Focus on Weed Control: Indaziflam Herbicidal Action: A Potent Cellulose Biosynthesis Inhibitor

Cellulose biosynthesis is a common feature of land plants. Therefore, cellulose biosynthesis inhibitors (CBIs) have a potentially broad-acting herbicidal mode of action and are also useful tools in decoding fundamental aspects of cellulose biosynthesis. Here, we characterize the herbicide indaziflam as a CBI and provide insight into its inhibitory mechanism. Indaziflam-treated seedlings exhibited the CBI-like symptomologies of radial swelling and ectopic lignification. Furthermore, indaziflam inhibited the production of cellulose within <1 h of treatment and in a dose-dependent manner. Unlike the CBI isoxaben, indaziflam had strong CBI activity in both a monocotylonous plant (Poa annua) and a dicotyledonous plant (Arabidopsis [Arabidopsis thaliana]). Arabidopsis mutants resistant to known CBIs isoxaben or quinoxyphen were not cross resistant to indaziflam, suggesting a different molecular target for indaziflam. To explore this further, we monitored the distribution and mobility of fluorescently labeled CELLULOSE SYNTHASE A (CESA) proteins in living cells of Arabidopsis during indaziflam exposure. Indaziflam caused a reduction in the velocity of YELLOW FLUORESCENT PROTEIN:CESA6 particles at the plasma membrane focal plane compared with controls. Microtubule morphology and motility were not altered after indaziflam treatment. In the hypocotyl expansion zone, indaziflam caused an atypical increase in the density of plasma membrane-localized CESA particles. Interestingly, this was accompanied by a cellulose synthase interacting1-independent reduction in the normal coincidence rate between microtubules and CESA particles. As a CBI, for which there is little evidence of evolved weed resistance, indaziflam represents an important addition to the action mechanisms available for weed management.Cellulose is a composite polymer of β-1,4-linked glucan chains and is the main load-bearing structure of plant cell walls (Jarvis, 2013). Although cellulose is a relatively simple polysaccharide molecule, its synthesis is quite complex. The principle catalytic unit is a plasma membrane (PM)-localized protein complex referred to as the cellulose synthase complex (CSC; Davis, 2012). In plants, the CSC, visualized with freeze fracture microscopy, is a solitary, hexagonal rosette-shaped complex (Herth and Weber, 1984; Delmer, 1999) and at least three of the catalytic CELLULOSE SYNTHASE A (CESA) proteins are required in each CSC for the production of cellulose (Desprez et al., 2007; Persson et al., 2007). In addition to CESAs, several accessory proteins have been discovered to be necessary for the production and deposition of cellulose, such as KORRIGAN (Lane et al., 2001), COBRA (Roudier et al., 2005) and CELLULOSE SYNTHASE INTERACTING1 (CSI1; Gu et al., 2010), as well as several others that are yet to be identified. The loss of function in any of the aforementioned proteins causes complete or partial loss of anisotropic growth in cells undergoing expansion, resulting in radial swelling. Severe radial swelling in rapidly expanding tissue is also a common symptomology observed in seedlings treated with cellulose biosynthesis inhibitors (CBIs). Therefore, numerous potential herbicidal targets exist (mechanisms of action) for the broad group of known CBIs.Classification of an herbicide to the CBI designation was traditionally achieved by short-term [¹⁴C]radioisotope tracer studies focused on the incorporation of Glc into cellulose (Heim et al., 1990; Sabba and Vaughn, 1999). More recently, time-lapse confocal microscopy of reporter-tagged CESA proteins (Paredez et al., 2006) has been used to further classify CBIs. CBIs can be classified into at least three primary groups based on how treatment disrupts the normal tracking and localization of fluorescently labeled CESAs (for review, see Brabham and DeBolt, 2012). The disruption is, it can be assumed, the result of the inhibitory mechanism of the CBI. In the first group, isoxaben and numerous other compounds cause YELLOW FLUORESCENT PROTEIN YFP):CESAs to be depleted from the PM and concomitantly accumulate in cytosolic vesicles (called small CESA compartments or microtubule-associated cellulose synthase compartments; Paredez et al., 2006; Crowell et al., 2009; Gutierrez et al., 2009) The second group, consisting only of dichlobenil (DCB), causes YFP:CESAs to become immobilized and hyperaccumulated at distinct foci in the PM (Herth, 1987; DeBolt et al., 2007b). The third group influences CSC-microtubule (MT)-associated functions resulting in errant movement and localization of YFP:CESAs (DeBolt et al., 2007a; Yoneda et al., 2007). These different disruption processes suggest that each CBI group targets a different aspect of the complex cellulose biosynthetic process.A lack of evolved weed resistance in the field suggests that CBIs are potentially underutilized tools for weed control (Sabba and Vaughn, 1999; Heap, 2014). CBIs have also been useful research tools in decoding fundamental aspects of cellulose biosynthesis. An exogenous application of a CBI provides spatial and temporal inhibition of cellulose. Resistance screens to CBIs have uncovered key genes in cellulose biosynthesis (Scheible et al., 2001; Desprez et al., 2002). Furthermore, CBIs such as isoxaben have also been effective in linking accessory proteins with CESAs in the CSC (Robert et al., 2005; Gu et al., 2010). Therefore, it is important to extend our range of CBI compounds. Indaziflam (Fig. 1A), an herbicide introduced by Bayer Crop Science, was recently proposed to be a CBI and was reported to have a photosystem II inhibition value of 9.4 (Meyer et al., 2009; Dietrich and Laber, 2012). Indaziflam is labeled for use in turf, for perennial crops, and for nonagricultural situations for preemergent control of grasses and broadleaf weeds (Meyer et al., 2009; Brosnan et al., 2011). The aim herein was to investigate indaziflam as a CBI and to characterize its inhibitory effect on cellulose biosynthesis.Open in a separate windowFigure 1.Indaziflam is a fluoroalkytriazine-containing compound that inhibits elongation in seedlings of P. annua and Arabidopsis. A, Chemical structure of indaziflam. B to D, Images of 7-d-old seedlings treated with increasing concentrations of indaziflam. B shows light-grown P. annua seedlings (indaziflam concentrations from left to right are 0, 100, 250, 500, 1,000, 5,000, and 10,000 pm). C and D show light-grown and dark-grown Arabidopsis seedlings, respectively (indaziflam concentrations from left to right are 0, 100, 250, 500, 1,000, and 2,500 pm). Indaziflam treatment induced swollen cells. E, Representative images of the primary root of P. annua grown in plates for 4 d with and without 10 nm indaziflam. F, Transgenic Arabidopsis seedlings expressing GFP:PIP2 were examined by laser scanning confocal microscopy and images represent visualization of the primary root grown vertically for 7-d plates without and with 250 pm indaziflam. PIP2, Plasma membrane intrinsic protein2. Bar = 10 mm in B, 5 mm in C and D, 2 mm in E, and 50 μm in F.     

Focus Issue on Roots: Root Nutrient Foraging

During a plant''s lifecycle, the availability of nutrients in the soil is mostly heterogeneous in space and time. Plants are able to adapt to nutrient shortage or localized nutrient availability by altering their root system architecture to efficiently explore soil zones containing the limited nutrient. It has been shown that the deficiency of different nutrients induces root architectural and morphological changes that are, at least to some extent, nutrient specific. Here, we highlight what is known about the importance of individual root system components for nutrient acquisition and how developmental and physiological responses can be coupled to increase nutrient foraging by roots. In addition, we review prominent molecular mechanisms involved in altering the root system in response to local nutrient availability or to the plant''s nutritional status.In natural and agricultural soils, the ability of plants to quickly and efficiently acquire nutrients may determine their competitive success and productivity. Because mineral elements interact differently with themselves and other soil constituents or are carried by water out of the rooted soil volume, their availability to plants may decrease and lead to nutrient deficiency. Under these conditions, plants activate foraging responses that include morphological changes, such as the modulation of root system architecture (RSA) or root hair formation, and physiological changes, such as the release of nutrient-mobilizing root exudates or the expression of nutrient transporters (Gojon et al., 2009; Hinsinger et al., 2009; Gruber et al., 2013). These responses are often spatially coupled to increase the root-soil interaction zone and improve the ability of the plant to intercept immobile nutrients. Noteworthy, although not discussed herein, symbiosis or associative rhizosphere microorganisms can also alter the RSA and enhance the foraging capacity of the plant (Gutjahr and Paszkowski, 2013). Here, we provide an update on the morphological responses induced by plants to forage sparingly available nutrients and some of the underlying molecular mechanisms known to date to be involved in RSA adaptations to nutrient availabilities.     

Focus on Weed Control: The Impact of Herbicide-Resistant Rice Technology on Phenotypic Diversity and Population Structure of United States Weedy Rice

The use of herbicide-resistant (HR) Clearfield rice (Oryza sativa) to control weedy rice has increased in the past 12 years to constitute about 60% of rice acreage in Arkansas, where most U.S. rice is grown. To assess the impact of HR cultivated rice on the herbicide resistance and population structure of weedy rice, weedy samples were collected from commercial fields with a history of Clearfield rice. Panicles from each weedy type were harvested and tested for resistance to imazethapyr. The majority of plants sampled had at least 20% resistant offspring. These resistant weeds were 97 to 199 cm tall and initiated flowering from 78 to 128 d, generally later than recorded for accessions collected prior to the widespread use of Clearfield rice (i.e. historical accessions). Whereas the majority (70%) of historical accessions had straw-colored hulls, only 30% of contemporary HR weedy rice had straw-colored hulls. Analysis of genotyping-by-sequencing data showed that HR weeds were not genetically structured according to hull color, whereas historical weedy rice was separated into straw-hull and black-hull populations. A significant portion of the local rice crop genome was introgressed into HR weedy rice, which was rare in historical weedy accessions. Admixture analyses showed that HR weeds tend to possess crop haplotypes in the portion of chromosome 2 containing the ACETOLACTATE SYNTHASE gene, which confers herbicide resistance to Clearfield rice. Thus, U.S. HR weedy rice is a distinct population relative to historical weedy rice and shows modifications in morphology and phenology that are relevant to weed management.Weedy rice (Oryza sativa), a conspecific weed of cultivated rice, is a global threat to rice production (Delouche et al., 2007). Classified as the same species as cultivated rice, it is highly competitive (Diarra et al., 1985; Pantone and Baker, 1991; Burgos et al., 2006), difficult to control without damaging cultivated rice, and can cause almost total crop failure (Diarra et al., 1985). The competition of cultivated rice with weedy rice can lead to yield losses from less than 5% to 100% (Kwon et al., 1991; Watanabe et al., 2000; Chen et al., 2004; Ottis et al., 2005; Shivrain et al., 2009b). Besides being difficult to control, weedy rice persists in rice fields because of key weedy traits, including variable emergence (Shivrain et al., 2009b), high degree of seed shattering (Eleftherohorinos, et al., 2002; Thurber et al., 2010), high diversity in seed dormancy (Do Lago, 1982; Noldin, 1995; Vidotto and Ferrero, 2000; Burgos et al., 2011; Tseng et al., 2013), and its seed longevity in soil (Goss and Brown, 1939). Weedy rice is a problem mainly in regions with large farm sizes where direct-seeded rice culture is practiced (Delouche et al., 2007). It is not a major problem in transplanted rice culture, where roguing weeds is possible and hand labor is available. The severity of the problem has increased in recent decades because of the significant shift to direct seeding from transplanting (Pandey and Velasco, 2002; Rao et al., 2007; Chauhan et al., 2013), which is driven by water scarcity (Kummu et al., 2010; Turral et al., 2011), increasing labor costs, and migration of labor to urban areas (Grimm et al., 2008).The herbicide-resistant (HR) Clearfield rice technology (Croughan, 2003) provides an option to control weedy rice in rice using imidazolinone herbicides, in particular, imazethapyr. Imidazolinones belong to group 2 herbicides, also known as ACETOLACTATE SYNTHASE (ALS) inhibitors. Examples of herbicides in this group are imazamox, imazapic, imazaquin, and imazethapyr. Developed through mutagenesis of the ALS locus (Croughan, 1998), Clearfield rice was first commercialized in 2002 in the southern U.S. rice belt (Tan et al., 2005). Low levels of natural hybridization are known to occur between the crop and weedy rice. Gene flow generally ranges from 0.003% to 0.25% (Noldin et al., 2002; Song et al., 2003; Messeguer et al., 2004; Gealy, 2005; Shivrain et al., 2007, 2008). After the adoption of Clearfield technology, resistant weedy outcrosses were soon detected in commercial fields (Fig. 1), generally after two cropping seasons of Clearfield rice, where escaped weedy rice was able to produce seed (Zhang et al., 2006; Burgos et al., 2007, 2008). Similar observations have been reported outside the United States, in other regions adopting the technology (Gressel and Valverde, 2009; Busconi et al., 2012).Open in a separate windowFigure 1.Suspected herbicide-resistant weedy rice in a rice field previously planted with Clearfield rice along the Mississippi River Delta in Arkansas. More than 10 morphotypes of weedy rice were observed in this field, with different maturity periods. In the foreground is a typical weedy rice with pale green leaves; the rice cultivar has dark green leaves. The inset shows a weedy morphotype that matured earlier than cultivated rice.Despite this complication, the adoption of Clearfield rice technology is increasing, albeit at a slower pace than that of glyphosate-resistant crops. After a decade of commercialization, 57% of the rice area in Arkansas was planted with Clearfield rice cultivars in 2013 (J. Hardke, personal communication). Clearfield technology has been very successful at controlling weedy rice, and polls among rice growers suggest that farmers have kept the problem of HR weeds in check by following the recommended stewardship practices (Burgos et al., 2008). The most notable of these are (1) implementation of herbicide programs that incorporate all possible modes of action available for rice production; (2) ensuring maximum efficacy of the herbicides used; (3) preventing seed production from escaped weedy rice, remnant weedy rice after crop harvest, or volunteer rice and weedy rice in the next crop cycle; (4) rotating Clearfield rice with other crops to break the weedy rice cycle; and (5) practicing zero tillage to avoid burying HR weedy rice seed (Burgos et al., 2008).Clearfield rice has gained a foothold in Asia, where rice cultivation originated (Londo and Schaal, 2007; Zong et al., 2007). Clearfield rice received government support for commercialization in Malaysia in 2010 (Azmi et al., 2012) because of the severity of the weedy rice problem there. Dramatic increases in rice yields (from 3.5 to 7 metric tons ha⁻¹) were reported in Malaysia where Clearfield rice was planted (Sudianto et al., 2013). However, the risk of gene flow and evolution of resistant weedy rice populations is high in the tropics, where up to three rice crops are planted each year, and freezing temperatures, which would reduce the density of volunteer plants, do not occur.In the United States, where Clearfield technology originated and has been used for the longest time, the interaction between HR cultivated rice and weedy rice is not yet fully understood. Two main populations of weedy rice are known to occur in the southern United States and can be found in the same cultivated rice fields. These populations are genetically differentiated, are largely distinct at the phenotypic level, and have separate evolutionary origins (Reagon et al., 2010). One group tends to have straw-colored hulls and is referred to as the SH population; a second group tends to have black-colored hulls and awns and is referred to as the BHA population (Reagon et al., 2010). Genomic evidence suggests that both groups descended from cultivated ancestors but not from the tropical japonica subgroup varieties that are grown commercially in the United States. Instead, the SH group evolved from indica, a subgroup of rice commonly grown in the lowland tropics, and the BHA group descended from aus, a related cultivated subgroup typically grown in Bangladesh and the West Bengal region (Reagon et al., 2010). Weed-weed and weed-crop hybrids are also known to occur, but prior to Clearfield commercialization, these hybrids had occurred at low frequency (Reagon et al., 2010; Gealy et al., 2012). With the advent and increased adoption of Clearfield cultivars, the impact on U.S. weedy rice population structure and the prevalence of the SH and BHA groups are unknown.Efforts to predict the possible consequences of HR or genetically modified rice on weedy rice have been a subject of discussion for many years. Both weedy rice and cultivated rice are primarily self-fertilizing, but, as mentioned above, low levels of gene flow are known to occur. Additional environmental and intrinsic genetic factors can act as prezygotic and postzygotic mating barriers between cultivated and weedy rice and influence the possibility and levels of gene flow between these groups (Craig et al., 2014; Thurber et al., 2014). However, once gene flow occurs between cultivated and weedy rice, and if the resulting hybrids are favored by selection, the resulting morphological, genetic, and physiological changes in weedy rice populations can alter the way that weedy rice evolves and competes. For example, herbicide-resistant weed outcrosses in an experimental field have been observed to be morphologically diverse (Shivrain et al., 2006), with some individuals carrying major weedy traits and well adapted to rice agriculture. Such weedy plants could be more problematic than their normal weedy counterparts. Thus, introgression of crop genes into weedy populations has the potential to change the population dynamic, genetic structure, and morphological profile of weedy plants. This, in turn, must alter our crop management practices. To increase our understanding of the impact of HR rice on the evolution of weedy rice, in this article we aim to (1) assess the frequency of herbicide resistance in weedy rice in southern U.S. rice fields with a history of Clearfield use; (2) characterize the weedy attributes of resistant populations; and (3) determine the genetic origins of herbicide-resistant weeds in U.S. fields.     

Focus Issue on Roots: Perennial Roots to Immortality,

Maximum lifespan greatly varies among species, and it is not strictly determined; it can change with species evolution. Clonal growth is a major factor governing maximum lifespan. In the plant kingdom, the maximum lifespans described for clonal and nonclonal plants vary by an order of magnitude, with 43,600 and 5,062 years for Lomatia tasmanica and Pinus longaeva, respectively. Nonclonal perennial plants (those plants exclusively using sexual reproduction) also present a huge diversity in maximum lifespans (from a few to thousands of years) and even more interestingly, contrasting differences in aging patterns. Some plants show a clear physiological deterioration with aging, whereas others do not. Indeed, some plants can even improve their physiological performance as they age (a phenomenon called negative senescence). This diversity in aging patterns responds to species-specific life history traits and mechanisms evolved by each species to adapt to its habitat. Particularities of roots in perennial plants, such as meristem indeterminacy, modular growth, stress resistance, and patterns of senescence, are crucial in establishing perenniality and understanding adaptation of perennial plants to their habitats. Here, the key role of roots for perennial plant longevity will be discussed, taking into account current knowledge and highlighting additional aspects that still require investigation.There is enormous diversity among the types of perennial plants and among their patterns of aging (Jones et al., 2014). Perennial plants can be divided into herbaceous (or perennial herbs) and woody perennials (trees and shrubs), and therefore, they represent very diverse organisms in size and complexity from some herbs that weigh a few grams to huge trees like sequoias (Sequoia sempervirens). Among perennial herbs, the slowest growing species described thus far, Borderea pyrenaica (a small geophyte growing in the Central Pyrenees of northeastern Spain), is also the one with the longest maximum lifespan (350 years; Fig. 1). Interestingly, fecundity of this species increases with aging, representing a case of negative senescence (Garcia et al., 2011; Morales et al., 2013). If mortality falls as size increases and if size increases with age, then mortality will fall with age, and negative senescence occurs (Vaupel et al., 2004). Negative senescence is not common in the tree of life, but it seems to occur in not only some perennial herbs, such as B. pyrenaica (Garcia et al., 2011) and Plantago lanceolata (Roach and Gampe, 2004), but also, other phylogenetically distant organisms, such as turtles (Jones et al., 2014). Other perennial herbs with higher biomass production rates and consequently, larger sizes, such as stinging nettle (Urtica dioica), are much shorter-lived (a few years only). In this case, however, perenniality is achieved by allocating an important part of their energy to asexual reproduction (production of stolons; i.e. clonal propagation), giving rise to new entire clonal plants (Koskela, 2002). Indeed, this process happens in several other plant species with rapid growth that we commonly find in gardens, such as strawberries (Fragaria × ananassa) or raspberries (Rubus idaeus). Stolons can be produced aboveground or underground (in the latter case, forming rhizomes). Van Dijk (2009) elegantly reviewed the direct and indirect methods currently used to estimate plant age in clonal and nonclonal plants, showing several examples of plant species using clonal propagation with maximum lifespans of thousands of years, with the most notable example, King’s Lomatia (Lomatia tasmanica), being dated at 43,600 years (Lynch et al., 1998). Only one wild-living clone of this species is known. Clonal propagation is the only means for propagation, because it is a sterile ancient clone. When a branch falls, that branch produces new roots, establishing a new plant that is genetically identical to its parent (Lynch et al., 1998). Here, the production of new roots becomes essential for achieving potential immortality. Another example of extreme longevity is the bristlecone pine (Pinus longaeva), with a maximum lifespan of 5,062 years. It holds the record of longevity of a single individual within the plant kingdom, which was observed by Tom Harlan during 2012 in a living individual of this species in the White Mountains (the location has not been reported; Earle, 2013).Open in a separate windowFigure 1.Examples of extreme longevity in perennial plants. A, B. pyrenaica, the perennial herb with the longest lifespan described to date. B, A cross section of the tuber of B. pyrenaica showing the scars left by the five meristematic points in the spiral. C, P. longaeva, the species with the individual with the longest lifespan ever recorded (not using clonal propagation). D, C. nodosa meadow, with a detail of the rhizomes (E) that allow clonal propagation and potential immortality in this species. [See online article for color version of this figure.]The enormous diversity in lifespans within a species responds to specific life history traits and mechanisms evolved by each individual to adapt to its habitat. Particularities of roots in perennial plants, such as meristem indeterminacy, modular growth, stress resistance, and patterns of senescence, are crucial in understanding adaptation of perennial plants to their habitats, explaining differences in longevity. Here, the key role of roots in providing long lifespans in perennial plants will be discussed, taking into account current knowledge and highlighting additional aspects that still require investigation.     

Focus Issue on Roots: Plant Nutrition: Root Transporters on the Move

Nutrient and water uptake from the soil is essential for plant growth and development. In the root, absorption and radial transport of nutrients and water toward the vascular tissues is achieved by a battery of specialized transporters and channels. Modulating the amount and the localization of these membrane transport proteins appears as a way to drive their activity and is essential to maintain nutrient homeostasis in plants. This control first involves the delivery of newly synthesized proteins to the plasma membrane by establishing check points along the secretory pathway, especially during the export from the endoplasmic reticulum. Plasma membrane-localized transport proteins are internalized through endocytosis followed by recycling to the cell surface or targeting to the vacuole for degradation, hence constituting another layer of control. These intricate mechanisms are often regulated by nutrient availability, stresses, and endogenous cues, allowing plants to rapidly adjust to their environment and adapt their development.Plants take up nutrients and water from the soil and transport them to the leaves to support photosynthesis and plant growth. However, most soils around the world do not provide optimal conditions for plant colonization. Consequently, plants have evolved sophisticated mechanisms to adjust to deficiency or excess of nutrients and water supply. Membrane transport proteins, including channels and transporters, play crucial roles in the uptake of nutrients and water from the soil and in their radial transport to the root vasculature. Newly synthesized membrane transport proteins have to be properly targeted to a defined compartment, usually the plasma membrane, to efficiently ensure their function. The trafficking of membrane transport proteins along the secretory pathway is tightly controlled and involves the recognition of exit signals by gatekeeper protein complexes. After reaching the plasma membrane, membrane transport proteins can be endocytosed and subsequently recycled to the cell surface or targeted to the vacuole for degradation. Because the subcellular localization of proteins directly influences their activity, modulating the localization of membrane transport proteins constitutes a powerful way to control nutrient and water uptake in plants. This review discusses the fundamental mechanisms at stake in membrane protein secretion and endocytosis, with a specific focus on membrane transport proteins, and how endogenous and exogenous cues affect their dynamics to integrate uptake of nutrients and water to plant growth conditions.     

Focus on Weed Control: Tandem Amplification of a Chromosomal Segment Harboring 5-Enolpyruvylshikimate-3-Phosphate Synthase Locus Confers Glyphosate Resistance in Kochia scoparia

Recent rapid evolution and spread of resistance to the most extensively used herbicide, glyphosate, is a major threat to global crop production. Genetic mechanisms by which weeds evolve resistance to herbicides largely determine the level of resistance and the rate of evolution of resistance. In a previous study, we determined that glyphosate resistance in Kochia scoparia is due to the amplification of the 5-Enolpyruvylshikimate-3-Phosphate Synthase (EPSPS) gene, the enzyme target of glyphosate. Here, we investigated the genomic organization of the amplified EPSPS copies using fluorescence in situ hybridization (FISH) and extended DNA fiber (Fiber FISH) on K. scoparia chromosomes. In both glyphosate-resistant K. scoparia populations tested (GR1 and GR2), FISH results displayed a single and prominent hybridization site of the EPSPS gene localized on the distal end of one pair of homologous metaphase chromosomes compared with a faint hybridization site in glyphosate-susceptible samples (GS1 and GS2). Fiber FISH displayed 10 copies of the EPSPS gene (approximately 5 kb) arranged in tandem configuration approximately 40 to 70 kb apart, with one copy in an inverted orientation in GR2. In agreement with FISH results, segregation of EPSPS copies followed single-locus inheritance in GR1 population. This is the first report of tandem target gene amplification conferring field-evolved herbicide resistance in weed populations.Glyphosate [N-(phosphonomethyl) Gly] is the most widely used agricultural pesticide globally (Duke and Powles, 2008). Originally, being a nonselective herbicide, its use was limited to vegetation management in noncrop areas; however, introduction of glyphosate-resistant (GR) crops in the late 1990s, coupled with their exceptional adoption, led to accelerated use totaling approximately 128 million ha worldwide in 2012 (James, 2012). GR crop technology has made a significant contribution to global agriculture and the environment, as it not only increased farm income by $32.2 billion (Brookes and Barfoot, 2013), but also moderated the negative environmental impacts of mechanical weed management practices (Gardner and Nelson, 2008; Bonny, 2011). Glyphosate offers a simple, effective, and economic weed management option in GR crops. In addition, it provides immense value in no-till crop production systems by enabling soil and moisture conservation. However, due to intensive glyphosate selection pressure, several weed populations globally have evolved resistance through a variety of mechanisms. Globally, herbicide resistance, in particular the recent proliferation of glyphosate resistance in weed species, is a major crop protection threat; nearly two dozen GR weed species have been reported in the last 15 years (Heap, 2014).Glyphosate, an aminophosphonic analog of the natural amino acid Gly, nonselectively inhibits 5-Enolpyruvylshikimate-3-Phosphate synthase (EPSPS) in plants, preventing the biosynthesis of the aromatic amino acids Phe, Tyr, and Trp (Steinrücken and Amrhein, 1980), resulting in the death of glyphosate-sensitive individuals. In plants, EPSPS is one of the key enzymes in the shikimate pathway (Herrmann and Weaver, 1999), and glyphosate inhibits EPSPS by binding to EPSPS-shikimate-3-P binary complex forming an EPSPS-shikimate-3-P-glyphosate complex (Alibhai and Stallings, 2001). Bradshaw et al. (1997) hypothesized against the likelihood of weeds evolving resistance to glyphosate, primarily because of its complex biochemical interactions in the shikimate pathway and also due to the absence of known glyphosate metabolism in plants. Nonetheless, several cases of glyphosate resistance, as a result of difference in glyphosate translocation (Preston and Wakelin, 2008) or mutations in the EPSPS, were confirmed (Baerson et al., 2002). More importantly, duplication/amplification of the EPSPS appears to be the basis for glyphosate resistance in several weeds (Sammons and Gaines, 2014). Here, we use duplication to refer to the formation of first repetition of a chromosomal segment and amplification to refer to increase in number of the repetitions (more than two repetitions of a chromosomal segment) under positive selection. The first case of EPSPS amplification as a basis for glyphosate resistance was reported in an Amaranthus palmeri population from GA (Gaines et al., 2010). In this A. palmeri population, there is a massive increase (>100-fold relative to glyphosate-susceptible [GS] plants) in EPSPS copies, and these copies are dispersed throughout the genome (Gaines et al., 2010).Field-evolved GR Kochia scoparia populations were first reported in western Kansas in 2007 (Heap, 2014). We previously determined that evolution of GR populations of K. scoparia in the U.S. Great Plains is also due to amplification of the EPSPS (A. Wiersma and P. Westra, unpublished data). Unlike in GR A. palmeri, we found relative EPSPS:acetolactate synthase (ALS) copies ranging from three to nine in GR K. scoparia populations. While it quickly became widespread in the region, its presence was reported in another five Great Plains states by 2013 (Heap, 2014). GR K. scoparia populations we tested were 3- to 11-times resistant (population level) to glyphosate compared with a GS population (Godar, 2014), and EPSPS expression positively correlated with genomic EPSPS copy number (A. Wiersma and P. Westra, unpublished data). Here, we reveal the genomic organization of the amplified EPSPS copies in two GR K. scoparia populations, an alternative mechanism of gene amplification to that reported in GR A. palmeri.     

Focus on Weed Control: In Vivo 31P-Nuclear Magnetic Resonance Studies of Glyphosate Uptake,Vacuolar Sequestration,and Tonoplast Pump Activity in Glyphosate-Resistant Horseweed

Horseweed (Conyza canadensis) is considered a significant glyphosate-resistant (GR) weed in agriculture, spreading to 21 states in the United States and now found globally on five continents. This laboratory previously reported rapid vacuolar sequestration of glyphosate as the mechanism of resistance in GR horseweed. The observation of vacuole sequestration is consistent with the existence of a tonoplast-bound transporter. ³¹P-Nuclear magnetic resonance experiments performed in vivo with GR horseweed leaf tissue show that glyphosate entry into the plant cell (cytosolic compartment) is (1) first order in extracellular glyphosate concentration, independent of pH and dependent upon ATP; (2) competitively inhibited by alternative substrates (aminomethyl phosphonate [AMPA] and N-methyl glyphosate [NMG]), which themselves enter the plant cell; and (3) blocked by vanadate, a known inhibitor/blocker of ATP-dependent transporters. Vacuole sequestration of glyphosate is (1) first order in cytosolic glyphosate concentration and dependent upon ATP; (2) competitively inhibited by alternative substrates (AMPA and NMG), which themselves enter the plant vacuole; and (3) saturable. ³¹P-Nuclear magnetic resonance findings with GR horseweed are consistent with the active transport of glyphosate and alternative substrates (AMPA and NMG) across the plasma membrane and tonoplast in a manner characteristic of ATP-binding cassette transporters, similar to those that have been identified in mammalian cells.Glyphosate is arguably the world’s most important herbicide (Duke and Powles, 2008). Environmental factors affecting its uptake and translocation in higher plants have been widely studied (Kells and Rieck, 1979; Coupland, 1983; Devine et al., 1983; Masiunas and Weller, 1988; Zhou et al., 2007). Notably, the role of light is important for effective uptake and translocation, suggesting that metabolic energy plays a role in this process (Simarmata et al., 2003; Shaner et al., 2005). Death of the whole plant requires effective glyphosate translocation from source to sink tissue, a process requiring ATP to maintain Suc gradients, which drive phloem movement (Bromilow et al., 1990; Dill et al., 2010).Weed species have developed glyphosate-resistant (GR) biotypes during the past decade (Heap, 2014). This has spurred interest in factors that may contribute to resistant attribute(s) as well as methods that can be used to screen plants for herbicide toxicity (Shaner, 2010). Resistance mechanisms have been reported for horseweed (Conyza canadensis; Feng et al., 2004; Zelaya et al., 2004; Ge et al., 2010, 2011), Palmer amaranth (Amaranthus palmeri; Gaines et al., 2010), and ryegrass (Lolium rigidum and Lolium multiflorum; Powles et al., 1998; Perez et al., 2004; Ge et al., 2012).Since glyphosate is foliar applied, glyphosate toxicity involves a multistep delivery process. Glyphosate must traverse the nonliving structures of the leaf cuticle and the cell walls of the epidermis, apoplast, and mesophyll prior to accessing the phloem for transport to sink tissues (Bromilow et al., 1990; Bromilow and Chamberlain, 2000). Indeed, restriction of glyphosate delivery to the plant cell cytoplasm (and chloroplast) by any means is, in itself, a resistance mechanism (Shaner, 2009; Ge et al., 2013). Elucidation of key factors governing delivery to the intracellular milieu of plant source leaves is critical for developing a complete understanding of the mechanism(s) of resistance to glyphosate.Glyphosate’s phosphono group offers the opportunity to employ in vivo ³¹P-NMR spectroscopy to track glyphosate movement and metabolism, additionally including monitoring of cellular pH, and gradients therein, and ATP levels, both indicators of tissue viability (Roberts, 1984). This laboratory has extended the ³¹P-NMR approach initially used by Gout et al. (1992) with suspension-cultured sycamore (Acer pseudoplatanus) cells. The initial findings, that source and sink leaf tissue from GR horseweed rapidly and avidly sequestered glyphosate within the vacuole compartment and that leaf tissue from glyphosate-sensitive (GS) horseweed did not, led to the hypothesis that vacuole sequestration was a key, perhaps the dominant, component of the resistance mechanism (Ge et al., 2010). It was then shown that GR horseweed acclimated and maintained at cold temperature (approximately 10°C–12°C) did not rapidly and avidly sequester glyphosate within the vacuole. Importantly, under such conditions, GR horseweed succumbed to the toxic effects of glyphosate. In short, by preventing glyphosate sequestration, GR horseweed became glyphosate sensitive, a laboratory finding confirmed in the field (Ge et al., 2011).The proposition that, by limiting the herbicide available for translocation, glyphosate vacuole sequestration could serve as an important if not dominant resistance mechanism was further strengthened by experiments that showed vacuolar glyphosate sequestration correlated with glyphosate resistance in ryegrass (Lolium spp.) from Australia, South America, and Europe (Ge et al., 2012). However, ³¹P-NMR studies of other weeds revealed that in some species, for example, Palmer amaranth, waterhemp (Amaranthus tuberculatus), and johnsongrass (Sorghum halepense), resistance correlated strongly with a lack of glyphosate uptake into the plant cell, a frontline resistance mechanism (Ge et al., 2013).Throughout these previous ³¹P-NMR studies, the finding that plants could regulate the compartmental access of glyphosate led us to speculate that the apoplast, tonoplast, and perhaps chloroplast possessed glyphosate-active transporters whose up-regulation or down-regulation and/or expression would confer resistance (Ge et al., 2010, 2011, 2012, 2013). This hypothesis motivated additional in vivo ³¹P-NMR experiments to further describe the determinants of glyphosate delivery in horseweed leaf tissue. Specifically, experiments with GR horseweed were designed with the goal of probing the transporter hypothesis.Findings from these experiments are reported herein and are consistent with the existence of a tonoplast transporter that is responsible for glyphosate resistance via vacuole sequestration. As described here, vacuole sequestration requires ATP, is active for multiple substrates, and shows substrate competition. Furthermore, glyphosate entry into the cell can be markedly inhibited by vanadate pretreatment. These characteristics are similar to those of ATP-binding cassette transporters in plants (Hetherington et al., 1998; Rea, 2007; Verrier et al., 2008; Prosecka et al., 2009; Conte and Lloyd, 2011) and mammalian cells (van de Ven et al., 2009; Ernst et al., 2010).