From genomics to functional markers in the era of next-generation sequencing.

The availability of complete genome sequences, along with other genomic resources for Arabidopsis, rice, pigeon pea, soybean and other crops, has revolutionized our understanding of the genetic make-up of plants. Next-generation DNA sequencing (NGS) has facilitated single nucleotide polymorphism discovery in plants. Functionally-characterized sequences can be identified and functional markers (FMs) for important traits can be developed at an ever-increasing ease. FMs are derived from sequence polymorphisms found in allelic variants of a functional gene. Linkage disequilibrium-based association mapping and homologous recombinants have been developed for identification of "perfect" markers for their use in crop improvement practices. Compared with many other molecular markers, FMs derived from the functionally characterized sequence genes using NGS techniques and their use provide opportunities to develop high-yielding plant genotypes resistant to various stresses at a fast pace.

Transgene excision in pollen using a codon optimized serine resolvase CinH-RS2 site-specific recombination system.

Transgene escape, a major environmental and regulatory concern in transgenic crop cultivation, could be alleviated by removing transgenes from pollen, the most frequent vector for transgene flow. A transgene excision vector containing a codon optimized serine resolvase CinH recombinase (CinH) and its recognition sites RS2 were constructed and transformed into tobacco (Nicotiana tabacum cv. Xanthi). CinH recombinase recognized 119 bp of nucleic acid sequences, RS2, in pollen and excised the transgene flanked by the RS2 sites. In this system, the pollen-specific LAT52 promoter from tomato was employed to control the expression of CinH recombinase. Loss of expression of a green fluorescent protein (GFP) gene under the control of the LAT59 promoter from tomato was used as an indicator of transgene excision. Efficiency of transgene excision from pollen was determined by flow cytometry (FCM)-based pollen screening. While a transgenic event in the absence of CinH recombinase contained about 70% of GFP-synthesizing pollen, three single-copy transgene events contained less than 1% of GFP-synthesizing pollen based on 30,000 pollen grains analyzed per event. This suggests that CinH-RS2 recombination system could be effectively utilized for transgene biocontainment.

Transgenic hybrid aspen overexpressing the Atwbc19 gene encoding an ATP-binding cassette transporter confers resistance to four aminoglycoside antibiotics.

Antibiotic-resistance genes of bacterial origin are invaluable markers for plant genetic engineering. However, these genes are feared to pose possible risk to human health by horizontal gene transfer from transgenic plants to bacteria, potentially resulting in antibiotic-resistant pathogenic bacteria; this is a considerable regulatory concern in some countries. The Atwbc19 gene, encoding an Arabidopsis thaliana ATP-binding cassette transporter, has been reported to confer resistance to kanamycin specifically as an alternative to bacterial antibiotic-resistance genes. In this report, we transformed hybrid aspen (Populus canescens x P. grandidentata) with the Atwbc19 gene. Unlike Atwbc19-transgenic tobacco that was only resistant to kanamycin, the transgenic Populus plants also showed resistance to three other aminoglycoside antibiotics (neomycin, geneticin, and paromomycin) at comparable levels to plants containing a CaMV35S-nptII cassette. Although it is unknown why the transgenic Populus with the Atwbc19 gene is resistant to all aminoglycoside antibiotics tested, the broad utility of the Atwbc19 gene as a reporter gene is confirmed here in a second dicot species. Because the Atwbc19 gene is plant-ubiquitous, it might serve as an alternative selectable marker to current bacterial antibiotic-resistance marker genes and alleviate the potential risk for horizontal transfer of bacterial-resistance genes in transgenic plants.

Green fluorescent protein as a marker for expression of a second gene in transgenic plants.

The use of transgenic crops has generated concerns about transgene movement to unintended hosts and the associated ecological consequences. Moreover, the in-field monitoring of transgene expression is of practical concern (e.g., the underexpression of an herbicide tolerance gene in crop plants that are due to be sprayed with herbicide). A solution to these potential problems is to monitor the presence and expression of an agronomically important gene by linking it to a marker gene, such as GFP. Here we show that GFP fluorescence can indicate expression of the Bacillus thuringiensus cry1Ac gene when co-introduced into tobacco and oilseed rape, as demonstrated by insect bioassays and western blot analysis. Furthermore we conducted two seasons of field experiments to characterize the performance of three different GFP genes in transgenic tobacco. The best gene tested was mGFP5er, a mutagenized GFP gene that is targeted to the endoplasmic reticulum. We also demonstrated that host plants synthesizing GFP in the field suffered no fitness costs.

Correlated expression of gfp and Bt cry1Ac gene facilitates quantification of transgenic hybridization between Brassicas.

Gene flow from transgenic oilseed rape (BRASSICA NAPUS) might not be avoidable, thus, it is important to detect and quantify hybridization events with its relatives in real time. Data are presented showing the correlation between genetically linked green fluorescent protein (GFP) with BACILLUS THURINGIENSIS (Bt) CRY1AC gene expression in hybrids formed between transgenic B. NAPUS "Westar" and a wild Chinese accession of wild mustard (B. JUNCEA) and hybridization between transgenic B. NAPUS and a conspecific Chinese landrace oilseed rape. Hybrids were obtained either by spontaneous hybridization in the field or by hand-crossing in a greenhouse. In all cases, transgenic hybrids were selected by GFP fluorescence among seedlings originating from seeds harvested from B. JUNCEA and the Chinese oilseed rape plants. Transgenicity was confirmed by PCR detection of transgenes. GFP fluorescence was easily and rapidly detected in the hybrids under greenhouse and field conditions. Results showed that both GFP fluorescence and Bt protein synthesis decreased as either plant or leaf aged, and GFP fluorescence intensity was closely correlated with Bt protein concentration during the entire vegetative lifetime in hybrids. These findings allow the use of GFP fluorescence as an accurate tool to detect gene-flow in time in the field and to conveniently estimate BT CRY1AC expression in hybrids on-the-plant.

Downregulation of a UDP-Arabinomutase Gene in Switchgrass (Panicum virgatum L.) Results in Increased Cell Wall Lignin While Reducing Arabinose-Glycans.

Background: Switchgrass (Panicum virgatum L.) is a C4 perennial prairie grass and a dedicated feedstock for lignocellulosic biofuels. Saccharification and biofuel yields are inhibited by the plant cell wall's natural recalcitrance against enzymatic degradation. Plant hemicellulose polysaccharides such as arabinoxylans structurally support and cross-link other cell wall polymers. Grasses predominately have Type II cell walls that are abundant in arabinoxylan, which comprise nearly 25% of aboveground biomass. A primary component of arabinoxylan synthesis is uridine diphosphate (UDP) linked to arabinofuranose (Araf). A family of UDP-arabinopyranose mutase (UAM)/reversible glycosylated polypeptides catalyze the interconversion between UDP-arabinopyranose (UDP-Arap) and UDP-Araf. Results: The expression of a switchgrass arabinoxylan biosynthesis pathway gene, PvUAM1, was decreased via RNAi to investigate its role in cell wall recalcitrance in the feedstock. PvUAM1 encodes a switchgrass homolog of UDP-arabinose mutase, which converts UDP-Arap to UDP-Araf. Southern blot analysis revealed each transgenic line contained between one to at least seven T-DNA insertions, resulting in some cases, a 95% reduction of native PvUAM1 transcript in stem internodes. Transgenic plants had increased pigmentation in vascular tissues at nodes, but were otherwise similar in morphology to the non-transgenic control. Cell wall-associated arabinose was decreased in leaves and stems by over 50%, but there was an increase in cellulose. In addition, there was a commensurate change in arabinose side chain extension. Cell wall lignin composition was altered with a concurrent increase in lignin content and transcript abundance of lignin biosynthetic genes in mature tillers. Enzymatic saccharification efficiency was unchanged in the transgenic plants relative to the control. Conclusion: Plants with attenuated PvUAM1 transcript had increased cellulose and lignin in cell walls. A decrease in cell wall-associated arabinose was expected, which was likely caused by fewer Araf residues in the arabinoxylan. The decrease in arabinoxylan may cause a compensation response to maintain cell wall integrity by increasing cellulose and lignin biosynthesis. In cases in which increased lignin is desired, e.g., feedstocks for carbon fiber production, downregulated UAM1 coupled with altered expression of other arabinoxylan biosynthesis genes might result in even higher production of lignin in biomass.

Insect Control and Dosage Effects in Transgenic Canola Containing a Synthetic Bacillus thuringiensis cryIAc Gene.

Zygotic hypocotyls of canola (Brassica napus L.) cv Oscar, cv Westar, and the breeding line UGA188-20B were transformed with a truncated synthetic Bacillus thuringiensis insecticidal crystal protein gene (Bt cryIAc) under the control of the cauliflower mosaic virus 35S promoter using Agrobacterium tumefaciens-mediated transformation. Fifty-seven independently transformed lines were produced, containing 1 to 12 copies of the transgenes. A range of cry expressors was produced from 0 to 0.4% Cry as a percentage of total extractable protein. The Brassica specialists, the diamondback month (Plutella xylostella L.) and the cabbage looper (Trichoplusia ni Hubner), were completely controlled by low-, medium-, and high-expressing lines. Whereas control of the generalist lepidopteran, the corn earworm (Helicoverpa zea Boddie), was nearly complete, the other generalist caterpillar tested, the beet armyworm (Spodoptera exigua Hubner), showed a dose response that had a negative association between defoliation and cry expression. These plants were produced as models for an ecological research assessment of the risk involved in the field release of naturalized transgenic plants harboring a gene (Bt) that confers higher relative fitness under herbivore-feeding pressure.

Transgenic plants and biosafety: science, misconceptions and public perceptions.

One usually thinks of plant biology as a non-controversial topic, but the concerns raised over the biosafety of genetically modified (GM) plants have reached disproportionate levels relative to the actual risks. While the technology of changing the genome of plants has been gradually refined and increasingly implemented, the commercialization of GM crops has exploded. Today's commercialized transgenic plants have been produced using Agrobacterium tumefaciens-mediated transformation or gene gun-mediated transformation. Recently, incremental improvements of biotechnologies, such as the use of green fluorescent protein (GFP) as a selectable marker, have been developed. Non-transformation genetic modification technologies such as chimeraplasty will be increasingly used to more precisely modify germplasm. In spite of the increasing knowledge about genetic modification of plants, concerns over ecological and food biosafety have escalated beyond scientific rationality. While several risks associated with GM crops and foods have been identified, the popular press, spurred by colorful protest groups, has left the general public with a sense of imminent danger. Reviewed here are the risks that are currently under research. Ecological biosafety research has identified potential risks associated with certain crop/transgene combinations, such as intra- and interspecific transgene flow, persistence and the consequences of transgenes in unintended hosts. Resistance management strategies for insect resistance transgenes and non-target effects of these genes have also been studied. Food biosafety research has focused on transgenic product toxicity and allergenicity. However, an estimated 3.5 x 10(12) transgenic plants have been grown in the U.S. in the past 12 years, with over two trillion being grown in 1999 and 2000 alone. These large numbers and the absence of any negative reports of compromised biosafety indicate that genetic modification by biotechnology poses no immediate or significant risks and that resulting food products from GM crops are as safe as foods from conventional varieties. We are increasingly convinced that scientists have a duty to conduct objective research and to effectively communicate the results--especially those pertaining to the relative risks and potential benefits--to scientists first and then to the public. All stakeholders in the technology need more effective dialogues to better understand risks and benefits of adopting or not adopting agricultural biotechnologies.

Applications of green fluorescent protein in plants.

Green fluorescent protein (GFP) is increasingly being used in plant biology from the cellular level to whole plant level. At the cellular level, GFP is being used as an in vivo reporter to assess frequency of transient and stable transformation. GFP has also proven to be an invaluable tool in monitoring trafficking and subcellular localization of protein. At the organ level and up, many exciting applications are rapidly emerging. The development of brighter GFP mutants with more robust folding properties has enabled better macroscopic visualization of GFP in whole leaves and plants. One interesting example has been the use of GFP to monitor virus movement in and among whole plants. GFP is also emerging as a powerful tool to monitor transgene movement and transgenic plants in the field. In a proof-of-concept study, tobacco was transformed with a modified version of the GFP gene controlled by a constitutive (35S) promoter. GFP expression in progeny plants ranged from 0% to 0.5%, and approximately 0.1% GFP was the minimal amount needed for unambiguous macroscopic detection. GFP is the first truly in vivo reporter system useful in whole plants, and we project its usefulness will increase even further as better forms of GFP genes become available.

Instrumentation and methodology for quantifying GFP fluorescence in intact plant organs.

The General Fluorescence Plant Meter (GFP-Meter) is a portable spectrofluorometer that utilizes a fiber-optic cable and a leaf clip to gather spectrofluorescence data. In contrast to traditional analytical systems, this instrument allows for the rapid detection and fluorescence measurement of proteins under field conditions with no damage to plant tissue. Here we discuss the methodology of gathering and standardizing spectrofluorescence data from tobacco and canola plants expressing GFP. Furthermore, we demonstrate the accuracy and effectiveness of the GFP-Meter. We first compared GFP fluorescence measurements taken by the GFP-Meter to those taken by a standard laboratory-based spectrofluorometer, the FluoroMax-2. Spectrofluorescence measurements were taken from the same location on intact leaves. When these measurements were tested by simple linear regression analysis, we found that there was a positive functional relationship between instruments. Finally, to exhibit that the GFP-Meter recorded accurate measurements over a span of time, we completed a time-course analysis of GFP fluorescence measurements. We found that only initial measurements were accurate; however, subsequent measurements could be used for qualitative purposes.

Disparity between formation of conditioned flavor aversions and neophobia during grooming in rats and mice.

Mice (Mus musculus) allowed to groom a paste containing saccharin from their fur before injection with lithium chloride displayed a saccharin aversion in subsequent drinking preference tests. No attenuation of neophobia was observed in mice grooming saccharin because the animals failed to display a neophobia towards saccharin in drinking tests. Rattus norvegicus displayed neophobia towards saccharin in two- and single-bottle drinking tests but this neophobia was not attenuated by grooming experience with the saccharin paste. Rats apparently learn that if a taste is hazardous in the grooming context it is also likely hazardous in an appetitive context. Learned safety in grooming, however, does not generalize into the appetitive context. The results support the view that neophobia and learned taste aversion depend upon different mechanisms.

Sodium detection during the water absorption response in Rana pipiens.

Although taste in vertebrates is typically associated with specialized receptors in the lingual epithelium, Hoff and Hillyard reported that the toad, Bufo punctatus, is able to "taste" sodium with the abdominal skin. This was reflected in a differential behavioral response to hypertonic NaCl. The present study tests for the presence of such abdominal chemoreceptors in the frog Rana pipiens. The experiment was a five-condition design in which frogs were placed on filter paper saturated with: deionized water, 250 mM NaCl, 350 mM NaCl, 12.9 microM amiloride, or 350 mM NaCl + 12.9 microM amiloride. The time that the frogs remained on the test substrate before moving to a surface of deionized water was recorded. It was necessary to dehydrate the frogs to 80% of their body weight to elicit a behavioral response to the NaCl whereas dehydration to 90% of their body weight has been reported effective in Bufo punctatus. The frogs displayed significantly shorter mean times to move on both concentrations of NaCl compared to deionized water, with the shortest times occurring when 350 mM NaCl was used. Amiloride alone did not have an effect upon times to move to deionized water, but did significantly reduce the response to 350 mM NaCl. Movement to amiloride + 350 mM NaCl did not differ significantly from that to deionized water. The results indicate that Rana pipiens, like Bufo punctatus, have epithelial chemoreceptors for the detection of NaCl on hydrated surfaces and that these receptors, like those of mammals, are amiloride sensitive.

Elevated shock threshold in sexually receptive female rats.

Previous studies have found cyclic differences in wheel running, extinction of conditioned avoidance responses, and open field behavior as a function of the estrous cycle in rodents. The purpose of this study was to investigate possible sensory changes associated with estrus in rodents. Female rats were monitored for behavioral and physiological changes related to the estrous cycle. Using the method of constant stimuli and foot shock, jump thresholds were determined during the estrous cycle stages of sexual receptivity (proestrus) and non-receptivity (metestrus). A significantly higher jump threshold was demonstrated by animals during proestrus as compared to metestrus. Possible explanations for the failure of previous investigators to find attenuated sensitivity as a function of the estrous cycle are discussed.

Profiling, mimicking and masking the flavor of a selected rodenticide.

In Experiment 1, rats drank strychnine solution followed by an injection of LiCl. Generalization of learned strychnine avoidance to 4 non-toxic flavors was then assessed. Additional conditioning and generalization trials followed until 24 flavors had been presented. In Experiment 2, rats were conditioned to avoid individual flavors, or flavor mixtures concocted on the basis of avoidance generalization observed in Experiment 1. Tests followed for generalization of learned avoidance from the simple flavors to the mixtures, from the mixtures to the simple flavors, and from either to strychnine. In Experiment 3, two concentrations of NaCl were mixed with strychnine or one of the flavors (SOA) used in the previous experiments. These stimuli, as well as SOA alone, strychnine alone, and each of the NaCl concentrations, were presented to rats during conditioning. Generalization followed, as in the previous experiments. In Experiment 1, strychnine avoidance generalized to 'bitter' flavors (ps less than 0.01). In Experiment 2, avoidance of flavor mixtures generalized more strongly to strychnine than did learned avoidance of simple flavors (ps less than 0.01). In Experiment 3, NaCl masked or otherwise suppressed the 'bitter' flavor of strychnine or SOA insofar as no groups conditioned with a 'bitter'-salt mixture generalized avoidance to 'bitter' alone (ps less than 0.01). Rats are therefore capable of recognizing the flavor components of strychnine. Moreover, when these components are mixed in proportion to the degree of generalized avoidance, a mimic (either in terms of flavor characteristics or perceived intensity) of strychnine is obtained. Avoidance learning appears useful in the development of rodenticide baits and pre-bait formulations.

Designing the perfect plant feedstock for biofuel production: using the whole buffalo to diversify fuels and products.

Petroleum-derived liquid fuels and commodities play a part in nearly every aspect of modern daily life. However, dependence on this one natural resource to maintain modern amenities has caused negative environmental and geopolitical ramifications. In an effort to replace petroleum, technologies to synthesize liquid fuels and other commodities from renewable biomass are being developed. Current technologies, however, only use a portion of plant biomass feedstocks for fuel and useful products. "Using the whole feedstock buffalo" or optimally using all portions and biochemicals present in renewable biomass will enhance the economic and environmental feasibility of biofuels and coproducts. To accomplish this optimization, greater understanding of the relationship between liquid fuel and bioproduct properties and plant chemistries is needed. Liquid fuel properties and how they relate to biochemistry and petrochemistry are discussed. Enhanced biofuel yields and high-value commodities from biomass are needed to sustainably replace petroleum-based products. Several metabolic engineering strategies are discussed. We will describe paths of possible fuel and product diversification using dedicated lignocellulosic biomass (e.g., switchgrass).