ACCase mutations in Avena sterilis populations and their impact on plant fitness

WGCNA and transcriptome profiling reveal hub genes for key development stage seed size/oil content between wild and cultivated soybean

BACKGROUND

Soybean is one of the most important oil crops in the world. The domestication of wild soybean has resulted in significant changes in the seed oil content and seed size of cultivated soybeans. To better understand the molecular mechanisms of seed formation and oil content accumulation, WDD01514 (E1), ZYD00463 (E2), and two extreme progenies (E23 and E171) derived from RILs were used for weighted gene coexpression network analysis (WGCNA) combined with transcriptome analysis.

RESULTS

In this study, both seed weight and oil content in E1 and E171 were significantly higher than those in E2 and E23, and 20 DAF and 30 DAF may be key stages of soybean seed oil content accumulation and weight increase. Pathways such as "Photosynthesis", "Carbon metabolism", and "Fatty acid metabolism", were involved in oil content accumulation and grain formation between wild and cultivated soybeans at 20 and 30 DAF according to RNA-seq analysis. A total of 121 oil content accumulation and 189 seed formation candidate genes were screened from differentially expressed genes. WGCNA identified six modules related to seed oil content and seed weight, and 76 candidate genes were screened from modules and network. Among them, 16 genes were used for qRT-PCR and tissue specific expression pattern analysis, and their expression-levels in 33-wild and 23-cultivated soybean varieties were subjected to correlation analysis; some key genes were verified as likely to be involved in oil content accumulation and grain formation.

CONCLUSIONS

Overall, these results contribute to an understanding of seed lipid metabolism and seed size during seed development, and identify potential functional genes for improving soybean yield and seed oil quantity.

Mechanism of metamifop resistance in Digitaria ciliaris var. chrysoblephara from Jiangsu, China

Digitaria ciliaris var. chrysoblephara is one of the most competitive and problematic grass weeds in China. Metamifop is an aryloxyphenoxypropionate (APP) herbicide that inhibits the activity of acetyl-CoA carboxylase (ACCase) of sensitive weeds. Following the introduction of metamifop to China in 2010, it has been continuously used in rice paddy fields, thereby substantially increasing selective pressure for resistant D. ciliaris var. chrysoblephara variants. Here, populations of D. ciliaris var. chrysoblephara (JYX-8, JTX-98, and JTX-99) were observed to be highly resistant to metamifop, with resistance index (RI) values of 30.64, 14.38, and 23.19, respectively. Comparison of resistant and sensitive population ACCase gene sequences revealed that a single nucleotide substitution from TGG to TGC resulted in an amino acid substitution from tryptophan to cysteine at position 2,027 in the JYX-8 population. No corresponding substitution was observed for JTX-98 and JTX-99 populations. The ACCase cDNA of D. ciliaris var. chrysoblephara was successfully obtained by PCR and RACE methods, representing the first amplification of full length ACCase cDNA from Digitaria spp. Investigation of the relative expressions of ACCase gene revealed the lack of significant differences between sensitive and resistant populations before and after herbicide treatments. ACCase activities in resistant populations were less inhibited than in sensitive populations and recovered to the same or even higher levels compared to untreated plants. Whole-plant bioassays were also conducted to assess resistance to other ACCase inhibitors, acetolactate synthase (ALS) inhibitors, auxin mimic herbicide, and protoporphyrinogen oxidase (PPO) inhibitor. Cross-resistance and some multi-resistance were observed in the metamifop-resistant populations. This study is the first to focus on the herbicide resistance of D. ciliaris var. chrysoblephara. These results provide evidence for a target-site resistance mechanism in metamifop-resistant D. ciliaris var. chrysoblephara, while providing a better understanding of cross- and multi-resistance characteristics of resistant populations that will help in the management of herbicide-resistant D. ciliaris var. chrysoblephara.

Investigating resistance levels to cyhalofop-butyl and mechanisms involved in Chinese sprangletop (Leptochloa chinensis L.) from Anhui Province, China

Chinese sprangletop (Leptochloa chinensis (L.) Nees) is a common grass species that severely threatens rice (Oryza sativa L.) cropping systems globally. Cyhalofop-butyl is a highly efficient acetyl-CoA carboxylase (ACCase)-inhibiting herbicide widely used for control of this species in China. However, some L. chinensis populations have gradually evolved resistance to this herbicide in recent years. To better understand the cyhalofop-butyl resistance status of L. chinensis in the major rice planting area of the middle-lower Yangtze River basin, 73 populations collected from the rice fields across Anhui Province were investigated for cyhalofop-butyl susceptibility and potential herbicide resistance-conferring mutations. Single-dose testing indicated that of the 73 populations, 25 had evolved resistance to cyhalofop-butyl and were separately classified as "RRR" and "RR" populations according to their fresh weight reductions, 8 had a high risk of evolving cyhalofop-butyl resistance and were classified as "R?" populations, and 40 were susceptible and classified as "S" populations. Whole-plant dose-response experiments showed that the resistance index (RI) of these R?, RR, and RRR populations to cyhalofop-butyl ranged from 2.47 to 36.94. Target gene sequencing identified seven ACCase resistance mutations (I1781L, W1999C, W2027S, W2027L, W2027C, I2041N, and D2078G), with W1999C and W2027C the two most common detected in about three quarters of all the resistant populations. Seven populations including LASC3, BBHY1, AQQS1, HFFD3, HFFD4, AQWJ1, and HFLJ6 each carrying a specific ACCase mutation were tested for their cross- and multiple-resistance patterns. Compared with a standard susceptible population HFLY1, the seven resistant populations showed distinct cross-resistance. All had low- to high-level cross-resistance to metamifop (RIs ranging from 6.16 to 17.65), fenoxaprop-P-ethyl (RIs ranging from 6.39 to 24.08), and quizalofop-P-ethyl (RIs ranging from 2.20 to 10.25), but responded differently to clodinafop-propargyl and clethodim. Multiple-resistance testing suggested that the seven resistant populations were all susceptible to the 4-hydroxyphenylpyruvate dioxygenase inhibitor tripyrasulfone, the protoporphyrinogen oxidase inhibitor oxyfluorfen, and the auxin mimic herbicide florpyrauxifen. In conclusion, this study has shown that cyhalofop-butyl resistance was prevalent in L. chinensis in Anhui Province, China, and target site mutation was one of the most common resistance mechanisms.

Mechanism of Resistance to Pyroxsulam in Multiple-Resistant Alopecurus myosuroides from China

Black grass (Alopecurus myosuroides Huds.) is a highly competitive weed in winter wheat fields of China. Due to repeated use of acetolactate synthase (ALS) inhibitors, many A. myosuroides populations have evolved resistance to pyroxsulam in some wheat fields. Research was conducted to determine the molecular basis of herbicide resistance in the AH93 A. myosuroides population. Whole-plant dose–response assay confirmed that the AH93 population was resistant to pyroxsulam with a resistance index of 4.2. Cross- and multiple-resistance assays indicated that the AH93 population was cross-resistant to mesosulfuron-methyl and multiple-resistant to pinoxaden. Sequencing of the ALS and ACCase gene revealed that there was no target-site mutation in ALS, but Trp-2027-Cys and Cys-2088-Arg amino acid mutations in ACCase in the AH93 population. A malathion pretreatment study indicated that the AH93 population might have cytochrome P450–mediated herbicide metabolic resistance. This is the first report of pyroxsulam resistance in a multiple-resistant A. myosuroides population in China, and the Cys-2088-Arg mutation is the first reported case of an ACCase mutant conferring herbicide resistance in A. myosuroides.

No fitness cost associated with Asn-2041-Ile mutation in winter wild oat (Avena ludoviciana) seed germination under various environmental conditions

Knowledge about the fitness cost imposed by herbicide resistance in weeds is instrumental in devising integrated management methods. The present study investigated the germination response of ACCase-resistant (R) and susceptible (S) winter wild oat under different environmental conditions. The DNA of the plants was sequenced after being extracted and purified. The segregated F₂ seeds were subjected to various temperatures, water potentials, NaCl concentrations, different pHs, darkness conditions, and burial depths. The results of the sequencing indicated that Ile-2041-Asn mutation is responsible for the evolution of resistance in the studied winter wild oat plants. The seeds were able to germinate over a wide range of temperatures, osmotic potentials, NaCl concentrations, and pHs. Germination percentage of R and S seeds under dark and light conditions was similar and ranged from 86.3 to 88.3%. The highest emergence percentage for both R and S plants was obtained in 0, 1, and 2 cm depths and ranged from 66.6 to 70.3%. In overall, no differences were observed in the germination response between the R and S winter wild oat plants under all studied conditions. No fitness cost at seed level indicates that control of R winter wild oats is more difficult, and it is essential to adopt crop and herbicide rotation to delay the further evolution of resistance.

Mechanisms of Lolium rigidum multiple resistance to ALS- and ACCase-inhibiting herbicides and their impact on plant fitness

Three putative resistant (R1, R2, R3) and one susceptible (S) Lolium rigidum populations originating from Greece were studied for resistance to ALS and ACCase inhibiting herbicides, using whole plant, sequencing of als and accase gene, and in vitro ALS activity assays. The S and two R (R1, R2) populations were also evaluated for fitness in competition with wheat. The whole plant assay indicated unsatisfactory control of the R populations with mesosulfuron-methyl + iodosulfuron-methyl or pinoxaden application, whereas sequencing of the als gene revealed that all ALS-resistant individuals had a Pro-197 substitution by Leu, Glu, Ser, Ala, Thr, or Gln. In addition, the accase gene of all pinoxaden resistant individuals had an Ile-2041 substitution by Asn or Thr. Furthermore, sequencing of the individuals surviving mesosulfuron-methyl + iodosulfuron-methyl or pinoxaden treatment revealed co-existence of point mutations in the accase or als genes, respectively, demonstrating multiple resistance. The in vitro activity of the ALS enzyme confirmed that resistance to mesosulfuron-methyl + iodosulfuron-methyl was due altered target-site. The recorded higher vigor and greater competitive ability of S population against wheat as compared with that of the R populations suggests an associated fitness cost with multiple resistance.

Detecting acetyl-coenzyme a carboxylase resistance gene in rice (Oryza sativa L.)

Herbicides inhibiting acetyl-coenzyme A carboxylase (ACCase) are very effective in controlling grass weeds including weedy-rice in paddy rice production systems. The ACCase inhibitor affects the enzyme by blocking fatty acid biosynthesis resulting in plant death. The herbicide resistance in rice is conferred by a single point mutation with an amino acid substitution of the carboxyl transferase domain of the ACCase gene. An assay based on the tetra-primer ARMS-PCR method was developed to detect the SNP G2027T that causes a tryptophan-cysteine substitution in the gene encoding chloroplastic ACCase in rice. The protocol was tested in 453 rice samples from a segregant population for validation of the assay. This technique can be exploited to monitor resistant lines in rice breeding programs to detect homozygous or heterozygous resistant genotypes and homozygous susceptible genotypes. The presence of resistant ACCase allele(s) can be detected with rapidity, simplicity, at low cost and can be used in any molecular biology laboratory with minimal equipment.

Fitness costs associated with acetyl-coenzyme A carboxylase mutations endowing herbicide resistance in American sloughgrass (Beckmannia syzigachne Steud.)

Weed resistance to herbicide can be conferred by gene mutations, and some mutations can cause pleiotropic effects in some cases. We investigated the pleiotropic effects associated with five specific ACCase mutations (Ile1781Leu, Trp2027Cys, Ile2041Asn, Asp2078Gly, and Gly2096Ala) on the plant growth, seed production, and resource competitiveness in American sloughgrass.Resistant plants (M/M) homozygous for specific ACCase mutation and susceptible wild-type plants (W/W) were derived from single heterozygous mother plant (M/W) by genotyping. Plant growth assay and neighborhood experiments were performed to quantify variation between M/M plants and W/W plants.The Ile1781Leu mutation resulted in slight increases in plant growth in pure stands and improved resource competitiveness under low-competition conditions in pot experiments, but no clear variation was observed under high competitive pressure or field conditions. During competition with wheat plants under field conditions, American sloughgrass plants containing Ile2041Asn ACCase exhibited a significantly lower (12.5%) aboveground biomass but no distinct differences in seed production or resource competitiveness. No significant detrimental pleiotropic effects associated with Gly2096Ala were detected in American sloughgrass.The Trp2027Cys mutation distinctly reduced seed production, especially under high competitive pressure, but did not significantly alter plant growth. The Asp2078Gly mutation consistently reduced not only plant growth and seed production but also resource competitiveness. Synthesis. The Trp2027Cys and Asp2078Gly mutations led to significant fitness costs, which may reduce the frequency of resistance alleles and reduce the propagation speed of resistant weeds in the absence of ACCase inhibitor herbicides. The Ile1781Leu, Ile2041Asn, and Gly2096Ala mutations displayed no obvious fitness costs or displayed very small fitness penalties, which would likely have no effect on the establishment of resistant weeds in the field.

Trp574 substitution in the acetolactate synthase of Sinapis arvensis confers cross-resistance to tribenuron and imazamox

Rate-response experiments with nine putative resistant wild mustard (Sinapis arvensis) populations from Greece showed cross-resistance to tribenuron and imazamox. The calculated GR₅₀ values [herbicide rate (gaiha^-1) required for 50% reduction of fresh weight] of the nine resistant (R) populations ranged from 51.8 to 555.6gaitribenuronha^-1 and from 66.3 to 900.4gaiimazamoxha^-1. Regarding the susceptible population, GR₅₀ value was not estimated for tribenuron as its lower treatment reduced fresh weight by >95%, whereas the respective value for imazamox was 0.5gaiha^-1. Gene sequencing of als revealed that a point mutation at Trp574 position, leading to amino acid substitution by Leu in the ALS enzyme was present and the likely cause of resistance. The in vitro activity of the ALS enzyme indicated I₅₀ values (herbicide concentration required for 50% reduction of the ALS activity) ranging from 19.11 to 217.45μM for tribenuron, whereas the respective value for the S population was 1.17μM. All populations were susceptible to MCPA at the recommended rate. These results strongly support that cross-resistance of 9 S. arvensis populations was due a point mutation of the als gene, which resulted in a less sensitive ALS enzyme.

Different Mutations Endowing Resistance to Acetyl-CoA Carboxylase Inhibitors Results in Changes in Ecological Fitness of Lolium rigidum Populations

Various mutations altering the herbicide target site (TS), can lead to structural modifications that decrease binding efficiency and results in herbicide resistant weed. In most cases, such a mutation will be associated with ecological fitness penalty under herbicide free environmental conditions. Here we describe the effect of various mutations, endowing resistance to acetyl-CoA carboxylase (ACCase) inhibitors, on the ecological fitness penalty of Lolium rigidum populations. The TS resistant populations, MH (substitution of isoleucine 1781 to leucine) and NO (cysteine 2088 to arginine), were examined and compared to a sensitive population (AL). Grain weight (GW) characterization of individual plants from both MH and NO populations, showed that resistant individuals had significantly lower GW compared with sensitive ones. Under high temperatures, both TS resistant populations exhibited lower germination rate as compared with the sensitive (AL) population. Likewise, early vigor of plants from both TS resistant populations was significantly lower than the one measured in plants of the sensitive population. Under crop-weed intra-species competition, we found an opposite trend in the response of plants from different populations. Relatively to inter-population competition conditions, plants of MH population were less affected and presented higher reproduction abilities compared to plants from both AL and NO populations. On the basis of our results, a non-chemical approach can be taken to favor the sensitive individuals, eventually leading to a decline in resistant individuals in the population.

Climate change increases the risk of herbicide-resistant weeds due to enhanced detoxification

Global warming will increase the incidence of metabolism-based reduced herbicide efficacy on weeds and, therefore, the risk for evolution of non-target site herbicide resistance. Climate changes affect food security both directly and indirectly. Weeds are the major biotic factor limiting crop production worldwide, and herbicides are the most cost-effective way for weed management. Processes associated with climatic changes, such as elevated temperatures, can strongly affect weed control efficiency. Responses of several grass weed populations to herbicides that inhibit acetyl-CoA carboxylase (ACCase) were examined under different temperature regimes. We characterized the mechanism of temperature-dependent sensitivity and the kinetics of pinoxaden detoxification. The products of pinoxaden detoxification were quantified. Decreased sensitivity to ACCase inhibitors was observed under elevated temperatures. Pre-treatment with the cytochrome-P450 inhibitor malathion supports a non-target site metabolism-based mechanism of herbicide resistance. The first 48 h after herbicide application were crucial for pinoxaden detoxification. The levels of the inactive glucose-conjugated pinoxaden product (M5) were found significantly higher under high- than low-temperature regime. Under high temperature, a rapid elevation in the level of the intermediate metabolite (M4) was found only in pinoxaden-resistant plants. Our results highlight the quantitative nature of non-target-site resistance. To the best of our knowledge, this is the first experimental evidence for temperature-dependent herbicide sensitivity based on metabolic detoxification. These findings suggest an increased risk for the evolution of herbicide-resistant weeds under predicted climatic conditions.