Somaclonal variation — a novel source of variability from cell cultures for plant improvement

Summary It is concluded from a review of the literature that plant cell culture itself generates genetic variability (somaclonal variation). Extensive examples are discussed of such variation in culture subclones and in regenerated plants (somaclones). A number of possible mechanisms for the origin of this phenomenon are considered. It is argued that this variation already is proving to be of significance for plant improvement. In particular the phenomenon may be employed to enhance the exchange required in sexual hybrids for the introgression of desirable alien genes into a crop species. It may also be used to generate variants of a commercial cultivar in high frequency without hybridizing to other genotypes.     

Analyzing somaclonal variation in micropropagated bananas (<Emphasis Type="Italic">Musa</Emphasis> spp.)

Summary In a micropropagation program, where it is of paramount importance to produce true-to-type planting material, somaclonal variation of any kind is undesirable. Variation among plants regenerated from tissue culture is termed ‘somaclonal variation’. In banana, somaclonal variants of different type have been reported with regard to plant morphology. This article discusses various factors due to which somaclonal variations may arise. Somaclonal variation may be detected by visual screening or by using molecular markers such as randomly amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), and by cytological studies. Although somaclonal variation is undesirable in the context of micropropagation, it can be used to advantage for genetic improvement of banana, as has been described.     

Recent progress in the understanding of tissue culture-induced genome level changes in plants and potential applications

In vitro cell and tissue-based systems have tremendous potential in fundamental research and for commercial applications such as clonal propagation, genetic engineering and production of valuable metabolites. Since the invention of plant cell and tissue culture techniques more than half a century ago, scientists have been trying to understand the morphological, physiological, biochemical and molecular changes associated with tissue culture responses. Establishment of de novo developmental cell fate in vitro is governed by factors such as genetic make-up, stress and plant growth regulators. In vitro culture is believed to destabilize the genetic and epigenetic program of intact plant tissue and can lead to chromosomal and DNA sequence variations, methylation changes, transposon activation, and generation of somaclonal variants. In this review, we discuss the current status of understanding the genomic and epigenomic changes that take place under in vitro conditions. It is hoped that a precise and comprehensive knowledge of the molecular basis of these variations and acquisition of developmental cell fate would help to devise strategies to improve the totipotency and embryogenic capability in recalcitrant species and genotypes, and to address bottlenecks associated with clonal propagation.     

植物体细胞无性系变异的细胞学和分子生物学研究进展

植物体细胞无性系变异是植物组织培养中的普遍现象,关于这些变异的起源存在多种观点,如转座因子的活化、DNA甲基化等。本文综述了植物体细胞无性系的研究进展,从细胞学和分子生物学两个层次对无性系变异的起源进行了讨论。     

植物体细胞无性系变异的细胞学和分子生物学研究进展

植物体细胞无性系变异是植物组织培养中的普遍现象,关于这些变异的起源存在多种观点,如转座因子的活化、ＤＮＡ甲基化等。本文综述了植物体细胞无性系的研究进展,从细胞学和分子生物学两个层次对无性系变异的起源进行了讨论     

Bacterial contamination of in vitro plant cultures: confounding effects on somaclonal variation and detection of contamination in plant tissues

Bacterial contamination represents a serious problem for plant tissue culture research and applications. Bacterial interference with normal plant physiology and morphology can generate misleading conclusions if the presence of bacteria is ignored. Bacterial contaminants in in vitro plant culture are typically detected by direct observation; thus, it is assumed that cultures without visible symptoms are bacteria free. Here, we demonstrate that contaminating Bacillus DNA in plant DNA solutions from asymptomatic plants can interfere with the analysis of somaclonal variation in chrysanthemum. We studied somaclonal variation in chrysanthemum using short semi-specific PCR primers based on conserved motifs in NBS–LRR disease resistance genes and in mobile elements. Instead of true somaclonal variation we found three polymorphic bands derived from contaminant bacterial DNA in plant extracts. Although the detection of asymptomatic bacteria in in vitro plant cultures is a major issue, we found that it has not been adequately addressed to date, particularly for studies on somaclonal variation. We reviewed the most commonly cited contaminant bacteria in in vitro plant culture and designed specific 16S rRNA gene-based PCR primers for the main genera causing contamination (Bacillus, Pseudomonas, Staphylococcus, Lactobacillus, Erwinia/Enterobacter and Xanthomonas). Using a panel of pure bacterial DNAs, artificial mixes of bacterial/plant DNAs, and in vitro plant cultures with and without visible contamination we demonstrated that our primers are in most instances both reliable and sensitive, and appropriate for the identification and tracking of the most frequent bacterial contaminants in plant in vitro cultures. Implications of bacterial identification to molecular analysis of somaclonal variation and plant culture decontamination are discussed.     

Genomic changes associated with somaclonal variation in banana (Musa spp.)

The molecular basis of somaclonal variation is not precisely known, but both genetic and epigenetic mechanisms have been proposed. The available evidence points toward the existence of labile portions of the genome that can be modulated when the cells undergo the stress of tissue culture. Therefore, the hypothesis that there are identifiable and predictable DNA markers for the early diagnosis of somaclonal variation has been tested. Representational difference analysis was used to isolate unique fragments of DNA (difference products) between visible culture-induced off-type and normal banana plants. Markers generated from six difference products differentiated between some of the off-type and normal pairs. The genomic region around one of these difference products has been extensively characterized and has a high degree of polymorphism, with variation in up to 10% of the nucleotides sequenced in the region. This same region has been shown to vary in other pairs of off-type and normal banana plants derived from tissue culture as well as in plants propagated commercially in vitro. The data are consistent with the hypothesis that there is at least one particularly labile portion of the genome that is especially susceptible to the stress imposed during tissue culture and that is associated with higher rearrangement and mutation rates than other portions of the genome. Consequently, the regions that are reported here have the potential to be used as early detection tools for identifying somaclonal variants.     

Somaclonal variation--genetic basis and breeding applications

Somaclonal variation, the recovery of genetic changes in plants regenerated from tissue culture, offers an opportunity to uncover natural variability and to use this variability for the development of new varieties. This review focuses on the unique variation generated by this technique and the current use of somaclonal variation to develop new plant varieties.     

Genetic fidelity of organized meristem-derived micropropagated plants: A critical reappraisal

Summary The commercial multiplication of a large number of diverse plant species represents one of the major success stories of urilizing tissue culture technology profitably. Micropropagation has now become a multibillion dollar industry, practised all over the world. Of the various methods used to micropropagate plants, somatic embryogenesis and enhanced axillary branching have become the principal methods of multiplication. Long-term benefits of this enterprise, however, lie in the production of clonally uniform plants. The concept of genetic uniformity among micropropagated plants derived through organized meristems was exploded by several convincing reports of the incidence of somaclonal variation at morphological, cytological (chromosome number and structure), cytochemical (genome size), biochemical (proteins and isozymes), and molecular (nuclear and organellar genomes) levels. Somaclonal variation is not limited to any particular group of plants; it has been reported, for example, in ornamentals, plantation crops, vegetable and food crops, forest species and fruit trees. The upsurge of these reports, facilitated to a large extent by the technical developments made in molecular biology, is a matter of great concern for any micropropagation system. The economic consequences of somaclonal variation can be enormous in forest trees and woody plants, as they have long life cycles. Therefore, somaclonal variation has to be dispensed with if large-scale micropropagation of diverse plant species is to become not only successful but also accepted by end-users. In the light of the various factors (genotype, ploidy level, in vitro culture age, explant and culture type, etc.) that lead to somaclonal variation of divergent genetic changes at the cellular and molecular levels, genetic analysis of micropropagated plants using a multidisciplinary approach, especially at the DNA sequence level, initially and at various cultural stages, is essential. The results obtained at early multiplication stages from these tests could help in modifying the protocol/s for obtaining genetically true-to-type plants, and ultimate usage by entrepneneurs without any ambiguity.     

Molecular markers applied to plant tissue culture

Summary The last decade has witnessed successful applications of plant tissue culture techniques in several crops. During that same period, studies in plant molecular genetics have also grown exponentially. Molecular markers (isozymes, RFLPs, and PCR-based markers such as RAPDs) are now used to study many of the current limitations of tissue culture. They have been used to investigate mechanisms that underlie somaclonal variation in the nuclear, mitochondrial, and chloroplast genomes. One recurrent problem with several tissue culture systems has been the difficulty of determining the origin of regenerants. Molecular markers represent powerful tools to determine precisely the origin of plants derived from microspore or anther culture, protoplast fusion, and other tissue culture studies where this information is important. With improvements in tissue culture techniques, populations of doubled haploid lines have been produced in several major crop species. Doubled haploid populations have proven useful in the production of molecular maps and in tagging important agronomic traits. This review describes the use of molecular markers to address fundamental and practical questions of plant tissue culture, and discusses the potential of improvements in molecular techniques and new molecular markers such as SCAR and STS along with high-resolution mapping strategies.     

Somaclonal Variation in Rice after Two Successive Cycles of Mature Embryo Derived Callus Culture in the Presence of NaCl

Two successive cycles of mature embryo-derived callus culture separated by one cycle of sexual reproduction of R₀ regenerated plants were performed using two rice (Oryza sativa L.) cultivars in order to gain information upon the nature of somaclonal variation in this species. Plants regenerated after one cycle of tissue culture exhibited higher variability and lower performances than those of initial cultivar. A second cycle performed using R₁ embryos as explants showed that the cellular component of salt resistance in terms of growth and regenerating abilities selected during the first cycle could be transmitted to the progenies. The extent and the nature of somaclonal variation depended on the identity of R₀ mother plant and culture conditions, somaclonal variation being strongly reduced in some families obtained from salt-treated calli.     

水稻体细胞无性系变异

水稻体细胞无性系变异研究取得了很大进展,获得了大量抗病、抗逆、优质、矮杆等突变体。对这些突变体遗传分析表明,大多数突变性状由1对或2对基因控制。水稻体细胞无性系变异的发生与基因型、性状、继代时间、培养方式等有关,并具有内在的机制,点突变和反转录转座子插入可能是引起水稻无性系变异的两个重要原因。     

Agronomic evaluation of inbred lines derived from tissue cultures of maize

Summary Tissue culture-induced variation has been proposed as a novel source of variation for crop improvement. In maize (Zea mays L.), chromosome aberrations and qualitative genetic variants have been induced during in vitro culture. The proportion of regenerated plants carrying such variants has been shown to increase with culture age. The objective of this research was to evaluate the relationship between culture age and somaclonal variation for several agronomic traits. Six sib-pollinated ears of S₀ (F₂) plants in four OH43 ms/A188 populations each provided control seed and embryos for culture initiation. S₂ lines derived from control seed and from plants regenerated 4 and 8 months after culture initiation were grouped according to their source ear and grown in 6 separate trials. A total of 305 tissue culture-derived and 48 control lines were evaluated as lines per se and in a testcross at each of three locations. Tissue culturederived lines and their testcrosses generally had lower grain yield and moisture. Since grain yield and moisture were not positively correlated in any trial, the highest yielding lines could be selected without increasing grain moisture. Grain yield and plant height tended to decrease with culture age. Although tissue culture-derived lines were, on average, inferior, the highest yielding line per se in three of six trials and the top-ranked line in five of six trials for yield and moisture were derived from tissue culture. The results indicate that tissue culture may generate variation for agronomic traits. Some of the variation, particularly the trend towards earlier maturity, could be useful. However, this method may require screening large populations because of the tendency to generate a large proportion of inferior lines.Contribution from Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108. Minnesota Agric. Exp. Stn. Scientific Journal Series Paper No. 15,172     

水稻体细胞无性系变异

水稻体细胞无性系变异研究取得了很大进展 ,获得了大量抗病、抗逆、优质、矮杆等突变体。对这些突变体遗传分析表明 ,大多数突变性状由 1对或 2对基因控制。水稻体细胞无性系变异的发生与基因型、性状、继代时间、培养方式等有关 ,并具有内在的机制 ,点突变和反转录转座子插入可能是引起水稻无性系变异的两个重要原因。     

Crop improvement through tissue culture

Plant tissue culture comprises a set of in vitro techniques, methods and strategies that are part of the group of technologies called plant biotechnology. Tissue culture has been exploited to create genetic variability from which crop plants can be improved, to improve the state of health of the planted material and to increase the number of desirable germplasms available to the plant breeder. Tissue-culture protocols are available for most crop species, although continued optimization is still required for many crops, especially cereals and woody plants. Tissueculture techniques, in combination with molecular techniques, have been successfully used to incorporate specific traits through gene transfer. In vitro techniques for the culture of protoplasts, anthers, microspores, ovules and embryos have been used to create new genetic variation in the breeding lines, often via haploid production. Cell culture has also produced somaclonal and gametoclonal variants with crop-improvement potential. The culture of single cells and meristems can be effectively used to eradicate pathogens from planting material and thereby dramatically improve the yield of established cultivars. Large-scale micropropagation laboratories are providing millions of plants for the commercial ornamental market and the agricultural, clonally-propagated crop market. With selected laboratory material typically taking one or two decades to reach the commercial market through plant breeding, this technology can be expected to have an ever increasing impact on crop improvement as we approach the new millenium.D.C.W. Brown is with Agriculture and Agri-Food Canada, Central Experimental Farm, Plant Research Centre, Ottawa, Ontario, K1A 0C6, Canada. T.A. Thorpe is with the Plant Physiology Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada     

Use of Tissue Culture and Biotechnology for the Genetic Improvement of Watermelon

Watermelon is an important vegetable crop world-wide with over 81 million metric tons produced annually. Despite these high production figures, million of metric tons of fruit are lost in fields to disease. Genetic improvement through tissue culture and biotechnology offer potential routes of improving fruit harvest by offering higher quality products, like seedless fruit, or by introducing recombinant genes or generating somaclonal variants with improved resistance to biotic or abiotic stresses. The purpose of this review is to highlight how tissue culture and biotechnology have been used for the genetic improvement of watermelon and provide suggestions for future application of these methods to facilitate further genetic improvement.     

植物体细胞无性系变异研究进展

植物体细胞无性系变异是植物组织培养中的普遍现象,泛指在植物细胞、组织和器官培养过程中, 培养细胞和再生植株中产生的遗传变异或表观遗传学变异。植物体细胞无性系变异的发生有其遗传学基础, 可从形态学、细胞学、生物化学和分子生物学等多个方面对其进行综合检测和鉴定。植物体细胞无性系变异是植物育种的有利资源, 但同时也是植物微繁和遗传转化工作中需要克服的一大难题,一直被众多研究者所关注。本文分别从细胞学和分子生物学两个层次综述了植物体细胞无性系变异的遗传学基础及其鉴定方法的研究进展,并就其在植物品质改良中的应用现状、存在的问题和应用前景进行了讨论。     

The effects of growth regulators on somaclonal variation in rye (Secale cereale L.) and selection of somaclonal variants with increased agronomic traits

The aim of this research was to characterize somaclonal variation in populations derived from embryos cultured on two types of induction medium (supplemented with either 2,4-D or dicamba), as well as to select and characterize several somaclonal lines. The sexual progenies of 40 R(0)regenerants - A somaclones (derived on the medium with 2,4-D) and B somaclones (derived on the medium with dicamba) - were analysed according to the following traits: plant height, total number of tillers, number of productive tillers, spike length, number of spikelets per spike, spike compactness, number of normally developed grains per spike, weight of grains per spike, and the weight of 1000 grains. The results for twenty-two R(1)plants surpassed the variability range for the control. The transmission of positive changes to the next generation was proved in the case of 8 originally chosen R(1) plants: 7 plants selected from the A somaclones and one plant from the B somaclones. Five out of the eight created somaclonal lines proved to be stable somaclonal variants. The absolute rate of the efficiency of positive somaclonal changes was calculated as 0.64%.     

Organ-specific and ploidy-dependent somaclonal variation; a new tool in breeding

The organ-specific somaclonal variation means the differences between the variability of somaclones originated from different somatic tissue of plant. Significant differences in some agronomical characters were achieved among somaclones of seed and plumule meristem origin. The ploidy-dependent somaclonal variation means the differences between the variability of somaclones originated from different ploidy-level tissue. Increased variation among regenerated plants was postulated by origin from cultured cells of reduced ploidy level. The comparison of somaclonal variation in the progenies of diploid plants regenerated from callus of haploid and diploid origin supported the ploidy dependent theory. The pollenhaploid somaclone method (PHS-method) was developed and tested for utilization somaclonal variation in rice breeding. The PHS-method comprises the two well-known and widely applied in vitro methods which are the androgenesis (another culture) and genetic instability of cultured haploid somatic cells (callus cultures). Developmental varieties produced by this breeding sheme are under certification in Hungary.     

Assessment of somaclonal variation in <Emphasis Type="Italic">Dieffenbachia</Emphasis> plants regenerated through indirect shoot organogenesis

The occurrence of somaclonal variation among regenerants derived through indirect shoot organogenesis from leaf explants of three Dieffenbachia cultivars Camouflage, Camille and Star Bright was evaluated. Three types of somaclonal variants (SV1, SV2, and SV3) were identified from regenerated plants of cv. Camouflage, one type from cv. Camille, but none from cv. Star Bright. The three variants had novel and distinct foliar variegation patterns compared to cv. Camouflage parental plants. Additionally, SV1 was taller with a larger canopy and longer leaves than parental plants and SV2. SV2 and SV3 did not produce basal shoots (single stem) but basal shoot numbers between SV1 and parental plants were similar ranging from three to four. The variant type identified from regenerated cv. Camille had lanceolate leaves compared to the oblong leaves of the parent. This variant type also grew taller and had a larger canopy than parental plants. The rates of somaclonal variation were up to 40.4% among regenerated cv. Camouflage plants and 2.6% for regenerated cv. Camille. The duration of callus culture had no effect on somaclonal variation rates of cv. Camouflage as the rates between plants regenerated from 8 months to 16 months of callus culture were similar. The phenotypes of the identified variants were stable as verified by their progenies after cutting propagation. This study demonstrated the potential for new cultivar development by selecting callus-derived somaclonal variants of Dieffenbachia.