.
3. Khan, IA, Gaj MD and Maluszynski M. In vitro
mutagenesis in sugarcane callus culture. Mutation
BreedingNewsletter. 1999; 44:19-20.
4. Raja S, Qamarunnisa S, Jamil I, Naqvi Q, Azhar A
and Qureshi A. Screening of sugarcane somaclones
of variety BL4 for Agronomic characteristics. Pak.
J. Bot. 2014; 46(4): 1531-1535.
5. Larkin PJ and Scowcroft WR. Somaclonal variation-
a novel source of variability from cell cultures for
plant improvement. Theor. Appl. Genet. 1981; 60:
197-214.
6. Ramos Leal MA, Maribona RH, RuizA, Korneva S,
Canales E, Dinkova TD, Izquierdo F, Coto O and
Rizo D. Somaclonal variation as a source of
resistance to eyespot disease of sugarcane. Plant
Breeding. 1996; 115: 37-42.
7. Rani V and Raina S. Genetic fidelity of organized
meristem derived micropropagated plants: a critical
reappraisal. InVitro Cellular Developmental Biology
Plant. 2000; 36: 319-330.
8. Singh A, Lal M, Singh M P, Lal K and Singh S B.
Variations for Red Rot Resistance in Somaclones of
Sugarcane. Sugar Tech. 2000; 2 (1&2): 56 - 58.
9. Singh G, Sandhu SK, Madhu Meeta Singh K, Gill R
and Gosal SS. In vitro induction and
characterization of somaclonal variation for red rot
and other agronomic traits in sugarcane. Euphytica.
2008;160: 35-47
10. SengarAS,Thind KS, Kumar B, Pallavi MandGosal
SS. In vitro selection at cellular level for red rot
resistance in sugarcane (Saccharum sp.). Plant.
Growth Regul. 2009; 58: 201-209.
11. PandeyRN, Singh SP, Rastogi J, Sharma ML and
Singh RK. Early assessment of genetic fidelity in
sugarcane (Saccharum officinarum) plantlets
regenerated through direct organogenesis with
RAPDandSSRmarkers.AJCS.2012; 6(4): 618-624.
12. Silvarolla MB. Plant genomic alternations due to
tissue culture. J. Brazil. Assoc. Adv. Sci. 1992; 44:
329-335.
13. Jain SM Tissue culture-derived variation in crop
improvement. Euphytica. 2000; 118: 153-166.
14. KhaliqA, Ashfaq M,Akram W, Choi JK and Lee JJ.

5. 15. Gill RS, Madhu M, Thind KS and Kumar B.
Identification of red rot resistant promisssing
crosses. Sugar Tech. 2007; 9: 321-324.
16. Heinz DJ 1973. Sugarcane improvement through
induced mutations using vegetative propagules and
cell culture techniques. In: Induced mutations in
vegetatively propagated plants. Proc. of a Panel,
Intern. Atomic Energy Agency, Vienna 11-15
September 1972; 53-59.
17. Heinz, DJ & Mee GWP. Morphologic, cytogenetic
and enzymatic variation in Saccharum species
hybrid clones drived from callus tissue. Am. J. Bot.
1971;58: 257-262.
18. Burner DM, andGrisham MP.Induction andstability
of phenotypic variation in sugarcane as affected
bypropagation procedure. Crop. Sci. 1995; 35: 875-
880.
19. HoyJW, BischoffKP, Milligan SB, and Gravois KA.
Effect of tissue culture explant source on sugarcane
yield components. Euphytica. 2003; 129: 237– 240.
20. Krishnamurthi M and Tlaskal J. Figi disease
resistant Saccharum ojjjcinarum var. Pindar sub-
clones from tissue cultures. Proc. Congr. Int. Sot.
Sugar Cane Technol. (South Africa) 1974; 15: 130-
137.
21. Liu MC and WH Chen. Tissue and cell culture as
aids to sugarcane breeding. Creation of genetic
variabilitythrough callus culture. Euphytica. 1976;
25:393-403.
22. Patade VY, Suprasanna P, Bapat VA, Kulkarni UG.
Selection for abiotic salinity and drought stress
tolerance and molecular characterization oftolerant
lines in sugarcane. BARC Newslett. 2006; 27: 244-
257.
23. Gandonou CB, Errabii T, Abrini J, Idaomar M and
Senhaji NS. Selection ofcalluscultures ofsugarcane
(Saccharum sp.) tolerant toNaCl and their response
tosalt tolerance. Plant Cell TissueOrgan Cult. 2006;
87:9-16.
Effect of plant factors, sugar contents, and control
methods on the Top Borer (Scirpophaga nivella F.)
Infestation in selected varieties of sugarcane.
Entomological Res. 2005; 35: 153-160.
24. Christophe B, Gandonou, Tomader E, Jamal A,
Mohamed I and Nadia SS. Selection of callus
cultures of sugarcane (Saccharum sp.) tolerant to
NaCl and their response to salt stress. Plant Cell
Tiss Organ Cult. 2006; 87: 9-16.
25. Wagih ME, Ala Aand Musa Y. Regeneration and
Evaluation of Sugarcane Somaclonal Variants for
Drought Tolerance. Sugar Tech. 2004; 6 (l&2): 35-
40.
26 Shomeili M, Majid N, Mosa M and Hamid RM.
Evaluation of sugarcane (Saccharum officinarum
L.) somaclonal variants tolerance to salinityin vitro
and in vivo cultures. African Journal of
Biotechnology. 2011; 10(46): 9337-9343l.
27. ZhambranoAY, DemeyJR, Fuch M, Gonzalez V, Rea
R, deSouza OandGutierrez Z. Slection ofsugarcane
clones resistant toSCMV. Plant Sci. 2003; 165: 221-
225.
28. Sobhakumari VP. Assessment of somaclonal
variation in sugarcane. African Journal of
Biotechnology. 2012; 11(87): 15303-15309.
29. Patade VY, Suprasanna P and Bapat VA. Gamma
irradiation of embryogenic callus cultures and in
vitro selection for salt tolerance in sugarcane
(Saccharum officinarum L.).Agric. Sci. China. 2008;
7(9):1147-1152.
30. Rajeswari S, Thirugnanakumar S, Anandan A and
Krishnamurthi M. Somaclonal variation in
sugarcane through tissue culture and evaluation
for quantitative and qualitytraits. Euphytica. 2009;
168:71-80.
31. Doule RB. Cane yield and Quality Characters of
Some Promising Somaclonal Variants ofSugarcane.
SugarTech. 2006; 8(2&3): 191-193.
32. Kumar P, Agarwal A,Tiwari AK, Lal M and Jabri
MRA. Possibilities of development of red rot
resistance in sugarcane through somaclonal
variation. SugarTech, 2012; 14(2): 192-194.
33. Krisnamurthi, Mand Tlaskal J. Fiji diseaseresistant.
Saccharum officinarum L. var. Pindar subclonefrom
tissueculture. Proc. ISSCT. 1974, 15:130-137.
34. Krishnamurthi M. Notes on disease resistance of
tissue culture subclones and fusion of sugarcane
protoplasts. Sugarcane Breed. Newsl. 1975; 35: 29-
26.
35. Heinz DJ, KrishnamurthiM,NickellLGandMaretzki
A. Cell, tissue and organ culture in sugarcane
improvement, In : Plant Cell, Tissue and Organ
Culture (J. Reinert andY.P.S. Bajaj, eds) Springer
Verlag, NewYork. 1977; 3-17.
36. Sreenivasan J and Sreenivasan TV. Somaclonal
variation for smut disease (Ustilago scitaminea
Syd.) resistance in sugarcane. Proc. Symp. Plant,
Cell and Tissue Cult. ofEconomically Imp. Plants.
(ed) Reddy, G.M. Hyderabad. 1987a: 259-264.
37. Sreenivasan J, Sreenivasan TV and Alexander KC.
Somaclonal Variation for rust resistance in
sugarcane Indian J. Genet. 1987b; 472 : 109-114.
38. Liu MC, Yeh HS and Chen WH.Ahigh sucrose and
vigorously growing calliclone. Rep. Taiwan Sugar
Res. Inst. 1984; 102: 1-11.
39. Jalaja NC, Sreenivasan TV, Pawar SM, Bhoi PGand
9 GERF Bulletin of Biosciences 2015, 6(1):5-10
www.gerfbb.com

6. Garker RM. Co 94012- A new sugarcane variety
through somaclonal variation. Sugar Tech. 2006; 8
(2&3):132-136.
40. AliA, Naz S, Alam S S and Iqbal J. In vitro induced
mutation for screening of red rot (Colletotrichum
falcatum) in sugarcane (Saccharum officinarum).
PakJ. Bot. 2007;39(6): 1979-1994.
41. Botstein D, White, RL, Skolnick M and Davis RW.
Construction of a genetic linkage map using
Restriction Fragment Length Polymorphisms.
American Journal ofHuman Genetics. 1980; 32: 314-
331.
42. Maria IZ, Hideto A, Vicente AM, Maria HPF and
Maria LCV. Genetic instabilityof sugarcane plants
derived from meristem cultures. Genetics and
Molecular Biology. 2002; 25 (1): 91-96.
43. Oropeza M, Guevara P, Garcia E and Ramirez JL.
Identification of sugarcane (Saccharum Spp.)
somaclonal variants resistant to sugarcane mosaic
virusvia RAPD marker. Plant Mol. Rep. 1995; 13(2):
182-192.
GERF Bulletin of Biosciences 2015, 6(1):5-10 10
www.gerfbb.com