Map-based cloning of a novel rice cytochrome P450 gene CYP81A6 that confers resistance to two different classes of herbicides

Comprehensive study of chiral herbicide flusulfinam uptake, translocation, degradation, and subcellular distribution in rice (Oryza sativa L.)

The biological behavior of flusulfinam, a potential commercial chiral herbicide for rice, has not been well explored. Herein, the uptake of chiral flusulfinam by rice and its transport, degradation, and subcellular distribution in rice (Oryza sativa L.) were investigated. The enantiomeric fraction (EF) in roots was 0.54 during 0 d to 7 d in hydroponic laboratory conditions. The bioconcentration factor of flusulfinam enantiomers was 2.1, suggesting an absence of observed enantioselectivity in the absorption process. Notably, the EF in the shoots decreased to 0.35 on the 7th day. The translocation factors of R- and S-flusulfinam were 0.12 and 0.27, respectively, indicating a preferential transfer of the S-flusulfinam from the root to the shoot. Flusulfinam was identified in the root after spraying. The translocation factors of R- and S-flusulfinam were consistently similar, signifying the capacity for downward movement without enantioselectivity. Interestingly, the degradation half-lives of R- and S-flusulfinam in the total plant were 5.50 and 5.06 d (p < 0.05), respectively, supporting the preferential degradation of S-flusulfinam throughout the total plant. Flusulfinam primarily entered the roots via the apoplastic pathway and was subsequently transported within the plant through aquaporins and ion channels. The subcellular distribution experiment revealed the predominant accumulation of flusulfinam enantiomers in soluble components (84%) with no enantioselectivity in these processes. There was upregulation lipid transfer protein-2 and carboxylesterases15 genes, which could explain the preferential transport and degradation of S-flusulfinam. This study is important in assessing the environmental risk associated with flusulfinam and ensuring food safety.

Transcriptomic analysis of maize uncovers putative genes involved in metabolic detoxification under four safeners treatment

Isoxadifen-ethyl (IDF) and cyprosulfamide (CSA) can effectively protect maize from nicosulfuron (NIC) injury, while mefenpyr-diethyl (MPR) and fenchlorazole-ethyl (FCO) did not. Their chemical diversity and requirement to use them in combination with the corresponding herbicides suggest that their elicitation of gene expression are complex and whether it is associated with the safening activity remains elusive. In this study, our first objective was to determine whether or not the ability of four safeners to enhance the metabolic rate of nicosulfuron. It was found that nicosulfuron degradation in maize was accelerated by IDF and CSA, but not by FCO and MPR. Transcriptomic analysis showed that the number of genes induced by IDF and CSA were larger than that induced by FCO and MPR. Overall, 34 genes associated with detoxification were identified, including glutathione S-transferase (GST), cytochrome P450 (CYP450), UDP-glucosyltransferase (UGT), transporter and serine. Moreover, 14 detoxification genes were screened for further verification by real-time PCR in two maize inbred lines. Two maize inbred lines exhibited high expression levels of four genes (GST31, GST39, AGXT2 and ADH) after IDF treatment. GST6, GST19, MATE, SCPL18 and UF3GT were specifically up-regulated in telerant maize inbred line under IDF and IDF + NIC treatments. Seven genes, namely GST31, GST6, GST19, UF3GT, MATE, ADH and SCPL18, are induced by IDF and CSA to play a vital role in regulating the detoxification process of NIC. Accordingly, the GST activity in maize was accelerated by IDF and CSA, but not by FCO and MPR. This result is consistent with transcriptome and metabolic data.These results indicate that the mitigation of NIC damage is associated with enhanced herbicide metabolism. IDF and CSA were more effective in protecting maize from NIC injury due to their ability to enhance the detoxification of specific types of herbicides, compared to FCO and MPR. The chemical specificity of four safeners is attributed to the up-regulated genes related to the detoxification pathway.

Cytochrome P450 Gene Families: Role in Plant Secondary Metabolites Production and Plant Defense

Cytochrome P450s (CYPs) are the most prominent family of enzymes involved in NADPH- and O2-dependent hydroxylation processes throughout all spheres of life. CYPs are crucial for the detoxification of xenobiotics in plants, insects, and other organisms. In addition to performing this function, CYPs serve as flexible catalysts and are essential for producing secondary metabolites, antioxidants, and phytohormones in higher plants. Numerous biotic and abiotic stresses frequently affect the growth and development of plants. They cause a dramatic decrease in crop yield and a deterioration in crop quality. Plants protect themselves against these stresses through different mechanisms, which are accomplished by the active participation of CYPs in several biosynthetic and detoxifying pathways. There are immense potentialities for using CYPs as a candidate for developing agricultural crop species resistant to biotic and abiotic stressors. This review provides an overview of the plant CYP families and their functions to plant secondary metabolite production and defense against different biotic and abiotic stresses.

Genome-Wide Identification and Expression Profiling of Cytochrome P450 Monooxygenase Superfamily in Foxtail Millet

The cytochrome P450 monooxygenases (CYP450) are the largest enzyme family in plant metabolism and widely involved in the biosynthesis of primary and secondary metabolites. Foxtail millet (Setaria italica (L.) P. Beauv) can respond to abiotic stress through a highly complex polygene regulatory network, in which the SiCYP450 family is also involved. Although the CYP450 superfamily has been systematically studied in a few species, the research on the CYP450 superfamily in foxtail millet has not been completed. In this study, three hundred and thirty-one SiCYP450 genes were identified in the foxtail millet genome by bioinformatics methods, which were divided into four groups, including forty-six subgroups. One hundred and sixteen genes were distributed in thirty-three tandem duplicated gene clusters. Chromosome mapping showed that SiCYP450 was distributed on seven chromosomes. In the SiCYP450 family of foxtail millet, 20 conserved motifs were identified. Cis-acting elements in the promoter region of SiCYP450 genes showed that hormone response elements were found in all SiCYP450 genes. Of the three hundred and thirty-one SiCYP450 genes, nine genes were colinear with the Arabidopsis thaliana genes. Two hundred SiCYP450 genes were colinear with the Setaria viridis genes, including two hundred and forty-five gene duplication events. The expression profiles of SiCYP450 genes in different organs and developmental stages showed that SiCYP450 was preferentially expressed in specific tissues, and many tissue-specific genes were identified, such as SiCYP75B6, SiCYP96A7, SiCYP71A55, SiCYP71A61, and SiCYP71A62 in the root, SiCYP78A1 and SiCYP94D9 in leaves, and SiCYP78A6 in the ear. The RT-PCR data showed that SiCYP450 could respond to abiotic stresses, ABA, and herbicides in foxtail millet. Among them, the expression levels of SiCYP709B4, SiCYP71A11, SiCYP71A14, SiCYP78A1, SiCYP94C3, and SiCYP94C4 were significantly increased under the treatment of mesotrione, florasulam, nicosulfuron, fluroxypyr, and sethoxydim, indicating that the same gene might respond to multiple herbicides. The results of this study will help reveal the biological functions of the SiCYP450 family in development regulation and stress response and provide a basis for molecular breeding of foxtail millet.

Comparative proteomic and physiological analyses reveal tribenuron-methyl phytotoxicity and nontarget-site resistance mechanisms in Brassica napus

The application of herbicides is the most effective strategy for weed control and the development of herbicide-resistant crops will facilitate the weed management. The acetolactate synthase-inhibiting herbicide, tribenuron-methyl (TBM), is broadly used for weed control. However, its application in rapeseed field is restricted since rapeseed is sensitive to TBM. Herein, an integrated study of cytological, physiological and proteomic analysis of the TBM-resistant rapeseed mutant M342 and its wild-type (WT) plants was conducted. After TBM spraying, M342 showed improved tolerance to TBM, and proteins implicated in non-target-site resistance (NTSR) to herbicides had a significantly higher level in M342 as compared with the WT. Differentially accumulated proteins (DAPs) between these two genotypes were enriched in glutathione metabolism and oxidoreduction coenzyme metabolic process, which protected the mutant from oxidative stress triggered by TBM. Important DAPs related to stress or defence response were up-accumulated in M342 regardless of the TBM treatment, which might serve as the constitutive part of NTSR to TBM. These results provide new clues for further exploration of the NTSR mechanism in plants and establish a theoretical basis for the development of herbicide-resistant crops.

Multiple resistance of Echinochloa phyllopogon to synthetic auxin, ALS-, and ACCase-inhibiting herbicides in Northeast China

Echinochloa phyllopogon is a self-pollinating allotetraploid weed and a serious threat to global rice production. One sensitive and three multiple-resistant populations collected from two provinces of Northeast China were used to analyze the mechanism of multiple resistance of E. phyllopogon to penoxsulam, metamifop, and quinclorac. Compared with the sensitive population LN12, LN1 showed higher resistance to these three herbicides; LN24 showed medium resistance to penoxsulam and metamifop and higher resistance to quinclorac (274-fold); HLJ4 showed low resistance to penoxsulam and high resistance to metamifop and quinclorac. Target sequence analysis showed no mutations in acetolactate synthase or acetyl-CoA carboxylase genes. In-vitro enzyme activity analysis showed that the activity of the target enzyme of multiple herbicide-resistant populations was similar to that of the sensitive population. The P450 inhibitor, malathion, noticeably increased the sensitivity of LN1, LN24, and HLJ4 to penoxsulam, LN1 to metamifop, and HLJ4 to quinclorac. Under all four treatments, the GSTs activities of resistant and sensitive populations showed an increasing trend from day 1 to day 5, but the sensitivity and activity of GSTs were higher in the multiple-resistant population than that in the sensitive population LN12. This study identified the development of multiple-resistant E. phyllopogon populations that pose a serious threat to rice production in rice fields in Northeast China, preliminarily confirming that multiple-resistance was likely due to non-target-site resistance mechanisms. These populations of E. phyllopogon are likely to be more difficult to control.

Identification of a Phase I mechanism gene of rice (OsCYP1) in response to isoproturon

The long-term use of isoproturon may threaten food security and human health. Cytochrome P450 (CYP or P450) can catalyze the biosynthetic metabolism, and play a crucial role in the modification of plant secondary metabolites. Therefore, it is of great importance to explore the genetic resources for isoproturon degradation. This research focused on a phase I metabolism gene (OsCYP1) with significant differential expression in rice under isoproturon pressure. Specifically, the high-throughput sequencing results of rice seedling transcriptome in response to isoproturon stress were analyzed. The molecular information and tobacco subcellular localization of OsCYP1 were studied. The subcellular localization of OsCYP1 in tobacco was assessed, where it is located in the endoplasmic reticulum. To analyze the expression of OsCYP1 in rice, the wild-type rice was treated with 0-1 mg/L isoproturon for 2 and 6 days, and qRT-PCR assays were conducted to detect the transcription levels. Compared with the control group, the expression of OsCYP1 in shoots was progressively upregulated after exposure to isoproturon, with 6.2-12.7-fold and 2.8-7.9-fold increases in transcription levels, respectively. Moreover, treatment with isoproturon upregulated the expression of OsCYP1 in roots, but the upregulation of transcripts was not significant except for 0.5 and 1 mg/L isoproturon at day 2. To confirm the role of OsCYP1 in enhancing isoproturon degradation, the vectors overexpressing OsCYP1 were transformed into recombinant yeast cells. After exposure to isoproturon, the growth of OsCYP1-transformed cells was better than the control cells, especially at higher stress levels. Furthermore, the dissipation rates of isoproturon were increased by 2.1-, 2.1- and 1.9-fold at 24, 48 and 72 h, respectively. These results further verified that OsCYP1 could enhance the degradation and detoxification of isoproturon. Collectively, our findings imply that OsCYP1 plays vital role in isoproturon degradation. This study provides a fundamental basis for the detoxification and regulatory mechanisms of OsCYP1 in crops via enhancing the degradation and/or metabolism of herbicide residues.

Metabolism Difference Is Involved in Mesosulfuron-Methyl Selectivity between Aegilops tauschii and Triticum aestivum

The acetolactate synthase (ALS) inhibitor mesosulfuron-methyl is currently the only selective herbicide to control Aegilops tauschii in wheat fields; however, the mechanism underlying this selectivity remains unclear. Results showed that the tolerance of Triticum aestivum to mesosulfuron-methyl was much higher than that of A. tauschii. Mesosulfuron-methyl inhibited the in vitro ALS activity of A. tauschii and T. aestivum similarly, but the predicted structural interactions of ALS with mesosulfuron-methyl and induced expression of als were different in the two species. Compared with T. aestivum, A. tauschii was found to absorb more mesosulfuron-methyl and metabolize much less mesosulfuron-methyl. The cytochrome P450 monooxygenase (CYP450) inhibitor, malathion, greatly increased the sensitivity of T. aestivum to mesosulfuron-methyl, while its synergistic effect was smaller in A. tauschii. Finally, 19 P450 genes were selected as candidate genes related with metabolism-based mesosulfuron-methyl selectivity. Collectively, different sensitivities to mesosulfuron-methyl in the two species were likely to be attributed to metabolism variances.

Comparison of herbicide specificity of CYP81A cytochrome P450s from rice and a multiple-herbicide resistant weed, Echinochloa phyllopogon

BACKGROUND

CYP81A cytochrome P450s (CYP81As) play a key role in herbicide detoxification in Poaceae plants. Crop CYP81As confer natural tolerance to multiple herbicides, whereas CYP81As in weeds disrupt herbicide action. Identifying differences in CYP81A herbicide specificity between crops and weeds could provide valuable information for controlling weeds. In this study, we quantitatively compared herbicide specificity between CYP81A6 from rice (Oryza sativa) and CYP81A12 and CYP81A21 from a weed, Echinochloa phyllopogon, using transgenic Escherichia coli and Arabidopsis.

RESULTS

All three CYP81As metabolized the five tested herbicides and formed similar metabolites, with the highest relative activities of 400 to 580% toward bentazone compared to their activity on bensulfuron-methyl (defined as 100%). However, they showed differing activity toward propyrisulfuron. The relative activities of Echinochloa phyllopogon CYP81A12 (12.2%) and CYP81A21 (34.4%) toward propyrisulfuron were lower than that of rice CYP81A6 (98.5%). Additionally, rice CYP81A6 produced O-demethylated propyrisulfuron and hydroxylated products, whereas Echinochloa phyllopogon CYP81As produced only hydroxylated products. Arabidopsis expressing CYP81A12 and CYP81A21 exhibited lower levels of resistance against propyrisulfuron compared to that in Arabidopsis expressing CYP81A6. Homology modeling and in silico docking revealed that bensulfuron-methyl docked well into the active centers of all three CYP81As, whereas propyrisulfuron docked into rice CYP81A6 but not into Echinochloa phyllopogon CYP81As.

CONCLUSION

The differing herbicide specificity displayed by rice CYP81A6 and Echinochloa phyllopogon CYP81A12 and CYP81A21 will help design inhibitors (synergists) of weed CYP81As, as well as develop novel herbicide ingredients that are selectively metabolized by crop CYP81As, to overcome the problem of herbicide resistance. © 2022 Society of Chemical Industry.

Development of a rice herbicide, fenquinotrione

Fenquinotrione is a novel rice herbicide that was discovered and developed by Kumiai Chemical Industry Co., Ltd. It can control a wide range of broadleaf and sedge weeds with excellent rice selectivity at 30 g a.i./10 a and is as effective as the wild type on acetolactate synthase inhibitor-resistant weeds. Our metabolic and molecular biological studies showed that CYP81A6-mediated demethylation and subsequent glucose conjugation are responsible for the safety of fenquinotrione in rice. Fenquinotrione was registered in Japan in 2018, and various products containing fenquinotrione have been launched. With its high efficacy and excellent rice selectivity, we believe that fenquinotrione will contribute to efficient food production in the future.

Transcriptional response of a target plant to benzoxazinoid and diterpene allelochemicals highlights commonalities in detoxification

BACKGROUND

Plants growing in proximity to other plants are exposed to a variety of metabolites that these neighbors release into the environment. Some species produce allelochemicals to inhibit growth of neighboring plants, which in turn have evolved ways to detoxify these compounds.

RESULTS

In order to understand how the allelochemical-receiving target plants respond to chemically diverse compounds, we performed whole-genome transcriptome analysis of Arabidopsis thaliana exposed to either the benzoxazinoid derivative 2-amino- 3H-phenoxazin-3-one (APO) or momilactone B. These two allelochemicals belong to two very different compound classes, benzoxazinoids and diterpenes, respectively, produced by different Poaceae crop species.

CONCLUSIONS

Despite their distinct chemical nature, we observed similar molecular responses of A. thaliana to these allelochemicals. In particular, many of the same or closely related genes belonging to the three-phase detoxification pathway were upregulated in both treatments. Further, we observed an overlap between genes upregulated by allelochemicals and those involved in herbicide detoxification. Our findings highlight the overlap in the transcriptional response of a target plant to natural and synthetic phytotoxic compounds and illustrate how herbicide resistance could arise via pathways involved in plant-plant interaction.

Characterization of Cytochrome P450s with Key Roles in Determining Herbicide Selectivity in Maize

Safeners such as metcamifen and benoxacor are widely used in maize to enhance the selectivity of herbicides through the induction of key detoxifying enzymes, notably cytochrome P450 monooxygenases (CYPs). Using a combination of transcriptomics, proteomics, and functional assays, the safener-inducible CYPs responsible for herbicide metabolism in this globally important crop have been identified. A total of 18 CYPs belonging to clans 71, 72, 74, and 86 were safener-induced, with the respective enzymes expressed in yeast and screened for activity toward thiadiazine (bentazon), sulfonylurea (nicosulfuron), and triketone (mesotrione and tembotrione) chemistries. Herbicide metabolism was largely restricted to family CYP81A members from clan 71, notably CYP81A9, CYP81A16, and CYP81A2. Quantitative transcriptomics and proteomics showed that CYP81A9/CYP81A16 were dominant enzymes in safener-treated field maize, whereas only CYP81A9 was determined in sweet corn. The relationship between CYP81A sequence and activities were investigated by splicing CYP81A2 and CP81A9 together as a series of recombinant chimeras. CYP81A9 showed wide ranging activities toward the three herbicide chemistries, while CYP81A2 uniquely hydroxylated bentazon in multiple positions. The plasticity in substrate specificity of CYP81A9 toward multiple herbicides resided in the second quartile of its N terminal half. Further phylogenetic analysis of CYP81A9 showed that the maize enzyme was related to other CYP81As linked to agrochemical metabolism in cereals and wild grasses, suggesting this clan 71 CYP has a unique function in determining herbicide selectivity in arable crops.

Transcriptome analysis and the identification of genes involved in the metabolic pathways of fenoxaprop-P-ethyl in rice treated with isoxadifen-ethyl hydrolysate

Fenoxaprop-P-ethyl (FE) is a highly effective weed control agent for rice fields, but it causes phytotoxicity in crops. A whole-plant bioassay has revealed that isoxadifen-ethyl hydrolysate (IH) can significantly improve the tolerance of rice to FE, but the molecular mechanisms underlying this phenomenon are still unclear. In this study, we performed RNA-Seq analysis using rice seedlings treated with FE and IH to determine the IH-regulated candidate genes involved in metabolic resistance to FE. We also analyzed spatiotemporal expression using quantitative reverse transcription polymerase chain reaction to reveal the expression patterns of these genes under different treatments. The results showed that genes encoding metabolic enzymes, such as cytochrome P450 monooxygenases, glutathione-s-transferases, UDP-glycosyltransferase, carboxylesterase, and ATP-binding cassette transporter, were influenced by the application of IH. Most of these genes were upregulated, and their products were involved in various stages of FE metabolism. Tolerance to FE was primarily mediated by CarE15, CYP86A1, GSTU6, GST4, UGT13248, UGT79, and ABCC4, all of which played a vital role in regulating the detoxification process of FE. Our findings elucidated the protective mechanisms of IH, which can help alleviate the phytotoxic effects of FE and expand its potential for application in agriculture.

CYP81A68 confers metabolic resistance to ALS and ACCase-inhibiting herbicides and its epigenetic regulation in Echinochloa crus-galli

Long-term and excessive herbicide use has led to some environmental concerns and especially, herbicide resistance evolution in weeds. Here, we confirmed acetolactate synthase (ALS) inhibiting herbicide penoxsulam resistance and cross resistance to acetyl-coenzyme carboxylase (ACCase) inhibiting herbicides (cyhalofop-butyl and metamifop) in a global weed Echinochloa crus-galli population resistant to these herbicides (R). Penoxsulam metabolism study indicated that degradation rate was significantly higher in R than susceptible E. crus-galli population (S). RNA-sequencing revealed that a cytochrome P450 (P450) gene, CYP81A68, expressed higher in R versus S. Rice seedlings overexpressing this CYP81A68 gene are resistant to penoxsulam, cyhalofop-butyl and metamifop, and penoxsulam resistance is due to enhanced metabolism via O-demethylation. Deletion analysis of the CYP81A68 gene promoter identified an efficient region, in which differential methylation of CpG islands occurred between R and S. Collectively, these results demonstrate that upregulation of E. crus-galli CYP81A68 gene endows generalist metabolic resistance to commonly used ALS- and ACCase-inhibiting herbicides in rice fields and epigenetic regulation may play a role in the resistance evolution. This research could contribute to strategies reducing herbicide environmental impacts by judicious selection of alternative herbicide and non-chemical control tactics.

Expression of a Cytochrome P450 Gene from Bermuda Grass Cynodon dactylon in Soybean Confers Tolerance to Multiple Herbicides

Bermuda grass (Cynodon dactylon) is notoriously difficult to control with some commonly used herbicides. We cloned a cytochrome P450 gene from Bermuda grass, named P450-N-Z1, which was found to confer tolerance to multiple herbicides in transgenic Arabidopsis. These herbicides include: (1) acetolactate synthase (ALS) inhibitor herbicides nicosulfuron and penoxsulam; (2) p-hydroxyphenylpyruvate dioxygenase (HPPD)-inhibiting herbicide mesotrione; (3) synthetic auxin herbicide dicamba; (4) photosynthesis inhibitor bentazon. We further generated transgenic soybean plants expressing P450-N-Z1, and found that these transgenic soybean plants gained robust tolerance to nicosulfuron, flazasulfuron, and 2,4-dichlorophenoxyacetic acid (2,4-D) in greenhouse assays. A field trial demonstrated that transgenic soybean is tolerant to flazasulfuron and 2,4-D at 4-fold and 2-fold the recommended rates, respectively. Furthermore, we also demonstrated that flazasulfuron and dicamba are much more rapidly degraded in vivo in the transgenic soybean than in non-transgenic soybean. Therefore, P450-N-Z1 may be utilized for engineering transgenic crops for herbicide tolerance.

Advances in gene editing without residual transgenes in plants

Transgene residuals in edited plants affect genetic analysis, pose off-target risks, and cause regulatory concerns. Several strategies have been developed to efficiently edit target genes without leaving any transgenes in plants. Some approaches directly address this issue by editing plant genomes with DNA-free reagents. On the other hand, DNA-based techniques require another step for ensuring plants are transgene-free. Fluorescent markers, pigments, and chemical treatments have all been employed as tools to distinguish transgenic plants from transgene-free plants quickly and easily. Moreover, suicide genes have been used to trigger self-elimination of transgenic plants, greatly improving the efficiency of isolating the desired transgene-free plants. Transgenes can also be excised from plant genomes using site-specific recombination, transposition or gene editing nucleases, providing a strategy for editing asexually produced plants. Finally, haploid induction coupled with gene editing may make it feasible to edit plants that are recalcitrant to transformation. Here, we evaluate the strengths and weaknesses of recently developed approaches for obtaining edited plants without transgene residuals.

Cytochrome P450 CYP709C56 metabolizing mesosulfuron-methyl confers herbicide resistance in Alopecurus aequalis

Multiple herbicide resistance in diverse weed species endowed by enhanced herbicide detoxification or degradation is rapidly growing into a great threat to herbicide sustainability and global food safety. Although metabolic resistance is frequently documented in the economically damaging arable weed species shortawn foxtail (Alopecurus aequalis Sobol.), relevant molecular knowledge has been lacking. Previously, we identified a field population of A. aequalis (R) that had evolved metabolic resistance to the commonly used acetolactate synthase (ALS)-inhibiting herbicide mesosulfuron-methyl. RNA sequencing was used to discover potential herbicide metabolism-related genes, and four cytochrome P450s (CYP709C56, CYP71R18, CYP94C117, and CYP94E14) were identified with higher expressions in the R vs. susceptible (S) plants. Here the full-length P450 complementary DNA transcripts were each cloned with identical sequences between the S and R plants. Transgenic Arabidopsis overexpressing CYP709C56 became resistant to the sulfonylurea herbicide mesosulfuron-methyl and the triazolo-pyrimidine herbicide pyroxsulam. This resistance profile generally but does not completely in accordance with what is evident in the R A. aequalis. Transgenic lines exhibited enhanced capacity for detoxifying mesosulfuron-methyl into O-demethylated metabolite, which is in line with the detection of O-demethylated herbicide metabolite in vitro in transformed yeast. Structural modeling predicted that mesosulfuron-methyl binds to CYP709C56 involving amino acid residues Thr-328, Thr-500, Asn-129, Gln-392, Phe-238, and Phe-242 for achieving O-demethylation. Constitutive expression of CYP709C56 was highly correlated with the metabolic mesosulfuron-methyl resistance in A. aequalis. These results indicate that CYP709C56 degrades mesosulfuron-methyl and its up-regulated expression in A. aequalis confers resistance to mesosulfuron-methyl.

Population genomic analysis reveals domestication of cultivated rye from weedy rye

Rye (Secale cereale) is an important crop with multiple uses and a valuable genetic resource for wheat breeding. However, due to its complex genome and outcrossing nature, the origin of cultivated rye remains elusive. The geneticist N.I. Vavilov proposed that cultivated rye had been domesticated from weedy rye, rather than directly from wild species like other crops. Unraveling the domestication history of rye will extend our understanding of crop evolution and upend our inherent understanding of agricultural weeds. To this end, in this study we generated the 8.5 Tb of whole-genome resequencing data from 116 worldwide accessions of wild, weedy, and cultivated rye, and demonstrated that cultivated rye was domesticated directly from weedy relatives with a similar but enhanced genomic selection by humans. We found that a repertoire of genes that experienced artificial selection is associated with important agronomic traits, including shattering, grain yield, and disease resistance. Furthermore, we identified a composite introgression in cultivated rye from the wild perennial Secale strictum and detected a 2-Mb introgressed fragment containing a candidate ammonium transporter gene with potential effect on the grain yield and plant growth of rye. Taken together, our findings unravel the domestication history of cultivated rye, suggest that interspecific introgression serves as one of the likely causes of obscure species taxonomy of the genus Secale, and provide an important resource for future rye and wheat breeding.

Identification of essential genes involved in metabolism-based resistance mechanism to fenoxaprop-P-ethyl in Polypogon fugax

BACKGROUND

Metabolic resistance is a worldwide concern for weed control but has not yet been well-characterized at the genetic level. Previously, we have identified an Asia minor bluegrass (Polypogon fugax Nees ex Steud.) population AHHY exhibiting cytochrome P450 (P450)-involved metabolic resistance to fenoxaprop-P-ethyl. In this study, we aimed to confirm the metabolic fenoxaprop-P-ethyl resistance in AHHY and uncover the potential herbicide metabolism-related genes in this economically damaging weed species.

RESULTS

Liquid chromatography-tandem mass spectrometry (LC-MS/MS) assays indicated the metabolic rates of fenoxaprop-P-ethyl were significantly faster in resistant (R, AHHY) than in susceptible (S, SDTS) plants. The amount of phytotoxic fenoxaprop-P peaked at 12 h after herbicide treatment (HAT) and started to decrease at 24 HAT in both biotypes. R and S plants at 24 HAT were sampled to conduct isoform-sequencing (Iso-Seq) and RNA-sequencing (RNA-Seq). A reference transcriptome containing 24 972 full-length isoforms was obtained, of which 24 329 unigenes were successfully annotated. Transcriptomic profiling identified 28 detoxifying enzyme genes constitutively and/or herbicide-induced up-regulated in R than in S plants. Real-time quantitative polymerase chain reaction (RT-qPCR) confirmed 17 genes were consistently up-regulated in R and its F1 generation plants. They were selected as potential fenoxaprop-P-ethyl metabolism-related genes, including ten P450s, one glutathione-S-transferase, one UDP-glucosyltransferase, and five adenosine triphosphate (ATP)-binding cassette transporters.

CONCLUSION

This study revealed that the enhanced rates of fenoxaprop-P-ethyl metabolism in P. fugax were very likely driven by the herbicide metabolism-related genes. The transcriptome data generated by Iso-Seq combined with RNA-Seq will provide abundant gene resources for understanding the molecular mechanisms of resistance in P. fugax.

Construction of a Novel Female Sterility System for Hybrid Rice

The main constraints of current hybrid rice technology using male sterility (MS) are the low yield and high labor costs of hybrid rice seed (HRS) production. Therefore, there is an urgent need for innovative new hybrid rice technology. Fortunately, we discovered a unique spontaneous sporophytic female-sterile rice mutant controlled by a single recessive locus in the nucleus. Because female-sterile mutant lines cannot produce any selfed-seeds but their pollen has totally normal functions, female sterility (FS) lines may be considered ideal pollen donors to replace the female-fertile pollen donor parent lines currently used in the HRS production. In this study, a genetically engineered FS-based system was constructed to propagate a pure transgene-free FS line using a bentazon herbicide screening. Additionally, the ability of the FS + MS (FM)-line system, with mixed plantings of FS and MS lines, to produce HRS was tested. The pilot field experiment results showed that HRS of the FM-line system was more efficient compared with the conventional FS to MS strip planting control mode. Thus, this study provides new insights into genetic engineering technology and a promising strategy for the utilization of FS in hybrid rice.

Transgene-free Genome Editing in Plants

Genome editing is widely used across plant species to generate and study the impact of functional mutations in crop improvement. However, transgene integration in plant genomes raises important legislative concerns regarding genetically modified organisms. Several strategies have been developed to remove or prevent the integration of gene editor constructs, which can be divided into three major categories: 1) elimination of transgenic sequences via genetic segregation; 2) transient editor expression from DNA vectors; and 3) DNA-independent editor delivery, including RNA or preassembled Cas9 protein-gRNA ribonucleoproteins (RNPs). Here, we summarize the main strategies employed to date and discuss the advantages and disadvantages of using these different tools. We hope that our work can provide important information concerning the value of alternative genome editing strategies to advance crop breeding.

Whole transcriptome analysis resulted in the identification of Chinese sprangletop (Leptochloa chinensis) genes involved in cyhalofop-butyl tolerance

Background

Chinese sprangletop [Leptochloa chinensis (L.) Nees] is an annual malignant weed, which can often be found in paddy fields. Cyhalofop-butyl is a specialized herbicide which is utilized to control L. chinensis. However, in many areas, L. chinensis has become tolerant to this key herbicide due to its continuous long-term use.

Results

In this study, we utilized a tolerant (LC18002) and a sensitive (LC17041) L. chinensis populations previously identified in our laboratory, which were divided into four different groups. We then employed whole transcriptome analysis to identify candidate genes which may be involved in cyhalofop-butyl tolerance. This analysis resulted in the identification of six possible candidate genes, including three cytochrome P450 genes and three ATP-binding cassette transporter genes. We then carried out a phylogenetic analysis to identify homologs of the differentially expressed cytochrome P450 genes. This phylogenetic analysis indicated that all genes have close homologs in other species, some of which have been implicated in non-target site resistance (NTSR).

Conclusions

This study is the first to use whole transcriptome analysis to identify herbicide non-target resistance genes in L. chinensis. The differentially expressed genes represent promising targets for better understanding herbicide tolerance in L. chinensis. The six genes belonging to classes already associated in herbicide tolerance may play important roles in the metabolic resistance of L. chinensis to cyhalofop-butyl, although the exact mechanisms require further study.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07856-z.

Investigation of clomazone-tolerance mechanism in a long-grain cultivar of rice

BACKGROUND

Clomazone is a potent herbicide for controlling weeds that have evolved resistance to other herbicides due to its unique mode of action. Clomazone is used in rice cultivation, but is limited to long-grain cultivars because other cultivars are highly sensitive to it. In this study, we investigated the mechanism of clomazone tolerance in a long-grain cultivar.

RESULTS

The long-grain cultivar Kasalath tolerated approximately five-fold higher doses of clomazone compared to two short-grain cultivars, Nipponbare and Koshihikari. While Arabidopsis thaliana transformed with a rice cytochrome P450, CYP81A6, showed resistance to clomazone, the cyp81a6 knockout Kasalath was unchanged in its clomazone sensitivity. The inheritance of clomazone sensitivity in the F1 and F2 of Kasalath and Nipponbare indicated the involvement of multiple loci for clomazone tolerance. Four chromosome segment substitution lines of Nipponbare/Kasalath and Koshihikari/Kasalath exhibited partial tolerance to clomazone. The overlapping DNA region among the four lines is on chromosome 5 within 11.5 Mb.

CONCLUSION

Multiple loci are involved in clomazone tolerance in Kasalath, one of which is located on chromosome 5. This information will help develop short-grain cultivars tolerant to clomazone. © 2021 Society of Chemical Industry.

Innate promiscuity of the CYP706 family of P450 enzymes provides a suitable context for the evolution of dinitroaniline resistance in weed

Increased metabolism is one of the main causes for evolution of herbicide resistance in weeds, a major challenge for sustainable food production. The molecular drivers of this evolution are poorly understood. We tested here the hypothesis that a suitable context for the emergence of herbicide resistance could be provided by plant enzymes with high innate promiscuity with regard to their natural substrates. A selection of yeast-expressed plant cytochrome P450 enzymes with well documented narrow to broad promiscuity when metabolizing natural substrates was tested for herbicide metabolism competence. The positive candidate was assayed for capacity to confer herbicide tolerance in Arabidopsis thaliana. Our data demonstrate that Arabidopsis thaliana CYP706A3, with the most promiscuous activity on monoterpenes and sesquiterpenes for flower defence, can also oxidize plant microtubule assembly inhibitors, dinitroanilines. Ectopic overexpression of CYP706A3 confers dinitroaniline resistance. We show, in addition, that the capacity to metabolize dinitroanilines is shared by other members of the CYP706 family from plants as diverse as eucalyptus and cedar. Supported by three-dimensional (3D) modelling of CYP706A3, the properties of enzyme active site and substrate access channel are discussed together with the shared physicochemical properties of the natural and exogenous substrates to explain herbicide metabolism.

Exploring Natural Allelic Variations of the β-Triketone Herbicide Resistance Gene HIS1 for Application in indica Rice and Particularly in Two-Line Hybrid Rice

BACKGROUND

Benzobicyclon (BBC) is a β-triketone herbicide (bTH) used in rice paddy fields. It has the advantages of high efficiency, low toxicity, high crop safety, and good environmental compatibility, and shows efficacy against paddy weeds resistant to other types of herbicides. However, as some important indica rice varieties are susceptible to BBC, BBC is currently only registered and applied in japonica rice cultivation areas.

RESULTS

By analyzing haplotypes of the bTHs broad-spectrum resistance gene HIS1 and phenotypes for BBC in 493 major indica rice accessions in China, we identified a novel non-functional allelic variant of HIS1 in addition to the previously reported 28-bp deletion. Through detection with markers specific to the two non-functional mutations, it was clear that 25.4% of indica conventional varieties, 59.9% of fertility restorers, and 15.9% of sterile lines were susceptible to BBC. In addition, due to natural allelic variations of the HIS1 gene in the sterile and restorer lines, some two-line hybrid sterile lines were sensitive to bTHs, and the corresponding restorers were resistant. We showed the potential effectiveness of using bTHs to address the issue of two-line hybrid rice seed purity stemming from the self-crossing of sterile lines during hybrid rice seed production. Finally, allelic variations of the HIS1 gene may also play an important role in the mechanized seed production of hybrid rice.

CONCLUSIONS

Our findings offer guidance for the application of BBC in indica rice areas and provide a non-transgenic approach to address the seed purity issue of two-line hybrid rice.

Cytochrome P450 CYP81A10v7 in Lolium rigidum confers metabolic resistance to herbicides across at least five modes of action

Rapid and widespread evolution of multiple herbicide resistance in global weed species endowed by increased capacity to metabolize (degrade) herbicides (metabolic resistance) is a great threat to herbicide sustainability and global food production. Metabolic resistance in the economically damaging crop weed species Lolium rigidum is well known but a molecular understanding has been lacking. We purified a metabolic resistant (R) subset from a field evolved R L. rigidum population. The R, the herbicide susceptible (S) and derived F₂ populations were used for candidate herbicide resistance gene discovery by RNA sequencing. A P450 gene CYP81A10v7 was identified with higher expression in R vs. S plants. Transgenic rice overexpressing this Lolium CYP81A10v7 gene became highly resistant to acetyl-coenzyme A carboxylase- and acetolactate synthase-inhibiting herbicides (diclofop-methyl, tralkoxydim, chlorsulfuron) and moderately resistant to hydroxyphenylpyruvate dioxygenase-inhibiting herbicide (mesotrione), photosystem II-inhibiting herbicides (atrazine and chlorotoluron) and the tubulin-inhibiting herbicide trifluralin. This wide cross-resistance profile to many dissimilar herbicides in CYP81A10v7 transgenic rice generally reflects what is evident in the R L. rigidum. This report clearly showed that a single P450 gene in a cross-pollinated weed species L. rigidum confers resistance to herbicides of at least five modes of action across seven herbicide chemistries.

Cytochrome P450-mediated herbicide metabolism in plants: current understanding and prospects

Cytochrome P450s (P450s) have been at the center of herbicide metabolism research as a result of their ability to endow selectivity in crops and resistance in weeds. In the last 20 years, ≈30 P450s from diverse plant species have been revealed to possess herbicide-metabolizing function, some of which were demonstrated to play a key role in plant herbicide sensitivity. Recent research even demonstrated that some P450s from crops and weeds metabolize numerous herbicides from various chemical backbones, which highlights the importance of P450s in the current agricultural systems. However, due to the enormous number of plant P450s and the complexity of their function, expression and regulation, it remains a challenge to fully explore the potential of P450-mediated herbicide metabolism in crop improvement and herbicide resistance mitigation. Differences in the substrate specificity of each herbicide-metabolizing P450 are now evident. Comparisons of the substrate specificity and protein structures of P450s will be beneficial for the discovery of selective herbicides and may lead to the development of crops with higher herbicide tolerance by transgenics or genome-editing technologies. Furthermore, the knowledge will help design sound management strategies for weed resistance including the prediction of cross-resistance patterns. Overcoming the ambiguity of P450 function in plant xenobiotic pathways will unlock the full potential of this enzyme family in advancing global agriculture and food security. © 2020 Society of Chemical Industry.

Expression and comparison of sweet corn CYP81A9s in relation to nicosulfuron sensitivity

BACKGROUND

Nicosulfuron, a sulfonylurea herbicide widely used for grass weed control in corn production, injures some sweet corn hybrids and inbreds. A specific cytochrome P450 (P450), CYP81A9, is suggested to be responsible for sensitivity to nicosulfuron and other P450-metabolized herbicides. Corn CYP81A9 enzymes were expressed in E. coli and investigated to find the factor(s) associated with their function and variation in metabolizing nicosulfuron.

RESULT

Recombinant expressed CYP81A9s from tolerant sweet corn inbreds produced an active form of P450, while CYP81A9 from a sensitive inbred produced an inactive form. Nicosulfuron bound to tolerant CYP81A9s, and produced reverse-type I ligand, while sensitive CYP81A9 showed no interaction with nicosulfuron. Investigation of 106 sweet corn inbreds showed variation in nicosulfuron injury. A survey of sweet corn CYP81A9 sequences showed mutations in codons for amino acids at 269, 284, 375, and 477 occurred in sweet corn inbreds with complete loss of P450 function (with mean injury >91%) and amino acid changes at 208 and 472 occurred in inbreds with moderate and complete loss of P450 function (with mean injury >14%).

CONCLUSION

Our results support that CYP81A9 enzyme is responsible for metabolizing nicosulfuron in sweet corn, and different types of amino acid changes in CYP81A9 sequence are associated with variation in nicosulfuron injury. Therefore, a careful selection of the tolerant allele will be critical for improving tolerance to nicosulfuron and several other P450-metabolized herbicides. © 2020 Society of Chemical Industry.

Toxicity of the herbicides used on herbicide-tolerant crops, and societal consequences of their use in France

In France, the implementation of mutant herbicide-tolerant crops and the use of the related herbicides - sulfonylureas and imidazolinones - have triggered a strong societal reaction illustrated by the intervening actions of environmentalist groups illegally mowing such crops. Trials are in progress, and therefore should be addressed the questions of the environmental risks and the toxicity of these herbicides for the animals and humans consuming the products derived from these plants. Regulatory authorities have allowed these mutant and herbicide-tolerant plants arguing that the herbicides against which they resist only target an enzyme found in 'weeds' (the acetolactate synthase, ALS), and that therefore all organisms lacking this enzyme would be endowed with immunity to these herbicides. The toxicological literature does not match with this argument: 1) Even in organisms displaying the enzyme ALS, these herbicides impact other molecular targets than ALS; 2) These herbicides are toxic for animals, organisms that do not possess the enzyme ALS, and especially invertebrates, amphibians and fish. In humans, epidemiological studies have shown that the use and handling of these toxins are associated with a significantly increased risk of colon and bladder cancers, and miscarriages. In agricultural soils, these herbicides have a persistence of up to several months, and water samples have concentrations of some of these herbicides above the limit value in drinking water.

Identification of chromosomes in Triticum aestivum possessing genes that confer tolerance to the synthetic auxin herbicide halauxifen-methyl

Natural tolerance in hexaploid bread wheat (Triticum aestivum L.) to synthetic auxin herbicides is primarily due to rapid metabolic detoxification, but genes encoding these herbicide-detoxifying enzymes have yet to be identified. Herbicide safeners are commonly applied in wheat to achieve herbicide tolerance by inducing the expression and activity of herbicide-detoxifying enzymes. While safeners have been utilized for decades, knowledge of mechanisms that induce gene expression is limited. Our objective was to identify wheat chromosomes possessing genes that endow natural or safener-induced tolerance to halauxifen-methyl (HM), a postemergence (POST) wheat-selective synthetic auxin herbicide, using alien substitution (the S genome of Aegilops searsii) and aneuploid lines. Two POST rates of HM were applied to seedlings with 1-2 leaves (Zadoks stages 11-12), and the highest HM rate was also applied with the safener cloquintocet-mexyl (CM). Wheat chromosomes possessing genes associated only with natural HM tolerance were identified because Ae. searsii is HM-sensitive but CM-responsive. Lines with substitutions for 5A and 5B displayed sensitivity to HM, and experiments with nullisomic-tetrasomic (NT) lines further indicated major genes associated with HM tolerance are present on 5A and 5B chromosomes. However, the genes on 5A appear to play a larger role because lines lacking 5A chromosomes displayed more sensitivity than lines lacking 5B. Overall, these results can be utilized to guide future transcriptome analyses to identify candidate genes that confer HM tolerance in wheat.

Role of Cytochrome P450 Enzymes in Plant Stress Response

Cytochrome P450s (CYPs) are the largest enzyme family involved in NADPH- and/or O₂-dependent hydroxylation reactions across all the domains of life. In plants and animals, CYPs play a central role in the detoxification of xenobiotics. In addition to this function, CYPs act as versatile catalysts and play a crucial role in the biosynthesis of secondary metabolites, antioxidants, and phytohormones in higher plants. The molecular and biochemical processes catalyzed by CYPs have been well characterized, however, the relationship between the biochemical process catalyzed by CYPs and its effect on several plant functions was not well established. The advent of next-generation sequencing opened new avenues to unravel the involvement of CYPs in several plant functions such as plant stress response. The expression of several CYP genes are regulated in response to environmental stresses, and they also play a prominent role in the crosstalk between abiotic and biotic stress responses. CYPs have an enormous potential to be used as a candidate for engineering crop species resilient to biotic and abiotic stresses. The objective of this review is to summarize the latest research on the role of CYPs in plant stress response.

Functional characterization of cytochrome P450 CYP81A subfamily to disclose the pattern of cross-resistance in Echinochloa phyllopogon

CYP81A P450s armor Echinochloa phyllopogon against diverse and several herbicide chemistries. CYP81A substrate preferences can be a basis for cross-resistance prediction and management in E. phyllopogon and other related species. Metabolism-based herbicide resistance is a major threat to agriculture, as it is unpredictable and could extend resistance to different chemical groups and modes of action, encompassing existing, novel and to-be-discovered herbicides. Limited information on the enzymes involved in herbicide metabolism has hindered the prediction of cross-resistance in weeds. Members of CYP81A subfamily in multiple herbicide resistant (MHR) Echinochloa phyllopogon were previously identified for conferring cross-resistance to six unrelated herbicide classes. This suggests a critical role of CYP81As in endowing unpredictable cross-resistances in E. phyllopogon, thus the functions of all its nine putative functional CYP81A genes to 33 herbicides from 24 chemical groups were characterized. Ectopic expression in Arabidopsis thaliana identified the CYP81As that can confer resistance to multiple and diverse herbicides. The CYP81As were further characterized for their enzymatic functions in Escherichia coli. CYP81A expression in E. coli was optimized via modification of the N-terminus, co-expression with HemA gene and culture at optimal temperature. CYP81As metabolized its herbicide substrates into hydroxylated, N-/O-demethylated or both products. The cross-resistance pattern conferred by CYP81As is geared towards all chemical groups of acetolactate synthase inhibitors and is expanded to herbicides inhibiting photosystem II, phytoene desaturase, protoporphyrinogen oxidase, 4-hydroxyphenylpyruvate dioxygenase, and 1-deoxy-D-xylulose 5-phosphate synthase. Cross-resistance to herbicides pyrimisulfan, propyrisulfuron, and mesotrione was predicted and confirmed in MHR E. phyllopogon. This study demonstrated that the functional characterization of the key enzymes for herbicide metabolism could disclose the cross-resistance pattern and identify appropriate chemical options to manage the existing and unexpected cross-resistances in E. phyllopogon.

Chemically induced herbicide tolerance in rice by the safener metcamifen is associated with a phased stress response

The closely related sulphonamide safeners, metcamifen and cyprosulfamide, were tested for their ability to protect rice from clodinafop-propargyl, a herbicide normally used in wheat. While demonstrating that both compounds were equally bioavailable in planta, only metcamifen prevented clodinafop from damaging seedlings, and this was associated with the enhanced detoxification of the herbicide. Transcriptome studies in rice cultures demonstrated that whereas cyprosulfamide had a negligible effect on gene expression over a 4 h exposure, metcamifen perturbed the abundance of 590 transcripts. Changes in gene expression with metcamifen could be divided into three phases, corresponding to inductions occurring over 30 min, 1.5 h and 4 h. The first phase of gene induction was dominated by transcription factors and proteins of unknown function, the second by genes involved in herbicide detoxification, while the third was linked to cellular homeostasis. Analysis of the inducible genes suggested that safening elicited similar gene families to those associated with specific biotic and abiotic stresses, notably those elicited by abscisic acid, salicylic acid, and methyl jasmonate. Subsequent experiments with safener biomarker genes induced in phase 1 and 2 in rice cell cultures provided further evidence of similarities in signalling processes elicited by metcamifen and salicylic acid.

Cost-effective detection of genome-wide signatures for 2,4-D herbicide resistance adaptation in red clover

Herbicide resistance is a recurrent evolutionary event that has been reported across many species and for all major herbicide modes of action. The synthetic auxinic herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) has been widely used since the 1940s, however the genetic variation underlying naturally evolving resistance remains largely unknown. In this study, we used populations of the forage legume crop red clover (Trifolium pratense L.) that were recurrently selected for 2,4-D resistance to detect genome-wide signatures of adaptation. Four susceptible and six derived resistant populations were sequenced using a less costly approach by combining targeted sequencing (Capture-Seq) with pooled individuals (Pool-Seq). Genomic signatures of selection were identified using: (i) pairwise allele frequency differences; (ii) genome scan for overly differentiated loci; and (iii) genome‐wide association. Fifty significant SNPs were consistently detected, most located in a single chromosome, which can be useful for marker assisted selection. Additionally, we searched for candidate genes at these genomic regions to gain insights into potential molecular mechanisms underlying 2,4-D resistance. Among the predicted functions of candidate genes, we found some related to the auxin metabolism, response to oxidative stress, and detoxification, which are also promising for further functional validation studies.

Exogenous Promoter Triggers APETALA3 Silencing through RNA-Directed DNA Methylation Pathway in Arabidopsis

The development of floral organs plays a vital role in plant reproduction. In our research, the APETALA3 (AP3) promoter-transgenic lines showed abnormal developmental phenotypes in stamens and petals. The aim of this study is to understand the molecular mechanisms of the morphological defects in transgenic plants. By performing transgenic analysis, it was found that the AP3-promoted genes and the vector had no relation to the morphological defects. Then, we performed the expression analysis of the class A, B, and C genes. A dramatic reduction of transcript levels of class B genes (AP3 and PISTILLATA) was observed. Additionally, we also analyzed the methylation of the promoters of class B genes and found that the promoter of AP3 was hypermethylated. Furthermore, combining mutations in rdr2-2, drm1/2, and nrpd1b-11 with the AP3-silencing lines rescued the abnormal development of stamens and petals. The expression of AP3 was reactivated and the methylation level of AP3 promoter was also reduced in RdDM-defective AP3-silencing lines. Our results showed that the RdDM pathway contributed to the transcriptional silencing in the transgenic AP3-silencing lines. Moreover, the results revealed that fact that the exogenous fragment of a promoter could trigger the methylation of homologous endogenous sequences, which may be ubiquitous in transgenic plants.

Role of CYP81A cytochrome P450s in clomazone metabolism in Echinochloa phyllopogon

Clomazone is a herbicide used in the cultivation of numerous crops due to its unique site of action and effectiveness on weeds. The differences in clomazone susceptibility among plants have been attributed to the differences in their complex clomazone metabolic pathways that are not fully understood. We previously identified two CYP81A cytochrome P450 monooxygenases that metabolize five chemically unrelated herbicides in multiple-herbicide resistant Echinochloa phyllopogon. Since the resistant E. phyllopogon have decreased clomazone susceptibility, involvement of these P450s in clomazone resistance was suggested. In this study, we revealed that each P450 gene endowed Arabidopsis thaliana (Arabidopsis) with clomazone resistance. Consistent with this, clomazone resistance co-segregated with resistance to other herbicides in F₆ progenies of crosses between susceptible and resistant E. phyllopogon, suggesting that the P450s are involved in differential clomazone susceptibility in E. phyllopogon. Arabidopsis transformations of the other seven CYP81As of E. phyllopogon found that two more genes, CYP81A15 and CYP81A24, decreased Arabidopsis susceptibility to clomazone. Differences in substrate preference between clomazone and a herbicide that inhibits acetolactate synthase were suggested among the four CYP81A P450s. This study provides insights into clomazone metabolism in plants.

Rapid identification of a candidate nicosulfuron sensitivity gene (Nss) in maize (Zea mays L.) via combining bulked segregant analysis and RNA-seq

A candidate nicosulfuron sensitivity gene Nss was identified by combining bulked segregant analysis and RNA-seq. Multiple mutations of this gene were discovered in nicosulfuron-sensitive maize compared with the tolerant. It has been demonstrated that variabilities exist in maize response to nicosulfuron. Two nicosulfuron-sensitive inbred lines (HB39, HB41) and two tolerant inbred lines (HB05, HB09) were identified via greenhouse and field trials. Genetic analysis indicated that the sensitivity to nicosulfuron in maize was controlled by a single, recessive gene. To precisely and rapidly map the nicosulfuron sensitivity gene (Nss), two independent F₂ segregating populations, Population A (HB41 × HB09) and Population B (HB39 × HB05), were constructed. By applying bulked segregant RNA-Seq (BSR-Seq), the Nss gene was, respectively, mapped on the short arm of chromosome 5 (chr5: 1.1-15.3 Mb) and (chr5: 0.5-18.2 Mb) using two populations, with 14.2 Mb region in common. Further analysis revealed that there were 43 and 119 differentially expressed genes in the mapping intervals, with 18 genes in common. Gene annotation results showed that a cytochrome P450 gene (CYP81A9) appeared to be the candidate gene of Nss associated with nicosulfuron sensitivity in maize. Sequence analysis demonstrated that two common deletion mutations existed in the sensitive maize, which might lead to the nicosulfuron sensitivity in maize. The results will make valuable contributions to the understanding of molecular mechanism of herbicide sensitivity in maize.

Non-target site-based resistance to tribenuron-methyl and essential involved genes in Myosoton aquaticum (L.)

BACKGROUND

Water chickweed (Myosoton aquaticum (L.)) is a dicot broadleaf weed that is widespread in winter fields in China, and has evolved serious resistance to acetolactate synthase (ALS) inhibiting herbicides.

RESULTS

We identified a M. aquaticum population exhibiting moderate (6.15-fold) resistance to tribenuron-methyl (TM). Target-site ALS gene sequencing revealed no known resistance mutations in these plants, and the in vitro ALS activity assays showed no differences in enzyme sensitivity between susceptible and resistant populations; however, resistance was reversed by pretreatment with the cytochrome P450 (CYP) monooxygenase inhibitor malathion. An RNA sequencing transcriptome analysis was performed to identify candidate genes involved in metabolic resistance, and the unigenes obtained by de novo transcriptome assembly were annotated across seven databases. In total, 34 differentially expressed genes selected by digital gene expression analysis were validated by quantitative real-time (qRT)-PCR. Ten consistently overexpressed contigs, including four for CYP, four for ATP-binding cassette (ABC) transporter, and two for peroxidase were further validated by qRT-PCR using additional plants from resistant and susceptible populations. Three CYP genes (with homology to CYP734A1, CYP76C1, and CYP86B1) and one ABC transporter gene (with homology to ABCC10) were highly expressed in all resistant plants.

CONCLUSION

The mechanism of TM resistance in M. aquaticum is controlled by NTSR rather than TSR. Four genes, CYP734A1, CYP76C1, CYP86B1, and ABCC10 could play essential role in metabolic resistance to TM and justify further functional studies. To our knowledge, this is the first large-scale transcriptome analysis of genes associated with NTSR in M. aquaticum using the Illumina platform. Our data provide resource for M. aquaticum biology, and will facilitate the study of herbicide resistance mechanism at the molecular level in this species as well as in other weeds.

The P450 gene CYP749A16 is required for tolerance to the sulfonylurea herbicide trifloxysulfuron sodium in cotton (Gossypium hirsutum L.)

BACKGROUND

Weed management is critical to global crop production and is complicated by rapidly evolving herbicide resistance in weeds. New sources of herbicide resistance are needed for crop plants so that applied herbicides can be rotated or combined to thwart the evolution of resistant weeds. The diverse family of cytochrome P450 proteins has been suggested to be a source of detoxifying herbicide metabolism in both weed and crop plants, and greater understanding of these genes will offer avenues for crop improvement and novel weed management practices.

RESULTS

Here, we report the identification of CYP749A16 (Gh_D10G1401) which is responsible for the natural tolerance exhibited by most cotton, Gossypium hirsutum L., cultivars to the herbicide trifloxysulfuron sodium (TFS, CGA 362622, commercial formulation Envoke). A 1-bp frameshift insertion in the third exon of CYP749A16 results in the loss of tolerance to TFS. The DNA marker designed from this insertion perfectly co-segregated with the phenotype in 2145 F₂ progeny of a cross between the sensitive cultivar Paymaster HS26 and tolerant cultivar Stoneville 474, and in 550 recombinant inbred lines of a multi-parent advanced generation inter-cross population. Marker analysis of 382 additional cotton cultivars identified twelve cultivars containing the 1-bp frameshift insertion. The marker genotypes matched perfectly with phenotypes in 188 plants from the selected twelve cultivars. Virus-induced gene silencing of CYP749A16 generated sensitivity in the tolerant cotton cultivar Stoneville 474.

CONCLUSIONS

CYP749A16 located on chromosome D10 is required for TFS herbicide tolerance in cotton. This finding should add to the repertoire of tools available to farmers and breeders for the advancement of agricultural productivity.

A 22-bp deletion in OsPLS3 gene encoding a DUF266-containing protein is implicated in rice leaf senescence

Key message The OsPLS3 locus was isolated by map-based cloning that encodes a DUF266-containing protein. OsPLS3 regulates the onset of leaf senescence in rice. Glycosyltransferases (GTs) are one of the most important enzyme groups required for the modification of plant secondary metabolites and play a crucial role in plant growth and development, however the biological functions of most GTs remain elusive. We reported here the identification and characterization of a novel Oryza sativa premature leaf senescence mutant (ospls3). Through map-based cloning strategy, we determined that 22-bp deletion in the OsPLS3 gene encoding a domain of unknown function 266 (DUF266)-containing protein, a member of GT14-like, underlies the premature leaf senescence phenotype in the ospls3 mutant. The OsPLS3 mRNA levels progressively declined with the age-dependent leaf senescence in wild-type rice, implying a negative role of OsPLS3 in regulating leaf senescence. Physiological analysis, and histochemical staining and transmission electron microscopy assays indicated that the ospls3 mutant accumulated higher levels of ethylene and reactive oxygen species than its wild type. Furthermore, the ospls3 mutant showed hypersensitivity to exogenous 1-aminocyclopropane-1-carboxylic acid, H₂O₂ and high level of cytokinins. Our results indicated that the DUF266-containing gene OsPLS3 plays an important role in the onset of leaf senescence, in part through cytokinin and ethylene signaling in rice.

Autophagy contributes to sulfonylurea herbicide tolerance via GCN2-independent regulation of amino acid homeostasis

Sulfonylurea (SU) herbicides inhibit branched-chain amino acid (BCAA) biosynthesis by targeting acetolactate synthase. Plants have evolved target-site resistance and metabolic tolerance to SU herbicides; the GCN2 (general control non-repressible 2) pathway is also involved in SU tolerance. Here, we report a novel SU tolerance mechanism, autophagy, which we call 'homeostatic tolerance,' is involved in amino acid signaling in Arabidopsis. The activation and reversion of autophagy and GCN2 by the SU herbicide tribenuron-methyl (TM) and exogenous BCAA, respectively, confirmed that TM-induced BCAA starvation is responsible for the activation of autophagy and GCN2. Genetic and biochemical analyses revealed a lower proportion of free BCAA and more sensitive phenotypes in atg5, atg7, and gcn2 single mutants than in wild-type seedlings after TM treatment; the lowest proportion of free BCAA and the most sensitive phenotypes were found in atg5 gcn2 and atg7 gcn2 double mutants. Immunoblotting and microscopy revealed that TM-induced activation of autophagy and GCN2 signaling do not depend on the presence of each other, and these 2 pathways may serve as mutually compensatory mechanisms against TM. TM inhibited the TOR (target of rapamycin), and activated autophagy in an estradiol-induced TOR RNAi line, suggesting that TM-induced BCAA starvation activates autophagy, probably via TOR inactivation. Autophagy and GCN2 were also activated, and independently contributed to TM tolerance in plants conferring metabolic tolerance. Together, these data suggest that autophagy is a proteolytic process for amino acid recycling and contributes to GCN2-independent SU tolerance, probably by its ability to replenish fresh BCAA.

Genome Editing in Rice: Recent Advances, Challenges, and Future Implications

Rice (Oryza sativa L.) is the major food source for more than three billion people of the world. In the last few decades, the classical, mutational, and molecular breeding approaches have brought about tremendous increase in rice productivity with the development of novel rice varieties. However, stagnation in rice yield has been reported in recent decade owing to several factors including the emergence of pests and phyto pathogens, climate change, and other environmental issues posing great threat to global food security. There is an urgent need to produce more rice and associated cereals to satisfy the mammoth task of feeding a still growing population expected to reach 9.7 billion by 2050. Advances in genomics and emergence of multiple genome-editing technologies through use of engineered site-specific nucleases (SSNs) have revolutionized the field of plant science and agriculture. Among them, the CRISPR/Cas9 system is the most advanced and widely accepted because of its simplicity, robustness, and high efficiency. The availability of huge genomic resources together with a small genome size makes rice more suitable and feasible for genetic manipulation. As such, rice has been increasingly used to test the efficiency of different types of genome editing technologies to study the functions of various genes and demonstrate their potential in genetic improvement. Recently developed approaches including CRISPR/Cpf1 system and base editors have evolved as more efficient and accurate genome editing tools which might accelerate the pace of crop improvement. In the present review, we focus on the genome editing strategies for rice improvement, thereby highlighting the applications and advancements of CRISPR/Cas9 system. This review also sheds light on the role of CRISPR/Cpf1 and base editors in the field of genome editing highlighting major challenges and future implications of these tools in rice improvement.

Genome Editing in Rice: Recent Advances, Challenges, and Future Implications

Rice (Oryza sativa L.) is the major food source for more than three billion people of the world. In the last few decades, the classical, mutational, and molecular breeding approaches have brought about tremendous increase in rice productivity with the development of novel rice varieties. However, stagnation in rice yield has been reported in recent decade owing to several factors including the emergence of pests and phyto pathogens, climate change, and other environmental issues posing great threat to global food security. There is an urgent need to produce more rice and associated cereals to satisfy the mammoth task of feeding a still growing population expected to reach 9.7 billion by 2050. Advances in genomics and emergence of multiple genome-editing technologies through use of engineered site-specific nucleases (SSNs) have revolutionized the field of plant science and agriculture. Among them, the CRISPR/Cas9 system is the most advanced and widely accepted because of its simplicity, robustness, and high efficiency. The availability of huge genomic resources together with a small genome size makes rice more suitable and feasible for genetic manipulation. As such, rice has been increasingly used to test the efficiency of different types of genome editing technologies to study the functions of various genes and demonstrate their potential in genetic improvement. Recently developed approaches including CRISPR/Cpf1 system and base editors have evolved as more efficient and accurate genome editing tools which might accelerate the pace of crop improvement. In the present review, we focus on the genome editing strategies for rice improvement, thereby highlighting the applications and advancements of CRISPR/Cas9 system. This review also sheds light on the role of CRISPR/Cpf1 and base editors in the field of genome editing highlighting major challenges and future implications of these tools in rice improvement.

Substrate specificity and safener inducibility of the plant UDP-glucose-dependent family 1 glycosyltransferase super-family

Plants contain large numbers of family 1 UDP-glucose-dependent glycosyltransferases (UGTs), including members that conjugate xenobiotics. Arabidopsis contains 107 UGT genes with 99 family members successfully expressed as glutathione transferase (GST)-fusion proteins in E. coli. A high-throughput catalytic screen was developed based on quantification of the fusion by measuring GST activity. UGT activity using UDP-glucose as donor was then determined using 11 synthetic acceptors bearing hydroxyl, amino and thiol groups that had been shown to undergo conjugation in plant extracts. In total, 44 UGTs, largely members of the D and E groups, were active towards xenobiotics, glucosylating phenol and thiol acceptors. In contrast, N-glucosyltransferase (NGT) activity was almost exclusively restricted to a single enzyme, UGT72B1. Using DNA microarrays, the induction of UGT transcripts following treatment with the herbicide safener fenclorim was compared in Arabidopsis and rice. D and L group members were the most safener-inducible UGTs in both species. The respective Arabidopsis enzymes showed low conjugating activity towards xenobiotics. Using Genevestigator, a small group of safened D and L UGTs were consistently induced in response to biotic and abiotic stress suggestive of protective activities beyond xenobiotic detoxification in both species. The induction of other detoxifying gene families following treatment with fenclorim, namely cytochromes P450 and glutathione transferases, further confirmed the selective enhancement of related subfamily members in the two species giving new insight into the safening response in cereals, where herbicide tolerance is enhanced compared with dicots, which are unresponsive to these treatments.

Autophagy contributes to sulfonylurea herbicide tolerance via GCN2-independent regulation of amino acid homeostasis

Sulfonylurea (SU) herbicides inhibit branched-chain amino acid (BCAA) biosynthesis by targeting acetolactate synthase. Plants have evolved target-site resistance and metabolic tolerance to SU herbicides; the GCN2 (general control non-repressible 2) pathway is also involved in SU tolerance. Here, we report a novel SU tolerance mechanism, autophagy, which we call 'homeostatic tolerance,' is involved in amino acid signaling in Arabidopsis. The activation and reversion of autophagy and GCN2 by the SU herbicide tribenuron-methyl (TM) and exogenous BCAA, respectively, confirmed that TM-induced BCAA starvation is responsible for the activation of autophagy and GCN2. Genetic and biochemical analyses revealed a lower proportion of free BCAA and more sensitive phenotypes in atg5, atg7, and gcn2 single mutants than in wild-type seedlings after TM treatment; the lowest proportion of free BCAA and the most sensitive phenotypes were found in atg5 gcn2 and atg7 gcn2 double mutants. Immunoblotting and microscopy revealed that TM-induced activation of autophagy and GCN2 signaling do not depend on the presence of each other, and these 2 pathways may serve as mutually compensatory mechanisms against TM. TM inhibited the TOR (target of rapamycin), and activated autophagy in an estradiol-induced TOR RNAi line, suggesting that TM-induced BCAA starvation activates autophagy, probably via TOR inactivation. Autophagy and GCN2 were also activated, and independently contributed to TM tolerance in plants conferring metabolic tolerance. Together, these data suggest that autophagy is a proteolytic process for amino acid recycling and contributes to GCN2-independent SU tolerance, probably by its ability to replenish fresh BCAA.

Intensive herbicide use has selected for constitutively elevated levels of stress-responsive mRNAs and proteins in multiple herbicide-resistant Avena fatua L

BACKGROUND

Intensive use of herbicides has led to the evolution of two multiple herbicide-resistant (MHR) Avena fatua (wild oat) populations in Montana that are resistant to members of all selective herbicide families available for A. fatua control in US small grain crops. We used transcriptome and proteome surveys to compare constitutive changes in MHR and herbicide-susceptible (HS) plants associated with non-target site resistance.

RESULTS

Compared to HS plants, MHR plants contained constitutively elevated levels of differentially expressed genes (DEGs) with functions in xenobiotic catabolism, stress response, redox maintenance and transcriptional regulation that are similar to abiotic stress-tolerant phenotypes. Proteome comparisons identified similarly elevated proteins including biosynthetic and multifunctional enzymes in MHR plants. Of 25 DEGs validated by RT-qPCR assay, differential regulation of 21 co-segregated with flucarbazone-sodium herbicide resistance in F₃ families, and a subset of 10 of these were induced or repressed in herbicide-treated HS plants.

CONCLUSION

Although the individual and collective contributions of these DEGs and proteins to MHR remain to be determined, our results support the idea that intensive herbicide use has selected for MHR populations with altered, constitutively regulated patterns of gene expression that are similar to those in abiotic stress-tolerant plants. © 2017 Society of Chemical Industry.

Physiological and Molecular Characterization of Hydroxyphenylpyruvate Dioxygenase (HPPD)-inhibitor Resistance in Palmer Amaranth (Amaranthus palmeri S.Wats.)

Herbicides that inhibit hydroxyphenylpyruvate dioxygenase (HPPD) such as mesotrione are widely used to control a broad spectrum of weeds in agriculture. Amaranthus palmeri is an economically troublesome weed throughout the United States. The first case of evolution of resistance to HPPD-inhibiting herbicides in A. palmeri was documented in Kansas (KS) and later in Nebraska (NE). The objective of this study was to investigate the mechansim of HPPD-inhibitor (mesotrione) resistance in A. palmeri. Dose response analysis revealed that this population (KSR) was 10-18 times more resistant than their sensitive counterparts (MSS or KSS). Absorbtion and translocation analysis of [¹⁴C] mesotrione suggested that these mechanisms were not involved in the resistance in A. palmeri. Importantly, mesotrione (>90%) was detoxified markedly faster in the resistant populations (KSR and NER), within 24 hours after treatment (HAT) compared to sensitive plants (MSS, KSS, or NER). However, at 48 HAT all populations metabolized the mesotrione, suggesting additional factors may contribute to this resistance. Further evaluation of mesotrione-resistant A. palmeri did not reveal any specific resistance-conferring mutations nor amplification of HPPD gene, the molecular target of mesotrione. However, the resistant populations showed 4- to 12-fold increase in HPPD gene expression. This increase in HPPD transcript levels was accompanied by increased HPPD protein expression. The significant aspects of this research include: the mesotrione resistance in A. palmeri is conferred primarily by rapid detoxification (non-target-site based) of mesotrione; additionally, increased HPPD gene expression (target-site based) also contributes to the resistance mechanism in the evolution of herbicide resistance in this naturally occurring weed species.

Transcriptional markers enable identification of rye-grass (Lolium sp.) plants with non-target-site-based resistance to herbicides inhibiting acetolactate-synthase

Molecular detection of herbicide non-target-site-based resistance (NTSR) classically requires extensively validated NTSR genes. We assessed the feasibility of predicting NTSR phenotypes using expression data of NTSR transcriptional markers, i.e., transcripts which expression levels are statistically correlated to NTSR. Markers were sought by comparative RNA-Seq analysis of untreated NTSR or sensitive plants from four rye-grass populations followed by expression quantification in 299 individual plants with characterised sensitivity to two acetolactate-synthase-inhibiting herbicides. Multivariate analyses were implemented to predict NTSR using combined marker expression data. Nineteen markers (four cytochromes P450, four glutathione-S-transferases, three glycosyltransferases, two ABC transporters, two hydrolases, one aldolase, one peptidase, one transferase and one esterase) expressed significantly higher in NTSR plants were identified. Expression was highest in the most resistant plants. Some markers appeared co-regulated. Combined marker expression data enabled prediction of NTSR phenotypes in individual plants or of resistant plant frequencies in populations. Thus, NTSR detection based on transcriptional markers proved feasible. Accuracy can be improved by identifying additional markers, especially markers associated to NTSR regulation. Additionally, our data suggest that NTSR mechanisms emerged in different populations via redundant evolution, and that NTSR can evolve by selection for higher constitutive expression of whole herbicide-response pathways.