Regenerant Arabidopsis lineages display a distinct genome-wide spectrum of mutations conferring variant phenotypes

Multicellular organisms can be regenerated from totipotent differentiated somatic cell or nuclear founders [1-3]. Organisms regenerated from clonally related isogenic founders might a priori have been expected to be phenotypically invariant. However, clonal regenerant animals display variant phenotypes caused by defective epigenetic reprogramming of gene expression [2], and clonal regenerant plants exhibit poorly understood heritable phenotypic ("somaclonal") variation [4-7]. Here we show that somaclonal variation in regenerant Arabidopsis lineages is associated with genome-wide elevation in DNA sequence mutation rate. We also show that regenerant mutations comprise?a distinctive molecular spectrum of base substitutions, insertions, and deletions that probably results from decreased DNA repair fidelity. Finally, we show that while regenerant base substitutions are a likely major genetic cause of the somaclonal variation of regenerant Arabidopsis lineages, transposon movement is unlikely to contribute substantially to that variation. We conclude that the phenotypic variation of regenerant plants, unlike that of regenerant animals, is substantially due to DNA sequence mutation.     

The use of phenotypic markers to identify Brassica oleracea genotypes for routine high-throughput Agrobacterium-mediated transformation

Doubled haploid (DH) genotypes from a genetic mapping population of Brassica oleracea were screened for ease of transformation. Candidate genotypes were selected based on prior knowledge of three phenotypic markers: susceptibility to Agrobacterium tumefaciens, shoot regeneration potential and mode of shoot regeneration. Mode of regeneration was found to be the most significant of the three factors. Transgenic plants were successfully obtained from genotypes that regenerated multiple shoots via a distinct swelling or callus phase. The absence of tissue culture blackening (associated with genotypes that formed callus) was found to be critical for transformation success. Transgenic shoots were obtained from genotypes that regenerated via an indirect callus mode, even when susceptibility to Agrobacterium was low. The most efficient genotype (DH AG1012) produced transgenic shoots at an average rate of 15% (percentage of inoculated explants giving rise to transgenic plants). The speed and efficiency of regeneration enabled the isolation of transgenic shoots 5–6 weeks after inoculation with A. tumefaciens. This line was also self-compatible, enabling the production of seed without the need for hand-pollination. A genetically uniform DH genotype, with an associated genetic map, make DH AG1012 highly desirable as a potential model B. oleracea genotype for studying gene function. The possibility of applying the same phenotypic tissue culture markers to other Brassica species is discussed.     

Early infection of scutellum tissue with Agrobacterium allows high-speed transformation of rice

Several approaches have recently been adopted to improve Agrobacterium-mediated transformation of rice, both to generate the large number of T-DNA insertion plants needed for functional analysis of the rice genome, and for production of rice with additional agronomical value. However, about 3 months of in vitro culture is still required for isolation of transgenic rice plants. Here, we report the competency of scutellum tissue from 1-day pre-cultured seeds for Agrobacterium-mediated transformation. Furthermore, early infection of rice seeds with Agrobacterium enhanced efficient selection of transformed calli. Using our system, we successfully regenerated transgenic rice plantlets within a month of the start of the aseptic culture of mature seeds. Our new system should reduce the somaclonal variation accompanying prolonged culture of rice cells in the dedifferentiated state and facilitate the molecular breeding of rice.     

Hygromycin B - An Alternative in Flax Transformant Selection

The in vitro regeneration of three flax (Linum usitatissimum L.) breeding lines (cv. Jitka, cv. Areco and NLN 245) and selection of transgenic plants were studied. A. tumefaciens derived binary vector GV3101 (pPM90RK)(pPCVRN4) bearing tetramer of 35S promoter enhancer was used in transformation experiments. Following 3 weeks of cultivation on shoot inducing Murashige and Skoog agar medium containing BAP (0.1 μM) and NAA (0.005 μM) from 82.6 % to 98 % of hypocotyl segments formed shoots. While ticarcillin (500 mg dm⁻³) used to eliminate Agrobacterium following the transformation decreased the organogenic response by about 10 % only, the addition of 20 mg dm⁻³ hygromycin to ticarcillin efficiently suppressed the regeneration of untransformed control plants. To look up for genomic mutations caused by T-DNA insertion from Agrobacterium transformation or originated from somaclonal variation over 500 regenerated plants have been cloned, transferred into soil and evaluated especially for their morphological characteristics. Up to now among plants of cv. Areco-background at least 8 genotypes showed changes either in flower or filament and stigma colour and one clone of plants with pollen sterility was identified. Among fifty four plant clones evaluated in 7 clones the presence of transgene specific sequence hpt was detected and simultaneously Agrobacterium contamination of tissues was firmly excluded. This revised version was published online in June 2006 with corrections to the Cover Date.     

Transformation of Lotus japonicus using the herbicide resistance bar gene as a selectable marker

Transgenic plants of the model legume Lotus japonicus were regenerated by hypocotyl transformation using a bar gene as a selectable marker. The bar encodes for Phosphinothricin Acetyl Transferase that detoxifies phosphinothricin (PPT), the active ingredient of herbicides such as Ignite (AgrEvo) and Basta (Hoechst). Transgenic L. japonicus plants resistant to PPT were positive upon PCR by bar gene-specific primers. In 5 out of 7 independent lines tested, PPT resistance segregated as a single dominant allele indicating a single T-DNA insertion into the plant genome. All regenerated plants were fertile and void of visible somaclonal abnormalities contrary to 14% infertility when antibiotic selectable markers were used. The lack of somaclonal variation, ease of PPT application and low cost of PPT makes this protocol an attractive alternative for the regeneration of transgenic L. japonicus. The production of PPT herbicide-resistant L. japonicus plants may have significant commercial applications in crop production.     

High-frequency regeneration via multiple shoot induction of an elite recalcitrant cotton (Gossypium hirsutum L. cv Narashima) by using embryo apex

Cotton (Gossypium hirsutum L.) is one of the most commercially important fiber crops in the world. Compared with other crops, cotton represents a recalcitrant species for regeneration protocols. The development of efficient and rapid regeneration protocol for elite Indian cotton variety could help improve the quality characteristics and biotic or abiotic stress tolerance. Here we report a novel regeneration protocol in Indian cotton cultivar Narashima. The maximum number of multiple shoots obtained was 16 per explants, performance which has never been achieved in any prior reports. The embryo apex explants were isolated from 2 d old in vitro growing seedlings. Explants were cultured on MS medium containing different plant growth regulator combinations in order to induce multiple shoots. Among the tested combinations, the 2 mg/l of 6-benzylaminopurine (BAP) and 2 mg/l kinetin (KIN) proved to be most suited for achieving the maximum number of multiple shoots. The elongation of multiple shoots was obtained in media supplemented with gibberellic acid (GA3). The regenerated plants were successfully hardened in earthen pots after adequate acclimatization. This method avoids callus tissue, the stage of regeneration which may lead to somaclonal variation. The important feature of the presented method is shortening of regeneration time, as well as the induction of a high number of multiple shoots per explants. The present protocol may provide an efficient and rapid regeneration tool for obtaining more stable transformants from embryo apex explants of Indian cotton cultivar Narashima.     

High frequency of tetraploidy in Agrobacterium-mediated transformants regenerated from tuber discs of diploid potato lines

Summary Variations in the ploidy level of 69 transgenic potato (Solanum tuberosum L.) plants regenerated from the tuber discs of 17 diploid lines were studied: 24 plants (35%) were diploid, the other 45 plants (65%) were tetraploid. Seventy-eight control regenerants obtained without Agrobacterium inoculation showed a relatively low tendency to tetraploidization (35%). The results obtained suggested that chromosome doubling occurred frequently in diploid potato lines during the tissue culture process for regeneration. Putative somaclonal changes in in vitro-formed tuber proteins were detected in three out of six transformants by electrophoretic analysis.     

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.     

Soybean transformation by electric discharge particle acceleration

By the use of a direct DNA-delivery system based on electric discharge particle acceleration we have been able to obtain transgenic soybean plants expressing the neomycin phosphotransferase II and the β-glucuronidase genes. Techniques for efficient introduction of foreign genes into agronomically important crop plants have been limited by the inability to regenerate fertile plants from single cells or by the limited hostrange of Agrobacterium vectors. In the case of soybean ( Glycine max ) the problem has been compounded due to the lack of a regeneration method compatible with existing transformation technology. In a commercial genetic engineering program the following points need to be considered: (a) not all crops/cultivars can be regenerated from transformed tissues, (b) long time frames are required for the regeneration of transgenic plants from callus, (c) Agrobacterium has a rather limited host specificity and (d) problems associated with somaclonal variation.     

Agrobacterium-mediated transformation of three economically important potato cultivars using sliced internodal explants: an efficient protocol of transformation

An efficient protocol has been developed for Agrobacterium-mediated transformation of internodal explants derived from three economically important Solanum tuberosum genotypes, namely Bintje, Désirée and Kaptah Vandel. By combining the best treatments, this protocol yielded an average transformation rate of 90% of treated longitudinal cut internodal explants. Seven to nine shoots per explant were obtained. The importance of zeatin riboside (0.8 mg^-1 l^-1) in the culture media, in controlling the development of highly organogenic micro-calli has been demonstrated. A total of 450 morphologically normal transgenic plants were regenerated. Stable integration and expression of the transgenes were confirmed by histochemical and molecular analyses. Short duration (7-8 weeks), high efficiency, genotype independence and low frequency of somaclonal variation make this system well suited for wider commercial applications of transgenic potato plants.Keywords: Solanum tuberosum L., potato, transformation, Agrobacterium tumefaciens.      

Influence of plant development and environment on transgene expression in potato and consequences for insect resistance

Clonal replicates of different transformed potato plants expressing transgene constructs containing the constitutive Cauliflower Mosaic Virus (CaMV) 35S promoter, and sequences encoding the plant defensive proteins snowdrop lectin (Galanthus nivalis agglutinin; GNA), and bean chitinase (BCH) were propagated in tissue culture. Plants were grown to maturity, at first under controlled environmental conditions, and later in the glasshouse. For a given transgene product, protein accumulation was found to vary between the different lines of clonal replicates (where each line was derived from a single primary transformant plant), as expected. However, variability was also found to exist within each line of clonal replicates, comparable to the variation of mean expression levels observed between the different clonal lines. Levels of GNA, accumulated in different parts of a transgenic potato plant, also showed variation but to a lesser extent than plant–plant variation in expression. With the majority of the clonal lines investigated, accumulation of the transgene product was found to increase as the potato plant developed, with maximum levels found in mature plants. The variation in accumulation of GNA among transgenic plants within a line of clonal replicates was exploited to demonstrate that the enhanced resistance towards larvae of the tomato moth, Lacanobia oleracea L., caused by expression of this protein in potato, was directly correlated with the level of GNA present in the plants, and that conditions under which the plants were grown affect the levels of GNA expression and subsequent levels of insect resistance.     

Comparative assessment of variation in the USA Arachis pintoi (Krap. and Greg.) germplasm collection using RAPD profiling and tissue culture regeneration ability

Arachis pintoi accessions were used to study genetic diversity using RAPD markers. Concurrently, two tissue culture protocols were evaluated for organogenesis and the capacity to generate somaclonal variation. Data were collected on callus growth, callus weight gain, and number of regenerated plants. Robust RAPD profiles were obtained and eight primers amplified 100 different bands with 98% polymorphisms. The proportion of polymorphic RAPD loci was 89%. Average genetic distance was 0.36 and indicated that a large amount of genetic diversity exists within the germplasm evaluated. Genetic distances were used to prepare a dendogram for the A. pintoi accessions that separated them into four groups. A large degree of variability for callus induction and callus weight gain was observed among the accessions. Shoot regeneration was achieved for several accessions on both media with no structures indicative of somatic embryogenesis detected. Root induction was difficult to obtain, and many shoots died during this process. RAPD band profiles of regenerated tissue culture plants were similar to their parent plants, and therefore no somaclonal variation was evident using these methods.     

Green fluorescent protein as a screenable marker to increase the efficiency of generating transgenic woody fruit plants

 The green fluorescent protein (GFP) from Aequorea victoria has been introduced into three different citrus genotypes [Citrus aurantium L., C. aurantifolia (Christm.) Swing. and C. sinensis L. Osbeck×Poncirus trifoliata (L.) Raf.] which are considered recalcitrant to transformation, mainly due to low transformation frequencies and to the regeneration of escape shoots at high frequencies from the Agrobacterium-inoculated explants. High-level GFP expression was detected in transgenic cells, tissues and plants. Using GFP as a vital marker has allowed us to localize the sites of transgene expression in specific cells, always occurring in callus tissue formed from the cambium of the cut ends of explants. Whereas green fluorescent shoots regenerated in all cases from this callus, most escapes regenerated directly from explants with almost no callus formation. Thus, development of callus from cambium is a prerequisite for citrus transformation. Furthermore, in vivo monitoring of GFP expression permitted a rapid and easy discrimination of transgenic and escape shoots. The selection of transgenic shoots could be easily favored by eliminating the escapes and/or by performing shoot-tip grafting of the transgenic buds soon after their origin. GFP-expressing shoots have also been observed in citrus explants co-cultivated with Agrobacterium but cultured in a medium without the selective agent kanamycin. This opens the possibility to rescue the transgenic sectors and to regenerate transgenic plants without using selectable marker genes conferring antibiotic or herbicide resistance, which is currently a topic of much discussion for the commercialization of transgenic plants. Received: 28 October 1998 / Accepted: 28 November 1998     

A robust genetic transformation protocol to obtain transgenic shoots of Solanum tuberosum L. cultivar ‘Kufri Chipsona 1’

The genetic transformation of plants is an important biotechnological tool used for crop improvement for many decades. The present study was focussed to investigate various factors affecting genetic transformation of potato cultivar ‘Kufri Chipsona 1’. It was observed that explants pre-cultured for 2 days on MS2 medium (MS medium containing 10 µM silver nitrate, 10 µM BA, 15 µM GA3), injured with a surgical blade and co-cultivated with Agrobacterium tumefaciens strain EHA105 [O.D600 (0.6)] for 2 days results in maximum transient β-glucuronidase (GUS) expression. The addition of 100 µM acetosyringone in MS2 medium also increased rate of transient GUS expression in both the explants. Clumps of putative transgenic shoots were regenerated using the optimised culture conditions from leaf and internodal explants. The stable integration of T-DNA was established using histochemical staining for GUS and amplification of DNA fragment specific to nptII and uidA genes. Within the clumps, around 67.85% of shoots showed uniform GUS expression in all the tissues and about 32.15% shoots show intermittent GUS expression establishing chimeric nature. Uniform GUS staining of the tissue was used as initial marker of non-chimeric transgenic shoots. Quantitative expression of nptII transgene was found to be directly proportional to uniformity of GUS staining in transgenic shoots. The present investigation indicated that manipulation of culture conditions and the medium composition may help to get transgenic shoots with uniform expression of transgene in all the tissues of potato cultivar ‘Kufri Chipsona 1’.     

Agrobacterium tumefaciens-mediated genetic transformation of rye (Secale cereale L.)

A system for the genetic transformation of rye by co-cultivation with Agrobacterium tumefaciens is described. A total of 45 independent transgenic plants were regenerated with a transformation efficiency of 1 to % of the inoculated explants. The co-cultivation of Agrobacterium-strain AGL0, harboring plasmid pJFnptII and rye im-mature embryos in liquid medium allowed a high throughput and facilitated washing of the cultures to avoid Agrobacterium overgrowth. Transgenic plants were phenotypically normal and fully fertile, which might be aconsequence of the short time in tissue culture. The selection with paromomycin exclusively during the regen-eration allowed the efficient recovery of transgenic events without interfering with somatic embryogenesis. Southern blot analysis confirmed the independent nature of the analyzed plants and indicated single copy inserts in more than 50% of them. Segregation analysis confirmed single locus integration and stable transgene expression in most of the lines, while one line with multiple locus integration was also observed. The analysis of T-DNA:: plant DNA boundary sequences revealed examples of exclusion of vector sequences, deletion of a few bases of the T-DNA or insertion of up to 29 bases of the vector backbone. This stresses the importance of detailed analysis of the inserted transgenes in order to identify events with the desired integration profile.     

Investigations of copy number of transgene,fertility and expression level of an introduced GUS gene in transgenic NERICA produced by <Emphasis Type="Italic">Agrobacterium</Emphasis>-mediated methods

In the use of genetic transformation in breeding, there are several possible problems including multiple copy insertion of transgene, sterility caused by somaclonal variation and gene silencing. In this study, we characterized transgenic New Rice for Africa (NERICA) produced by Agrobacterium-mediated methods with respect to copy number of transgene, fertility, and expression level of an introduced GUS gene. Southern blot analysis of primary transformants demonstrated that about half of the events carried a single copy of the transgene regardless of the cell density of Agrobacerium for inoculation. We examined ten procedures, consisting of different time periods and times of subculture for callus formation and the starting times of hygromycin-based selection of transformed cells, for transformation of NERICA cultivars to produce transformants within a short culture period at high frequency. A new culture method developed in this study required only about 1.5 mo from the beginning of tissue culture to transformants, whereas a standard protocol we developed previously needed about 2 mo of culture; however, it did not significantly reduce percentages of sterile plants. Fertile T₀ plants produced fertile T₁ plants at higher frequency. However, fertility was not inherited in a simple fashion: both fertile and partially sterile T₀ plants produced fertile, partially sterile and sterile T₁ plants. Expression assay of an introduced GUS gene revealed position effects in seven independent homozygous transformed lines carrying one copy of the transgene. Points to pay attention to in the use of genetic transformation in breeding are discussed.     

Developmental and hormonal regulation of direct shoot organogenesis and somatic embryogenesis in sugarcane (Saccharum spp. interspecific hybrids) leaf culture

Rapid and efficient in vitro regeneration methods that minimise somaclonal variation are critical for the genetic transformation and mass propagation of commercial varieties. Using a transverse thin cell layer culture system, we have identified some of the developmental and physiological constraints that limit high-frequency regeneration in sugarcane leaf tissue. Tissue polarity and consequently the orientation of the explant in culture, size and developmental phase of explant, and auxin concentration play a significant role in determining the organogenic potential of leaf tissue in culture. Both adventitious shoot production and somatic embryogenesis occurred on the proximal cut surface of the explant, and a regeneration gradient, decreasing gradually from the basal to the distal end, exists in the leaf roll. Importantly, auxin, when added to the culture medium, reduced this spatial developmental constraint, as well as the effect of genotype on plant regeneration. Transverse sections (1-2 mm thick) obtained from young leaf spindle rolls and orienting explants with its distal end facing the medium (directly in contact with medium) are critical for maximum regeneration. Shoot regeneration was observed as early as 3 weeks on MS medium supplemented with alpha-naphthalenencetic acid (NAA) and 6-benzyladenine, while somatic embryogenesis or both adventitious shoot organogenesis and somatic embryogenesis occurred on medium with NAA and chlorophenoxyacetic acid. Twenty shoots or more could be generated from a single transverse section explant. These shoots regenerated roots and successfully established after transplanted to pots. Large numbers of plantlets can be regenerated directly and rapidly using this system. SmartSett, the registered name for this process and the plants produced, will have significant practical applications for the mass propagation of new cultivars and in genetic modification programs. The SmartSett system has already been used commercially to produce substantial numbers of plants of orange rust-resistant and new cultivars in Australia.     

Genetic stability of micropropagated almond plantlets,as assessed by RAPD and ISSR markers

Almond shoots produced by axillary branching from clone VII derived from a seedling of cultivar Boa Casta were evaluated for somaclonal variation using randomly amplified polymorphic DNA (RAPD) and inter-simple sequence repeats (ISSR) analysis. To verify genetic stability we compared RAPD and ISSR patterns of plantlets obtained after 4 and 6 years of in vitro multiplication. A total of 64 RAPD and 10 ISSR primers gave 326 distinct and reproducible band classes, monomorphic across all 22 plantlets analysed. Thus, a total of 7,172 bands were generated, exhibiting homogeneous RAPD and ISSR patterns for the plantlets tested. These results suggest that the culture conditions used for axillary branching proliferation are appropriate for clonal propagation of almond clone VII, as they do not seem to interfere with the integrity of the regenerated plantlets. These results allowed us to establish the use of axillary branching plantlets (mother-plants) as internal controls for the analysis of somaclonal variation of shoots regenerated from other in vitro culture processes performed with clone VII (adventitious regeneration, regeneration from meristem culture, virus sanitation programs and genetic engineering).M. Martins and D. Sarmento contributed equally to this paper     

Clonal Fidelity and Variation in Plantain (Musa AAB) Regenerated from Vegetative Stem and Floral Axis Tips in vitro

Recognition of a phenotypically distinct 'French-type' plantain(Musa AAB) designated 'Superplatano' (Superplantain) promptedevaluation of in vitro micropropagation as a means of generatingsufficient numbers of plants for field evaluation in three locationsin Puerto Rico. A multi-faceted study designed to evaluate relationshipsbetween different aseptic culture procedures and morphologicalorigins of primary explants was carried out. Vegetative budsfrom various positions relative to the mother corm (definedby cardinal points on the compass) and explants from the floralaxis of 'Maricongo' (the 'False-Horn', or florally determinatetype 'progenitor' of 'Superplatano'), and 'Superplatano' (a'French-type') were used as starting materials. Responses underfield conditions were studied using a number of parameters includingyield of commercially marketable fruits. We compared four populationsof shoots, each of which derived from at least three differentshoots from within one mat, shoots derived from vegetative andfloral material from the same mat for both 'Maricongo' and 'Superplatano',and shoots derived from a number of floral buds of the sameclone ('Maricongo') all of which were in culture for the samelength of time. 'Superplatano' was stable whether from vegetativecorm or floral bud apex. This shows conclusively that if thestarting point in the micropropagation process is a stable Musaclone, our tissue culture procedure is reliable. Considerablevariation in bunch phenotype was observed, however, in plantsregenerated from ten of 12 shoot and floral meristems startedfrom the 'False-Horn'-type 'Maricongo'. Change from 'False-Horn'-type(determinate) to 'French'-phenotype (indeterminate) was evidentin each of the three locations. Frequency of bunch reversionvaried from 0·4 to 100%, but was confined to individualoriginating stem tips rather than clones. The most dramaticbunch phenotypic change occurred in plants regenerated fromclone 3. All plants regenerated from shoot 3-North bore 100%'French-type' bunches. However, reversion in plants regeneratedfrom shoot 3-West was only 1·8%, and no bunch phenotypicchange was observed in plants from shoot 3-East. Plants regeneratedfrom both shoot and male floral axis tips in 'Maricongo' clone4 also bore 'French-type' bunches. Frequency of bunch reversionfrom shoot 4-East was 0·4% as compared to 2·6%from 4-floral. Bunch reversion occurred at the frequency of2·0% when plants were regenerated from clone 6-floral.No bunch reversion was observed in plants regenerated from asingle shoot tip in clones 1-West and 5-floral. No dwarfismwas encountered in any of the tissue culture-derived plants.We conclude that tissue culture per se plays a very small role,if any, in the direct induction of off-types. Pre-existing characteristicsof the primary explant determines whether products of a multiplicationshow fidelity or not. Our data suggest that 'Maricongo' is achimera and that 'Superplatano' is revertant off-type that resultswhen breakdown of the chimera occurs. Large numbers of stable'Superplatano' were produced from unstable 'Maricongo' and thisaffirms the value of micropropagation for generation of cloneswith desirable bunch phenotype.Copyright 1993, 1999 AcademicPress Musa, plantains, bananas, tissue culture, clonal multiplication, somaclonal variation, phenotype