Stefan Malepszy

Unintended consequences of plant transformation: a molecular insight.

Plant genomes are dynamic structures having both the system to maintain and accurately reproduce the information encoded therein and the ability to accept more or less random changes, which is one of the foundations of evolution. Crop improvement and various uncontrolled stress factors can induce unintended genetic and epigenetic variations. In this review it is attempted to summarize factors causing such changes and the molecular nature of these variations in transgenic plants. Unintended effects in transgenic plants can be divided into three main groups: first, pleiotropic effects of integrated DNA on the host plant genome; second, the influence of the integration site and transgene architecture on transgene expression level and stability; and third, the effect of various stresses related to tissue handling, regeneration and clonal propagation. Many of these factors are recently being redefined due to new researches, which apply modern highly sensitive analytical techniques and sequenced model organisms. The ability to inspect large portions of genomes clearly shows that tissue culture contributes to a vast majority of observed genetic and epigenetic changes. Nevertheless, monitoring of thousands transcripts, proteins and metabolites reveals that unintended variation most often falls in the range of natural differences between landraces or varieties. We expect that an increasing amount of evidence on many important crop species will support these observations in the nearest future.

The Genome Sequence of the North-European Cucumber (Cucumis sativus L.) Unravels Evolutionary Adaptation Mechanisms in Plants

Cucumber (Cucumis sativus L.), a widely cultivated crop, has originated from Eastern Himalayas and secondary domestication regions includes highly divergent climate conditions e.g. temperate and subtropical. We wanted to uncover adaptive genome differences between the cucumber cultivars and what sort of evolutionary molecular mechanisms regulate genetic adaptation of plants to different ecosystems and organism biodiversity. Here we present the draft genome sequence of the Cucumis sativus genome of the North-European Borszczagowski cultivar (line B10) and comparative genomics studies with the known genomes of: C. sativus (Chinese cultivar – Chinese Long (line 9930)), Arabidopsis thaliana, Populus trichocarpa and Oryza sativa. Cucumber genomes show extensive chromosomal rearrangements, distinct differences in quantity of the particular genes (e.g. involved in photosynthesis, respiration, sugar metabolism, chlorophyll degradation, regulation of gene expression, photooxidative stress tolerance, higher non-optimal temperatures tolerance and ammonium ion assimilation) as well as in distributions of abscisic acid-, dehydration- and ethylene-responsive cis-regulatory elements (CREs) in promoters of orthologous group of genes, which lead to the specific adaptation features. Abscisic acid treatment of non-acclimated Arabidopsis and C. sativus seedlings induced moderate freezing tolerance in Arabidopsis but not in C. sativus. This experiment together with analysis of abscisic acid-specific CRE distributions give a clue why C. sativus is much more susceptible to moderate freezing stresses than A. thaliana. Comparative analysis of all the five genomes showed that, each species and/or cultivars has a specific profile of CRE content in promoters of orthologous genes. Our results constitute the substantial and original resource for the basic and applied research on environmental adaptations of plants, which could facilitate creation of new crops with improved growth and yield in divergent conditions.

Variable properties of transgenic cucumber plants containing the thaumatin II gene from Thaumatococcus daniellii

Thaumatin represents a unique class of the sweet-tasting plant proteins. Transgenic cucumber (Cucumis sativus L.) plants with stable integrated constructs consisting of the cauliflower mosaic virus 35S promoter and thaumatin II cDNA were produced. Transformed cucumber plants were obtained using Agrobacterium tumefaciens, with one, two or five integration sites in diploid cucumber and with inheritance confirmed by a 3:1 Mendelian ratio and normal morphologies and viable seeds. Inter- and intra-transformant variabilities in the expression of the thaumatin II gene were observed. The variability was independent of integrated copy number of the T-DNA. Variation in thaumatin II protein accumulation levels in the ripe fruits and the lack of correlation between protein and mRNA levels were observed, suggesting that thaumatin may be controlled at the levels of both transcription and translation. Transgenic fruits accumulating thaumatin II protein exhibited sweet phenotype and positive correation between thaumatin accumulation levels and sweet taste intensity was noticed. Thaumatin II belongs to the pathogenesis-related (PR) proteins family. Some of the T2 progeny plants expressing thaumatin II protein did not exhibit tolerance for pathogenic fungus Pseudoperonospora cubensis. These results, together with previously reported results, suggest no relationship between transgenic protein levels and the increased tolerance phenotype.

The DefH9-iaaM-containing construct efficiently induces parthenocarpy in cucumber.

Parthenocarpy (seedless fruits) is a desirable trait that has been achieved in many plant cultivars. We generated parthenocarpic cucumber fruits by introducing the chimeric DefH9-iaaM construct into the cucumber genome using an Agrobacterium tumefaciens-mediated protocol. The construct consists of the DefH9 promoter from Antirrhinum majus and the iaaM coding sequence from Pseudomonas syringae. Transgenic plants were obtained from nine independent transformation events: half of these were tetraploid and did not produce seeds following self-pollination, while the remaining half were capable of displaying parthenocarpy in the subsequent reproductive generation. Of the fruits produced by the transgenic lines, 70–90% were parthenocarpic. The segregation of the marker gene in the transgenic T1 progeny indicated single gene inheritance. The seed set in the transgenic lines and their F1 hybrids was lower than in the non-transgenic control plants. Some of the methodological details and the practical significance of the results are discussed.

Characterization of CsSEF1 gene encoding putative CCCH-type zinc finger protein expressed during cucumber somatic embryogenesis.

Somatic embryos obtained in vitro are a form of vegetative reproduction that can be used in artificial seed technology, as well as a model to study the principles of plant development. In order to isolate the genes involved in somatic embryogenesis of the cucumber (Cucumis sativus L.), we utilized the suppression subtractive hybridization (SSH). One of the obtained sequences was the CsSEF1 clone (Cucumis sativus Somatic Embryogenesis Zinc Finger 1), with a level of expression that sharply increased with the induction of embryogenesis. The full length cDNA of CsSEF1 encodes the putative 307 amino acid long protein containing three zinc finger motifs, two with CCCH and one with the atypical CHCH pattern. The CsSEF1 protein shows significant similarity to other proteins from plants, in which the zinc fingers arrangement and patterns are very similar. Transcripts of CsSEF1 were localized in the apical part of somatic embryos, starting as early as the polarity was visible and in later developmental stages marking the cotyledon primordia and procambium tissues. As a result of transferring an antisense fragment of CsSEF1 into Arabidopsis thaliana abnormalities in zygotic embryos and also in cotyledons and root development were observed.

The relationship between the regeneration system and genetic variability in the cucumber (Cucumis sativus L.)

Somaclonal variation in the Borszczagowski line of Cucumis sativus L. was determined for five regeneration systems: micropropagation (MP), direct leaf callus regeneration (DLR), leaf callus regeneration (LCR), recurrent leaf callus regeneration (RLCR), and direct protoplast regeneration (DPR). The frequency at which new phenotypes appeared in R1 lines and the stability of the rDNA region analysed using of five probes were investigated. MP was not subject to change, while DLR caused only infrequent changes. The highest frequency of change arose through DPR (90% of lines) and RLCR (42.8%), as opposed to 5.9% with LCR. Tetraploids were produced only in the case of LCR (4.7%) and RLCR (28%).

The complete structure of the cucumber (Cucumis sativus L.) chloroplast genome: Its composition and comparative analysis

The complete nucleotide sequence of the cucumber (C. sativus L. var. Borszczagowski) chloroplast genome has been determined. The genome is composed of 155,293 bp containing a pair of inverted repeats of 25,191 bp, which are separated by two single-copy regions, a small 18,222-bp one and a large 86,688-bp one. The chloroplast genome of cucumber contains 130 known genes, including 89 protein-coding genes, 8 ribosomal RNA genes (4 rRNA species), and 37 tRNA genes (30 tRNA species), with 18 of them located in the inverted repeat region. Of these genes, 16 contain one intron, and two genes and one ycf contain 2 introns. Twenty-one small inversions that form stem-loop structures, ranging from 18 to 49 bp, have been identified. Eight of them show similarity to those of other species, while eight seem to be cucumber specific. Detailed comparisons of ycf2 and ycf15, and the overall structure to other chloroplast genomes were performed.

Relationship between somaclonal variation and type of culture in cucumber

Highly inbred B line of cucumber was used to compare the effect of four types of in vitro culture on somaclonal variation. The plants were regenerated from the following types of culture: twelve- and eighteen-month-old liquid culture of meristematic clumps (LMC12(18)), ten-month-old embryogenic cytokinin-dependent suspension (CDS), eighteen-month-old embryogenic cytokinin-dependent suspension in medium with modified NH+4/NO3- ratio (CDS 1.7), twelve-month-old embryogenic auxin-dependent suspension (ADS), thirty six-month-old embryogenic auxin-dependent suspension in medium with modified NH+4/NO3- ratio (ADS 1.7) and recurrent leaf callus regeneration (RLC) – repeated 5 times. The differences in the incidence of the following properties were observed: the ploidy of R0 plants, the segregation of new morphological traits in R1 and the germination ability of R1 seeds. R1 families with the segregation of new phenotypes were most numerous in CDS (62.5%) and LMC18 (57.9%), next in CDS1.7 (35.7%), while the smallest number was found in LMC12 (11.1%) and RLC (3.4%).Tetraploid and mixoploid plants occurred in ADS1.7 and ADS (100%) whereas CDS and RLC were observed to contain only tetraploids, respectively 33.3% and 55.2%. There were no changes of ploidy after LMC12, LMC18 and CDS1.7. Among new phenotypes there were such that have not been described so far in cucumber: ginkgolike leaf (gll), yellow-green chlorophyll mutants (y-gc), serrate margin of corolla in male and female flowers (smc).

The MADS-box gene CUS1 is expressed during cucumber somatic embryogenesis

Abstract We report the isolation and characterisation of cDNA and genomic clones of a MADS-box gene which is expressed in cucumber fruit and somatic embryos. The cDNA clone was isolated using a heterologous probe, MADS-box cDNA fragments from Antirrhinum majus. The CUS1 cDNA clone was sequenced and the deduced amino acid sequence is highly similar to the products of the the PLENA gene from Antirrhinum majus, of the FBP6 gene from Petunia hybrida and of the AGL1 and AGL5 genes from Arabidopsis thaliana. The presence of single copy of CUS1 and a family of related genes in the cucumber genome was demonstrated by Southern blots. The 1050 bases long CUS1 transcript was only detected in embryogenic callus, in fruit and weakly in female flowers, and was absent in non-embryogenic callus and other organs of the seedling and mature plant. More specifically the CUS1 transcript was detected only in the outer cell layers of the radicular part of the heart stage somatic embryo, in transmitting tissue of female flowers and in tissues surrounding the ovules. The structure of the CUS1 gene was determined.

The influence of genotype and medium on rye (Secale cereale L.) anther culture

Anthers of three rye inbred lines - L9, L318, Dw28, one synthetic hybrid - F1(5) and one variety, Dańkowskie Zote (DZ), were cultured on two media based on N6, and two based on P2 components. The induction rate significantly depended on genotype - the best results were obtained for line L318 and the lowest percentage of responding anthers was noticed in line L9. There was no universal medium for all tested genotypes. The highest induction rate (IR) for lines L318, L9 and hybrid F1(5) was obtained on medium CI (11.94, 0.71 and 1.75 respectively). For DZ, the P2I medium was better than the others while for Dw28 CIP turned to be as suitable as CI. A highly significant interaction between genotype and medium was proved. Single anthers of DZ, L318 and L9 produced embryos on CI, CIP and P2I media. They did not develop into plants but after transferring them to CS1.7 medium, a secondary, embryogenic callus was obtained. Such a reaction has not been described in rye until now. In spite of a relatively high IR, plant regeneration was rather poor. An elaboration of this step in haploid production is needed. Most of the analyzed calluses and microspore derived regenerants proved to be haploids, according to flow cytometry analysis. Plants treated with colchicine were doubled haploids.