Comparative analysis reveals changes in transcriptomes of sugarcane upon infection by Leifsoniaxyli subsp. xyli

Ratoon stunting disease (RSD) caused by bacterium Leifsoniaxyli subsp. xyli (Lxx) is a devastating disease of sugarcane over a large part of the world. Genetic improvement for RSD‐resistant varieties is considered the most effective method to control the disease. However, genetic improvement of sugarcane is hindered by the limited information about the molecular mechanisms underlying Lxx pathogenicity and defence responses in sugarcane. In this study, genome‐wide gene expression profiling was used to compare RSD‐resistant (CP72‐2086) and RSD‐susceptible (GT11) genotypes at different infection time points in order to identify the candidate regulators for RSD resistance. A total of 14,494 differentially expressed genes (DEGs) were identified, indicating that dramatic changes had occurred in gene expression upon Lxx infection, especially in the susceptible genotype. Enrichment analysis showed that a large number of genes related to plant hormone signal transduction, phenylalanine metabolism, phenylpropanoid biosynthesis and starch and sucrose metabolism was responsible for sugarcane response to Lxx infection. Plant hormone signalling pathway genes were significantly differentially expressed at the early infection stage between the two genotypes. The resistant genotype chose the jasmonic acid‐ and ethylene‐dependent host‐defence pathways to resist Lxx infection, whereas the susceptible genotype preferred the salicylic acid‐dependent host‐defence pathways. These findings help unravel the molecular mechanisms of sugarcane plant–Lxx interactions and may pave the way for sugarcane breeding for disease resistance.     

Incidence and Severity of Leifsonia xyli subsp. xyli Infection of Sugarcane in Sao Paulo State,Brazil

Sugarcane covers 8.53 million hectares with production of 596.63 million tonnes in Brazil. Despite its importance, little information is available on ratoon stunt (RSD), caused by Leifsonia xyli subsp xyli (Lxx). Our objective was to examine the incidence and severity of Lxx among sugarcane cultivars in 2009, 2010 and 2011. Sap from 100 stalks from each field was sent for a routine RSD analyses that allowed examination of Lxx incidence. The presence of bacterium was checked by dot blot enzyme immunoassay to detect its presence and relative concentration. Analyses of 187 fields from 35 cultivars in 2009, 166 fields from 33 cultivars in 2010 and 221 fields from 30 cultivars in 2011 found Lxx incidence of 23.6% of fields of 23 cultivars in 2009, 27.1% of fields of 15 cultivars in 2010 and 25.8% of fields of 15 cultivars in 2011. RB867515, the major cultivar in Sao Paulo, had within‐field incidence of up to 70% in 2009, 48% in 2010 and 88% in 2011. Highest incidence and populations of Lxx infection were found for cvs RB867515, RB855453, SP81‐3250, RB855536 and RB92579, demonstrating their susceptibility to RSD.     

Characterization of new IS elements and studies of their dispersion in two subspecies of <Emphasis Type="Italic">Leifsonia xyli</Emphasis>

Background  

Leifsonia xyli is a xylem-inhabiting bacterial species comprised of two subspecies: L. xyli subsp. xyli (Lxx) and L. xyli subsp. cynodontis (Lxc). Lxx is the causal agent of ratoon stunting disease in sugarcane commercial fields and Lxc colonizes the xylem of several grasses causing either mild or no symptoms of disease. The completely sequenced genome of Lxx provided insights into its biology and pathogenicity. Since IS elements are largely reported as an important source of bacterial genome diversification and nothing is known about their role in chromosome architecture of L. xyli, a comparative analysis of Lxc and Lxx elements was performed.     

Gibberellins and indole-3-acetic acid producing rhizospheric bacterium Leifsonia xyli SE134 mitigates the adverse effects of copper-mediated stress on tomato

Beneficial bacteria Supplemental data for this article can be accessed at https://doi.org/10.1080/17429145.2017.1370142.View all notesliving in the rhizosphere pose several implications on plant growth promotion and are highly desirable for sustainable agriculture. In the current study, we explored the ameliorative capacity of Leifsonia xyli SE134, a plant growth-promoting rhizobacteria (PGPR), against copper (Cu) stress on tomato grown under elevated Cu levels of 50 and 100?mM. Initially, L. xyli SE134 modulated innate gibberellins (GAs) and indole-3-acetic acid (IAA) metabolism in response to elevated Cu toxicity. The IAA contents increased, whereas that of bioactive GAs decreased in relation to Cu concentration gradient in the broth media. Furthermore, exposure to elevated Cu caused detrimental effects on the physiological attributes as revealed by attenuated shoot length, root length, stem diameter, shoot dry weight, root dry weight, and chlorophyll content in non-inoculated tomatoes as compared to L. xyli SE134 inoculated plants. The growth rescuing effect of L. xyli SE134 may be attributed to the modulation of endogenous amino acids contents in plants, such as glutamic acid, threonine, phenylalanine, glycine, proline, and arginine. Moreover, L. xyli SE134 inoculation stimulated total polyphenol and flavonoid content, reduced super oxide dismutase activity, strongly inhibited Cu, and increased phosphorus and iron content in plants grown under elevated Cu stress. In the absence of Cu toxicity, L. xyli SE134 significantly enhanced amino acid content, improved total flavonoids, and increased phosphorus content, thus resulting in higher plant growth.     

Response of eight sugarcane cultivars to glyphosine and glyphosate ripeners

Studies were conducted on eight sugarcane (Saccharum spp. hydrid) cultivars during the 1982–83 (plant crop) and 1983–84 (ratoon crop) growing seasons to determine the effects of glyphosine (Polaris) (N,N-bis (phosphonomethyl) glycine) and glyphosate (Polado) (sodium-N-(phosphonomethyl) glycine) on stalk sucrose content and yield. Difference due to crops (plant vs. ratoon) for sugarcane quality, kilograms of sugar per ton of cane (S/T), sugarcane yield, tons of cane per hectare (TCH), and sugar yield, tons of sugar per hectare (TSH) were significant. Significant differences were found in quality for the ratoon crop and cane and sugar yield in both crops due to ripener treatment. Cultivars in both crops differed significantly in quality and yield. Harvest dates were significantly different for all plant characteristics. Interactions of cultivar by treatment for the plant crop, harvest date by treatment for the ratoon crop, and cultivar by harvest date for both crops for cane quality also were significant. Time from ripener application to achievement of maximum sugar concentration also depended on cultivar. This is important in determining the economic benefits of a ripener treatment. Climatic conditions may also affect the benefits of such applications.Mention of trade name or proprietary product does not imply or constitute an endorsement or recommendation by the USDA or the University of Florida.     

Infection and Colonization of Sugar Cane and Other Graminaceous Plants by Endophytic Diazotrophs

Agriculturally important grasses such as sugar cane (Saccharum sp.), rice (Oryza sativa), wheat (Triticum aestivum) sorghum (Sorghum bicolor), maize (Zea mays), Panicum maximum, Brachiaria spp., and Pennisetum purpureum contain numerous diazotrophic bacteria, such as, Acetobacter diazotrophicus, Herbaspirillum spp., Azospirillum spp. These bacteria do not usually cause disease symptoms in the plants with which they are associated and the more numerous of them, for example, Herbaspirillum spp. and A. diazotrophicus, are obligate or facultative endo-phytes that do not survive well (or at all) in native soil; these are thought to be spread from plant generation to plant generation via seeds, vegetative propagation, dead plant material, and possibly by insect sap feeders. By contrast, Azospirillum spp. are not wholly endophytic but are root-associated, soil-dwelling bacteria that are also often found within plants, probably entering host plants via seeds or via wounds/cracks at lateral root junctions. Endophytic diazotrophs have been isolated from a number of grasses in which significant biological N₂ fixation (BNF) has been demonstrated, particularly Brazilian sugar cane varieties, but also in rice, maize, and sorghum. However, although the endophytic diazotrophs are held to be the causative agents of the observed BNF, direct evidence for this is lacking. Therefore, in this review we examine probable sites of bacterial multiplication and/or BNF within endophyte-containing grasses and discuss these in terms of potential benefits (or not) to both host plants and bacteria. In particular, we examine how potentially large numbers of bacteria, especially Herbaspirillum spp., A. diazotrophicus, and Azospirillum spp., can exist extracellularly within non-specialized (for symbiotic purposes) regions such as xylem vessels and intercellular spaces. The processes of infection and colonization of various grasses (particularly sugar cane) by diazotrophic endophytes are also described, and these are compared with those of important (nondiazotrophic) endophytic sugar cane pathogens such as Clavibacter xyli subsp. xyli and Xanthomonas albilineans.     

Response of eight sugarcane cultivars to glyphosine and glyphosate ripeners

Studies were conducted on eight sugarcane (Saccharum spp. hydrid) cultivars during the 1982–83 (plant crop) and 1983–84 (ratoon crop) growing seasons to determine the effects of glyphosine (Polaris) (N,N-bis (phosphonomethyl) glycine) and glyphosate (Polado) (sodium-N-(phosphonomethyl) glycine) on stalk sucrose content and yield. Difference due to crops (plant vs. ratoon) for sugarcane quality, kilograms of sugar per ton of cane (S/T), sugarcane yield, tons of cane per hectare (TCH), and sugar yield, tons of sugar per hectare (TSH) were significant. Significant differences were found in quality for the ratoon crop and cane and sugar yield in both crops due to ripener treatment. Cultivars in both crops differed significantly in quality and yield. Harvest dates were significantly different for all plant characteristics. Interactions of cultivar by treatment for the plant crop, harvest date by treatment for the ratoon crop, and cultivar by harvest date for both crops for cane quality also were significant. Time from ripener application to achievement of maximum sugar concentration also depended on cultivar. This is important in determining the economic benefits of a ripener treatment. Climatic conditions may also affect the benefits of such applications.     

Field performance of transgenic sugarcane produced using Agrobacterium and biolistics methods

Future genetic improvement of sugarcane depends, in part, on the ability to produce high‐yielding transgenic cultivars with improved traits such as herbicide and insect resistance. Here, transgenic sugarcane plants generated by different transformation methods were assessed for field performance over 3 years. Agrobacterium‐mediated (Agro) transgenic events (35) were produced using four different Agrobacterium tumefaciens strains, while biolistic (Biol) transgenic events (48) were produced using either minimal linearized DNA (LDNA) transgene cassettes with 5′, 3′ or blunt ends or whole circular plasmid (PDNA) vectors containing the same transgenes. A combined analysis showed a reduction in growth and cane yield in Biol, Agro as well as untransformed tissue culture (TC) events, compared with the parent clone (PC) Q117 (no transformation or tissue culture) in the plant, first ratoon and second ratoon crops. However, when individual events were analysed separately, yields of some transgenic events from both Agro and Biol were comparable to PC, suggesting that either transformation method can produce commercially suitable clones. Interestingly, a greater percentage of Biol transformants were similar to PC for growth and yield than Agro clones. Crop ratoonability and sugar yield components (Brix%, Pol%, and commercial cane sugar (CCS)) were unaffected by transformation or tissue culture. Transgene expression remained stable over different crop cycles and increased with plant maturity. Transgene copy number did not influence transgene expression, and both transformation methods produced low transgene copy number events. No consistent pattern of genetic changes was detected in the test population using three DNA fingerprinting techniques.     

Biological nitrogen fixation associated with sugar cane

A recent¹⁵N dilution/N balance study confirmed that certain sugar cane varieties are capable of obtaining large contributions of nitrogen from plant-associated N₂ fixation. It was estimated that up to 60 to 80% of plant N could be derived from this source, and under good conditions of water and mineral nutrient supply, it may be possible to dispense with N fertilization of these varieties altogether. The recently discovered bacterium,Acetobacter diazotrophicus, apparently responsible for this N₂ fixation associated with the plants, has unique physiological properties for a diazotroph, such as tolerance to low pH, and high sugar and salt concentrations, lack of nitrate reductase, and nitrogenase activity which tolerates short-term exposure to ammonium. Furthermore, it also behaves as an endophyte, in that it is unable to infect sugar cane plants unless through damaged tissue or by means of VA mycorrhizae and is propagated via the planting material (stem pieces).     

Biological Nitrogen Fixation in Sugar Cane: A Key to Energetically Viable Biofuel Production

The advantages of producing biofuels to replace fossil energy sources are derived from the fact that the energy accumulated in the biomass is captured directly from photosynthesis and is thus renewable, and that the cycle of carbon dioxide fixation by the crop, followed by burning of the fuel makes no overall contribution to atmospheric CO₂ or, consequently, to global warming. However, these advantages are negated if large quantities of fossil fuels need to be used to grow or process the biofuel crop. In this regard, the Brazilian bioethanol program, based on the fermentation/distillation of sugar cane juice, is particularly favorable, not only because the crop is principally hand harvested, but also because of the low nitrogen fertilizer use on sugar cane in Brazil. Recent ¹⁵N and N balance studies have shown that in some Brazilian cane varieties, high yields are possible without N fertilization because the plants are able to obtain large contributions of nitrogen from plant-associated biological N₂ fixation (BNF). The N₂-fixing acid-tolerant bacterium Acetobacter diazotrophicus was first found to occur within roots, stems, and leaves of sugar cane. Subsequently, two species of Herbaspirillum also have been found to occur within the interior of all sugar cane tissues. The discovery of these, and other N₂-fixing bacteria that survive poorly in soil but thrive within plant tissue (endophytic bacteria), may account for the high BNF contributions observed in sugar cane. Further study of this system should allow the gradual elimination of N fertilizer use on sugar cane, at least in Brazil, and opens up the possibility of the extension of this efficient N₂-fixing system to cereal and other crops with consequent immense potential benefits to tropical agriculture.     

Silicon impedes stalk penetration by the borer Eldana saccharina in sugarcane

Many plants grown in soils amended with silicon (Si) display increased levels of resistance to attack by insect herbivores. This study aimed to determine if Si treatment impeded Eldana saccharina Walker (Lepidoptera: Pyralidae) stalk penetration and subsequent damage, as well as borer mass gain, on the node and internode of a susceptible (N11) and a resistant (N33) sugarcane cultivar. Sugarcane [Saccharum spp. (Poaceae)] cultivars were grown in a pot trial in Si‐deficient river sand, with (Si+) and without (Si–) calcium silicate. Sugarcane was infested with 2‐week‐old E. saccharina larvae and harvested at four times, 24, 48, 72, and 96 h after infestation. Silicon‐treated plants showed significant increases in Si content compared to controls, and the external rind was significantly harder for Si+ cane than Si– cane. Silicon treatment significantly decreased borer penetration, stalk damage, and larval mass gain. The results are consistent with the hypothesis that Si contributes to sugarcane stalk borer resistance by impeding larval penetration. Silicon appears to contribute to the suppression of E. saccharina directly through reduced larval growth and feeding damage to the crop, and indirectly by delaying stalk penetration, resulting most likely in increased exposure time of young larvae to natural enemies, adverse climatic factors, or control measures that target young larvae (e.g., insecticides).     

Root dynamics in plant and ratoon crops of sugar cane

The root system of a sugar cane crop on an Ultisol in northeastern Brazil was examined throughout the plant and first ratoon crop cycles, using both coring and minirhizotron methods. Total root masses (living plus dead, 0.9–1.1 kg m^-2) and live root lengths (14.0–17.5 km m^-2) were greater during the ratoon cycle than at the end of the plant cane cycle (0.75 kg m^-2 and 13.8 km m^-2, respectively). Root die-back during the two weeks following ratoon harvest was estimated to be 0.15 kg m^-2, about 17% of the total root mass. Root die-back after the plant cane harvest was lower because fire was not used at this harvest and soil humidity was higher under the accumulated litter. A small amount of fine roots proliferated in the litter layer, amounting to 1% of the total mass and 3% of the total length. Root turnover could not be accurately assessed from minirhizotron observations due to variation in the relationship between coring data and the minirhizotron data with both time and soil depth.     

Deletion of fucose residues in plant N‐glycans by repression of the GDP‐mannose 4,6‐dehydratase gene using virus‐induced gene silencing and RNA interference

Production of pharmaceutical glycoproteins in plants has many advantages in terms of safety and reduced costs. However, plant‐produced glycoproteins have N‐glycans with plant‐specific sugar residues (core β‐1,2‐xylose and α‐1,3‐fucose) and a Lewis a (Le^a) epitope, i.e., Galβ(1‐3)[Fucα(1‐4)]GlcNAc. Because these sugar residues and glycan structures seemed to be immunogenic, several attempts have been made to delete them by repressing their respective glycosyltransferase genes. However, until date, such deletions have not been successful in completely eliminating the fucose residues. In this study, we simultaneously reduced the plant‐specific core α‐1,3‐fucose and α‐1,4‐fucose residues in the Le^a epitopes by repressing the Guanosine 5′‐diphosphate (GDP)‐D‐mannose 4,6‐dehydratase (GMD) gene, which is associated with GDP‐L‐fucose biosynthesis, in Nicotiana benthamiana plants. Repression of GMD was achieved using virus‐induced gene silencing (VIGS) and RNA interference (RNAi). The proportion of fucose‐free N‐glycans found in total soluble protein from GMD gene‐repressed plants increased by 80% and 95% following VIGS and RNAi, respectively, compared to wild‐type plants. A small amount of putative galactose substitution in N‐glycans from the NbGMD gene‐repressed plants was observed, similar to what has been previously reported GMD‐knockout Arabidopsis mutant. On the other hand, the recombinant mouse granulocyte‐macrophage colony‐stimulating factor (GM‐CSF) with fucose‐deleted N‐glycans was successfully produced in NbGMD‐RNAi transgenic N. benthamiana plants. Thus, repression of the GMD gene is thus very useful for deleting immunogenic total fucose residues and facilitating the production of pharmaceutical glycoproteins in plants.     

低氮条件下甘蔗-大豆间作对甘蔗产量、品质及经济效益的影响

为探究甘蔗-大豆间作对甘蔗产量、品质及经济效益的影响,在施用尿素150 kg·hm^-2条件下,选择3个甘蔗品种(B8、ROC22及GT21)进行了甘蔗单作、甘蔗-大豆间作两种种植模式的试验.结果表明： 甘蔗-大豆间作对甘蔗的有效茎数、茎径以及原料蔗、蔗糖产量均有显著影响,而对原料蔗品质影响不大;与单作相比,间作大豆处理的宿根蔗茎径大小、有效茎数、蔗茎产量和糖产量分别提高5.1%～8.7%、7.9%～31.0%、9.0%～40.5%和5.6%～39.5%;每公顷原料蔗+大豆、糖+大豆可分别增收5.89～7.93万元和5.83～7.72万元;3个品种中,ROC22间作大豆的经济收益最高,而宿根蔗B8和GT21的产量均高于ROC22.表明甘蔗-大豆间作是减少氮肥施用、提高经济收入的有效栽培措施.     

Sugar homeostasis mediated by cell wall invertase GRAIN INCOMPLETE FILLING 1 (GIF1) plays a role in pre‐existing and induced defence in rice

Sugar metabolism and sugar signalling are not only critical for plant growth and development, but are also important for stress responses. However, how sugar homeostasis is involved in plant defence against pathogen attack in the model crop rice remains largely unknown. In this study, we observed that the grains of gif1, a loss‐of‐function mutant of the cell wall invertase gene GRAIN INCOMPLETE FILLING 1 (GIF1), were hypersusceptible to postharvest fungal pathogens, with decreased levels of sugars and a thinner glume cell wall in comparison with the wild‐type. Interestingly, constitutive expression of GIF1 enhanced resistance to both the rice bacterial pathogen Xanthomonas oryzae pv. oryzae and the fungal pathogen Magnaporthe oryzae. The GIF1‐overexpressing (GIF1‐OE) plants accumulated higher levels of glucose, fructose and sucrose compared with the wild‐type plants. More importantly, higher levels of callose were deposited in GIF1‐OE plants during pathogen infection. Moreover, the cell wall was much thicker in the infection sites of the GIF1‐OE plants when compared with the wild‐type plants. We also found that defence‐related genes were constitutively activated in the GIF1‐OE plants. Taken together, our study reveals that sugar homeostasis mediated by GIF1 plays an important role in constitutive and induced physical and chemical defence.     

RNAi-directed downregulation of betaine aldehyde dehydrogenase 1 (OsBADH1) results in decreased stress tolerance and increased oxidative markers without affecting glycine betaine biosynthesis in rice (Oryza sativa)

Chemically inducible gene switches can provide precise control over gene expression, enabling more specific analyses of gene function and expanding the plant biotechnology toolkit beyond traditional constitutive expression systems. The alc gene expression system is one of the most promising chemically inducible gene switches in plants because of its potential in both fundamental research and commercial biotechnology applications. However, there are no published reports demonstrating that this versatile gene switch is functional in transgenic monocotyledonous plants, which include some of the most important agricultural crops. We found that the original alc gene switch was ineffective in the monocotyledonous plant sugar cane, and describe a modified alc system that is functional in this globally significant crop. A promoter consisting of tandem copies of the ethanol receptor inverted repeat binding site, in combination with a minimal promoter sequence, was sufficient to give enhanced sensitivity and significantly higher levels of ethanol inducible gene expression. A longer CaMV 35S minimal promoter than was used in the original alc gene switch also substantially improved ethanol inducibility. Treating the roots with ethanol effectively induced the modified alc system in sugar cane leaves and stem, while an aerial spray was relatively ineffective. The extension of this chemically inducible gene expression system to sugar cane opens the door to new opportunities for basic research and crop biotechnology.     

Genetic control of yield related stalk traits in sugarcane

A major focus of sugarcane variety improvement programs is to increase sugar yield, which can be accomplished by either increasing the sugar content of the cane or by increasing cane yield, as the correlation between these traits is low. We used a cross between an Australian sugarcane variety Q165, and a Saccharum officinarum accession, IJ76-514, to dissect the inheritance of yield-related traits in the complex polyploid sugarcane. A population of 227 individuals was grown in a replicated field trial and evaluated over 3 years for stalk weight, stalk diameter, stalk number, stalk length and total biomass. Over 1,000 AFLP and SSR markers were scored across the population and used to identify quantitative trait loci (QTL). In total, 27 regions were found that were significant at the 5% threshold using permutation tests with at least one trait; individually, they explained from 4 to 10% of the phenotypic variation and up to 46% were consistent across years. With the inclusion of digeneic interactions, from 28 to 60% of the variation was explained for these traits. The 27 genomic regions were located on 22 linkage groups (LGs) in six of the eight homology groups (HGs) indicating that a number of alleles or quantitative trait alleles (QTA) at each QTL contribute to the trait; from one to three alleles had an effect on the traits for each QTL identified. Alleles of a candidate gene, TEOSINTE BRANCHED 1 (TB1), the major gene controlling branching in maize, were mapped in this population using either an SSR or SNP markers. Two alleles showed some association with stalk number, but unlike maize, TB1 is not a major gene controlling branching in sugarcane but only has a minor and variable effect.     

Endless Hide-and-Seek： Dynamic Co-evolution in Plant-Bacterium Warfare

Plants possess innate Immune systems to prevent most potential Infections. The ancient and conserved innate immune responses are triggered by microbe-associated molecular patterns （MAMPs） and play important roles in broad-spectrum defenses. However, successful bacterial pathogens evolved type Ⅲ virulence effectors to suppress MAMP-medlated immunity. To survive, plants further developed highly specific resistance （R） genes to trigger gene-for-gene-mediated immunity and turn the virulent pathogens into avirulent ones. We summarize here the very recent advances in this dynamic coevolution of plantbacterium interaction.