Application of qRT-PCR and RNA-Seq analysis for the identification of housekeeping genes useful for normalization of gene expression values during Striga hermonthica development.

Striga is a root parasitic weed that attacks many of the staple crops in Africa, India and Southeast Asia, inflicting tremendous losses in yield and for which there are few effective control measures. Studies of parasitic plant virulence and host resistance will be greatly facilitated by the recent emergence of genomic resources that include extensive transcriptome sequence datasets spanning all life stages of S. hermonthica. Functional characterization of Striga genes will require detailed analyses of gene expression patterns. Quantitative real-time PCR is a powerful tool for quantifying gene expression, but correct normalization of expression levels requires identification of control genes that have stable expression across tissues and life stages. Since no S. hermonthica housekeeping genes have been established for this purpose, we evaluated the suitability of six candidate housekeeping genes across key life stages of S. hermonthica from seed conditioning to flower initiation using qRT-PCR and high-throughput cDNA sequencing. Based on gene expression analysis by qRT-PCR and RNA-Seq across heterogeneous Striga life stages, we determined that using the combination of three genes, UBQ1, PP2A and TUB1 provides the best normalization for gene expression throughout the parasitic life cycle. The housekeeping genes characterized here provide robust standards that will facilitate powerful descriptions of parasite gene expression patterns.

Procaryotic genomic DNA inhibits mammalian cell transformation.

Ltk- mouse cells were transformed to thymidine kinase prototrophy in the presence of carrier DNAs isolated from different organisms. Procaryotic genomic and phage DNA was consistently less effective as a carrier than was eucaryotic DNA. Mixing experiments indicate that DNA of procaryotic origin inhibits mammalian cell transformation.

Host-plant recognition by parasitic Scrophulariaceae.

Parasitic plants in the Scrophulariaceae invade the roots of neighboring plants in order to rob them of water and nutrients. A distinctive feature of these parasites is their ability to cue their development to small molecules released by host-plant roots. Evidence is continuing to emerge that parasite perception of host factors occurs via a redox-associated mechanism. Genes predicted to function during the early stages of parasite-host interactions have been cloned from both plant partners, and their characterization is providing a genetic framework on which to model subterranean plant-plant interactions.

Parasitic plant responses to host plant signals: a model for subterranean plant-plant interactions.

The ability of plants to fulfill nutritional needs by parasitizing neighboring plants has originated several times in angiosperm evolution. Molecular tools are now being exploited to investigate the evolutionary origins of plant parasitism and to dissect the genetic mechanisms governing parasitic plant-host plant interactions. Investigating the nature of signal exchanges between parasitic plants and their hosts serves as a tractable system for understanding how plants in general communicate in the environment. This work should also lead to the development of novel strategies for minimizing the devastation caused by parasitic weeds in international agriculture.

Ac-induced instability at the Xanthophyllic locus of tomato.

To detect genomic instability caused by Ac elements in transgenic tomatoes, we used the incompletely dominant mutation Xanthophyllic-1 (Xa-1) as a whole plant marker gene. Xa-1 is located on chromosome 10 and in the heterozygote state causes leaves to be yellow. Transgenic Ac-containing tomato plants which differed in the location and number of their Ac elements were crossed to Xa-1 tester lines and F1 progeny were scored for aberrant somatic sectoring. Of 800 test and control F1 progeny screened, only four plants had aberrantly high levels of somatic sectors. Three of the plants had twin sectors consisting of green tissue adjacent to white tissue, and the other had twin sectors comprised of green tissue adjacent to tissue more yellow than the heterozygote background. Sectoring was inherited and the two sectoring phenotypes mapped to opposite homologs of chromosome 10; the green/yellow sectoring phenotype mapped in coupling to Xa-1 while the green/white sectoring phenotype mapped in repulsion. The two sectoring phenotypes cosegregated with different single, non-rearranged Acs, and loss of these Acs from the genome corresponded to the loss of sectoring. Sectoring was still observed after transposition of the Ac to a new site which indicated that sectoring was not limited to a single locus. In both sectored lines, meiotic recombination of the sectoring Ac to the opposite homolog caused the phenotype to switch between the green/yellow and the green/white phenotypes. Thus the two different sectoring phenotypes arose from the same Ac-induced mechanism; the phenotype depended on which chromosome 10 homolog the Ac was on. We believe that the twin sectors resulted from chromosome breakage mediated by a single intact, transposition-competent Ac element.

Sexual transmission of transposed activator elements in transgenic tomatoes.

The transmission of transposed Ac elements in progeny derived by self-pollination of ten transformed tomato plants has been examined by Southern hybridization analysis. We show that six of these primary transformants have transmitted a transposed Ac to at least one progeny. One of the families was segregating for at least two different insertion events. In five of ten families, progeny were detected that contained a transposed Ac but no donor T-DNA sequences, indicating that a recombination event occurred between the original and new Ac insertion site. Somatic transposition of Ac as late as the R2 generation is evidenced. One family contained an empty donor site fragment but Ac was not detected in either the parent or progeny, indicating Ac was lost in this population early in regeneration. While four of ten families were segregating for aberrant phenotypes, there was no evidence that the mutated gene was linked to a transposed Ac.

Complementation of the Tomato anthocyanin without (aw) Mutant Using the Dihydroflavonol 4-Reductase Gene.

We isolated the dihydroflavonol 4-reductase (DFR) gene from tomato (Lycopersicon esculentum) using a previously characterized cDNA as probe. Earlier studies had indicated that the DFR gene is present in tomato as a single gene located on chromosome 2 near the locus anthocyanin without (aw). Mutant alleles of the aw locus result in the complete absence of anthocyanin pigmentation throughout all stages of plant development. When the genomic DFR clone was introduced by Agrobacterium-mediated transformation into plants bearing the aw mutation, primary transgenic seedlings accumulated anthocyanins that could be observed while the plants were still in tissue culture and which continued to be observed as the plants matured. Progeny of self pollinated and backcrossed transgenic plants segregated for anthocyanin pigmentation, and Southern hybridization analyses indicated the presence of the DFR transgene exclusively in those plants with pigmentation. These data indicate that the aw locus likely corresponds to the structural gene for DFR and that DFR can be used as a visual, nondestructive, plant-derived marker gene for tomato.

Differential RNA expression of alpha-expansin gene family members in the parasitic angiosperm Triphysaria versicolor (Scrophulariaceae).

Haustoria are parasitic plant specific organs that locate, attach to, and invade host plant tissues. Parasitic species of the Scrophulariaceae develop haustoria on their roots in response to chemical signals released by host plant roots. Haustorium development was induced in vitro in roots of the parasitic Scrophulariaceae Triphysaria versicolor by treating them with exudates obtained from maize roots, the chemical 2,6-dimethoxybenzoquinone (DMBQ) or the cytokinin 6-benzylaminopurine (BAP). Morphological responses of T. versicolor roots to these haustoria inducing factors (HIFs) included localized swelling and epidermal hair proliferation near the root tips. These responses were not observed when roots of the non-parasitic Scrophulariaceae Lindenbergia muraria were similarly treated. Because expansin proteins are closely associated with plant cell wall expansion and growth, we examined the expression of expansin genes in response to HIFs. We isolated cDNAs homologous to transcripts encoding three distinct alpha-expansin proteins in T. versicolor. Northern-blot analyses indicated that these transcripts were differentially abundant in different tissues. Steady-state levels of two expansin transcripts increased in T. versicolor roots exposed to BAP, but not DMBQ or maize root exudates. Expansin transcript abundance also increased in L. muraria in response to BAP treatment. These results suggest that the expansins examined fulfill functions distinct from haustorium development.

Host-root exudates increase gene expression of asparagine synthetase in the roots of a hemiparasitic plant Triphysaria versicolor (Scrophulariaceae).

Triphysaria is a facultative root parasite in the Scrophulariaceae family. Similar to other related parasites, the development of the parasitic life cycle is initiated by molecular signals released from appropriate host roots. Using a differential display, we isolated cDNAs preferentially abundant in T. versicolor roots exposed to Trifolium repens (white clover) root exudates in vitro. Sequence analysis indicated that one of the differentially expressed cDNAs had significant homology to the nitrogen-assimilating enzyme, asparagine synthetase (AS). T. versicolor AS cDNA clones were isolated and placed into three distinct classes on the basis of nucleotide sequence variations. All three classes encoded identical AS proteins. AS was expressed in both roots and shoots of in-vitro-cultured T. versicolor. Steady-state levels of AS mRNA increased in T. versicolor roots several-fold when seedlings were exposed to exudate obtained from hydroponically grown Arabidopsis thaliana roots. Therefore, AS transcript levels increased in response to exudates from two different hosts (Trifolium and Arabidopsis). The T. versicolor AS message levels increased to a similar magnitude when seedlings were incubated in the dark. Interestingly, AS levels were unaffected by treatment with the Striga haustoria inducer 2,6-dimethoxybenzoquinone. The potential role of AS in root parasitism is discussed.

Characterization of the gene encoding dihydroflavonol 4-reductase in tomato.

A cDNA clone (DFR) encoding dihydroflavonol 4-reductase was identified from tomato hypocotyls. Nucleotide and amino acid sequence comparisons to Petunia hybrida, Antirrhinum majus and Zea mays DFR sequences confirmed that the cDNA encodes the structural DFR gene. In tomato, the DFR sequence appeared to be present as a single gene and mapped to a region on chromosome 2 near two loci affecting anthocyanin pigmentation, are and aw. DFR was expressed in both leaf and hypocotyl tissue. Sequencing data from two DFR cDNA clones indicated there are alternative polyadenylation sites on DFR.

Rapid proliferation of the maize transposable element Activator in transgenic tomato.

We have found that the maize transposable element Activator (Ac) can rapidly proliferate when transformed into tomato plants. The fate of transposed Ac elements in self-pollinated progeny of independent transgenic tomato plants was examined by DNA gel blot hybridizations. When a single copy of Ac was introduced into a transformant, the number of copies usually remained low in subsequent generations. In one lineage, however, the number of Ac elements increased from one to more than 15 copies in only two generations. DNA gel blot analyses indicated that the amplified elements were not grossly rearranged. Amplified copies of Ac resided at unique sites in the genome, and segregation analysis indicated that these sites were not tightly linked at one genetic locus. Taken together, these observations indicate that the mechanism of Ac amplification is associated with transposition.

A genetic analysis of mutations recovered from tomato following Agrobacterium-mediated transformation with the maize transposahle elements Activator and Dissociation.

The maize autonomous transposable element, Activator (Ac), and the nonautonomous element Dissociation (Ds), were introduced into the tomato cultivars VF36 and VFNT Cherry by Agrobacterium-mediated transformation. Progeny families from 145 primary transformants were scored at the seedling stage for phenotypically variant individuals. When VF36 was transformed, 20% of families had progeny with aberrant phenotypes. The mutation frequency in VFNT Cherry transformants was lower; in this cultivar 7% of the transformants had progeny segregating for seedling mutations. The majority of the mutations showed monogenic inheritance in the R1 population, suggesting that the mutations occurred early in the transformation/regeneration process. One mutation, however, was recovered at low frequency in the R1, suggesting a late mutagenesis event. When tomato was transformed with either the Ac or Ds elements, no differences in mutation frequencies were observed. Since Ac is transpositionally active in tomato transformants while Ds is not, these numbers indicate that the mutation frequency inherent to the transformation process is higher than the mutational activity of Ac. These results demonstrate that efficient gene tagging using heterologous transposable elements will require screening for transposon-induced mutations in later generations.

A species-specific recognition system directs haustorium development in the parasitic plant Triphysaria (Scrophulariaceae).

Parasitic plants use host molecules to trigger development programs essential for parasitism. One such program governs the initiation, development, and function of haustoria, parasite-specific organs responsible for attachment and invasion of host tissues. Haustoria development can be initiated by several different molecules produced by appropriate host species. We are interested in understanding how these signals are interpreted by two related facultative parasites, Triphysaria eriantha (Benth). Chuang and Heckard, and T. versicolor Fischer and C. Meyer, to distinguish their own roots from those of potential hosts. We used an in vitro bioassay to determine what proportion of different Triphysaria populations formed haustoria in the presence and absence of closely related and unrelated host species. We found that the proportion of plants with haustoria was the same whether the plants were grown in isolation or with a conspecific host. In contrast, a significantly higher proportion of plants made haustoria when the host was a congeneric Triphysaria. Plants with haustoria neither enhanced nor inhibited other plants' propensity to form haustoria. Together these results indicate that qualitative differences exist in haustorium-inducing factors exuded by closely related species. The highest proportion of Triphysaria had haustoria when growth with Arabidopsis thaliana (L.) Heynh. Even in this case, however, some Triphysaria failed to develop haustoria. Interestingly, the percentage of haustoria that had vessel elements was higher when connections were made with Arabidopsis than with another Triphysaria. These results demonstrate that host recognition can be manifested at multiple points in haustorium development.

Ploidy levels in transgenic tomato plants determined by chloroplast number.

We determined germline ploidy of primary tomato transformants by counting meiotic chromosomes. We then determined the number of chloroplasts in stomatal cells by cytological staining. A correlation of these values indicated that diploid transformants had significantly fewer chloroplasts than tetraploid transformants. By maximum likelihood, we estimate that less than 1% of diploid transformants will have chloroplast values in the tetraploid range. Transformed plants generally had more chloroplasts than plants derived from seed. Also, there was more variability between transformed than seed derived plants. Less than 5% of transformed plants were chimeric when comparing leaf and pollen ploidy levels. Of 129 transgenic plants examined, 29 (22%) were polyploid.

Unstable transmission and frequent rearrangement of two closely linked transposed Ac elements in transgenic tomato.

We are examining the behavior of the maize transposable element Ac in transgenic tomato with the goal of developing an efficient insertional mutagenesis system. Among the self progeny of a transgenic tomato plant containing an active Ac element, we identified six plants that contained the same germinally transposed Ac. In one of these plants, we found a second Ac element inserted in the same orientation and approximately 2 kb to the 5′ side of the original Ac insertion. Transmission of this composite structure was significantly reduced with less than one-quarter of the self progeny inheriting Ac either in the form of the intact parental allele (two neighboring Ac's) or derivatives of it. The derivative alleles that arose were complex in structure and could not be explained solely on the basis of the excision of one or the other Ac element. These results illustrate the potential of transposable elements to cause genetic instabilities and complex chromosomal rearrangements.

Biological assay of prokaryotic genes in mouse cells following DNA mediated transformation.

Genes coding for leucine biosynthesis in Bacillus subtilis were introduced into mouse LTK- cells by co-transformation with thymidine kinase+ (tk) DNA. Genomic DNA from the tk+ transformants was used to transform competent cultures of different B. subtilis leucine auxotrophs. Each auxotroph was transformed to prototrophy at a similar frequency and the number of leucine gene sequences per transformant genome as deduced by the B. subtilis bioassay strongly correlated with the number estimated by hybridization methods. Tk- subclones were obtained by plating the transformants in 5'-bromodeoxyuridine. One subclone still contained the non-selected leucine gene sequences and could transform auxotrophs of B. subtilis. No deletions or rearrangements in the linkage relationships of the leucine genes occurred in the LTK- cells that inhibited transformation of B. subtilis.

Independent transposition of multiple Ac elements in the same transgenic tomato cell.

To effectively use transposable elements for the genetic manipulation of plant species lacking well characterized endogenous elements, it is important to evaluate the behavior of known transposable elements following their introduction into heterologous host species. One critical parameter concerns the timing of transposition in relation to the development of the transgenic host since this will affect the frequency with which transposition events are captured in the gametes. In order to examine whether different elements in the same cell are differentially active during development, we used Southern hybridizations to assess the activity of Activator (Ac) elements in progeny plants derived from a tomato transformant carrying five Ac's at two loci. All of the elements at one locus transposed in the primary transformant at a developmental stage resulting in the transmission of newly transposed elements to the next generation. In contrast, one or more of the Ac's at the second locus were not active at this stage and were transmitted to the next generation at the original donor T-DNA insertion site. These elements were, however, transpositionally active in somatic tissue. These results demonstrated that individual transposable elements in the same transformed cell can be differentially activated during development.

Insertional inactivation of the tomato polygalacturonase gene.

The site-selected insertion (SSI) procedure was used to generate insertional knockout mutations in the gene for tomato polygalacturonase (PG), a critical enzyme in fruit ripening. Previously, it had been shown that the Dissociation (Ds) elements in a select group of tomato plants frequently inserted into PG, at least in somatic tissues. DNA isolated from pollen produced by progeny of these plants was screened by SSI to identify plants likely to transmit the insertions in PG to progeny. These results identified one family as likely candidate for yielding germinally transmitted insertions. Four thousand progeny were screened and five were found containing germinally transmitted Ds insertions in PG, one of which contained two Ds insertions in PG. The Ds elements were stabilized by genetically removing the transposase and four of the five insertions were recovered as homozygous in the next generation. Enzymatic analysis of fruit from these individuals demonstrated that there was at least a 1000-fold reduction in polygalacturonase levels in those plants bearing Ds insertions in PG exons. Individuals with modified PG sequences due to the sequence footprint, resulting from excision of the element, were identified using the single-strand conformational polymorphism (SSCP) method. Enzymatic analysis of fruit from a plant homozygous for one such excision allele showed a significant reduction in polygalacturonase activity. Since there is no transgenic material left in PG, this demonstrates the ability to modify a gene of commercial value in planta and subsequently removing all transgenic material.

Mox: a novel modifier of the tomato Xa locus.

We have isolated a novel mutation that caused variegated leaf color in a tomato plant which had multiple maize Ac transposable elements and the tomato Xa allele. Xa is a previously characterized semi-dominant mutation that causes tomato leaves to be bright yellow when heterozygous (Xa/xa+). The mutation responsible for the new phenotype was named Mox (Modifier of Xa). The Mox mutation modified the Xa/xa+ yellow leaf phenotype in two ways: it compensated for the Xa allele resulting in a plant with a wildtype green color, and it caused somatic variegation which appeared as white and yellow sectors on the green background. Somatic variegation was visible only if the plant contained both the Mox and Xa loci. Genetic studies indicated that the Mox locus was linked in repulsion to Xa and that the Mox locus was genetically transmitted at a reduced frequency through the male gamete. Molecular characterization of the Ac elements in lines segregating for Mox identified an Ac insertion that appeared to cosegregate with Mox variegation. We propose a model in which the Mox mutation consists of a duplication of the xa+ allele and subsequent Ac-induced breakage of the duplicated region causes variegation.