Particle bombardment technology and its applications in plants

Particle bombardment, or biolistics, has emerged as an excellent alternative approach for plant genetic transformation which circumvents the limitations of Agrobacterium-mediated genetic transformation. The method has no biological constraints and can transform a wide range of plant species. Besides, it has been the most efficient way to achieve organelle transformation (for both chloroplasts and mitochondria) so far. Along with the recent advances in genome editing technologies, conventional gene delivery tools are now being repurposed to deliver targeted gene editing reagents into the plants. One of the key advantages is that the particle bombardment allows DNA-free gene editing of the genome. It enables the direct delivery of proteins, RNAs, and RNPs into plants. Owing to the versatility and wide-range applicability of the particle bombardment, it will likely remain one of the major genetic transformation methods in the future. This article provides an overview of the current status of particle bombardment technology and its applications in the field of plant research and biotechnology.

Integration, abundance, and transmission of mutations and transgenes in a series of CRISPR/Cas9 soybean lines

BACKGROUND

As with many plant species, current genome editing strategies in soybean are initiated by stably transforming a gene that encodes an engineered nuclease into the genome. Expression of the transgene results in a double-stranded break and repair at the targeted locus, oftentimes resulting in mutation(s) at the intended site. As soybean is a self-pollinating species with 20 chromosome pairs, the transgene(s) in the T0 plant are generally expected to be unlinked to the targeted mutation(s), and the transgene(s)/mutation(s) should independently assort into the T1 generation, resulting in Mendellian combinations of transgene presence/absence and allelic states within the segregating family. This prediction, however, is not always consistent with observed results.

RESULTS

In this study, we investigated inheritance patterns among three different CRISPR/Cas9 transgenes and their respective induced mutations in segregating soybean families. Next-generation resequencing of four T0 plants and four T1 progeny plants, followed by broader assessments of the segregating families, revealed both expected and unexpected patterns of inheritance among the different lineages. These unexpected patterns included: (1) A family in which T0 transgenes and mutations were not transmitted to progeny; (2) A family with four unlinked transgene insertions, including two respectively located at paralogous CRISPR target break sites; (3) A family in which mutations were observed and transmitted, but without evidence of transgene integration nor transmission.

CONCLUSIONS

Genome resequencing provides high-resolution of transgene integration structures and gene editing events. Segregation patterns of these events can be complicated by several potential mechanisms. This includes, but is not limited to, plant chimeras, multiple unlinked transgene integrations, editing of intended and paralogous targets, linkage between the transgene integration and target site, and transient expression of the editing reagents without transgene integration into the host genome.

Biolistic Transformation of Wheat

The wheat genome encodes some 100,000 genes. To understand how the expression of these genes is regulated it will be necessary to carry out many genetic transformation experiments. Robust protocols that allow scientists to transform a wide range of wheat genotypes are therefore required. In this chapter, we describe a protocol for biolistic transformation of wheat that uses immature embryos and small quantities of DNA cassettes. An original method for DNA cassette purification is also described. This protocol can be used to transform a wide range of wheat genotypes and other related species.

Agrobacterium-Mediated Transformation of Leaf Base Segments

Agrobacterium-mediated transformation has become a routine method of genetic engineering of cereals, gradually replacing the biolistic protocols. Simple integration patterns of transgenic loci, decent transformation efficiency, and technical simplicity are the main advantages offered by this method. Here we present a detailed protocol for the production of transgenic oat plants by Agrobacterium-mediated transformation of leaf base segments. The use of leaf explants as target tissues for transformation and in vitro regeneration of transgenic plants may be a good alternative for genotypes which are not susceptible to regeneration from immature or mature embryos. We also describe the biochemical and molecular analysis procedures of the transgenic plants including a GUS histochemical assay, and Southern blot, both of which are optimized for application in oat.

Extended Chromatin and DNA Fibers from Active Plant Nuclei for High-resolution FISH

The conventional protocol for isolation of cell wall free nuclei for release of DNA fibers for plants involves mechanical removal of the cell wall and separation of debris by sieve filtration. The mechanical grinding pressure applied during the process leaves only the more tolerant G(1) nuclei intact, and all other states of active nuclei that may be present in the target tissues (e.g., leaf) are simply crushed/disrupted during the isolation process. Here we describe an alternative enzymatic protocol for isolation of nuclei from root tip tissue. Cell wall free nuclei at a given stage of cell cycle, free of any cell debris, could be realized in suspension that are fit for preparation of extended fibers suitable for fiber FISH applications. The protocol utilizes selective harvest of active nuclei from root tip tissue in liquid suspension under the influence of cell wall-degrading enzymes, and provides opportunities to target cell cycle-specific nuclei from interphase through division phase for the release of extended DNA fibers. Availability of cell cycle-specific fibers may have added value in transcriptional analysis, DNA:RNA hybridization, visualization of DNA replication and replication forks, and improved FISH efficiency.

High-throughput analysis pipeline for achieving simple low-copy wheat and barley transgenics

Transgenic (or genetically modified-GM) plant breeding is increasingly being used as a supplementary tool to many classical plant-breeding programs. Currently the range of transgenic traits accepted for commercial use is largely restricted to herbicide and pest resistance. Given the fact that transgenics can offer an alternative and novel source of genetic variation, pre-breeding research is now increasingly exploiting this technology to tackle a greater spectrum of traits. These traits range from abiotic stress tolerance to improved product quality and nutritional characteristics. Likewise there is an increasing demand for high-throughput methodologies for transgenic plant generation, characterization and phenotyping. Selecting simple low-copy number transgenic events that are both heritable and stably expressed "in planta" is considered a prerequisite to systematic phenotyping for traits of interest. Furthermore, this assessment relies heavily on comparisons to appropriate control plants, in the case of wheat and barley transgenics this is both wild-type and null siblings. This chapter presents a general scheme on which to base selection of transgenics and respective null siblings using wheat and barley as an example. This scheme can be adapted to other similar crop species. Overall this strategy reduces the total number of plants to be genotyped and phenotyped at each generational step, and therefore resulting in significant savings in time, effort, and resources.

Oat (Avena sativa L.)

Agrobacterium-mediated transformation is a suitable method to transform different cultivars using different systems of A. tumefaciens strains and binary vectors as well as selection cassettes. We describe here a detailed protocol for two cultivars, one naked and one husked, using the AGL1 strain and the pGreen vector containing the nptII selection cassette ( http://www.pgreen.ac.uk/ ), suitable for oat as well as other cereals. The pGreen vector system was recently developed for pBract ( http://www.bract.org/ ) and its transformation ability for cereals was proved. Assuming our experience and the latest knowledge on Agrobacterium-mediated transformation of cereals, we suggest using in the protocol one of the newly developed pBract or pCAMBIA ( http://www.cambia.org/daisy/cambia/ ) vector systems which carry different selection cassettes. The commonly used selection genes nptII, bar, and hpt were proved to be applicable for oat transformation and might be used as needed.

Evaluation of designer crops for biosafety--a scientist's perspective

With the advent of transgenic technology, it has become possible to mobilize and express foreign genes into plants and to design crop varieties with better agronomic attributes and adaptability to challenging environmental conditions. Recent advances in transgenic technology have led to concerns about safety of transgenic crops to human and animal health and environment. Biosafety focuses on preventing, minimizing and eliminating risks associated with the research, production, and use of transgenic crops. Food biosafety involves studies of substantial equivalence related to compositional analysis, toxicity and allergenicity. Environmental biosafety involves glasshouse and field trials and study of unintended effects on non-target organisms. Transgenics are characterized at phenotypic and molecular levels for understanding the location of transgene insertion site, ploidy level, copy number, integrated vector sequences, protein expression and stability of the transgene. Various techniques employed for transgene characterization include flow cytometry, southern, northern and western analyses, real-time (qRT) PCR, competitive PCR, FISH, fiber-FISH, DNA micro-arrays, mRNA profiling, 2DE-MS, iTRAQ, FT-MS, NMR, GC-MS, CE-MS and biosensor-based approaches. Evaluation of transgene expression involves the application of integrated phenomics, transcriptomics, proteomics and metabolomics approaches. However, the relevance and application of these approaches may vary in different cases. The elaborate analysis of transgenic crops will facilitate the safety assessment and commercialization of transgenics and lead to global food security for the future.

The application of GMOs in agriculture and in food production for a better nutrition: two different scientific points of view

This commentary is a face-to-face debate between two almost opposite positions regarding the application of genetic engineering in agriculture and food production. Seven questions on the potential benefits of the application of genetic engineering in agriculture and on the potentially adverse impacts on the environment and human health were posed to two scientists: one who is sceptical about the use of GMOs in Agriculture, and one who views GMOs as an important tool for quantitatively and qualitatively improving food production.

An affinity-based genome walking method to find transgene integration loci in transgenic genome

Identifying a good transgenic event from the pool of putative transgenics is crucial for further characterization. In transgenic plants, the transgene can integrate in either single or multiple locations by disrupting the endogenes and/or in heterochromatin regions causing the positional effect. Apart from this, to protect the unauthorized use of transgenic plants, the signature of transgene integration for every commercial transgenic event needs to be characterized. Here we show an affinity-based genome walking method, named locus-finding (LF) PCR (polymerase chain reaction), to determine the transgene flanking sequences of rice plants transformed by Agrobacterium tumefaciens. LF PCR includes a primary PCR by a degenerated primer and transfer DNA (T-DNA)-specific primer, a nested PCR, and a method of enriching the desired amplicons by using a biotin-tagged primer that is complementary to the T-DNA. This enrichment technique separates the single strands of desired amplicons from the off-target amplicons, reducing the template complexity by several orders of magnitude. We analyzed eight transgenic rice plants and found the transgene integration loci in three different chromosomes. The characteristic illegitimate recombination of the Agrobacterium sp. was also observed from the sequenced integration loci. We believe that the LF PCR should be an indispensable technique in transgenic analysis.

Agrobacterium-mediated transformation of oat (Avena sativa L.) cultivars via immature embryo and leaf explants

This paper reports on the successful Agrobacterium-mediated transformation of oat, and on some factors influencing this process. In the first step of the experiments, three cultivars, two types of explant, and three combinations of strain/vectors, which were successfully used for transformation of other cereals were tested. Transgenic plants were obtained from the immature embryos of cvs. Bajka, Slawko and Akt and from leaf base explants of cv. Bajka after transformation with A. thumefaciens strain LBA4404(pTOK233). The highest transformation rate (12.3%) was obtained for immature embryos of cv. Bajka. About 79% of the selected plants proved to be transgenic; however, only 14.3% of the T(0) plants and 27.5% of the T(1) showed GUS expression. Cell competence of both types of explant differed in terms of their transformation ability and transgene expression. The next step of the study was to test the suitability for oat transformation of the pGreen binary vector combined with different selection cassettes: nptII or bar under the nos or 35S promoter. Transgenic plants were selected in combinations transformed with nos::nptII, 35S::nptII and nos::bar. The highest transformation efficiency (5.3%) was obtained for cv. Akt transformed with nos::nptII. A detailed analysis of the T(0) plants selected from a given callus line and their progeny revealed that they were the mixture of transgenic, chimeric-transgenic and non-transgenic individuals. Southern blot analysis of T(0) and T(1) showed simple integration pattern with the low copy number of the introduced transgenes.

Characterisation of 3' transgene insertion site and derived mRNAs in MON810 YieldGard maize

The construct inserted in YieldGard MON810 maize, produced by Monsanto, contains the CaMV 35S promoter, the hsp70 intron of maize, the cryI(A)b gene for resistance to lepidopterans and the NOS terminator. In a previous work a truncation event at the 3' end of the cryI(A)b gene leading to the complete loss of the NOS terminator was demonstrated. The 3' maize genome junction region was isolated in the same experiment not showing any homology with known sequences. The aim of the experiments here reported was therefore to isolate and characterize a larger portion of the 3' integration junction from genomic DNA of two commercial MON810 maize lines. Specific primers were designed on the 3' integration junction sequence for the amplification of a 476 bp fragment downstream of the sequence previously detected. In silico analysis identified the whole isolated 3' genomic region as a gene putatively coding for the HECT E3 ubiquitin ligase. RT-PCR performed in this region produced cDNA variants of different length. In silico translation of these transcripts identified 2 and 18 putative additional aminoacids in different variants, all derived from the adjacent host genomic sequences, added to the truncated CRY1A protein. These putative recombinant proteins did not show homology with any known protein domains. Our data gave new insights on the genomic organization of MON810 in the YieldGard maize and confirmed the previous suggestion that the integration in the genome of maize caused a complex recombination event without, apparently, interfering with the activity of the partial CRY1A endotoxin and both the vigor and yield of the YieldGard maize.

Variable T-DNA linkage configuration affects inheritance of carotenogenic transgenes and carotenoid accumulation in transgenic indica rice

Transgenics for the expression of beta-carotene biosynthetic pathway in the endosperm were developed in indica rice background by introducing phytoene synthase (psy) and phytoene desaturase (crtI) genes through Agrobacterium-mediated transformation, employing non-antibiotic positive selectable marker phosphomannose isomerase (pmi). Twenty-seven transgenic lines were characterized for the structural organization of T-DNA inserts and the expression of transgenes in terms of total carotenoid and beta-carotene accumulation in the endosperm. Ten lines were also studied for the inheritance of transgenic loci to the T(1) progenies. Copy number and sites of integration of the transgenes ranged from one to four. Almost 50% of the transgenic lines showed rearrangement of T-DNA inserts. However, most of the rearrangements occurred in the crtI expression cassette which is adjacent to the right T-DNA border. Differences in copy numbers of psy and crtI were also observed indicating partial T-DNA integration. Beyond T-DNA border transfer was also detected in 25% of the lines. Fifty percent of the lines studied showed single Mendelian locus inheritance, while two lines showed bi-locus inheritance in the T(1) progenies. Some of the lines segregating in 3:1 ratio showed two sites of integration on restriction digestion analysis indicating that the T-DNA insertion sites were tightly linked. Three transgenic lines showed nonparental types in the segregating progenies, indicating unstable transgenic locus. Evidences from the HPLC analysis showed that multiple copies of transgenes had a cumulative effect on the accumulation of carotenoid in the endosperm. T(1) progenies, in general, accumulated more carotenoids than their respective parents, the highest being 6.77 mug/g of polished seeds. High variation in the carotenoid accumulation was observed within the T(1) progenies which could be attributed to the variation in the structural organization and expression of transgenes, minor variations in the genetic background within the progeny plants, or differences in the plant microenvironments. The study identified lines worthy of further multiplication and breeding based on transgene structural integrity in the segregating progeny and high expression levels in terms of the beta-carotene accumulation.

Microsatellite megatracts in the maize (Zea mays L.) genome

Long tracts (megatracts) of (CAG)n, (TAG)n, and (GAA)n microsatellite sequences capable of forming composite DNA segments were found in the maize (Zea mays L.) genome. Some of the (CAG)n and (TAG)n megatracts were organized in clusters of up to 1 Mb on several chromosomes, as detected by fluorescence in situ hybridization (FISH), as well as on extended DNA fibers. Extensive polymorphism was found among different maize inbred lines with respect to the number and size of microsatellite megatract clusters on the A chromosomes. Polymorphism was also common among B chromosomes of different nuclei in the inbred line Zapalote Chico. Different retrotransposable elements were often inserted into the microsatellite tracts. Size variation in some (TAG)n and (GAA)n megatracts was observed in consecutive generations among siblings of the inbred lines, indicating that these loci are highly unstable and predisposed to dynamic mutations similar to those described in mammalian systems.

In situ methods to localize transgenes and transcripts in interphase nuclei: a tool for transgenic plant research

Genetic engineering of commercially important crops has become routine in many laboratories. However, the inability to predict where a transgene will integrate and to efficiently select plants with stable levels of transgenic expression remains a limitation of this technology. Fluorescence in situ hybridization (FISH) is a powerful technique that can be used to visualize transgene integration sites and provide a better understanding of transgene behavior. Studies using FISH to characterize transgene integration have focused primarily on metaphase chromosomes, because the number and position of integration sites on the chromosomes are more easily determined at this stage. However gene (and transgene) expression occurs mainly during interphase. In order to accurately predict the activity of a transgene, it is critical to understand its location and dynamics in the three-dimensional interphase nucleus. We and others have developed in situ methods to visualize transgenes (including single copy genes) and their transcripts during interphase from different tissues and plant species. These techniques reduce the time necessary for characterization of transgene integration by eliminating the need for time-consuming segregation analysis, and extend characterization to the interphase nucleus, thus increasing the likelihood of accurate prediction of transgene activity. Furthermore, this approach is useful for studying nuclear organization and the dynamics of genes and chromatin.

Transgene integration in plants: poking or patching holes in promiscuous genomes?

Transgene integration in plants transformed by either Agrobacterium or direct DNA delivery methods occurs through illegitimate recombination (IR). The precise mechanism(s) for IR-mediated transgene integration and the role of host double-strand break repair enzymes remain unknown. A recent wealth of sequenced transgene loci and investigations aimed at genetically dissecting transgene integration mechanism(s) have provided new insights into the process.

Simple and complex nuclear loci created by newly transferred chloroplast DNA in tobacco

Transfer of organelle DNA into the nuclear genome has been significant in eukaryotic evolution, because it appears to be the origin of many nuclear genes. Most studies on organelle DNA transfer have been restricted to evolutionary events but experimental systems recently became available to monitor the process in real time. We designed an experimental screen to detect plastid DNA (ptDNA) transfers to the nucleus in whole plants grown under natural conditions. The resultant genotypes facilitated investigation of the evolutionary mechanisms underlying ptDNA transfer and nuclear integration. Here we report the characterization of nuclear loci formed by integration of newly transferred ptDNA. Large, often multiple, fragments of ptDNA between 6.0 and 22.3 kb in size are incorporated into chromosomes at single Mendelian loci. The lack of chloroplast transcripts of comparable size to the ptDNA integrants suggests that DNA molecules are directly involved in the transfer process. Microhomology (2-5 bp) and rearrangements of ptDNA and nuclear DNA were frequently found near integration sites, suggesting that nonhomologous recombination plays a major role in integration. The mechanisms of ptDNA integration appear similar to those of biolistic transformation of plant cells, but no sequence preference was identified near junctions. This article provides substantial molecular analysis of real-time ptDNA transfer and integration that has resulted from natural processes with no involvement of cell injury, infection, and tissue culture. We highlight the impact of cytoplasmic organellar genome mobility on nuclear genome evolution.

Complex transgene locus structures implicate multiple mechanisms for plant transgene rearrangement

To more fully characterize the internal structure of transgene loci and to gain further understanding of mechanisms of transgene locus formation, we sequenced more than 160 kb of complex transgene loci in two unrelated transgenic oat (Avena sativa L.) lines transformed using microprojectile bombardment. The transgene locus sequences from both lines exhibited extreme scrambling of non-contiguous transgene and genomic fragments recombined via illegitimate recombination. A perfect direct repeat of the delivered DNA, and inverted and imperfect direct repeats were detected in the same transgene locus indicating that homologous recombination and synthesis-dependent mechanism(s), respectively, were also involved in transgene locus rearrangement. The most unexpected result was the small size of the fragments of delivered and genomic DNA incorporated into the transgene loci via illegitimate recombination; 50 of the 82 delivered DNA fragments were shorter than 200 bp. Eleven transgene and genomic fragments were shorter than the DNA lengths required for Ku-mediated non-homologous end joining. Detection of these small fragments provided evidence that illegitimate recombination was most likely mediated by a synthesis-dependent strand-annealing mechanism that resulted in transgene scrambling. Taken together, these results indicate that transgene locus formation involves the concerted action of several DNA break-repair mechanisms.