Somaclonal variations and their applications in horticultural crops improvement
Identifieur interne : 000717 ( Pmc/Corpus ); précédent : 000716; suivant : 000718Somaclonal variations and their applications in horticultural crops improvement
Auteurs : Hare Krishna ; Mahdi Alizadeh ; Dhurendra Singh ; Udayvir Singh ; Nitesh Chauhan ; Maliheh Eftekhari ; Radha Kishan SadhSource :
- 3 Biotech [ 2190-5738 ] ; 2016.
Abstract
The advancements made in tissue culture techniques has made it possible to regenerate various horticultural species in vitro as micropropagation protocols for commercial scale multiplication are available for a wide range of crops. Clonal propagation and preservation of elite genotypes, selected for their superior characteristics, require high degree of genetic uniformity amongst the regenerated plants. However, plant tissue culture may generate genetic variability, i.e., somaclonal variations as a result of gene mutation or changes in epigenetic marks. The occurrence of subtle somaclonal variation is a drawback for both in vitro cloning as well as germplasm preservation. Therefore, it is of immense significance to assure the genetic uniformity of in vitro raised plants at an early stage. Several strategies have been followed to ascertain the genetic fidelity of the in vitro raised progenies comprising morpho-physiological, biochemical, cytological and DNA-based molecular markers approaches. Somaclonal variation can pose a serious problem in any micropropagation program, where it is highly desirable to produce true-to-type plant material. On the other hand, somaclonal variation has provided a new and alternative tool to the breeders for obtaining genetic variability relatively rapidly and without sophisticated technology in horticultural crops, which are either difficult to breed or have narrow genetic base. In the present paper, sources of variations induced during tissue culture cycle and strategies to ascertain and confirm genetic fidelity in a variety of in vitro raised plantlets and potential application of variants in horticultural crop improvement are reviewed.
Url:
DOI: 10.1007/s13205-016-0389-7
PubMed: NONE
PubMed Central: 4752953
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Somaclonal variations and their applications in horticultural crops improvement</title><author><name sortKey="Krishna, Hare" sort="Krishna, Hare" uniqKey="Krishna H" first="Hare" last="Krishna">Hare Krishna</name><affiliation><nlm:aff id="Aff1">ICAR-Central Institute for Arid Horticulture, Beechwal, Bikaner, Rajasthan 334 006 India</nlm:aff></affiliation></author><author><name sortKey="Alizadeh, Mahdi" sort="Alizadeh, Mahdi" uniqKey="Alizadeh M" first="Mahdi" last="Alizadeh">Mahdi Alizadeh</name><affiliation><nlm:aff id="Aff2">Department of Horticulture, Faculty of Agriculture, Gorgan University of Agricultural Sciences and Natural Resources (GUASNR), Golestan, Gorgan, Iran</nlm:aff></affiliation></author><author><name sortKey="Singh, Dhurendra" sort="Singh, Dhurendra" uniqKey="Singh D" first="Dhurendra" last="Singh">Dhurendra Singh</name><affiliation><nlm:aff id="Aff1">ICAR-Central Institute for Arid Horticulture, Beechwal, Bikaner, Rajasthan 334 006 India</nlm:aff></affiliation></author><author><name sortKey="Singh, Udayvir" sort="Singh, Udayvir" uniqKey="Singh U" first="Udayvir" last="Singh">Udayvir Singh</name><affiliation><nlm:aff id="Aff1">ICAR-Central Institute for Arid Horticulture, Beechwal, Bikaner, Rajasthan 334 006 India</nlm:aff></affiliation></author><author><name sortKey="Chauhan, Nitesh" sort="Chauhan, Nitesh" uniqKey="Chauhan N" first="Nitesh" last="Chauhan">Nitesh Chauhan</name><affiliation><nlm:aff id="Aff1">ICAR-Central Institute for Arid Horticulture, Beechwal, Bikaner, Rajasthan 334 006 India</nlm:aff></affiliation></author><author><name sortKey="Eftekhari, Maliheh" sort="Eftekhari, Maliheh" uniqKey="Eftekhari M" first="Maliheh" last="Eftekhari">Maliheh Eftekhari</name><affiliation><nlm:aff id="Aff2">Department of Horticulture, Faculty of Agriculture, Gorgan University of Agricultural Sciences and Natural Resources (GUASNR), Golestan, Gorgan, Iran</nlm:aff></affiliation></author><author><name sortKey="Sadh, Radha Kishan" sort="Sadh, Radha Kishan" uniqKey="Sadh R" first="Radha Kishan" last="Sadh">Radha Kishan Sadh</name><affiliation><nlm:aff id="Aff1">ICAR-Central Institute for Arid Horticulture, Beechwal, Bikaner, Rajasthan 334 006 India</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmc">4752953</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4752953</idno><idno type="RBID">PMC:4752953</idno><idno type="doi">10.1007/s13205-016-0389-7</idno><idno type="pmid">NONE</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">000717</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Somaclonal variations and their applications in horticultural crops improvement</title><author><name sortKey="Krishna, Hare" sort="Krishna, Hare" uniqKey="Krishna H" first="Hare" last="Krishna">Hare Krishna</name><affiliation><nlm:aff id="Aff1">ICAR-Central Institute for Arid Horticulture, Beechwal, Bikaner, Rajasthan 334 006 India</nlm:aff></affiliation></author><author><name sortKey="Alizadeh, Mahdi" sort="Alizadeh, Mahdi" uniqKey="Alizadeh M" first="Mahdi" last="Alizadeh">Mahdi Alizadeh</name><affiliation><nlm:aff id="Aff2">Department of Horticulture, Faculty of Agriculture, Gorgan University of Agricultural Sciences and Natural Resources (GUASNR), Golestan, Gorgan, Iran</nlm:aff></affiliation></author><author><name sortKey="Singh, Dhurendra" sort="Singh, Dhurendra" uniqKey="Singh D" first="Dhurendra" last="Singh">Dhurendra Singh</name><affiliation><nlm:aff id="Aff1">ICAR-Central Institute for Arid Horticulture, Beechwal, Bikaner, Rajasthan 334 006 India</nlm:aff></affiliation></author><author><name sortKey="Singh, Udayvir" sort="Singh, Udayvir" uniqKey="Singh U" first="Udayvir" last="Singh">Udayvir Singh</name><affiliation><nlm:aff id="Aff1">ICAR-Central Institute for Arid Horticulture, Beechwal, Bikaner, Rajasthan 334 006 India</nlm:aff></affiliation></author><author><name sortKey="Chauhan, Nitesh" sort="Chauhan, Nitesh" uniqKey="Chauhan N" first="Nitesh" last="Chauhan">Nitesh Chauhan</name><affiliation><nlm:aff id="Aff1">ICAR-Central Institute for Arid Horticulture, Beechwal, Bikaner, Rajasthan 334 006 India</nlm:aff></affiliation></author><author><name sortKey="Eftekhari, Maliheh" sort="Eftekhari, Maliheh" uniqKey="Eftekhari M" first="Maliheh" last="Eftekhari">Maliheh Eftekhari</name><affiliation><nlm:aff id="Aff2">Department of Horticulture, Faculty of Agriculture, Gorgan University of Agricultural Sciences and Natural Resources (GUASNR), Golestan, Gorgan, Iran</nlm:aff></affiliation></author><author><name sortKey="Sadh, Radha Kishan" sort="Sadh, Radha Kishan" uniqKey="Sadh R" first="Radha Kishan" last="Sadh">Radha Kishan Sadh</name><affiliation><nlm:aff id="Aff1">ICAR-Central Institute for Arid Horticulture, Beechwal, Bikaner, Rajasthan 334 006 India</nlm:aff></affiliation></author></analytic><series><title level="j">3 Biotech</title><idno type="eISSN">2190-5738</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The advancements made in tissue culture techniques has made it possible to regenerate various horticultural species in vitro as micropropagation protocols for commercial scale multiplication are available for a wide range of crops. Clonal propagation and preservation of elite genotypes, selected for their superior characteristics, require high degree of genetic uniformity amongst the regenerated plants. However, plant tissue culture may generate genetic variability, i.e., somaclonal variations as a result of gene mutation or changes in epigenetic marks. The occurrence of subtle somaclonal variation is a drawback for both in vitro cloning as well as germplasm preservation. Therefore, it is of immense significance to assure the genetic uniformity of in vitro raised plants at an early stage. Several strategies have been followed to ascertain the genetic fidelity of the in vitro raised progenies comprising morpho-physiological, biochemical, cytological and DNA-based molecular markers approaches. Somaclonal variation can pose a serious problem in any micropropagation program, where it is highly desirable to produce true-to-type plant material. On the other hand, somaclonal variation has provided a new and alternative tool to the breeders for obtaining genetic variability relatively rapidly and without sophisticated technology in horticultural crops, which are either difficult to breed or have narrow genetic base. In the present paper, sources of variations induced during tissue culture cycle and strategies to ascertain and confirm genetic fidelity in a variety of in vitro raised plantlets and potential application of variants in horticultural crop improvement are reviewed.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Abreu, Is" uniqKey="Abreu I">IS Abreu</name></author><author><name sortKey="Carvalho, Cr" uniqKey="Carvalho C">CR Carvalho</name></author><author><name sortKey="Clarindo, Wr" uniqKey="Clarindo W">WR Clarindo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Afrasiab, H" uniqKey="Afrasiab H">H Afrasiab</name></author><author><name sortKey="Iqbal, J" uniqKey="Iqbal J">J Iqbal</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ahloowalia, Bs" uniqKey="Ahloowalia B">BS Ahloowalia</name></author></analytic></biblStruct><biblStruct><analytic><author><name 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<front><journal-meta><journal-id journal-id-type="nlm-ta">3 Biotech</journal-id><journal-id journal-id-type="iso-abbrev">3 Biotech</journal-id><journal-title-group><journal-title>3 Biotech</journal-title></journal-title-group><issn pub-type="epub">2190-5738</issn><publisher><publisher-name>Springer Berlin Heidelberg</publisher-name><publisher-loc>Berlin/Heidelberg</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmc">4752953</article-id><article-id pub-id-type="publisher-id">389</article-id><article-id pub-id-type="doi">10.1007/s13205-016-0389-7</article-id><article-categories><subj-group subj-group-type="heading"><subject>Review Article</subject></subj-group></article-categories><title-group><article-title>Somaclonal variations and their applications in horticultural crops improvement</article-title></title-group><contrib-group><contrib contrib-type="author" corresp="yes"><name><surname>Krishna</surname><given-names>Hare</given-names></name><address><phone>+91 1512250960</phone><email>kishun@rediffmail.com</email></address><xref ref-type="aff" rid="Aff1"></xref></contrib><contrib contrib-type="author"><name><surname>Alizadeh</surname><given-names>Mahdi</given-names></name><xref ref-type="aff" rid="Aff2"></xref></contrib><contrib contrib-type="author"><name><surname>Singh</surname><given-names>Dhurendra</given-names></name><xref ref-type="aff" rid="Aff1"></xref></contrib><contrib contrib-type="author"><name><surname>Singh</surname><given-names>Udayvir</given-names></name><xref ref-type="aff" rid="Aff1"></xref></contrib><contrib contrib-type="author"><name><surname>Chauhan</surname><given-names>Nitesh</given-names></name><xref ref-type="aff" rid="Aff1"></xref></contrib><contrib contrib-type="author"><name><surname>Eftekhari</surname><given-names>Maliheh</given-names></name><xref ref-type="aff" rid="Aff2"></xref></contrib><contrib contrib-type="author"><name><surname>Sadh</surname><given-names>Radha Kishan</given-names></name><xref ref-type="aff" rid="Aff1"></xref></contrib><aff id="Aff1"><label></label>ICAR-Central Institute for Arid Horticulture, Beechwal, Bikaner, Rajasthan 334 006 India</aff><aff id="Aff2"><label></label>Department of Horticulture, Faculty of Agriculture, Gorgan University of Agricultural Sciences and Natural Resources (GUASNR), Golestan, Gorgan, Iran</aff></contrib-group><pub-date pub-type="epub"><day>13</day><month>2</month><year>2016</year></pub-date><pub-date pub-type="pmc-release"><day>13</day><month>2</month><year>2016</year></pub-date><pub-date pub-type="ppub"><month>12</month><year>2016</year></pub-date><volume>6</volume><issue>1</issue><elocation-id>54</elocation-id><history><date date-type="received"><day>26</day><month>8</month><year>2015</year></date><date date-type="accepted"><day>20</day><month>10</month><year>2015</year></date></history><permissions><copyright-statement>© The Author(s) 2016</copyright-statement><license license-type="OpenAccess"><license-p><bold>Open Access</bold>This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link>), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.</license-p></license></permissions><abstract id="Abs1"><p>The advancements made in tissue culture techniques has made it possible to regenerate various horticultural species in vitro as micropropagation protocols for commercial scale multiplication are available for a wide range of crops. Clonal propagation and preservation of elite genotypes, selected for their superior characteristics, require high degree of genetic uniformity amongst the regenerated plants. However, plant tissue culture may generate genetic variability, i.e., somaclonal variations as a result of gene mutation or changes in epigenetic marks. The occurrence of subtle somaclonal variation is a drawback for both in vitro cloning as well as germplasm preservation. Therefore, it is of immense significance to assure the genetic uniformity of in vitro raised plants at an early stage. Several strategies have been followed to ascertain the genetic fidelity of the in vitro raised progenies comprising morpho-physiological, biochemical, cytological and DNA-based molecular markers approaches. Somaclonal variation can pose a serious problem in any micropropagation program, where it is highly desirable to produce true-to-type plant material. On the other hand, somaclonal variation has provided a new and alternative tool to the breeders for obtaining genetic variability relatively rapidly and without sophisticated technology in horticultural crops, which are either difficult to breed or have narrow genetic base. In the present paper, sources of variations induced during tissue culture cycle and strategies to ascertain and confirm genetic fidelity in a variety of in vitro raised plantlets and potential application of variants in horticultural crop improvement are reviewed.</p></abstract><kwd-group xml:lang="en"><title>Keywords</title><kwd>Micropropagation</kwd><kwd>Somaclones</kwd><kwd>Oxidative stress</kwd><kwd>Epignetic variation</kwd><kwd>Molecular markers</kwd><kwd>Crop improvement</kwd></kwd-group><custom-meta-group><custom-meta><meta-name>issue-copyright-statement</meta-name><meta-value>© The Author(s) 2016</meta-value></custom-meta></custom-meta-group></article-meta></front><body><sec id="Sec1"><title>Introduction</title><p>Plant tissue culture techniques proffer a substitute method of vegetative propagation of horticultural crops (Krishna et al. <xref ref-type="bibr" rid="CR105">2005</xref>; Alizadeh et al. <xref ref-type="bibr" rid="CR5">2010</xref>). Clonal propagation through tissue culture (popularly known as micropropagation) can be realized relatively rapidly within a small space (Krishna et al. <xref ref-type="bibr" rid="CR106">2008</xref>; Eftekhari et al. <xref ref-type="bibr" rid="CR46">2012</xref>). The uniformity of individual plants within a clone population is a major advantage of clonal cultivars in commercial production (Krishna and Singh <xref ref-type="bibr" rid="CR104">2013</xref>). However, genetic variations do occur in undifferentiated cells, isolated protoplasts, calli, tissues and morphological traits of in vitro raised plants (Bairu et al. <xref ref-type="bibr" rid="CR11">2011</xref>; Currais et al. <xref ref-type="bibr" rid="CR32">2013</xref>). In 1981, Larkin and Scowkraft coined a general term “somaclonal variation” for plant variants derived from any form of cell or tissue cultures.</p><p>At present, micropropagated plants, in various crops, such as strawberry, papaya, banana, grapes, pineapple, citrus, tomato, cucumber, watermelon, rhododendron, orchids, etc., are preferred over plants propagated through conventional means. However, ever since the first formal report of morphological variants in sugarcane plants produced in vitro in 1971 (Heinze and Mee <xref ref-type="bibr" rid="CR68">1971</xref>), several instances of somaclonal variations have been reported in different horticultural crops. The notable example could be banana in which occurrence of off-types from tissue cultured plantlets ranged from 6 to 38 % in Cavendish cultivars (Sahijram et al. <xref ref-type="bibr" rid="CR177">2003</xref>); however, it could be as high as 90 % (Smith <xref ref-type="bibr" rid="CR192">1988</xref>). From the point of commercial micropropagation, variation of any kind, in particular, genetic variations may be considered obstructive and worthless; since, such variations may lead to loss of genetic fidelity. However, plant cell and tissue cultures render increased genetic variability comparatively faster and without applying a sophisticated technology. This technology holds ample scope in crop improvement of horticultural crops, which are largely propagated vegetatively, partly, due to reasons like longer juvenile phase as in perennial fruit crops, occasional inbreeding depression, self and cross incompatibility, narrow genetic base especially in ornamentals, etc. Further, somaclonal variations require less space and time for screening of desirable traits in vitro unlike cross seedlings of perennial crops, which require a great deal of land area and time. Somaclones may itself have numerous applications in plant breeding and genetic improvements and recovery of such novel variants can be enhanced by applying suitable in vitro selection pressure (Jain <xref ref-type="bibr" rid="CR85">2001</xref>; Lestari <xref ref-type="bibr" rid="CR114">2006</xref>).</p></sec><sec id="Sec2"><title>Sources of variations detected in plant tissue culture</title><p>Tissue culture is an efficient method of clonal propagation; however, the resulting regenerants often has a number of somaclonal variations (Larkin and Scowcroft <xref ref-type="bibr" rid="CR112">1981</xref>). These somaclonal variations are mainly caused by newly generated mutations arising from tissue culture process (Sato et al. <xref ref-type="bibr" rid="CR183">2011b</xref>). The triggers of mutations in tissue culture had been attributed to numerous stress factors, including wounding, exposure to sterilants during sterilization, tissue being incomplete (protoplasts as an extreme example), imbalances of media components such as high concentration of plant growth regulators (auxin and cytokinins), sugar from the nutrient medium as a replacement of photosynthesis in the leaves, lighting conditions, the disturbed relationship between high humidity and transpiration (Joyce et al. <xref ref-type="bibr" rid="CR91">2003</xref>; Sato et al. <xref ref-type="bibr" rid="CR183">2011b</xref>; Smulders and de Klerk <xref ref-type="bibr" rid="CR193">2011</xref>).</p><p>Much of the variability expressed in micropropagated plants may be the result of, or related to, oxidative stress damage inflicted upon plant tissues during in vitro culture (Cassells and Curry <xref ref-type="bibr" rid="CR27">2001</xref>; Tanurdzic et al. <xref ref-type="bibr" rid="CR198">2008</xref>; Nivas and DSouza <xref ref-type="bibr" rid="CR152">2014</xref>). Oxidative stress results in elevated levels of pro-oxidants or reactive oxygen species (ROS) such as superoxide, hydrogen peroxide, hydroxyl, peroxyl and alkoxyl radicals. These ROS may involve in altered hyper- and hypo-methylation of DNA (Wacksman <xref ref-type="bibr" rid="CR208">1997</xref>); changes in chromosome number from polyploidy to aneuploidy, chromosome strand breakage, chromosome rearrangements, and DNA base deletions and substitutions (Czene and Harms-Ringdahl <xref ref-type="bibr" rid="CR33">1995</xref>), which in turn may lead to mutations in plant cells in vitro (Fig. <xref rid="Fig1" ref-type="fig">1</xref>). Somaclonal variation shows a similar spectrum of genetic variation to induced mutation as both of them result in qualitatively analogous gamut of DNA changes (Cassells et al. <xref ref-type="bibr" rid="CR28">1998</xref>). Different factors affect the frequency of development of somaclones under in vitro conditions.<fig id="Fig1"><label>Fig. 1</label><caption><p>Mechanism of somaclonal variation in micropropagated plants as a result of oxidative burst upon in vitro culture</p></caption><graphic xlink:href="13205_2016_389_Fig1_HTML" id="MO1"></graphic></fig></p><sec id="Sec3"><title>Explant/explant source</title><p>Differences in both the frequency and nature of somaclonal variation may occur when regeneration is achieved from different tissue sources (Sahijram et al. <xref ref-type="bibr" rid="CR177">2003</xref>). Highly differentiated tissues such as roots, leaves, and stems generally produce more variations than explants with pre-existing meristems, such as axillary buds and shoot tips (Duncan <xref ref-type="bibr" rid="CR44">1997</xref>). In general, the older and/or the more specialized the tissue is used for regeneration, the greater the chances that variation will be recovered in the regenerated plants (Table <xref rid="Tab1" ref-type="table">1</xref>) as under such conditions, adventitious shoot regeneration (shoot organogenesis) takes place from atypical points of origin directly or indirectly through a callus stage (e.g., from leaves, petioles, shoot internodes, root segments, anthers, hypocotyls, cotyledons, etc.; Pijut et al. <xref ref-type="bibr" rid="CR166">2012</xref>). Somaclonal variation can also arise from somatic mutations already present in the donor plant, i.e., presence of chimera in explants (Karp <xref ref-type="bibr" rid="CR96">1994</xref>).<table-wrap id="Tab1"><label>Table 1 </label><caption><p>Occurrence of somaclonal variations as affected by the choice of explants</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="left">S. no.</th><th align="left">Crop species</th><th align="left">Explants/explants source</th><th align="left">Presence or absence of somaclonal variations (+/−)</th><th align="left">References</th></tr></thead><tbody><tr><td align="left">1</td><td align="left">African violet (<italic>Saintpaulia</italic> sp.)</td><td align="left">Leaf segments</td><td align="left">+</td><td align="left">Matsuda et al. (<xref ref-type="bibr" rid="CR128">2014</xref>)</td></tr><tr><td align="left">2</td><td align="left">Almond (<italic>Prunus dulcis</italic>)</td><td align="left">Axillary branching</td><td align="left">−</td><td align="left">Martins et al. (<xref ref-type="bibr" rid="CR124">2004</xref>)</td></tr><tr><td align="left" rowspan="3">3</td><td align="left">Chimeric ‘Maricongo’ banana</td><td align="left">Vegetative and floral axis tip</td><td align="left">+</td><td align="left">Krikorian et al. (<xref ref-type="bibr" rid="CR102">1993</xref>)</td></tr><tr><td align="left">Cavendish group of bananas (<italic>Musa</italic> sp.)</td><td align="left">Chimeric shoot tip</td><td align="left">+</td><td align="left">Israeli et al. (<xref ref-type="bibr" rid="CR82">1995</xref>)</td></tr><tr><td align="left">Banana cv. Martaman</td><td align="left">Shoot tip</td><td align="left">−</td><td align="left">Ray et al. (<xref ref-type="bibr" rid="CR173">2006</xref>)</td></tr><tr><td align="left" rowspan="2">4</td><td align="left" rowspan="2">Brinjal (<italic>Solanum melongena</italic>)</td><td align="left">Hypocotyl</td><td align="left">−</td><td align="left">Mallaya and Ravishankar (<xref ref-type="bibr" rid="CR121">2013</xref>)</td></tr><tr><td align="left">Callus induction on leaves, nodes and intermodal explants</td><td align="left">+</td><td align="left">Naseer and Mahmood (<xref ref-type="bibr" rid="CR145">2014</xref>)</td></tr><tr><td align="left">5</td><td align="left">Chrysanthemum (<italic>Dendranthema grandiflora</italic>)</td><td align="left">Callus from leaves and internodes</td><td align="left">+</td><td align="left">Miler and Zalewska (<xref ref-type="bibr" rid="CR132">2014</xref>)</td></tr><tr><td align="left">6</td><td align="left">European violet (<italic>Viola uliginosa</italic> Besser)</td><td align="left">Leaf and petiole fragments</td><td align="left">+</td><td align="left">Slazak et al. (<xref ref-type="bibr" rid="CR191">2015</xref>)</td></tr><tr><td align="left">7</td><td align="left">Gerbera (<italic>Gerbera</italic><italic>jamesonii</italic> Bolus)</td><td align="left">Capitulum</td><td align="left">−</td><td align="left">Bhatia et al. (<xref ref-type="bibr" rid="CR20">2009</xref>, <xref ref-type="bibr" rid="CR21">2011</xref>)</td></tr><tr><td align="left">8</td><td align="left">Gloxinia</td><td align="left">Leaf explants</td><td align="left">+</td><td align="left">Hu and Xu (<xref ref-type="bibr" rid="CR77">2010</xref>)</td></tr><tr><td align="left">9</td><td align="left"><italic>Hedychium coronarium</italic> Koen.</td><td align="left">Axillary bud explants</td><td align="left">−</td><td align="left">Parida et al. (<xref ref-type="bibr" rid="CR157">2013</xref>)</td></tr><tr><td align="left">10</td><td align="left">Hop (<italic>Humulus lupulus</italic> L.)</td><td align="left">Meristem tissue</td><td align="left">−</td><td align="left">Patzak (<xref ref-type="bibr" rid="CR160">2003</xref>)</td></tr><tr><td align="left">11</td><td align="left"><italic>Kaempferia galanga</italic></td><td align="left">Buds of rhizomes</td><td align="left">−</td><td align="left">Mohanty et al. (<xref ref-type="bibr" rid="CR136">2011</xref>)</td></tr><tr><td align="left">12</td><td align="left">Kiwifruit (<italic>Actinidia deliciosa</italic> (Chev.) Liang and Ferguson) cv. ‘Tomuri’</td><td align="left">Leaf blades and petioles</td><td align="left">+</td><td align="left">Prado et al. (<xref ref-type="bibr" rid="CR168">2007</xref>)</td></tr><tr><td align="left" rowspan="3">13</td><td align="left" rowspan="3">Oil palm (<italic>Elaeis guineensis</italic> Jacq.)</td><td align="left">Mature zygotic embryos</td><td align="left">+</td><td align="left">Rival et al. (<xref ref-type="bibr" rid="CR175">2013</xref>)</td></tr><tr><td align="left">Immature zygotic embryo</td><td align="left">+</td><td align="left">Sanputawong and Te-chato (<xref ref-type="bibr" rid="CR180">2011</xref>)</td></tr><tr><td align="left">Immature leaves</td><td align="left">+</td><td align="left">Lucia et al. (<xref ref-type="bibr" rid="CR120">2011</xref>)</td></tr><tr><td align="left">14</td><td align="left">Papaya (<italic>Carica papaya</italic> L.)</td><td align="left">Axillary shoot tips underwent cryopreservation</td><td align="left">+</td><td align="left">Kaity et al. (<xref ref-type="bibr" rid="CR93">2009</xref>)</td></tr><tr><td align="left">15</td><td align="left">Patchouli (<italic>Pogostemon patchouli</italic>)</td><td align="left">Callus induction on internodal and leaf explants</td><td align="left">+</td><td align="left">Ravindra et al. (<xref ref-type="bibr" rid="CR172">2012</xref>)</td></tr><tr><td align="left" rowspan="2">16</td><td align="left" rowspan="2">Potato (<italic>Solanum tuberosum</italic>)</td><td align="left">Callus cultures of stem explant</td><td align="left">+</td><td align="left">Thieme and Griess (<xref ref-type="bibr" rid="CR199">2005</xref>)</td></tr><tr><td align="left">Callus induction via fresh sprouts</td><td align="left">+</td><td align="left">Munir et al. (<xref ref-type="bibr" rid="CR142">2011</xref>)</td></tr><tr><td align="left">17</td><td align="left">Sweet cherry (<italic>Prunus avium</italic>)</td><td align="left">Shoot apical portions</td><td align="left">+</td><td align="left">Piagnani and Chiozzotto (<xref ref-type="bibr" rid="CR165">2010</xref>)</td></tr><tr><td align="left">18</td><td align="left">Rootstock Mr.S 2/5, selected from a half-sib progeny from <italic>Prunus cerasifera</italic> Erhr</td><td align="left">Leaf</td><td align="left">+</td><td align="left">Muleo et al. (<xref ref-type="bibr" rid="CR141">2006</xref>)</td></tr><tr><td align="left">19</td><td align="left"><italic>Swertia chirayita</italic></td><td align="left">Axillary multiplication</td><td align="left">−</td><td align="left">Joshi and Dhawan (<xref ref-type="bibr" rid="CR90">2007</xref>)</td></tr><tr><td align="left" rowspan="3">20</td><td align="left" rowspan="3">Turmeric (<italic>Curcuma longa</italic> L.)</td><td align="left">Latent axillary buds of rhizome</td><td align="left">−</td><td align="left">Nayak et al. (<xref ref-type="bibr" rid="CR149">2010</xref>)</td></tr><tr><td align="left">Axillary buds of unsprouted rhizome</td><td align="left">−</td><td align="left">Panda et al. (<xref ref-type="bibr" rid="CR156">2007</xref>)</td></tr><tr><td align="left">Callus cultures established from rhizome segments</td><td align="left">+</td><td align="left">Kar et al. (<xref ref-type="bibr" rid="CR94">2014</xref>)</td></tr><tr><td align="left">21</td><td align="left"><italic>Vitis</italic> spp.</td><td align="left">Nodal segment</td><td align="left">−</td><td align="left">Alizadeh et al. (<xref ref-type="bibr" rid="CR4">2008</xref>)</td></tr></tbody></table></table-wrap></p></sec><sec id="Sec4"><title>Mode of regeneration</title><p>Both culture initiation and subsequent subculture expose explants to oxidative stress (Krishna et al. <xref ref-type="bibr" rid="CR106">2008</xref>), which may result in mutations (Cassells and Curry <xref ref-type="bibr" rid="CR27">2001</xref>). It seems evident that ‘extreme’ procedures such as protoplast culture and also callus formation impose stress (Smulders and de Klerk <xref ref-type="bibr" rid="CR193">2011</xref>). Magnitude of this stress depends on the tissue culture technique. Therefore, the production of plants via axillary branching does not normally result in the production of variants, while cultures that go through a callus phase are the ones that theoretically promote a higher mutation rate (Zayova et al. <xref ref-type="bibr" rid="CR213">2010</xref>).</p><p>Investigations indicate more chromosome variability in the callus phase than in adventitious shoots (Saravanan et al. <xref ref-type="bibr" rid="CR181">2011</xref>), indicating a loss of competence in the more seriously disturbed genomes. This could be explained by the different grade of disturbance with which the cells are confronted. In the first case, cells follow a pattern of division which is the normal one in the developing plant. On the other hand, callus formation implies a dedifferentiation phase followed by uncontrolled cell divisions (Vázquez <xref ref-type="bibr" rid="CR203">2001</xref>). Some types of tissue culture mimic, in some aspects, other stressful situations as, for example, protoplast preparation in which cell wall degradation resembles the infective process of some pathogens. Therefore, the type and magnitude of the stress imposed on cultured cells varies according to the technique used. In contrast to popular belief that the growth of unorganized callus is necessary for induction of genetic variation, variability could be noticed in plants regenerated from explants adventitiously (Farahani et al. <xref ref-type="bibr" rid="CR50">2011</xref>; Bhojwani and Dantu <xref ref-type="bibr" rid="CR22">2013</xref>).</p><p>Sometimes for regeneration under in vitro conditions, somatic embryogenesis is the preferred pathway for generating propagules. It has been suggested that regeneration via embryogenesis has better chance of obtaining genetically uniform plants than through organogenic differentiation (Vázquez <xref ref-type="bibr" rid="CR203">2001</xref>). This is so, because DNA in the initial stages of development in somatic embryogenesis contains lower levels of methylation than in the later stages (Sahijram et al. <xref ref-type="bibr" rid="CR177">2003</xref>). Variation in in vitro cultures raised through somatic embryogenesis has been reported in several horticultural crops like hazel nut (Diaz-Sala et al. <xref ref-type="bibr" rid="CR41">1995</xref>), <italic>Citrus paradisi</italic> (Hao et al. <xref ref-type="bibr" rid="CR65">2004</xref>), oil palm (Jaligot et al. <xref ref-type="bibr" rid="CR86">2004</xref>), rose (Xu et al. <xref ref-type="bibr" rid="CR210">2004</xref>), potato (Sharma et al. <xref ref-type="bibr" rid="CR186">2007</xref>), grapevine (Schellenbaum et al. <xref ref-type="bibr" rid="CR185">2008</xref>), coffee (Menéndez-Yuffá et al. <xref ref-type="bibr" rid="CR129">2010</xref>), olive (Leva et al. <xref ref-type="bibr" rid="CR115">2012</xref>), tamarillo (Currais et al. <xref ref-type="bibr" rid="CR32">2013</xref>) and brinjal (Naseer and Mahmood <xref ref-type="bibr" rid="CR145">2014</xref>).</p></sec><sec id="Sec5"><title>Effect of length of culture period and number of subculture cycles</title><p>The longer a culture is maintained in vitro, the greater the somaclonal variation is (Kuznetsova et al. <xref ref-type="bibr" rid="CR111">2006</xref>; Gao et al. <xref ref-type="bibr" rid="CR52">2010</xref>; Farahani et al. <xref ref-type="bibr" rid="CR50">2011</xref>; Jevremović et al. <xref ref-type="bibr" rid="CR89">2012</xref>; Sun et al. <xref ref-type="bibr" rid="CR195">2013</xref>). Variant karyotypes are found to amass with increasing age of callus and as a result the chances of variant plants produced during successive subculture also increases, in general (Zayova et al. <xref ref-type="bibr" rid="CR213">2010</xref>). Furthermore, the rapid multiplication of a tissue, during micropropagation, may affect its genetic stability. Khan et al. (<xref ref-type="bibr" rid="CR99">2011</xref>) reported that after the eighth subculture, the number of somaclonal variants increased with a simultaneous decrease in the multiplication rate of propagules in banana.</p><p>Similarly, Clarindo et al. (<xref ref-type="bibr" rid="CR31">2012</xref>) suggested a limit of less than 4 months storage of coffee cell aggregate suspensions for true-to-type mass propagation as ploidy instability was noticed in long-term in vitro culture. Similarly when Farahani et al. (<xref ref-type="bibr" rid="CR50">2011</xref>) raised olive cultivars, under in vitro conditions, through internode cuttings, significant difference was observed in morphological characters among the regenerated plants after seventh subculture, which was later confirmed by RAPD analysis. However, C-value analysis showed that no significant change has occurred during subculturing in both olive genotypes. This indicates that the genetic changes accompanied by somaclonal variation could be due to the changes in the nucleotide content of the genome, probably, owing to mutations (insertions/deletions) and not due to quantitative changes.</p><p>Not only the number of subculture but their duration also contributes to enhancing the rate of somaclonal variations, especially cell suspension and callus cultures (Bairu et al. <xref ref-type="bibr" rid="CR10">2006</xref>; Sun et al. <xref ref-type="bibr" rid="CR195">2013</xref>). Studies have shown that somaclonal variation is more apparent in plants regenerated from long-term cultures (Etienne and Bertrand <xref ref-type="bibr" rid="CR48">2003</xref>). Rival et al. (<xref ref-type="bibr" rid="CR175">2013</xref>) noticed that in vitro proliferation induces DNA hypermethylation in a time-dependent fashion and changes in DNA methylation is involved in modulating the expression of embryogenic capacity of oil palm during tissue culture.</p></sec><sec id="Sec6"><title>Culture environment</title><p>External factors like growth regulators, temperature, light, osmolarity and agitation rate of the culture medium are known to influence the cell cycle in vivo in plants, considerably, which indicates that inadequate control of cell cycle in vitro is one of the causes of somaclonal variation (Karp <xref ref-type="bibr" rid="CR96">1994</xref>; Nwauzoma and Jaja <xref ref-type="bibr" rid="CR153">2013</xref>). Normal cell cycle controls, which prevent cell division before the completion of DNA replication, are presumed to be disrupted by tissue culture, resulting in chromosomal breakage (Phillips et al. <xref ref-type="bibr" rid="CR164">1994</xref>). Chromosome breakage and its consequences (deletions, duplications, inversions, and translocations) cause aberrations in vitro (Duncan <xref ref-type="bibr" rid="CR44">1997</xref>). Plant growth regulators can affect the rate of somaclonal variation both directly and indirectly by increasing the multiplication rate and inducing adventitious shoots (Gao et al. <xref ref-type="bibr" rid="CR52">2010</xref>). According to D’Amato (<xref ref-type="bibr" rid="CR34">1985</xref>), it cannot be excluded that some plant growth regulators (PGRs) at certain concentrations or in combination with other growth regulators and/or particular constituents of a culture medium, may act as mutagens.</p><p>Several growth regulators, such as 2,4-dichlorophenoxy acetic acid (2,4-D), naphthalene acetic acid (NAA) and BAP (6-benzylaminopurine), synthetic phenylurea derivatives (4-CPPU, PBU and 2,3-MDPU) have been most frequently considered to be responsible for genetic variability (Siragusa et al. <xref ref-type="bibr" rid="CR189">2007</xref>; Sun et al. <xref ref-type="bibr" rid="CR195">2013</xref>; Sales and Butardo <xref ref-type="bibr" rid="CR179">2014</xref>).</p><p>Prolonged cultivation in medium containing 2,4-D influences higher DNA ploidy levels in callus cells (da Silva and Carvalho <xref ref-type="bibr" rid="CR35">2014</xref>). In their experiment with banana, Sales and Butardo (<xref ref-type="bibr" rid="CR179">2014</xref>) observed that addition of synthetic auxin 2,4-D in culture medium led to high level of methylation events, particularly, cytosine methylation either at the internal or external cytosine end, which largely resulted in variations in tissue cultured plants. Alteration in genomic DNA methylation rate is being attributed for the development of ‘mantled’ somaclonal variant in oil palm (Eeuwens et al. <xref ref-type="bibr" rid="CR45">2002</xref>; Jaligot et al. <xref ref-type="bibr" rid="CR87">2011</xref>). Similarly, Arnhold-Schmitt (<xref ref-type="bibr" rid="CR9">1993</xref>) observed that indole-3-acetic acid (IAA) and inositol in the growth medium induced DNA rearrangements and methylation changes in carrot (<italic>Daucus carota</italic>) callus cultures. Matsuda et al. (<xref ref-type="bibr" rid="CR128">2014</xref>) observed that percentage of somaclonal variations dramatically increased when PGRs (0.5 ppm BA and 0.1 ppm NAA) were added to the medium inoculated with leaf/leaf segments explants of African violet.</p><p>Kinetin has been shown to cause extensive hypomethylation of DNA in proliferating cultures of carrot root explants within 2 weeks (Arnhold-Schmitt <xref ref-type="bibr" rid="CR9">1993</xref>), and auxins, including NAA, have the opposite effect and cause hypermethylation (LoSchiavo et al. <xref ref-type="bibr" rid="CR119">1989</xref>). Moreover, there is evidence that differential expression in chromatin remodeling genes and histone methylation genes happens during tissue culture, which leads to disruption in the methylation pathway in a non-specific manner and hypo/hypermethylation patterns of DNA induced in tissue culture. This can be stabilized and transmitted to plants regenerated from these cultures (Shearman et al. <xref ref-type="bibr" rid="CR187">2013</xref>). Not only the concentration, but also the ratio of different growth regulators affects the occurrence of variations in vitro. Eeuwens et al. (<xref ref-type="bibr" rid="CR45">2002</xref>) observed that, in general, a relatively high auxin/cytokinin ratio resulted in the lowest incidence of variant ‘mantled’ flowering in oil palm, while using media supplemented with relatively high cytokinins/auxin ratio resulted in a high incidence of mantled flowering. The role of cytokinin was further confirmed by Ooi et al. (<xref ref-type="bibr" rid="CR154">2013</xref>), who noticed that the mantled inflorescences of oil palm contained higher levels of cytokinins like isopentenyladenine 9-glucoside and lower levels of trans-zeatin 9-glucoside, dihydrozeatin riboside, and dihydrozeatin riboside 5′-monophosphate compared with normal inflorescences.</p></sec><sec id="Sec7"><title>Genotype and ploidy</title><p>Though, the in vitro morphogenesis seems to be highly dependent on plant growth regulators and media used for culture, it is again genotype specific (Alizadeh et al. <xref ref-type="bibr" rid="CR5">2010</xref>; Eftekhari et al. <xref ref-type="bibr" rid="CR46">2012</xref>). Among factors affecting somaclonal variation, plant genotype is probably the most important determinant of variation (Shen et al. <xref ref-type="bibr" rid="CR188">2007</xref>; Tican et al. <xref ref-type="bibr" rid="CR200">2008</xref>; Nwauzoma and Jaja <xref ref-type="bibr" rid="CR153">2013</xref>). Earlier, Eeuwens et al. (<xref ref-type="bibr" rid="CR45">2002</xref>) characterized oil palm clones as low/moderate risk and high risk with regard to ‘mantle’ flowering (wherein anther primordia in both male and female flowers turn into fleshy supplementary carpels), on the basis of terminal inflorescence data generated under in vitro conditions. Clones classified as high risk at the outset gave a significantly higher incidence of mantled flowering in the field than low/medium risk clones, confirming that data on terminal inflorescences produced in vitro allows effective screening of material with regard to the risk of mantled flowering. It is likely that this result from a combination of differences in genotype and differences in epigenetically inherited changes are induced during the pre-embryogenic stages of the culture process, i.e., callus initiation and maintenance.</p></sec></sec><sec id="Sec8"><title>Identification of variation in tissue culture</title><p>Both genetic and epigenetic alterations are associated with in vitro propagation, which may have phenotypic consequences, and are collectively called somaclonal variation (Larkin and Scowcroft <xref ref-type="bibr" rid="CR112">1981</xref>; Guo et al. <xref ref-type="bibr" rid="CR59">2007</xref>). As a result, somaclonal variation is characterized by the intricacy of the changes, which are exhibited at various levels, including phenotypic, cytological, biochemical and genetic/epigenetic (Kaeppler et al. <xref ref-type="bibr" rid="CR92">2000</xref>). Therefore, the strategy for the detection of somaclones should be based on such manifestations.</p><p>A wide variety of tools are available for the detection and characterization of somaclonal variants which are primarily based on the differences in morphological traits (Pérez et al. <xref ref-type="bibr" rid="CR161">2009</xref>, <xref ref-type="bibr" rid="CR162">2011</xref>; Nhut et al. <xref ref-type="bibr" rid="CR151">2013</xref>), cytogenetical analysis for the determination of numerical and structural variation in the chromosomes (Clarindo et al. <xref ref-type="bibr" rid="CR31">2012</xref>; Currais et al. <xref ref-type="bibr" rid="CR32">2013</xref>; Abreu et al. <xref ref-type="bibr" rid="CR1">2014</xref>), biochemical (Vujovic et al. <xref ref-type="bibr" rid="CR207">2010</xref>; Kar et al. <xref ref-type="bibr" rid="CR94">2014</xref>), molecular DNA markers (Krishna and Singh <xref ref-type="bibr" rid="CR103">2007</xref>; Pathak and Dhawan <xref ref-type="bibr" rid="CR158">2012</xref>; Hossain et al. <xref ref-type="bibr" rid="CR76">2013</xref>; Bello-Bello et al. <xref ref-type="bibr" rid="CR15">2014</xref>) or their combinations (Horáček et al. <xref ref-type="bibr" rid="CR74">2013</xref>; Dey et al. <xref ref-type="bibr" rid="CR39">2015</xref>; Stanišić et al. <xref ref-type="bibr" rid="CR194">2015</xref>). The best test for assessing somaclonal variation is to fruit out the plants and conduct an extensive horticultural evaluation, which is unfortunately a long-term endeavor with woody fruit crops, particularly (Grosser et al. <xref ref-type="bibr" rid="CR56">1996</xref>). Every tool has its own advantages and limitations in assessment of the variations (Table <xref rid="Tab2" ref-type="table">2</xref>), which govern their use for restricted or large-scale application. The choice of technique for any given application depends upon the material used and the nature of the question being addressed (Karp <xref ref-type="bibr" rid="CR98">2000</xref>).<table-wrap id="Tab2"><label>Table 2</label><caption><p>Strengths and weaknesses of different marker systems for the assessment of clonal fidelity</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="left">Advantages</th><th align="left">Disadvantages</th></tr></thead><tbody><tr><td align="left" colspan="2"><bold>Morphological traits</bold></td></tr><tr><td align="left">Visual differentiation</td><td align="left">Sensitive to ontogenic changes and other environmental factors</td></tr><tr><td align="left">Does not require any laboratory facility</td><td align="left">Limited in numbers</td></tr><tr><td align="left">Suitable for preliminary detection</td><td align="left">Time-consuming</td></tr><tr><td align="left" colspan="2"><bold>Cytological markers (flow-cytometry)</bold></td></tr><tr><td align="left">Sample preparation and analysis is convenient and rapid in case of in flow-cytometry</td><td align="left">Cytosolic compounds may interfere with quantitative DNA staining in flow-cytometry</td></tr><tr><td align="left">Rapid and efficient method for routine large-scale studies of ploidy level</td><td align="left">Absence of a set of internationally agreed DNA reference standards in case of in flow-cytometry</td></tr><tr><td align="left">Unfailing detection of even the smallest modifications in chromosome number</td><td align="left">Time-consuming chromosome counting</td></tr><tr><td align="left" colspan="2"><bold>Isozyme markers</bold></td></tr><tr><td align="left">Codominant expression</td><td align="left">Sensitive to ontogenic changes and other environmental factors</td></tr><tr><td align="left">Ease of performance</td><td align="left">Limited in numbers<break></break>Not all of these reagent systems work efficiently with all plant species<break></break>Tissue-specific expression</td></tr><tr><td align="left" colspan="2"><bold>DNA markers</bold></td></tr><tr><td align="left">Codominant expression<break></break>Any source DNA can be used for the analysis<break></break>Phenotypically neutral<break></break>Not sensitive to ontogenic changes and other environmental factors<break></break>Capability to detect culture-induced variation both at the DNA sequence and methylation pattern levels</td><td align="left">RAPD markers are dominant and do not permit the scoring of heterozygous individuals. Besides, they exclusively identify sequence changes<break></break>Possible non-homology of similar sized fragments as ISSR is a multilocus technique<break></break>Disadvantages of AFLPs include the need for purified, high molecular weight DNA, the dominance of alleles and the possible non-homology of comigrating fragments belonging to different loci<break></break>Involvement of high development costs in SSR markers if adequate primer sequences for the crop species of interest are unavailable. Further, mutations in the primer annealing sites may result in the occurrence of null alleles (no amplification of the intended PCR product), which may lead to errors in scoring</td></tr></tbody></table></table-wrap></p></sec><sec id="Sec9"><title>Molecular basis of somaclonal variation</title><p>How a single plant genotype can result in a variety of phenotypic outcomes under the same in vitro culture conditions is still far from being completely understood. Several bases for somaclonal variation have been proposed, which include changes in chromosome number (Mujib et al. <xref ref-type="bibr" rid="CR140">2007</xref>; Leva et al. <xref ref-type="bibr" rid="CR115">2012</xref>), point mutations (D’Amato <xref ref-type="bibr" rid="CR34">1985</xref>; Ngezahayo et al. <xref ref-type="bibr" rid="CR150">2007</xref>), somatic crossing over and sister chromatid exchange (Duncan <xref ref-type="bibr" rid="CR44">1997</xref>; Bairu et al. <xref ref-type="bibr" rid="CR11">2011</xref>), chromosome breakage and rearrangement (Czene and Harms-Ringdahl <xref ref-type="bibr" rid="CR33">1995</xref>; Alvarez et al. <xref ref-type="bibr" rid="CR6">2010</xref>), somatic gene rearrangement, DNA amplification (Karp <xref ref-type="bibr" rid="CR97">1995</xref>; Tiwari et al. <xref ref-type="bibr" rid="CR201">2013</xref>), changes in organelle DNA (Cassells and Curry <xref ref-type="bibr" rid="CR27">2001</xref>; Bartoszewski et al. <xref ref-type="bibr" rid="CR13">2007</xref>), DNA methylation (Guo et al. <xref ref-type="bibr" rid="CR59">2007</xref>; Linacero et al. <xref ref-type="bibr" rid="CR117">2011</xref>), epigenetic variation (Kaeppler et al. <xref ref-type="bibr" rid="CR92">2000</xref>; Guo et al. <xref ref-type="bibr" rid="CR58">2006</xref>; Smulders and de Klerk <xref ref-type="bibr" rid="CR193">2011</xref>), histone modifications and RNA interference (Miguel and Marum <xref ref-type="bibr" rid="CR131">2011</xref>), segregation of pre-existing chimeral tissue (Brar and Jain <xref ref-type="bibr" rid="CR25">1998</xref>; Vázquez <xref ref-type="bibr" rid="CR203">2001</xref>; Ravindra et al. <xref ref-type="bibr" rid="CR172">2012</xref>; Nwauzoma and Jaja <xref ref-type="bibr" rid="CR153">2013</xref>) and insertion or excision of transposable elements (Gupta <xref ref-type="bibr" rid="CR60">1998</xref>; Sato et al. <xref ref-type="bibr" rid="CR183">2011b</xref>). In particular, transposable elements are one of the causes of genetic rearrangements in in vitro culture (Hirochika et al. <xref ref-type="bibr" rid="CR72">1996</xref>; Sato et al. <xref ref-type="bibr" rid="CR182">2011a</xref>).</p><p>Tissue culture is reported to activate silent transposable elements, resulting in somaclonal variations. Insertions of transposable elements and retrotransposons can function as insertional mutagens of plant genomes, whereas widespread activation may result in a wide gamut of chromosomal rearrangements (Tanurdzic et al. <xref ref-type="bibr" rid="CR198">2008</xref>). In turn, these rearrangements can lead to misregulation of genes, aneuploidy and new transposon insertions (Smulders and de Klerk <xref ref-type="bibr" rid="CR193">2011</xref>).</p><p>However, many aspects of the mechanisms, which result in somaclonal variations, remain undefined. It is therefore, inevitable to explore the genome-wide change through sequencing of whole-genome of the concerned crop. Next-generation sequencing technology has enabled the whole-genome sequencing of individual plants (Miyao et al. <xref ref-type="bibr" rid="CR134">2012</xref>). A new generation of sequencing technologies, from Illumina/Solexa, ABI/SOLiD, 454/Roche, and Helicos, has provided unprecedented opportunities for high-throughput functional genomic research (Morozova and Marra <xref ref-type="bibr" rid="CR138">2008</xref>; Metzker <xref ref-type="bibr" rid="CR130">2010</xref>).</p></sec><sec id="Sec10"><title>Somaclonal variations vis-à-vis crop improvement</title><p>Genetic variation is an essential component of any conventional crop breeding program. The typical crop improvement cycle takes 10–15 years to complete and includes germplasm manipulations, genotype selection and stabilization, variety testing, variety increase, proprietary protection and crop production stages. Plant tissue culture is an enabling technology from which many novel tools have been developed to assist plant breeders (Karp <xref ref-type="bibr" rid="CR95">1992</xref>; Mathur <xref ref-type="bibr" rid="CR126">2013</xref>). Tissue culture-induced somaclonal variation is akin to variations induced with chemical and physical mutagens (Jain <xref ref-type="bibr" rid="CR85">2001</xref>) and offers an opportunity to uncover natural variability for their potential exploitation in crop improvement.</p><p>Like any other technology, in vitro induced somaclonal variation has its own merits and demerits, like the two sides of the same coin.</p><sec id="Sec11"><title>Advantages</title><p>The advantages comprise: (1) it is cheaper than other methods of genetic manipulation and does not require ‘containment’ procedures. (2) Tissue culture systems are available for more plant species than can be manipulated by somatic hybridization and transformation at the present time. (3) It is not necessary to have identified the genetic basis of the trait, or indeed, in the case of transformation, to have isolated and cloned it. (4) Novel variants have been reported among somaclones, and evidences indicate that both the frequency and distribution of genetic recombination events can be altered by passage though tissue culture. This implies that variation may be generated from different locations of the genome than those, which are accessible to conventional and mutation breeding (Karp <xref ref-type="bibr" rid="CR95">1992</xref>). (5) There is no possibility of obtaining chimeric expression if somaclones are raised through cell culture (Evans <xref ref-type="bibr" rid="CR49">1989</xref>).</p><p>Somaclonal variation has been most successful in crops with limited genetic systems (e.g., apomicts, vegetative reproducers) and/or narrow genetic bases. In ornamental plants, for instance, the exploitation of in vitro-generated variability has become part of the routine breeding practice of many commercial enterprises.</p></sec><sec id="Sec12"><title>Disadvantages</title><p>One of the serious limitations of somaclonal variation which makes it comparatively difficult to use is that, despite the identification of factors affecting the variation response of a given plant species, it is still not possible to predict the outcome of a somaclonal program (Karp <xref ref-type="bibr" rid="CR95">1992</xref>) as it is random and lacks reproducibility. Further, as a large number of genetic changes are based on point mutations or chromosome rearrangements, most R<sub>1</sub> segregate. Therefore for quantitative traits such as yield, it is virtually impossible to select individuals with improvements in the R<sub>1</sub> generation. Though techniques for selection of somaclones resistant to various biotic and abiotic stresses had been worked out in many horticultural crops, unfortunately, no in vitro selection methods exist for complicated traits such as yield, soluble solids, sweetness, texture or shelf life (Evans <xref ref-type="bibr" rid="CR49">1989</xref>).</p><p>Somaclonal variation can become a part of plant breeding provided they are heritable and genetically stable. Only a limited numbers of promising varieties so far had been released using somaclonal variations. This is perhaps due to the lack of interaction between plant breeders and tissue culture scientists, and non-predictability of somaclones (Jain <xref ref-type="bibr" rid="CR85">2001</xref>). Further, though the new varieties have been produced by somaclonal variation, in a large number of cases improved variants have not been selected due to (1) the variations were all negative; (2) positive changes were also altered in negative ways; (3) the changes were not novel, or (4) the changes were not stable after selfing or crossing (Karp <xref ref-type="bibr" rid="CR95">1992</xref>).</p></sec></sec><sec id="Sec13"><title>Recovery of somaclonal variants</title><p>The recovery of variants can be improved by promoting the factors which are responsible for the development of somaclonal variations such as protoplast culture (Kothari et al. <xref ref-type="bibr" rid="CR101">2010</xref>) and employing callus and cell suspension culture for several cycles and regeneration of large number of plants from long-term cultures (Barakat and El-Sammak <xref ref-type="bibr" rid="CR12">2011</xref>). Indirect organogenesis is an important means of retrieving genetic variation through somaclones with useful traits of agronomic or industrial use. Besides, plant genotype is a major factor, which determines the type and frequency of somaclonal variation. For instances, Solanaceous plants like potato (Sharma et al. <xref ref-type="bibr" rid="CR186">2007</xref>) and tomato (Bhatia et al. <xref ref-type="bibr" rid="CR19">2005</xref>) produce a gamut of somaclonal variation than many other commercial horticultural crops. However, to be of practical value, the frequency of somaclonal variation should be sufficient enough to select desirable traits, and the selected lines should perform well under multiple environments (Duncan <xref ref-type="bibr" rid="CR44">1997</xref>). The efficiency of recovering variants in vitro can further be enhanced by applying selection pressure through screening of desirable traits, e.g., in vitro selection for tolerance against abiotic and biotic stresses (Barakat and El-Sammak <xref ref-type="bibr" rid="CR12">2011</xref>). This attains more significance in view of the fact that the selection of desirable traits takes several years and many generations under field conditions. In vitro selection can shorten considerably the time for the selection of desirable traits under in vitro selection pressure with minimal environmental interaction, and can complement field selection (Jain <xref ref-type="bibr" rid="CR85">2001</xref>).</p><p>The recovery of somaclones can be increased by combining micropropagation with induced mutagenesis in vitro (Afrasiab and Iqbal <xref ref-type="bibr" rid="CR2">2010</xref>). Kuksova et al. (<xref ref-type="bibr" rid="CR110">1997</xref>) noted that somaclonal variation and mutagens can be combined to increase the frequency of induced mutation. Likewise, irradiation followed by adventitious bud regeneration has been reported to have allowed the recovery of mutants with useful agronomic traits in <italic>Gypsophila paniculata</italic> L. (Barakat and El-Sammak <xref ref-type="bibr" rid="CR12">2011</xref>). Yang and Schmidt (<xref ref-type="bibr" rid="CR211">1994</xref>) treated in vitro leaves of the cherry rootstock ‘209/1’ (<italic>Prunus cerasus</italic> × <italic>P. canescens</italic>) with X-rays with LD50 close to 20 Gy. Among plants regenerated from leaves with 20 Gy, one was phenotypically different, and was subsequently isolated and cloned. This somaclone was extremely dwarfed and was stable in both greenhouse and field tests. Employing more than one mutagen results in further improvement in recovery of somaclones in vitro. Murti et al. (<xref ref-type="bibr" rid="CR143">2013</xref>) exposed the strawberry ‘DNKW001’ to the doses of 0, 30, 80, 130, 180, 230, 280, 300 and 325 Gy and similar doses of gamma rays + EMS 7 µM treatments. Their results showed that Gamma ray irradiation + EMS was more effective to generate more type and magnitude of variants. Purwati and Sudarsono (<xref ref-type="bibr" rid="CR169">2007</xref>) regenerated four variant lines in abaca banana from (1) embryogenic calli; (2) ethyl methyl sulphonate (EMS)-treated embryogenic calli; (3) EMS-treated embryogenic calli, followed by in vitro selection on Foc (<italic>Fusarium oxysporum</italic> f.sp. cubense) culture filtrate (EMS + CF line) and (4) EMS-treated embryogenic calli, followed by in vitro selection on fusaric acid. The Foc resistance abaca variants were successfully identified from four tested abaca variant lines, although with different frequencies. However, more Foc resistance abaca plants were identified from EMS + CF line than the others. Earlier, Bidabadi et al. (<xref ref-type="bibr" rid="CR23">2012</xref>) suggested that the subjecting of shoot tips cultures of banana to EMS (200 mM) treatments could provide an alternative strategy for inducing variants. Recently, Iuliana and Cerasela (<xref ref-type="bibr" rid="CR83">2014</xref>) suggested irradiation of in vitro raised plants with ultraviolet radiations (UV-C) for induction of somaclones in potato.</p></sec><sec id="Sec14"><title>Application of somaclonal variations</title><p>It is well accepted that somaclonal variations arising out of unique tissue culture environment are very often noticed phenomenon in clonally propagated plants, which can advantageously be utilized as a source of new variation in horticultural crops (Karp <xref ref-type="bibr" rid="CR97">1995</xref>). However, suitable tools for detection, evaluation, identification and improvement of resistant clones should be designed in order to realize the benefits of such variations (Sahijram et al. <xref ref-type="bibr" rid="CR177">2003</xref>). Crop improvement through somaclonal variation enables breeders to obtain plants tolerant to the biotic or abiotic stress, such as drought, high salinity, high or low soil pH and disease tolerance (Yusnita et al. <xref ref-type="bibr" rid="CR212">2005</xref>). A number of cultivars have been developed through somaclonal variation in different horticultural crops for a range of useful traits, which are presented in Table <xref rid="Tab3" ref-type="table">3</xref>.<table-wrap id="Tab3"><label>Table 3</label><caption><p>In vitro selection of desirable traits and development of some commercially exploited varieties through somaclonal variation in different horticultural crops</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="left">S. no.</th><th align="left">Horticultural crop</th><th align="left">Characteristic of somaclone</th><th align="left">References</th></tr></thead><tbody><tr><td align="left">1</td><td align="left"><italic>Aglaonema</italic></td><td align="left">Cultivar ‘Moonlight Bay’ and ‘Diamond Bay’ from ‘Silver Bay,’ and ‘Emerald Bay,’ from ‘Golden Bay’</td><td align="left">Henny et al. (<xref ref-type="bibr" rid="CR70">1992</xref>, <xref ref-type="bibr" rid="CR71">2003</xref>)</td></tr><tr><td align="left">2</td><td align="left">Apple (<italic>Malus</italic> × <italic>domestica</italic> Borkh.)</td><td align="left">Resistance to <italic>Erwinia amylovora</italic></td><td align="left">Chevreau et al. (<xref ref-type="bibr" rid="CR30">1998</xref>)</td></tr><tr><td align="left">3</td><td align="left">Apple rootstocks M 26 and MM 106 (<italic>Malus pumila</italic> Mill.)</td><td align="left">Resistance to <italic>Phytophthora</italic><italic>cactorum</italic></td><td align="left">Rosati et al. (<xref ref-type="bibr" rid="CR176">1990</xref>)</td></tr><tr><td align="left">4</td><td align="left">Apple rootstock Malling 7</td><td align="left">Resistance to white root rot (<italic>Dematophora necatrix</italic>)</td><td align="left">Modgil et al. (<xref ref-type="bibr" rid="CR135">2012</xref>)</td></tr><tr><td align="left">5</td><td align="left"><italic>Anthurium</italic> sp.</td><td align="left">‘Orange Hot’ derived from ‘Red Hot’ clone</td><td align="left">Henny and Chen (<xref ref-type="bibr" rid="CR69">2011</xref>)</td></tr><tr><td align="left" rowspan="7">6</td><td align="left" rowspan="7">Banana (<italic>Musa acuminata</italic> L.)</td><td align="left">Semi-dwarf and resistant to <italic>Fusarium</italic> wilt TC1-229</td><td align="left">Tang et al. (<xref ref-type="bibr" rid="CR197">2000</xref>)</td></tr><tr><td align="left">Larger bunch size var. TC2-425; Resistant to <italic>Fusarium</italic><italic>oxysporum</italic> f. sp. cubense (Foc) race 4; bunch 40 % heavier than cv. Formosana</td><td align="left">Hwang (<xref ref-type="bibr" rid="CR78">2002</xref>)</td></tr><tr><td align="left"><italic>Fusarium</italic> wilt-resistant somaclonal variants of banana cv. Rasthali</td><td align="left">Ghag et al. (<xref ref-type="bibr" rid="CR53">2014</xref>)</td></tr><tr><td align="left">Var. CIEN-BTA-03, resistant to yellow Sigatoka</td><td align="left">Giménez et al. (<xref ref-type="bibr" rid="CR54">2001</xref>)</td></tr><tr><td align="left">10 somaclones; GCTCV215-1 released for commercial planting</td><td align="left">Hwang and Ko (<xref ref-type="bibr" rid="CR79">1992</xref>, <xref ref-type="bibr" rid="CR80">2004</xref>)</td></tr><tr><td align="left">Var. CUDBT-B1, reduced height and early flowering</td><td align="left">Martin et al. (<xref ref-type="bibr" rid="CR123">2006</xref>)</td></tr><tr><td align="left">Var. Tai-Chiao No. 5, superior horticultural traits and resistance to <italic>Fusarium</italic> wilt</td><td align="left">Lee et al. (<xref ref-type="bibr" rid="CR113">2011</xref>)</td></tr><tr><td align="left">7</td><td align="left">Begonia (<italic>Begonia</italic> × <italic>elatior</italic>)</td><td align="left">Plant morphology, number of flowers per plant, and flower size</td><td align="left">Jain (<xref ref-type="bibr" rid="CR84">1997</xref>)</td></tr><tr><td align="left">8</td><td align="left">Brinjal (<italic>Solanum melongena</italic> L.)</td><td align="left">Stress-tolerant somaclone selection</td><td align="left">Ferdausi et al. (<xref ref-type="bibr" rid="CR51">2009</xref>)</td></tr><tr><td align="left">9</td><td align="left">Blackberry</td><td align="left">Thornless var. ‘Lincoln Logan’</td><td align="left">Hall et al. (<xref ref-type="bibr" rid="CR62">1986</xref>)</td></tr><tr><td align="left">10</td><td align="left">Capsicum (<italic>Capsicum annuum</italic> L.)</td><td align="left">Yellow fruited var. Bell sweet</td><td align="left">Morrison et al. (<xref ref-type="bibr" rid="CR139">1989</xref>)</td></tr><tr><td align="left">11</td><td align="left"><italic>Calthea roseopicta</italic></td><td align="left">Developed common cultivars like Angela, Cora, Dottie, Eclipse and Saturn</td><td align="left">Chao et al. (<xref ref-type="bibr" rid="CR29">2005</xref>)</td></tr><tr><td align="left" rowspan="2">12</td><td align="left" rowspan="2">Carrot (<italic>Daucus carota</italic> L.)</td><td align="left">Resistance to leaf spot (<italic>Alternaria dauci</italic>)</td><td align="left">Dugdale et al. (<xref ref-type="bibr" rid="CR43">2000</xref>)</td></tr><tr><td align="left">Resistant to drought</td><td align="left">Rabiei et al. (<xref ref-type="bibr" rid="CR170">2011</xref>)</td></tr><tr><td align="left">13</td><td align="left">Carnation (<italic>Dianthus caryoplyllus</italic> L.)</td><td align="left">Resistant to <italic>Fusarium oxysporum</italic> f. sp. <italic>dianthi</italic></td><td align="left">Esmaiel et al. (<xref ref-type="bibr" rid="CR47">2012</xref>)</td></tr><tr><td align="left" rowspan="2">14</td><td align="left" rowspan="2">Celery (<italic>Apium graveolens</italic> L.)</td><td align="left"><italic>Fusarium</italic> resistant var. UC-TC</td><td align="left">Heath-Pagliuso and Rappaport (<xref ref-type="bibr" rid="CR67">1990</xref>)</td></tr><tr><td align="left">Multiple-resistant (insect resistance against <italic>Spodoptera</italic><italic>exigua</italic> and disease resistance against <italic>Fusarium</italic> yellow) somaclones K-26, K-108 and K-128</td><td align="left">Diawara et al. (<xref ref-type="bibr" rid="CR40">1996</xref>)</td></tr><tr><td align="left">15</td><td align="left"><italic>Celosia argentea</italic> L.</td><td align="left">Resistance to nematode</td><td align="left">Opabode and Adebooye (<xref ref-type="bibr" rid="CR155">2005</xref>)</td></tr><tr><td align="left">16</td><td align="left"><italic>Cereus peruvianus</italic></td><td align="left">Shoots with different areoles characteristics</td><td align="left">Resende et al. (<xref ref-type="bibr" rid="CR174">2010</xref>)</td></tr><tr><td align="left">17</td><td align="left">Chili pepper (<italic>Capsicum annuum</italic> L.)</td><td align="left">Early flowering and increase of yield components</td><td align="left">Hossain et al. (<xref ref-type="bibr" rid="CR75">2003</xref>)</td></tr><tr><td align="left" rowspan="3">18</td><td align="left" rowspan="3">Chrysanthemum (<italic>Dendranthema grandiflora</italic>)</td><td align="left">Variation in leaf, flower shape and petal size</td><td align="left">Ahloowalia (<xref ref-type="bibr" rid="CR3">1992</xref>)</td></tr><tr><td align="left">Daisy type chrysanthemum</td><td align="left">Jevremović et al. (<xref ref-type="bibr" rid="CR89">2012</xref>)</td></tr><tr><td align="left">Attractive variants with changed inflorescence colors</td><td align="left">Miler and Zalewska (<xref ref-type="bibr" rid="CR132">2014</xref>)</td></tr><tr><td align="left" rowspan="2">19</td><td align="left" rowspan="2"><italic>Citrus</italic> spp.</td><td align="left">Resistant to <italic>Phoma tracheiphila</italic></td><td align="left">Deng et al. (<xref ref-type="bibr" rid="CR37">1995</xref>)</td></tr><tr><td align="left">Salinity tolerance</td><td align="left">Ben-Hayyim and Goffer (<xref ref-type="bibr" rid="CR16">1989</xref>)</td></tr><tr><td align="left">20</td><td align="left"><italic>Cuphea viscosissima</italic> Jacq.</td><td align="left">Significantly superior over the parents for mean plant height, leaf area, seed yield, per cent caprylic acid and lauric acid contents</td><td align="left">Ben-Salah and Roath (<xref ref-type="bibr" rid="CR17">1994</xref>)</td></tr><tr><td align="left" rowspan="3">21</td><td align="left" rowspan="2"><italic>Cymbopogon winterianus</italic> Jowitt</td><td align="left">Aromatic grass var. CIMAP/Bio-13 with 50–60 % increased oil yield</td><td align="left">Mathur et al. (<xref ref-type="bibr" rid="CR127">1988</xref>)</td></tr><tr><td align="left">Increased total oil yield and quality with high geraniol content</td><td align="left">Nayak et al. (<xref ref-type="bibr" rid="CR148">2003</xref>)</td></tr><tr><td align="left"><italic>Cymbopogon martinii</italic></td><td align="left">Increased oil content</td><td align="left">Patnaik et al. (<xref ref-type="bibr" rid="CR159">1999</xref>)</td></tr><tr><td align="left">22</td><td align="left"><italic>Dieffenbachia</italic> sp.</td><td align="left">Novel and distinct foliar variegation with taller, larger canopy and longer leaves than ‘Camouflage’ parental plants</td><td align="left">Shen et al. (<xref ref-type="bibr" rid="CR188">2007</xref>)</td></tr><tr><td align="left" rowspan="2">23</td><td align="left" rowspan="2">Garlic (<italic>Allium</italic><italic>sativum</italic> L.)</td><td align="left">Consistently higher bulb yield than the parental clone</td><td align="left">Vidal et al. (<xref ref-type="bibr" rid="CR205">1993</xref>)</td></tr><tr><td align="left">Resistance against the pathogenic fungi ‘<italic>Sclerotium</italic><italic>cepivorum’</italic></td><td align="left">Zhang et al. (<xref ref-type="bibr" rid="CR215">2012</xref>)</td></tr><tr><td align="left" rowspan="3">24</td><td align="left" rowspan="3"><italic>Geranium</italic> spp.</td><td align="left">Vigourous and attractive flower</td><td align="left">Skirvin and Janick (<xref ref-type="bibr" rid="CR190">1976</xref>)</td></tr><tr><td align="left">Isomenthone-rich somaclonal mutant</td><td align="left">Gupta et al. (<xref ref-type="bibr" rid="CR61">2001</xref>)</td></tr><tr><td align="left">Cv. ‘CIM Pawan, a somaclone of the Bourbon type variety Bipuli, with more herbage and essential oil yield than Bipuli</td><td align="left">Saxena et al. (<xref ref-type="bibr" rid="CR184">2008</xref>)</td></tr><tr><td align="left">25</td><td align="left">Gerbera (<italic>Gerbera jamesonii</italic> Bolus)</td><td align="left">Novel cultivars</td><td align="left">Minerva and Kumar (<xref ref-type="bibr" rid="CR133">2013</xref>)</td></tr><tr><td align="left">26</td><td align="left">Ginger (<italic>Zingiber officinale</italic> Rosc.)</td><td align="left">Tolerant to wilt pathogen (<italic>Fusarium oxysporum</italic> f.sp. <italic>zingiberi</italic> Trujillo)</td><td align="left">Bhardwaj et al. (<xref ref-type="bibr" rid="CR18">2012</xref>)</td></tr><tr><td align="left">27</td><td align="left">Grapevine (<italic>Vitis vinifera</italic> L.)</td><td align="left">Resistant to <italic>Botrytis cinerea</italic> and <italic>Plasmopara viticola</italic></td><td align="left">Kuksova et al. (<xref ref-type="bibr" rid="CR110">1997</xref>)</td></tr><tr><td align="left">28</td><td align="left"><italic>Haemerocallis</italic> spp.</td><td align="left">Dwarf, short flowers, male sterile var. Yellow Tinkerbell</td><td align="left">Griesbach (<xref ref-type="bibr" rid="CR55">1989</xref>)</td></tr><tr><td align="left">29</td><td align="left"><italic>Hedychium</italic> (ornamental ginger)</td><td align="left">Ramata, dwarf and variegated cultivar</td><td align="left">Sakhanokho et al. (<xref ref-type="bibr" rid="CR178">2012</xref>)</td></tr><tr><td align="left">30</td><td align="left"><italic>Java citronella</italic> (<italic>Cymbopogon winterianus</italic>)</td><td align="left">Somaclonal variant variety CIMAP/Bio-13, which yields 37 % more oil and 39 % more citronellon than the control variant</td><td align="left">Mathur (<xref ref-type="bibr" rid="CR125">2010</xref>)</td></tr><tr><td align="left">31</td><td align="left">Kiwi fruit (<italic>Actinidia deliciosa</italic>)</td><td align="left">5 somaclones, derived from cv. Tamuri, tolerant to NaCl</td><td align="left">Caboni et al. (<xref ref-type="bibr" rid="CR26">2003</xref>)</td></tr><tr><td align="left">32</td><td align="left">Mango (<italic>Mangifera indica</italic> L.)</td><td align="left">Resistant to <italic>Colletotrichum gleosporiensis</italic></td><td align="left">Litz et al. (<xref ref-type="bibr" rid="CR118">1991</xref>)</td></tr><tr><td align="left">33</td><td align="left">Mint (<italic>Mentha arvensis</italic>)</td><td align="left">Increased herb and oil yield</td><td align="left">Kukreja et al. (<xref ref-type="bibr" rid="CR108">1991</xref>; <xref ref-type="bibr" rid="CR109">2000</xref>)</td></tr><tr><td align="left">34</td><td align="left">Myrobolan (<italic>Prunus cerasifera</italic> Erhr)</td><td align="left">Water logging-tolerant clone variant (S.4) of myrobolan rootstcock Mr.S 2/5 for peach cv. Sun Crest</td><td align="left">Iacona et al. (<xref ref-type="bibr" rid="CR81">2013</xref>)</td></tr><tr><td align="left">35</td><td align="left">Olive (<italic>Olive europea</italic>)</td><td align="left">Bush olive somaclone (BOS), columnar olive somaclone (COS)</td><td align="left">Leva et al. (<xref ref-type="bibr" rid="CR115">2012</xref>)</td></tr><tr><td align="left">36</td><td align="left">Patchouli (<italic>Pogostemon patchouli</italic>)</td><td align="left">Higher herb yield and essential oil content</td><td align="left">Ravindra et al. (<xref ref-type="bibr" rid="CR172">2012</xref>)</td></tr><tr><td align="left">37</td><td align="left">Pea (<italic>Pisum sativum</italic> L.)</td><td align="left">Resistance to <italic>Fusarium solani</italic></td><td align="left">Horáček et al. (<xref ref-type="bibr" rid="CR74">2013</xref>)</td></tr><tr><td align="left" rowspan="3">38</td><td align="left" rowspan="3">Peach (<italic>Prunus persica</italic> L.)</td><td align="left">Somaclones S156 and S122 resistant to leaf spot, moderately resistant to canker in cvs. Sunhigh and Red haven</td><td align="left">Hammerschlag and Ognjanov (<xref ref-type="bibr" rid="CR64">1990</xref>)</td></tr><tr><td align="left">Resistant to root-knot nematode (<italic>Meloidogyne</italic><italic>incognita</italic> Kofoid and White)</td><td align="left">Hashmi et al. (<xref ref-type="bibr" rid="CR66">1995</xref>)</td></tr><tr><td align="left">Somaclone S 122-1 was found resistant to bacterial canker (<italic>Pseudomonas syringae</italic> pv. <italic>syringae</italic>)</td><td align="left">Hammerschlag (<xref ref-type="bibr" rid="CR63">2000</xref>)</td></tr><tr><td align="left" rowspan="2">39</td><td align="left">Pear (<italic>Pyrus</italic> sp.)</td><td align="left">Resistant to <italic>Erwinia amylovora</italic></td><td align="left">Viseur (<xref ref-type="bibr" rid="CR206">1990</xref>)</td></tr><tr><td align="left">Pear rootstock (<italic>Pyrus communis</italic> L.) ‘Old Home × Farmingdale (OHF 333)’</td><td align="left">Tolerance to the fire blight</td><td align="left">Nacheva et al. (<xref ref-type="bibr" rid="CR144">2014</xref>)</td></tr><tr><td align="left">40</td><td align="left"><italic>Philodendron</italic></td><td align="left">Cultivars ‘Baby Hope’ from ‘Hope’</td><td align="left">Devanand et al. (<xref ref-type="bibr" rid="CR38">2004</xref>)</td></tr><tr><td align="left">41</td><td align="left"><italic>Picrorhiza kurroa</italic></td><td align="left">Higher glycoside contents including kutkoside and picroside I in somaclone 14-P derived through <italic>Agrobacterium</italic><italic>rhizogenes</italic> mediated transformed hairy root cultures of <italic>P. kurroa</italic></td><td align="left">Mondal et al. (<xref ref-type="bibr" rid="CR137">2013</xref>)</td></tr><tr><td align="left" rowspan="2">42</td><td align="left" rowspan="2">Pineapple (<italic>Ananas comosus</italic> L., Merr.)</td><td align="left">Spineless variant</td><td align="left">Jaya et al. (<xref ref-type="bibr" rid="CR88">2002</xref>)</td></tr><tr><td align="left">Cvs. P3R5 and Dwarf, variation in fruit color, growth habit, fruit size and length of plant generation cycle</td><td align="left">Pérez et al. (<xref ref-type="bibr" rid="CR161">2009</xref>, <xref ref-type="bibr" rid="CR163">2012</xref>)</td></tr><tr><td align="left" rowspan="7">43</td><td align="left" rowspan="7">Potato (<italic>Solanum tuberosum</italic> L.)</td><td align="left">Non-browning var. White Baron</td><td align="left">Arihara et al. (<xref ref-type="bibr" rid="CR8">1995</xref>)</td></tr><tr><td align="left">Somaclones for heat tolerance</td><td align="left">Das et al. (<xref ref-type="bibr" rid="CR36">2000</xref>)</td></tr><tr><td align="left">Somaclones IBP-10, IBP-27 and IBP-30, derived from cultivar Desiree, showed higher resistance to <italic>Alternaria solani</italic> and <italic>Streptomyces scabiei</italic></td><td align="left">Veitia-Rodriguez et al. (<xref ref-type="bibr" rid="CR204">2002</xref>)</td></tr><tr><td align="left">Improved size, shape, appearance, starch content and starch yield</td><td align="left">Thieme and Griess (<xref ref-type="bibr" rid="CR199">2005</xref>)</td></tr><tr><td align="left">Superior processing attributes than cv. ‘Russet Burbank’</td><td align="left">Nassar et al. (<xref ref-type="bibr" rid="CR146">2011</xref>)</td></tr><tr><td align="left">High-yielding genotype SVP-53</td><td align="left">Hoque and Morshad (<xref ref-type="bibr" rid="CR73">2014</xref>)</td></tr><tr><td align="left">Increased phytonutrient and antioxidant components over cv. ‘Russet Burbank’</td><td align="left">Nassar et al. (<xref ref-type="bibr" rid="CR147">2014</xref>)</td></tr><tr><td align="left">44</td><td align="left">Quince A (<italic>Cydonia oblonga</italic>)</td><td align="left">High soil pH</td><td align="left">Dolcet-Sanjuan et al. (<xref ref-type="bibr" rid="CR42">1992</xref>), Marino et al. (<xref ref-type="bibr" rid="CR122">2000</xref>)</td></tr><tr><td align="left">45</td><td align="left"><italic>Stevia rebaudiana</italic></td><td align="left">High glycoside contents (steviol, stevioside, and rebaudioside)</td><td align="left">Khan et al. (<xref ref-type="bibr" rid="CR100">2014</xref>)</td></tr><tr><td align="left" rowspan="6">46</td><td align="left" rowspan="6">Strawberry (<italic>Fragaria</italic> sp.)</td><td align="left">Resistant to <italic>Fusarium oxysporum f. sp. fragariae</italic></td><td align="left">Toyoda et al. (<xref ref-type="bibr" rid="CR202">1991</xref>)</td></tr><tr><td align="left">Resistant to <italic>Alternaria alternate</italic></td><td align="left">Takahashi et al. (<xref ref-type="bibr" rid="CR196">1993</xref>)</td></tr><tr><td align="left">Resistant to <italic>Phytophthora cactorum</italic></td><td align="left">Battistini and Rosati (<xref ref-type="bibr" rid="CR14">1991</xref>)</td></tr><tr><td align="left">Improved horticultural traits</td><td align="left">Biswas et al. (<xref ref-type="bibr" rid="CR24">2009</xref>)</td></tr><tr><td align="left">Resistant to <italic>Verticillium dahliae</italic> Kleb</td><td align="left">Zebrowska (<xref ref-type="bibr" rid="CR214">2010</xref>)</td></tr><tr><td align="left">‘Serenity’, a paler skin-colored, late season, resistant to powdery mildew and <italic>Verticillium</italic> wilt somaclonal variant of the short-day cv. ‘Florence’</td><td align="left">Whitehouse et al. (<xref ref-type="bibr" rid="CR209">2014</xref>)</td></tr><tr><td align="left">47</td><td align="left">Sweet potato (<italic>Ipomea batatas</italic> L. Lam.)</td><td align="left">Tolerant to salinity</td><td align="left">Anwar et al. (<xref ref-type="bibr" rid="CR7">2010</xref>)</td></tr><tr><td align="left">48</td><td align="left">Sweet orange (<italic>Citrus sinensis</italic> (L.) Osb.)</td><td align="left">Somaclone of OLL (Orie Lee Late) sweet orange; late maturing; suitable for fresh market or processing, exceptional juice quality and flavor</td><td align="left">Grosser et al. (<xref ref-type="bibr" rid="CR57">2015</xref>)</td></tr><tr><td align="left">49</td><td align="left">St. Augustine grass [<italic>Stenotaphrum</italic><italic>secundatum</italic> (Walt.) Kuntze]</td><td align="left">Freeze-tolerant somaclonal variant SVC3</td><td align="left">Li et al. (<xref ref-type="bibr" rid="CR116">2010</xref>)</td></tr><tr><td align="left">50</td><td align="left"><italic>Syngonium podophyllum</italic> Schott</td><td align="left">22 cultivars, derived from original ‘White Butterfly’ clone, with distinct and stable foliage characteristics</td><td align="left">Henny and Chen (<xref ref-type="bibr" rid="CR69">2011</xref>)</td></tr><tr><td align="left">51</td><td align="left">Tomato (<italic>Lycopersicon esculentum</italic> L.)</td><td align="left">High solid contents var. DNAP9</td><td align="left">Evans (<xref ref-type="bibr" rid="CR49">1989</xref>)</td></tr><tr><td align="left">52</td><td align="left">Tulip (<italic>Tulipa</italic> sp.)</td><td align="left">“Bs6”, selected from among the micropropagated plants of the cultivar ‘Blue Parrot’ with red-violet colored longer flower and stem</td><td align="left">Podwyszynska et al. (<xref ref-type="bibr" rid="CR167">2010</xref>)</td></tr><tr><td align="left">53</td><td align="left">Torenia (<italic>Torenia fournieri</italic>)</td><td align="left">Flower color somaclonal variants</td><td align="left">Nhut et al. (<xref ref-type="bibr" rid="CR151">2013</xref>)</td></tr><tr><td align="left" rowspan="2">54</td><td align="left" rowspan="2">Turmeric (<italic>Curcuma longa</italic> L.)</td><td align="left">High essential oil yielding somaclones</td><td align="left">Kar et al. (<xref ref-type="bibr" rid="CR94">2014</xref>)</td></tr><tr><td align="left">Turmeric somaclone resistant to <italic>Fusarium oxysporum</italic> f.sp. Zingiberi</td><td align="left">Kuanar et al. (<xref ref-type="bibr" rid="CR107">2014</xref>)</td></tr><tr><td align="left">55</td><td align="left">Indian ginseng (<italic>Withania somnifera</italic> (L.) Dunal)</td><td align="left">Withanolide (12-deoxywithastramonolide)-rich somaclonal variant</td><td align="left">Rana et al. (<xref ref-type="bibr" rid="CR171">2012</xref>)</td></tr></tbody></table></table-wrap></p></sec><sec id="Sec15"><title>Conclusions</title><p>Several strategies have been followed to ascertain the genetic fidelity of the in vitro produced progenies in view of the fact that the commercial viability of micropropagation technology is reliant upon maintenance of genetic fidelity in the regenerated plants. Therefore, a thorough assessment of micropropagated plants becomes very critical, especially, for perennial crops such as fruit species, which have a long pre-bearing growth period. The efficiency and sensitivity of new molecular tools has enabled us to detect somaclonal variation at an early stage. These tools have become very useful for the rapid detection and accurate identification of variants. Nevertheless, the morphological and cytological assays should continue to remain as the primary and essential assay for the sustained success of fidelity tests associated with production of clonal plants. Though, on one hand, tissue culture-induced variations pose a major threat to the genomic integrity of regenerated plants, they provide tools for improvement to plant breeders, particularly for crops with a narrow genetic base, i.e., self pollinated and vegetatively propagated. Irrespective of our goal either for production of true-to-the type planting material or creation of variability, a multidisciplinary approach (involving concerned sciences of horticulture, genetics and plant breeding, physiology, cytology and molecular biology) with all our previous knowledge and experience should be followed to achieve the desideratum.</p></sec></body><back><ack><p>Authors are grateful to the Dr. S.K. 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