A target-site mutation is present in a glyphosate-resistant Lolium rigidum population

Annual ryegrass (Lolium rigidum) is the only weed species to have evolved resistance to the broad‐spectrum herbicide glyphosate in Australia. A population that had failed to be controlled by glyphosate was collected from a vineyard in the Adelaide Hills region of South Australia. Dose–response experiments on this population (SLR 77) showed that it was glyphosate resistant, with an LD₅₀ that was 1.9–3.4 times higher than that of a susceptible population (VLR 1). The movement of radiolabelled glyphosate within SLR 77 plants showed that this population did not have the differential glyphosate translocation mechanism of resistance common to several other Australian glyphosate‐resistant populations. Subsequent analysis of shikimic acid accumulation within the plant after glyphosate treatment showed that this population accumulated significantly less shikimic acid than a susceptible population, but more than a glyphosate‐resistant population with the translocation mechanism, indicating the possible involvement of another mechanism of resistance. Sequencing of a portion of the SLR 77 5‐enolpyruvylshikimate‐3‐phosphate synthase gene was carried out and a mutation causing an amino acid change at position 106 from proline to threonine was identified. This mutation is likely to be responsible for glyphosate resistance in this population, as mutations in this position have been found to be responsible for glyphosate resistance in goosegrass (Eleusine indica) from Malaysia. This paper represents the first report of target‐site glyphosate resistance in L. rigidum and provides evidence that this species has at least two mechanisms of glyphosate resistance present in Australia.     

Glyphosate resistance in four different populations of Lolium rigidum is associated with reduced translocation of glyphosate to meristematic zones

Weed populations with resistance to glyphosate have evolved over the last 7 years, since the discovery of the first glyphosate‐resistant populations of Lolium rigidum in Australia. Four populations of L. rigidum from cropping, horticultural and viticultural areas in New South Wales and South Australia were tested for resistance to glyphosate by dose–response experiments. All populations required considerably more glyphosate to achieve 50% control compared with a known susceptible population, indicating they were resistant to glyphosate. Translocation of glyphosate within these resistant populations was examined by following the movement of radiolabelled glyphosate applied to a mature leaf. All resistant plants translocated significantly more herbicide to the tip of the treated leaf than did susceptible plants. Susceptible plants translocated twice as much herbicide to the stem meristematic portion of the plant compared with resistant plants. These different translocation patterns suggest an association between glyphosate resistance in L. rigidum and the ability of glyphosate to accumulate in the shoot meristem.     

Simulating evolution of glyphosate resistance in Lolium rigidum I: population biology of a rare resistance trait

Despite frequent use for the past 25 years, resistance to glyphosate has evolved in few weed biotypes. The propensity for evolution of resistance is not the same for all herbicides, and glyphosate has a relatively low resistance risk. The reasons for these differences are not entirely understood. A previously published two‐herbicide resistance model has been modified to explore biological and management factors that account for observed rates of evolution of glyphosate resistance. Resistance to a post‐emergence herbicide was predicted to evolve more rapidly than it did to glyphosate, even when both were applied every year and had the same control efficacy. Glyphosate is applied earlier in the growing season when fewer weeds have emerged and hence exerts less selection pressure on populations. The evolution of glyphosate resistance was predicted to arise more rapidly when glyphosate applications were later in the growing season. In simulations that assumed resistance to the post‐emergence herbicide did not evolve, the evolution of glyphosate resistance was less rapid, because post‐emergence herbicides were effectively controlling rare glyphosate‐resistant individuals. On their own, these management‐related factors could not entirely account for rates of evolution of resistance to glyphosate observed in the field. In subsequent analyses, population genetic parameter values (initial allele frequency, dominance and fitness) were selected on the basis of empirical data from a glyphosate‐resistant Lolium rigidum population. Predicted rates of evolution of resistance were similar to those observed in the field. Together, the timing of glyphosate applications, the rarity of glyphosate‐resistant mutants, the incomplete dominance of glyphosate‐resistant alleles and pleiotropic fitness costs associated with glyphosate resistance, all contribute to its relatively slow evolution in the field.     

Non‐target‐site mechanism of glyphosate resistance in Italian ryegrass (Lolium multiflorum)

In Shizuoka Prefecture, Japan, glyphosate‐resistant Lolium multiflorum is a serious problem on the levees of rice paddies and in wheat fields. The mechanism of resistance of this biotype was analyzed. Based on LD₅₀, the resistant population was 2.8–5.0 times more resistant to glyphosate than the susceptible population. The 5‐enolpyruvyl‐shikimate‐3‐phosphate synthase (EPSPS) gene sequence of the resistant biotype did not show a non‐synonymous substitution at Pro106, and amplification of the gene was not observed in the resistant biotype. The metabolism and translocation of glyphosate were examined 4 days after application through the direct detection of glyphosate and its metabolite aminomethylphosphonic acid (AMPA) using liquid chromatograph‐tandem mass spectrometer (LC‐MS/MS). AMPA was not detected in either biotype in glyphosate‐treated leaves or the other plant parts. The respective absorption rates of the susceptible and resistant biotypes were 37.90 ± 3.63% and 41.09 ± 3.36%, respectively, which were not significantly different. The resistant biotype retained more glyphosate in a glyphosate‐treated leaf (91.36 ± 1.56% of absorbed glyphosate) and less in the untreated parts of shoots (5.90 ± 1.17%) and roots (2.76 ± 0.44%) compared with the susceptible biotype, 79.58 ± 3.73%, 15.77 ± 3.06% and 4.65 ± 0.89%, respectively. The results indicate that the resistance mechanism is neither the acquisition of a metabolic system nor limiting the absorption of glyphosate but limited translocation of the herbicide in the resistant biotype of L. multiflorum in Shizuoka Prefecture.     

Development of microsatellite markers and their effectiveness in Lolium temulentum

Screening a genomic library of Lolium temulentum (darnel) with synthetic (GT)₁₅ and (GA)₁₅ oligonucleotides, we identified microsatellite‐containing clones. Based on the sequence data of the clones, specific primer pairs were synthesized and their effectiveness examined using 10 L. temulentum and two L. persicum accessions from Asia, Africa and Europe. Fifteen primer pairs amplified single fragments, and five of them showed polymorphism in polyacrylamide gel electrophoresis in the L. temulentum and L. persicum accessions. Fifteen primer pairs reported in L. perenne (perennial ryegrass) were also applied in this study. Nine of them amplified the microsatellite alleles, and two of the nine showed polymorphic alleles in L. temulentum and L. persicum. For the polymorphic markers, polymorphic information content values ranged from 0.60 to 0.86 with an average of 0.76 among 10 L. temulentum accessions. The microsatellite markers developed for L. temulentum and L. perenne should be informative and powerful in analysing the intraspecific genetic diversity and the phylogenetic relationships of L. temulentum and L. persicum.     

Phylogeography based on the nuclear ribosomal DNA internal transcribed spacer region of native Miscanthus sinensis (Poaceae) populations in Japan

Nucleotide sequence variations were investigated with respect to the geographical distribution patterns of Miscanthus sinensis populations that were sampled from 26 Japanese national parks and three populations of the Ryukyu Islands. Twelve homozygous sequences in the nuclear ribosomal DNA internal transcribed spacer region were detected. The populations of M. sinensis in mainland Japan mainly were composed of a monophyletic group with a symapomorphic character, whereas those in the Ryukyu Islands included a polyphyletic group. Only an internal transcribed spacer haplotype with a plesiomorphic character was found in both mainland Japan and the Ryukyu Islands. Thus, no clear geographical isolation was observed in this species. These facts might be caused by the ability of M. sinensis as a pioneer plant to have a high migration potential and high gene flow by outcrossing. On the basis of the results of this study (nuclear ribosomal DNA) and the previous study (chloroplast DNA), a phylogeographical history of M. sinensis was presumed where the ancestral and derived lineages were distributed in the southern and northern regions of Japan, respectively, without strict geographical isolation.     

SSR-based genetic linkage analysis of resistance to crown rust (Puccinia coronata f. sp. lolii) in perennial ryegrass (Lolium perenne)

Crown rust (caused by Puccinia coronata f. sp. lolii) is a serious foliar disease of the pasture and turfgrass perennial ryegrass (Lolium perenne). Previous genetic studies have detected both qualitative and quantitative resistance mechanisms, and interpretation of the genetic system is complicated by variation within the sexually reproducing pathogen. Resistant and susceptible parental genotypes of ryegrass were identified using a composite urediniospore population collected from three geographically distinct locations. A two-way pseudo-testcross mapping population was obtained as the F₁ progeny of the pair-cross between ryegrass parental genotypes Vedette₆ and Victorian₉. Both parents showed intermediate resistance against a pathogen population collected in a single geographical zone (Hamilton, Victoria), but in the F₁ population, significant variation for a range of resistance-associated characters was detected. Statistical analysis of phenotypic data suggested a major gene effect, hence bulked segregant analysis with map-assigned simple sequence repeat (SSR) markers was used to scan the genome. A marker showing strong association with resistance was assigned to linkage group (LG) 2 of perennial ryegrass. Analysis of 11 LG2 SSR markers defined an interval between loci xlpssrh03f03 and xlpssrk02e02 as containing the gene or genes (LpPc1) conferring crown rust resistance. Resistance gene determinants were inherited from both parents, with up to 80% of the total phenotypic variation explained by markers segregating from Vedette₆ and up to 26% of the variation explained by markers segregating from Victorian₉. The two contributions together resulted in an additive increase in effect, with fully resistant individuals requiring determinants from both parents. A conserved syntenic relationship was observed with linkage group B of Avena strigosa, which is the location of a cluster of resistance genes to the oat form of crown rust. The implications of this study for marker-assisted selection of disease resistance in perennial ryegrass are discussed.     

PCR‐based identification of Pythium spp. causing cavity spot in carrots and sensitive detection in soil samples

On the basis of ITS sequences PCR primers were designed for the identification of the five Pythium species found to be most important for the development of carrot cavity spot in Norway: P. intermedium, P. sulcatum, P. sylvaticum, P. violae and P. ‘vipa’. The P. ‘vipa’ isolates had a unique ITS sequence, differed morphologically from all other Pythium isolates, and thus probably represent a new species. The PCR primers were species‐specific with no cross‐reaction to other Pythium species or to fungal isolates from carrot tested. The detection limits varied for the different primer pairs. The two most sensitive assays allowed detection of as little as 5 fg DNA. All five Pythium species could be detected in lesions from diseased carrots. Weak positive signals were obtained from some carrot samples without symptoms. PCR assays allowed detection of pathogens in soil. In samples of soil known to produce cavity spots on cropped carrots, strong signals were obtained. In several soil samples more than one of the five Pythium species could be detected. The utilization of this diagnostic PCR assay in analysis of field soil and carrot tissue might in the future be exploited to reduce the incidence of this serious carrot disease.     

An aspartate to glycine change in the carboxyl transferase domain of acetyl CoA carboxylase and non‐target‐site mechanism(s) confer resistance to ACCase inhibitor herbicides in a Lolium multiflorum population

BACKGROUND: The increasing use of ACCase‐inhibiting herbicides has resulted in evolved resistance in key grass weeds infesting cereal cropping systems worldwide. Here, a thorough and systematic approach is proposed to elucidate the basis of resistance to three ACCase herbicides in a Lolium multiflorum Lam. (Italian rye grass) population from the United Kingdom (UK24). RESULTS: Resistance to sethoxydim and pinoxaden was always associated with a dominant D2078G (Alopecurus myosuroides Huds. equivalent) target‐site mutation in UK24. Conversely, whole‐plant herbicide assays on predetermined ACCase genotypes showed very high levels of resistance to diclofop‐methyl for all three wild DD2078 and mutant DG2078 and GG2078 ACCase genotypes from the mixed resistant population UK24. This indicates the presence of other diclofop‐methyl‐specific resistance mechanism(s) yet to be determined in this population. The D2078G mutation could be detected using an unambiguous DNA‐based dCAPS procedure that proved very transferable to A. myosuroides, Avena fatua L., Setaria viridis (L.) Beauv. and Phalaris minor Retz. CONCLUSION: This study provides further understanding of the molecular basis of resistance to ACCase inhibitor herbicides in a Lolium population and a widely applicable PCR‐based method for monitoring the D2078G target‐site resistance mutation in five major grass weed species. Copyright © 2010 Society of Chemical Industry     

香蕉炭疽菌rDNA ITS区的分子鉴定与检测

 香蕉炭疽病菌(Colletordchum muscat)是一种引起香蕉采后病害的最重要病原,本研究用真菌18S~28S间的内转录间隔区(internal transcribed spacer,ITS)通用引物18SF和28SR扩增香蕉炭疽菌和其它外群真菌的基因组DNA,扩增出约510bp的片段;通过克隆测序香蕉炭疽菌的ITS全序列并与GenBank中炭疽菌属其它种的ITS序列比对,设计出香蕉炭疽菌的特异性引物ColM1和ColM2。用此特异引物可以从香蕉炭疽菌株中扩增出382bp的特异性片段,而其余20个参试菌株和香蕉组织的PCR反应结果为阴性,灵敏度实验证明可以检测到目标DNA的浓度为0.1Pg。该方法可用于快速、准确和灵敏地检测香蕉炭疽菌,为快速监测组织中有无香蕉炭疽病菌潜伏侵染与及早采取防治措施提供积极的指导意义。     

Influence of weed management measures on glyphosate resistance and endophyte infection in naturalized Italian ryegrass (Lolium multiflorum)

Recently, glyphosate‐resistant Italian ryegrass (Lolium multiflorum Lam.) was found on rice paddy levees in a western region of Shizuoka Prefecture, Japan. Naturalized populations of Italian ryegrass are frequently infected with fungal Epichloë endophytes. Endophytes often confer benefits to their host grasses. This study investigated the influence of five weed management treatments on glyphosate resistance and endophyte infection in Italian ryegrass that was growing on paddy levees where glyphosate‐resistant individuals were dominant. The weed management treatments were: (i) mowing once before the grass flowered; (ii) mowing once during flowering; (iii) mowing twice during flowering; (iv) glyphosate application before flowering; and (v) no treatment. The seeds were collected from the treatment plots in 2013 and 2014. The seeds were examined for endophyte infection and the seedlings that had been grown from the seeds were tested for the frequency of glyphosate resistance. The seedlings that had been derived from the glyphosate treatment showed higher frequencies of glyphosate resistance than those seedlings that had been derived from all the other treatments. Endophytes were found in all populations of the seeds from the paddy levees, with higher infection rates in the seeds that had been derived from the glyphosate treatment and the twice‐mowed treatment. There was a significant relationship between the endophyte infection frequency in the seeds and glyphosate resistance in the seedlings that had been grown from the same populations. The results indicate that where glyphosate herbicides are frequently used, selection for glyphosate‐resistant Italian ryegrass occurs, and along with this, the frequency of endophyte infection also increases.     

PCR-based detection of resistance to acetyl-CoA carboxylase-inhibiting herbicides in black-grass (Alopecurus myosuroides Huds) and ryegrass (Lolium rigidum gaud)

A simple method based upon allele-specific PCR was developed to detect an isoleucine-leucine substitution in the gene encoding chloroplastic acetyl-coenzyme A carboxylase (ACCase) in two gramineous weeds: Lolium rigidum Gaud and Alopecurus myosuroides Huds. Analysis of 1800 A myosuroides and 750 L rigidum seedlings showed that the presence of ACCase leucine allele(s) conferred cross-resistance to the cyclohexanedione herbicide cycloxydim and to the aryloxyphenoxypropionate herbicides fenoxaprop-P-ethyl and diclofop-methyl. Seedlings containing ACCase leucine allele(s) could be either sensitive or resistant to the aryloxyphenoxypropionate herbicides haloxyfop-P-methyl and clodinafop-propargyl. Successful detection of resistant plants in a field population of A myosuroides was achieved using this PCR assay. Using it with basic molecular biology laboratory equipment, the presence of resistant leucine ACCase allele(s) can be detected within one working day.     

Introgression of crown rust (Puccinia coronata) resistance from meadow fescue (Festuca pratensis) into Italian ryegrass (Lolium multiflorum): genetic mapping and identification of associated molecular markers

Crown rust ( Puccinia coronata ) resistance (CRres), which had been introgressed from meadow fescue ( Festuca pratensis ) into the Italian ryegrass ( Lolium multiflorum ) background, was genetically mapped with amplified fragment length polymorphism (AFLP) and sequence tagged site (STS) markers to a terminal segment of chromosome 5. Comparative mapping had previously shown that this region of the Lolium / Festuca genome has a degree of conserved genetic synteny with chromosomes 11 and 12 of rice. Sequences from rice chromosome 12 were used as templates for identifying further STS markers that cosegregated with CRres. The relative genomic positions of molecular markers associated with CRres in L. multiflorum , L. perenne , F. pratensis and oats is discussed, along with their relationships to physical positions on rice chromosomes C11 and C12.     

ISSR variation in a worldwide collection of velvetleaf (Abutilon theophrasti) and the genetic background of weedy strains mingled in grains imported into Japan

Velvetleaf seeds have been found in imported grains in Japan. The plants from these seeds show a weedy growth habit, such as that seen in the noxious velvetleaf which has recently emerged in Japan and noted in our previous study. To elucidate the genetic background of the velvetleaf strains found in imported grains we evaluated the genetic variation of six strains and an additional 39 worldwide velvetleaf accessions using the intersimple sequence repeat (ISSR) polymorphism. Cluster analysis based on the ISSR polymorphism emitted two major clusters which corresponded well with classification by growth habit, that is, crop type and weed type. Five of the six strains from the imported grains formed a small cluster. All six strains united into one major cluster containing the weed type accessions, while all of the old Japanese accessions formed another major cluster containing the crop type accessions. The genetic difference between imported weedy velvetleaf and old Japanese accessions suggests that imported velvetleaves are the source of the recent outbreak of the noxious velvetleaf in Japan.