Quinclorac resistance induced by the suppression of the expression of 1-aminocyclopropane-1-carboxylic acid (ACC) synthase and ACC oxidase genes in Echinochloa crus-galli var. zelayensis

Epigenetic Regulation of CYP72A385-Mediated Metabolic Resistance to Novel Auxin Herbicide Florpyrauxifen-benzyl in Echinochloa crus-galli (L.) P. Beauv

Weed's metabolic resistance to herbicides has undermined the sustainability of herbicides and global food security. Notably, we identified an Echinochloa crus-galli (L.) P. Beauv population (R) that evolved resistance to the never-used florpyrauxifen-benzyl, in which florpyrauxifen-benzyl was metabolized faster than the susceptible E. crus-galli population (S). RNA-seq identified potential metabolism-related genes, EcCYP72A385 and EcCYP85A1, whose expression in yeast exhibited the capacity to degrade florpyrauxifen-benzyl. Region-2 in the EcCYP72A385 promoter showed significant demethylation after florpyrauxifen-benzyl treatment in the R population. DNA methyltransferase inhibitors induce EcCYP72A385 overexpression in the S population and endow it with tolerance to florpyrauxifen-benzyl. Moreover, methyltransferase-like 7A (EcMETTL7A) was overexpressed in the S population and specifically bound to the EcCYP72A385 promoter. Transgenic EcCYP72A385 in Arabidopsis and Oryza sativa L. exhibited resistance to florpyrauxifen-benzyl, whereas EcMETTL7A transgenic plants were sensitive. Overall, EcCYP72A385 is the principal functional gene for conferring resistance to florpyrauxifen-benzyl and is regulated by EcMETTL7A in E. crus-galli.

Comparative Analysis of Whole Chloroplast Genomes of Three Common Species of Echinochloa (Gramineae) in Paddy Fields

Echinochloa crus-galli var. crus-galli, E. crus-galli var. zelayensis, and E. glabrescens, morphologically similar at the seedling stage, are the most pernicious barnyard grass species in paddy fields worldwide. Chloroplast (cp) genomes could be conducive to their identification. In this study, we assembled the complete cp genome sequences of Echinochloa crus-galli var. crus-galli (139,856 bp), E. crus-galli var. zelayensis (139,874 bp), and E. glabrescens (139,874 bp), which exhibited a typical circular tetramerous structure, large and small single-copy regions, and a pair of inverted repeats. In Echinochloa crus-galli var. crus-galli, there were 136 simple sequence (SSRs) and 62 long (LRs) repeats, and in the other two species, 139 SSRs and 68 LRs. Each cp genome contains 92 protein-encoding genes. In Echinochloa crus-galli var. crus-galli and E. glabrescens, 321 and 1 single-nucleotide polymorphisms were detected compared to Echinochloa crus-galli var. zelayensis. IR expansion and contraction revealed small differences between the three species. The phylogenetic tree based on cp genomes demonstrated the phylogenetic relationship between ten barnyard grass species and other common Gramineae plants, showing new genetic relationships of the genus Echinochloa. This study provides valuable information on cp genomes, useful for identifying and classifying the genus Echinochloa and studying its phylogenetic relationships and evolution.

Comparison of quintrione and quinclorac on mechanism of action

Quintrione is a new post-emergence herbicide developed for use in rice; however, the mechanism of action remains unclear. We determined the phytotoxicity of quintrione, and the contributions of hormone levels and lipid peroxidation to phytotoxicity, by comparing them to those induced by quinclorac. We also investigated 4-hydroxyphenylpyruvate dioxygenase (HPPD) activity and carotenoid content following treatment with quintrione by comparing them to those induced by quinclorac and mesotrione. We found that quintrione and quinclorac both inhibited the growth of Echinochloa crusgalli var. zelayensis, but that quinclorac was a little more effective. At 24 h, quintrione and quinclorac significantly increased ethylene production and the contents of abscisic acid (ABA) and indole acetic acid (IAA) compared with the control. No significant differences were observed between quintrione and quinclorac on the three plant hormones. Quintrione and quinclorac also induced the formation of malondialdehyde (MDA), which is associated with lipid peroxidation, with no significant difference between them. Carotenoid content was reduced in E. crusgalli var. zelayensis following treatments with quintrione, quinclorac, and mesotrione. At 120 h, carotenoid contents were significantly higher following the quintrione and quinclorac treatments, in comparison with mesotrione treatment. There were no significant differences between quintrione and quinclorac in the inhibition of HPPD activity, and the effects of both were significantly less than the effect of mesotrione. In summary, E. crusgalli var. zelayensis was susceptible to both quintrione and quinclorac. The mechanism of action of quintrione, like that of quinclorac, was related to levels of plant hormones and lipid peroxidation; however, quintrione was a poor inhibitor of HPPD activity compared to mesotrione.

The phytotoxicity mechanism of florpyrauxifen-benzyl to Echinochloa crus-galli (L.) P. Beauv and weed control effect

Weeds infest rice causing high yield losses, leading to the increasing use of herbicides for weed control. However, many weeds have evolved resistance to common commercial herbicides, including penoxsulam, metamifop and quinclorac. This study investigated the weed control effect and the phytotoxicity mechanism of florpyrauxifen-benzyl, a novel synthetic auxin herbicide registered for weed management in rice fields in China. The greenhouse study showed that florpyrauxifen-benzyl was highly efficient (GR₅₀ < 6 and GR₉₀ < 15 g a.i ha^-1) at controlling 10 weed species commonly found in rice fields, including penoxsulam- and quinclorac- resistant(R) biotypes of Echinochloa Beauv. and bensulfuron-methyl-R biotype of Ammannia arenaria. The typical plant hormone content showed that following florpyrauxifen-benzyl treatment, indole-3-acetic acid (IAA) production changed only slightly at 12 h, while abscisic acid (ABA) production increased with time in the treated group, whose content was significantly higher than that of the control. Besides, ethylene biosynthesis was stimulated by florpyrauxifen-benzyl, ethylene production, 1-aminocyclopropane-1-carboxylic acid (ACC) content, and 1-aminocyclopropane-1-carboxylate synthase (ACS) and 1-aminocyclopropane-1-carboxylate oxidase (ACO) activities, which evidently increased in the treated group, and ethylene peaked at 36 h. For the antioxidant enzyme activities and malondialdehyde (MDA) content in the treated group, results showed that MDA content continuously increased with time and was greater than that in the untreated group at 48 h and 72 h, superoxide dismutase (SOD) activity changed with exposure time and was significantly higher in the treatment group than the control at 48 h. A similar phenomenon was observed in peroxidase (POD) activity, which reached a peak at 48 h, and no distinct difference in catalase (CAT) activity was observed among groups except for the higher activity in the treated groups than control at 36 h and 48 h. Our results showed that that the stimulation ethylene biosynthesis and accumulation of ABA and reactive oxygen species (ROS) play important roles in the phytotoxicity mechanism of florpyrauxifen-benzyl in plants. Our findings demonstrate the potential of florpyrauxifen-benzyl to provide an alternative weed management strategy for rice fields.

Magnetic mesoporous nanomaterials with AIE properties for selective detection and removal of CN- from water under magnetic conditions

We have prepared a type of magnetic mesoporous nanomaterial with aggregation-induced emission properties (Fe₃O₄@mSiO₂@TPA@BA, hence abbr. FSTB) to detect and remove cyanide ions (CN^-) under magnetic conditions. FSTB has a large specific surface area and improved fluorescence performance to identify CN^-, and its superparamagnetic behavior plays an important role in removing CN^-. The magnetic sensor FSTB shows excellent selectivity and anti-interference for the detection of CN^- in aqueous solutions. It is obvious from the equation LOD = 3δ/S that the limit of detection (LOD) of FSTB for CN^- is significantly lower than the permissible level of CN^- in drinkable water recommended by the World Health Organization. Therefore, the magnetic sensor FSTB has a wide range of applications for detecting and removing harmful CN^-.

Transcriptome analysis reveals gene responses to herbicide, tribenuron methyl, in Brassica napus L. during seed germination

Background

Tribenuron methyl (TBM) is an herbicide that inhibits sulfonylurea acetolactate synthase (ALS) and is one of the most widely used broad-leaved herbicides for crop production. However, soil residues or drifting of the herbicide spray might affect the germination and growth of rapeseed, Brassica napus, so it is imperative to understand the response mechanism of rape to TBM during germination. The aim of this study was to use transcriptome analysis to reveal the gene responses in herbicide-tolerant rapeseed to TBM stress during seed germination.

Results

2414, 2286, and 1068 differentially expressed genes (DEGs) were identified in TBM-treated resistant vs sensitive lines, treated vs. control sensitive lines, treated vs. control resistant lines, respectively. GO analysis showed that most DEGs were annotated to the oxidation-reduction pathways and catalytic activity. KEGG enrichment was mainly involved in plant-pathogen interactions, α-linolenic acid metabolism, glucosinolate biosynthesis, and phenylpropanoid biosynthesis. Based on GO and KEGG enrichment, a total of 137 target genes were identified, including genes involved in biotransferase activity, response to antioxidant stress and lipid metabolism. Biotransferase genes, CYP450, ABC and GST, detoxify herbicide molecules through physical or biochemical processes. Antioxidant genes, RBOH, WRKY, CDPK, MAPK, CAT, and POD regulate plant tolerance by transmitting ROS signals and triggering antioxidant enzyme expression. Lipid-related genes and hormone-related genes were also found, such as LOX3, ADH1, JAZ6, BIN2 and ERF, and they also played an important role in herbicide resistance.

Conclusions

This study provides insights for selecting TBM-tolerant rapeseed germplasm and exploring the molecular mechanism of TBM tolerance during germination.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07614-1.

Synthetic auxin herbicides: finding the lock and key to weed resistance

Synthetic auxin herbicides are designed to mimic indole-3-acetic acid (IAA), an integral plant hormone affecting cell growth, development, and tropism. In this review, we explore target site genes in the auxin signaling pathway including SCF^TIR1/AFB, Aux/IAA, and ARFs that are confirmed or proposed mechanisms for weed resistance to synthetic auxin herbicides. Resistance to auxin herbicides by metabolism, either by enhanced cytochrome P450 detoxification or by loss of pro-herbicide activation, is a major non-target-site resistance pathway. We speculate about potential fitness costs of resistance due to effects of resistance-conferring mutations, provide insight into the role of polyploidy in synthetic auxin resistance evolution, and address the genetic resources available for weeds. This knowledge will be the key to unlock the long-standing questions as to which components of the auxin signaling pathway are most likely to have a role in resistance evolution. We propose that an ambitious research effort into synthetic auxin herbicide/target site interactions is needed to 1) explain why some synthetic auxin chemical families have activity on certain dicot plant families but not others and 2) fully elucidate target-site cross-resistance patterns among synthetic auxin chemical families to guide best practices for resistance management.

Barnyard Millet for Food and Nutritional Security: Current Status and Future Research Direction

Barnyard millet (Echinochloa species) has become one of the most important minor millet crops in Asia, showing a firm upsurge in world production. The genus Echinochloa comprises of two major species, Echinochloa esculenta and Echinochloa frumentacea, which are predominantly cultivated for human consumption and livestock feed. They are less susceptible to biotic and abiotic stresses. Barnyard millet grain is a good source of protein, carbohydrate, fiber, and, most notably, contains more micronutrients (iron and zinc) than other major cereals. Despite its nutritional and agronomic benefits, barnyard millet has remained an underutilized crop. Over the past decades, very limited attempts have been made to study the features of this crop. Hence, more concerted research efforts are required to characterize germplasm resources, identify trait-specific donors, develop mapping population, and discover QTL/gene (s). The recent release of genome and transcriptome sequences of wild and cultivated Echinochloa species, respectively has facilitated in understanding the genetic architecture and decoding the rapport between genotype and phenotype of micronutrients and agronomic traits in this crop. In this review, we highlight the importance of barnyard millet in the current scenario and discuss the up-to-date status of genetic and genomics research and the research gaps to be worked upon by suggesting directions for future research to make barnyard millet a potential crop in contributing to food and nutritional security.

Ethylene Biosynthesis Inhibition Combined with Cyanide Degradation Confer Resistance to Quinclorac in Echinochloa crus-galli var. mitis

Echinochloa crus-galli var. mitis has rarely been reported for herbicide resistance, and no case of quinclorac resistance has been reported so far. Synthetic auxin-type herbicide quinclorac is used extensively to control rice weeds worldwide. A long history of using quinclorac in Chinese rice fields escalated the resistance in E. crus-galli var. mitis against this herbicide. Bioassays in Petri plates and pots exhibited four biotypes that evolved into resistance to quinclorac ranking as JS01-R > AH01-R > JS02-R > JX01-R from three provinces of China. Ethylene production in these biotypes was negatively correlated with resistance level and positively correlated with growth inhibition. Determination of the related ethylene response pathway exhibited resistance in biotypes that recorded a decline in 1-aminocyclopropane-1-carboxylic acid (ACC) content, ACC synthase oxidase activities, and less inducible ACS and ACO genes expressions than the susceptible biotype, suggesting that there was a positive correlation between quinclorac resistance and ethylene biosynthesis inhibition. Cyanides produced during the ethylene biosynthesis pathway mainly degraded by the activity of β-cyanoalanine synthase (β-CAS). Resistant biotypes exhibited higher β-CAS activity than the susceptible ones. Nucleotide changes were found in the EcCAS gene of resistant biotypes as compared to sensitive ones that caused three amino acid substitutions (Asn-105-Lys, Gln-195-Glu, and Gly-298-Val), resulting in alteration of enzyme structure, increased binding residues in the active site with its cofactor, and decreased binding free energy; hence, its activity was higher in resistant biotypes. Moreover, these mutations increased the structural stability of the enzyme. In view of the positive correlation between ethylene biosynthesis inhibition and cyanide degradation with resistance level, it is concluded that the alteration in ethylene response pathway or at least variation in ACC synthase and ACC oxidase enzyme activities—due to less relative expression of ACS and ACO genes and enhanced β-CAS activity, as well as mutation and increased relative expression of EcCAS gene—can be considered as a probable mechanism of quinclorac resistance in E. crus-galli var. mitis.

Transcriptome profiling to identify cytochrome P450 genes involved in penoxsulam resistance in Echinochloa glabrescens

Cytochrome P450s (P450s) confer resistance against herbicides, and this is increasingly becoming a concern for weed control. As a widespread Gramineae weed in paddy fields, Echinocloa glabrescens has become resistant to the acetolactate synthase (ALS)-inhibiting triazolopyrimidine herbicide penoxsulam. In this study, we found that the GR₅₀ of the resistant population (SHQP-R) decreased substantially from 25.6 to 5.0 and 6.2 g a.i. ha^-1 after treatment with the P450 inhibitors piperonyl butoxide (PBO) and malathion, respectively. However, P450 inhibitors almost had no effects on the susceptibility of the sensitive population (JYJD-S) to penoxsulam. To investigate the mechanisms of metabolic resistance, transcriptome sequencing analysis was performed to find candidate genes that may confer resistance to penoxsulam in E. glabrescens. A total of 233 P450 differentially expressed genes (DEGs) were identified by transcriptome sequencing. We found that the metabolic process and metabolic pathways were the most highly enriched in DEGs. Further, twenty-seven candidate P450 DEGs were selected for qPCR validation analyses. After penoxsulam treatment, the relative expression levels were significantly higher in SHQP-R than in JYJD-S. Among these, the relative expression of twenty-three P450 DEGs (eighteen from the CYP72A-71C-74A-96A-734A subfamily; five from CYP81E1-94C1-94B3-714C1-714C2) were upregulated and four P450 DEGs (from CYP724B1-711A1-707A7-97B2) were downregulated. Changes in the expression of these candidate P450 genes in E. glabrescens were in response to penoxsulam, which provides preliminary evidence for the role of P450s in herbicide metabolism in E. glabrescens. However, further functional studies on metabolic resistance to penoxsulam in a resistant E. glabrescens population are required.

Mechanisms of the IAA and ACC-deaminase producing strain of Trichoderma longibrachiatum T6 in enhancing wheat seedling tolerance to NaCl stress

BACKGROUND

Trichoderma species, a class of plant beneficial fungi, may provide opportunistic symbionts to induce plant tolerance to abiotic stresses. Here, we determined the possible mechanisms responsible for the indole acetic acid (IAA) and 1-aminocyclopropane-1-carboxylate-deaminase (ACC-deaminase) producing strain of Trichoderma longibrachiatum T6 (TL-6) in promoting wheat (Triticum aestivum L.) growth and enhancing plant tolerance to NaCl stress.

RESULTS

Wheat treated with or without TL-6 was grown under different levels of salt stress in controlled environmental conditions. TL-6 showed a high level of tolerance to 10 mg ml^- 1 of NaCl stress and the inhibitory effect was more pronounced at higher NaCl concentrations. Under NaCl stress, the activity of ACC-deaminase and IAA concentration in TL-6 were promoted, with the activity of ACC-deaminase increased by 26% at the salt concentration of 10 mg ml^- 1 and 31% at 20 mg ml^- 1, compared with non-saline stress; and the concentration of IAA was increased by 10 and 7%, respectively (P < 0.05). The increased ACC-deaminase and IAA concentration in the TL-6 strain may serve as an important signal to alleviate the negative effect of NaCl stress on wheat growth. As such, wheat seedlings with the ACC-deaminase and IAA producing strain of TL-6 treatment under NaCl stress increased the IAA concentration by an average of 11%, decreased the activity of ACC oxidase (ACO) by an average of 12% and ACC synthase (ACS) 13%, and decreased the level of ethylene synthesis and the content of ACC by 12 and 22%, respectively (P < 0.05). The TL-6 treatment decreased the transcriptional level of ethylene synthesis genes expression, and increased the IAA production genes expression significantly in wheat seedlings roots; down-regulated the expression of ACO genes by an average of 9% and ACS genes 12%, whereas up-regulated the expression of IAA genes by 10% (P < 0.05). TL-6 treatments under NaCl stress decreased the level of Na⁺ accumulation; and increased the uptake of K⁺ and the ratio of K⁺/Na⁺, and the transcriptional level of Na⁺/H⁺ antiporter gene expression in both shoots and roots.

CONCLUSIONS

Our results indicate that the strain of TL-6 effectively promoted wheat growth and enhanced plant tolerance to NaCl stress through the increased ACC-deaminase activity and IAA production in TL-6 stain that modulate the IAA and ethylene synthesis, and regulate the transcriptional levels of IAA and ethylene synthesis genes expression in wheat seedling roots under salt stress, and minimize ionic toxicity by disturbing the intracellular ionic homeostasis in the plant cells. These biochemical, physiological and molecular responses helped promote the wheat seedling growth and enhanced plant tolerance to salt stress.