Genome Editing, Gene Drives, and Synthetic Biology: Will They Contribute to Disease-Resistant Crops, and Who Will Benefit?

Genetically engineered crops have been grown for more than 20 years, resulting in widespread albeit variable benefits for farmers and consumers. We review current, likely, and potential genetic engineering (GE) applications for the development of disease-resistant crop cultivars. Gene editing, gene drives, and synthetic biology offer novel opportunities to control viral, bacterial, and fungal pathogens, parasitic weeds, and insect vectors of plant pathogens. We conclude that there will be no shortage of GE applications totackle disease resistance and other farmer and consumer priorities for agricultural crops. Beyond reviewing scientific prospects for genetically engineered crops, we address the social institutional forces that are commonly overlooked by biological scientists. Intellectual property regimes, technology regulatory frameworks, the balance of funding between public- and private-sector research, and advocacy by concerned civil society groups interact to define who uses which GE technologies, on which crops, and for the benefit of whom. Ensuring equitable access to the benefits of genetically engineered crops requires affirmative policies, targeted investments, and excellent science.

Role of Glutamine Synthetase Isogenes and Herbicide Metabolism in the Mechanism of Resistance to Glufosinate in Lolium perenne L. spp. multiflorum Biotypes from Oregon.

Glufosinate-resistant Lolium perenne L. spp. multiflorum biotypes from Oregon exhibited resistance levels up to 2.8-fold the field rate. One resistant biotype (MG) had an amino acid substitution in glutamine synthetase 2 (GS2), whereas the other (OR) exhibited the wild-type genotype. We hypothesized that the amino acid substitution in GS2 is involved in the resistance mechanism in MG and that non-target site resistance mechanisms are present in OR. OR metabolized glufosinate faster than the other two biotypes, with >75% of the herbicide metabolized in comparison to 50% in MG and the susceptible biotype. A mutation in GS2 co-segregating with resistance in MG did not reduce the enzyme activity, with results further supported by our enzyme homology models. This research supports the conclusion that a metabolism mechanism of glufosinate resistance is present in OR and that glufosinate resistance in MG is not due to an altered target site.

Identification of glyphosate resistance in Salsola tragus in north-eastern Oregon.

BACKGROUND: Farmers in the low-rainfall region of eastern Oregon rely on repeated applications of non-selective herbicides, predominately glyphosate, to control Salsola tragus in no-till fallow systems. Reports of poor glyphosate effectiveness have increased in recent years. Reduced efficacy is often attributed to dust, water stress, or generally poor growing conditions during application. Inadequate control also may be the result of the evolution of glyphosate resistance. Therefore, studies were undertaken to determine if glyphosate-resistant S. tragus populations occur in Oregon. RESULTS: Results from dose-response studies confirmed glyphosate resistance in three of 10 Oregon Salsola tragus populations. The ratio I50R /I50S from dose-response curves was, on average, 3.1 for the relative dry biomass per plant and 3.2 for the % of surviving plants per pot in these three populations. Plant mortality at recommended glyphosate doses for the resistant populations was less than 30% 3 weeks after treatment. CONCLUSIONS: Glyphosate resistance in S. tragus highlights the imperative need to diversify weed control strategies to preserve the longevity and sustainability of herbicides in semi-arid cropping systems of the Pacific Northwest. © 2017 Society of Chemical Industry.

Impact of transgene genome location on gene migration from herbicide-resistant wheat (Triticum aestivum L.) to jointed goatgrass (Aegilops cylindrica Host).

BACKGROUND: Wheat (Triticum aestivum) (ABD) and jointed goatgrass (Aegilops cylindrica) (CD) can cross and produce hybrids that can backcross to either parent. Such backcrosses can result in progeny with chromosomes and/or chromosome segments retained from wheat. Thus, a herbicide resistance gene could migrate from wheat to jointed goatgrass. In theory, the risk of gene migration from herbicide-resistant wheat to jointed goatgrass is more likely if the gene is located on the D genome and less likely if the gene is located on the A or B genome of wheat. RESULTS: BC1 populations (jointed goatgrass as a recurrent parent) were analyzed for chromosome numbers and transgene transmission rates under sprayed and non-sprayed conditions. Transgene retention in the non-sprayed BC1 generation for the A, B and D genomes was 84, 60 and 64% respectively. In the sprayed populations, the retention was 81, 59 and 74% respectively. CONCLUSION: The gene transmission rates were higher than the expected 50% or less under sprayed and non-sprayed conditions, possibly owing to meiotic chromosome restitution and/or chromosome non-disjunction. Such high transmission rates in the BC1 generation negates the benefits of gene placement for reducing the potential of gene migration from wheat to jointed goatgrass. © 2016 Society of Chemical Industry.

Identification and phytotoxicity of a new glucosinolate breakdown product from Meadowfoam (Limnanthes alba) seed meal.

Meadowfoam (Limnanthes alba Hartw. ex Benth.) is an oilseed crop grown in the Willamette Valley of Oregon. Meadowfoam seed meal (MSM), a byproduct after oil extraction, contains 2-4% glucosinolate (glucolimnanthin). Activated MSM, produced by adding freshly ground myrosinase-active meadowfoam seeds to MSM, facilitates myrosinase-mediated formation of glucosinolate-derived degradation products with herbicidal activity. In the activated MSM, glucolimnanthin was converted into 3-methoxybenzyl isothiocyanate ("isothiocyanate") within 24 h and was degraded by day three. 3-Methoxyphenylacetonitrile ("nitrile") persisted for at least 6 days. Methoxyphenylacetic acid (MPAA), a previously unknown metabolite of glucolimnanthin, appeared at day three. Its identity was confirmed by LC-UV and high resolution LC-MS/MS comparisons with a standard of MPAA. Isothiocyanate inhibited lettuce germination 8.5- and 14.4-fold more effectively than MPAA and nitrile, respectively. Activated MSM inhibited lettuce germination by 58% and growth by 72% compared with the control. Results of the study suggest that MSM has potential uses as a pre-emergence bioherbicide.

Characterization of multiple-herbicide-resistant Italian ryegrass (Lolium perenne spp. multiflorum).

BACKGROUND: Multiple-herbicide resistance in Lolium perenne spp. multiflorum has evolved in many areas in Oregon. To manage the resistant populations, the resistance patterns must be determined. In this study, a population (CT) suspected to be resistant to sulfometuron and hexazinone was collected from a Christmas tree plantation. RESULTS: The CT population is resistant to at least six herbicides with four different mechanisms of action: atrazine (>16-fold), diuron (2.4-fold), glyphosate (7.4-fold), hexazinone (3.1-fold), imazapyr (1.8-fold) and sulfometuron (>16-fold). Two mutations, Trp-591-Leu and Ser-264-Gly, were identified in the acetolactate synthase (ALS) and psbA gene respectively. No previously reported mutation in the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene was found. Less shikimic acid accumulated in the CT plants than in the susceptible plants after treatment with glyphosate at 0.6 kg AE ha(-1) . CONCLUSION: This study suggests that the multiple resistance patterns of Lolium perenne spp. multiflorum populations can be complex, but that chemical control options to manage these populations exist. These remaining chemical options should be integrated with non-chemical management strategies to slow the spread of multiple-resistant biotypes in agroecosystems.

Development of a chloroplast DNA marker for monitoring of transgene introgression in Brassica napus L.

Chloroplast molecular markers can provide useful information for high-resolution analysis of inter- and intra-specific variation in Brassicaceae and for differentiation between its species. Combining data generated from nuclear and chloroplast markers enables the study of seed and pollen movement, and assists in the assessment of gene-flow from genetically modified (GM) plants through hybridization studies. To develop chloroplast DNA markers for monitoring of transgene introgression in Brassica napus L., we searched for sequence variations in the chloroplast (cp) genome, and developed a simple cpDNA marker that is reliable, time-saving, and easily discriminates among 4 species (B. napus, B. rapa, Raphanus sativus, and Sinapis alba) based on PCR-product length polymorphism. This marker will be useful to identify maternal lineages and to estimate transgene movement of GM canola.

Crossing the divide: gene flow produces intergeneric hybrid in feral transgenic creeping bentgrass population.

Gene flow is the most frequently expressed public concern related to the deregulation of transgenic events (Snow 2002; Ellstrand 2003). However, assessing the potential for transgene escape is complex because it depends on the opportunities for unintended gene flow, and establishment and persistence of the transgene in the environment (Warwick et al. 2008). Creeping bentgrass (Agrostis stolonifera L.), a turfgrass species widely used on golf courses, has been genetically engineered to be resistant to glyphosate, a nonselective herbicide. Outcrossing species, such as creeping bentgrass (CB), which have several compatible species, have greater chances for gene escape and spontaneous hybridization (i.e. natural, unassisted sexual reproduction between taxa in the field), which challenges transgene containment. Several authors have emphasized the need for evidence of spontaneous hybridization to infer the potential for gene flow (Armstrong et al. 2005). Here we report that a transgenic intergeneric hybrid has been produced as result of spontaneous hybridization of a feral-regulated transgenic pollen receptor (CB) and a nontransgenic pollen donor (rabbitfoot grass, RF, Polypogon monspeliensis (L.) Desf.). We identified an off-type transgenic seedling and confirmed it to be CB × RF intergeneric hybrid. This first report of a transgenic intergeneric hybrid produced in situ with a regulated transgenic event demonstrates the importance of considering all possible avenues for transgene spread at the landscape level before planting a regulated transgenic crop in the field. Spontaneous hybridization adds a level of complexity to transgene monitoring, containment, mitigation and remediation programmes.

Gene flow from herbicide-resistant crops: it's not just for transgenes.

Gene flow was raised as one of the first issues related to the development and release of genetically engineered (GE) crops. Gene flow has remained a topic of discussion for more than 20 years and is still used as an argument against the release of transgenic crops. With respect to herbicide-resistant crops, gene flow does not differ whether the herbicide resistance trait is introduced via genetic engineering or via conventional breeding techniques. Conventional breeding and genetic engineering techniques have been used to produce herbicide resistance in many of the same crop species. In addition, conventional breeding has been used to produce a broader range of herbicide-resistant crops than have been genetically engineered for herbicide resistance. Economic, political, and social concerns center on the breeding technique, but the results of gene flow for weed management are the same irrespective of breeding technique. This paper will focus on gene flow from nonGE herbicide-resistant crops in North America.

Development of novel chloroplast microsatellite markers to identify species in the Agrostis complex (Poaceae) and related genera.

We needed a reliable way to identify species and confirm potential interspecific and intergeneric hybrids in a landscape level study of gene flow from transgenic glyphosate-resistant Agrostis stolonifera (Poaceae) to compatible relatives. We developed 12 new polymorphic chloroplast microsatellite markers to aid in identifying species recipient of transgenic pollen both within the Agrostis complex and the related genera Polypogon.

Investigating the mechanisms of glyphosate resistance in Lolium multiflorum.

Evolved resistance to the herbicide glyphosate has been reported in eleven weed species, including Lolium multiflorum. Two glyphosate-resistant L. multiflorum populations were collected, one from Chile (SF) and one from Oregon, USA (OR), and the mechanisms conferring glyphosate resistance were studied. Based on a Petri dish dose-response bioassay, the OR and the SF populations were two and fivefold more resistant to glyphosate when compared to the susceptible (S) population, respectively; however, based on a whole-plant dose-response bioassay, both OR and SF populations were fivefold more resistant to glyphosate than the S population, implying that different resistance mechanisms might be involved. The S population accumulated two and three times more shikimic acid in leaf tissue 96 h after glyphosate application than the resistant OR and SF populations, respectively. There were no differences between the S and the glyphosate-resistant OR and SF populations in 14C-glyphosate leaf uptake; however, the patterns of 14C-glyphosate translocation were significantly different. In the OR population, a greater percentage of 14C-glyphosate absorbed by the plant moved distal to the treated section and accumulated in the tip of the treated leaf. In contrast, in the S and in the SF populations, a greater percentage of 14C-glyphosate moved to non-treated leaves and the stem. cDNA sequence analysis of the EPSP synthase gene indicated that the glyphosate-resistant SF population has a proline 106 to serine amino acid substitution. Here, we report that glyphosate resistance in L. multiflorum is conferred by two different mechanisms, limited translocation (nontarget site-based) and mutation of the EPSP synthase gene (target site-based).

Introgression of an imidazolinone-resistance gene from winter wheat (Triticum aestivum L.) into jointed goatgrass (Aegilops cylindrica Host).

Imidazolinone-resistant winter wheat (Triticum aestivum L.) is being commercialized in the USA. This technology allows wheat growers to selectively control jointed goatgrass (Aegilops cylindrica Host), a weed that is especially problematic because of its close genetic relationship with wheat. However, the potential movement of the imidazolinone-resistance gene from winter wheat to jointed goatgrass is a concern. Winter wheat and jointed goatgrass have the D genome in common and can hybridize and backcross under natural field conditions. Since the imidazolinone-resistance gene (Imi1) is located on the D genome, it is possible for resistance to be transferred to jointed goatgrass via hybridization and backcrossing. To study the potential for gene movement, BC(2)S(2) plants were produced artificially using imidazolinone-resistant winter wheat (cv. FS-4) as the female parent and a native jointed goatgrass collection as the male recurrent parent. FS-4, the jointed goatgrass collection, and 18 randomly selected BC(2)S(2) populations were treated with imazamox. The percentage of survival was 100% for the FS-4, 0% for the jointed goatgrass collection and 6 BC(2)S(2) populations, 40% or less for 2 BC(2)S(2) populations, and 50% or greater for the remaining 10 BC(2)S(2) populations. Chromosome counts in BC(2)S(3) plants showed a restoration of the chromosome number of jointed goatgrass, with four out of four plants examined having 28 chromosomes. Sequencing of AHASL1D in BC(2)S(3) plants derived from BC(2)S(2)-6 revealed the sexual transmission of Imi1 from FS-4 to jointed goatgrass. Imi1 conferred resistance to the imidazolinone herbicide imazamox, as shown by the in vitro assay for acetohydroxyacid synthase (AHAS) activity.

psbA mutation (Asn266 to Thr) in Senecio vulgaris L. confers resistance to several PS II-inhibiting herbicides.

DNA sequence analysis of the psbA gene encoding the D1 protein of photosystem II (PS II), the target site of PS II-inhibiting herbicides, identified a point mutation (Asn266 to Thr) in a bromoxynil-resistant Senecio vulgaris L. population collected from peppermint fields in Oregon. Although this mutation has been previously reported in Synechocystis, this is the first report of this particular point mutation in a higher plant exhibiting resistance to PS II-inhibiting herbicides. The resistant population displayed high-level resistance to bromoxynil and terbacil (R/S ratio 10.1 and 9.3, respectively) and low-level resistance to metribuzin and hexazinone (R/S ratio 4.2 and 2.6, respectively) when compared with the susceptible population. However, the population was not resistant to the triazine herbicides atrazine and simazine or to the urea herbicide diuron. A chlorophyll fluorescence assay confirmed the resistance levels and patterns of cross-resistance of the whole-plant studies. The resistant S. vulgaris plants produced fewer seeds. Differences in cross-resistance patterns to PS II-inhibiting herbicides and the difference in fitness cost could be exploited in a weed management program.

Chloroplast and nuclear microsatellite analysis of Aegilops cylindrica.

Aegilops cylindrica Host (2n = 4x = 28, genome CCDD) is an allotetraploid formed by hybridization between the diploid species Ae. tauschii Coss. (2n = 2x = 14, genome DD) and Ae. markgrafii (Greuter) Hammer (2n = 2x = 14, genome CC). Previous research has shown that Ae. tauschii contributed its cytoplasm to Ae. cylindrica. However, our analysis with chloroplast microsatellite markers showed that 1 of the 36 Ae. cylindrica accessions studied, TK 116 (PI 486249), had a plastome derived from Ae. markgrafii rather than Ae. tauschii. Thus, Ae. markgrafii has also contributed its cytoplasm to Ae. cylindrica. Our analysis of chloroplast and nuclear microsatellite markers also suggests that D-type plastome and the D genome in Ae. cylindrica were closely related to, and were probably derived from, the tauschii gene pool of Ae. tauschii. A determination of the likely source of the C genome and the C-type plastome in Ae. cylindrica was not possible.