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Kababji AM, Butt H, Mahfouz M. Synthetic directed evolution for targeted engineering of plant traits. FRONTIERS IN PLANT SCIENCE 2024; 15:1449579. [PMID: 39286837 PMCID: PMC11402689 DOI: 10.3389/fpls.2024.1449579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Accepted: 08/12/2024] [Indexed: 09/19/2024]
Abstract
Improving crop traits requires genetic diversity, which allows breeders to select advantageous alleles of key genes. In species or loci that lack sufficient genetic diversity, synthetic directed evolution (SDE) can supplement natural variation, thus expanding the possibilities for trait engineering. In this review, we explore recent advances and applications of SDE for crop improvement, highlighting potential targets (coding sequences and cis-regulatory elements) and computational tools to enhance crop resilience and performance across diverse environments. Recent advancements in SDE approaches have streamlined the generation of variants and the selection processes; by leveraging these advanced technologies and principles, we can minimize concerns about host fitness and unintended effects, thus opening promising avenues for effectively enhancing crop traits.
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Affiliation(s)
- Ahad Moussa Kababji
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Haroon Butt
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Magdy Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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Kersten S, Rabanal FA, Herrmann J, Hess M, Kronenberg ZN, Schmid K, Weigel D. Deep haplotype analyses of target-site resistance locus ACCase in blackgrass enabled by pool-based amplicon sequencing. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1240-1253. [PMID: 36807472 PMCID: PMC10214753 DOI: 10.1111/pbi.14033] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 12/27/2022] [Accepted: 02/06/2023] [Indexed: 05/27/2023]
Abstract
Rapid adaptation of weeds to herbicide applications in agriculture through resistance development is a widespread phenomenon. In particular, the grass Alopecurus myosuroides is an extremely problematic weed in cereal crops with the potential to manifest resistance in only a few generations. Target-site resistances (TSRs), with their strong phenotypic response, play an important role in this rapid adaptive response. Recently, using PacBio's long-read amplicon sequencing technology in hundreds of individuals, we were able to decipher the genomic context in which TSR mutations occur. However, sequencing individual amplicons are costly and time-consuming, thus impractical to implement for other resistance loci or applications. Alternatively, pool-based approaches overcome these limitations and provide reliable allele frequencies, although at the expense of not preserving haplotype information. In this proof-of-concept study, we sequenced with PacBio High Fidelity (HiFi) reads long-range amplicons (13.2 kb), encompassing the entire ACCase gene in pools of over 100 individuals, and resolved them into haplotypes using the clustering algorithm PacBio amplicon analysis (pbaa), a new application for pools in plants and other organisms. From these amplicon pools, we were able to recover most haplotypes from previously sequenced individuals of the same population. In addition, we analysed new pools from a Germany-wide collection of A. myosuroides populations and found that TSR mutations originating from soft sweeps of independent origin were common. Forward-in-time simulations indicate that TSR haplotypes will persist for decades even at relatively low frequencies and without selection, highlighting the importance of accurate measurement of TSR haplotype prevalence for weed management.
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Affiliation(s)
- Sonja Kersten
- Institute of Plant Breeding, Seed Science and Population GeneticsUniversity of HohenheimStuttgartGermany
- Department of Molecular BiologyMax Planck Institute for Biology TübingenTübingenGermany
| | - Fernando A. Rabanal
- Department of Molecular BiologyMax Planck Institute for Biology TübingenTübingenGermany
| | | | | | | | - Karl Schmid
- Institute of Plant Breeding, Seed Science and Population GeneticsUniversity of HohenheimStuttgartGermany
| | - Detlef Weigel
- Department of Molecular BiologyMax Planck Institute for Biology TübingenTübingenGermany
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Vázquez-García JG, de Portugal J, Torra J, Osuna MD, Palma-Bautista C, Cruz-Hipólito HE, De Prado R. Comparison between the mechanisms of Clearfield ® wheat and Lolium rigidum multiple resistant to acetyl CoA carboxylase and acetolactate synthase inhibitors. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 306:119438. [PMID: 35561797 DOI: 10.1016/j.envpol.2022.119438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 04/28/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
Clearfield® wheat (Triticum aestivum) have helped eliminate the toughest grasses and broadleaf weeds in Spain since 2005. This crop production system includes other tolerant cultivars to the application of imidazolinone (IMI) herbicides. However, the continuous use and off-label rates of IMI herbicides can contribute to the development of resistance in Lolium rigidum and other weed species. In this research, the main objectives were to study the resistance mechanisms to acetolactate synthase (ALS) and acetyl coenzyme A carboxylase (ACCase) inhibitors in a L. rigidum accession (LrR) from a Clearfield® wheat field, with a long history rotating these IMI-tolerant crops and compare them with those present in the IMI-tolerant wheat. The resistance to ACCase inhibitors in LrR was due to point mutations (Ile1781Leu plus Asp2078Gly) of the target site gene plus an enhanced herbicide metabolism (EHM), on the other hand, in wheat accessions was due only by EHM. Mechanisms involved in the resistance to ALS inhibitors were both point mutations of the target gene and EHM in the IMI-tolerant wheat, while only evidence of mutation (Trp574Leu) was found in the multiple herbicide resistant L. rigidum accession. This research demonstrates that if crop rotation is not accompanied by the use of alternative sites of action in herbicide-tolerant crops, resistant weeds to herbicide to which crops are tolerant, can easily be selected. Moreover, repeated and inappropriate use of Clearfield® crops and herbicide rotations can lead to the evolution of multiple resistant weeds, as shown in this study, and have also inestimable environmental impacts.
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Affiliation(s)
- José G Vázquez-García
- Department of Agricultural Chemistry, Edaphology and Microbiology, University of Córdoba, 14014, Córdoba, Spain.
| | - Joao de Portugal
- Biosciences Department, Polytechnic Institute of Beja, Beja, Portugal; VALORIZA-Research Centre for Endogenous Resource Valorization, Polytechnic Institute of Portalegre, Portalegre, Portugal
| | - Joel Torra
- Department d'Hortofructicultura, Botànica i Jardineria, Agrotecnio-CERCA Center, Universitat de Lleida, Lleida, Spain
| | - Maria D Osuna
- Plant Protection Department, Extremadura Scientific and Technological Research Center (CICYTEX), Ctra. de AV, km 372, Badajoz, 06187, Guadajira, Spain
| | - Candelario Palma-Bautista
- Department of Agricultural Chemistry, Edaphology and Microbiology, University of Córdoba, 14014, Córdoba, Spain
| | | | - Rafael De Prado
- Department of Agricultural Chemistry, Edaphology and Microbiology, University of Córdoba, 14014, Córdoba, Spain
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Ioannou E, Papageorgiou AC, Labrou NE. Directed Evolution of Phi Class Glutathione Transferases Involved in Multiple-Herbicide Resistance of Grass Weeds and Crops. Int J Mol Sci 2022; 23:ijms23137469. [PMID: 35806486 PMCID: PMC9267659 DOI: 10.3390/ijms23137469] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/30/2022] [Accepted: 07/01/2022] [Indexed: 11/16/2022] Open
Abstract
The extensive application of herbicides in crop cultivation has indisputably led to the emergence of weed populations characterized by multiple herbicide resistance (MHR). This phenomenon is associated with the enhanced metabolism and detoxifying ability of endogenous enzymes, such as phi class glutathione transferases (GSTFs). In the present work, a library of mutant GSTFs was created by in vitro directed evolution via DNA shuffling. Selected gstf genes from the weeds Alopecurus myosuroides and Lolium rigidum, and the cereal crops Triticum durum and Hordeum vulgare were recombined to forge a library of novel chimeric GSTFs. The library was activity screened and the best-performing enzyme variants were purified and characterized. The work allowed the identification of enzyme variants that exhibit an eight-fold improvement in their catalytic efficiency, higher thermal stability (8.3 °C) and three-times higher inhibition sensitivity towards the herbicide butachlor. The crystal structures of the best-performing enzyme variants were determined by X-ray crystallography. Structural analysis allowed the identification of specific structural elements that are responsible for kcat regulation, thermal stability and inhibition potency. These improved novel enzymes hold the potential for utilization in biocatalysis and green biotechnology applications. The results of the present work contribute significantly to our knowledge of the structure and function of phi class plant GSTs and shed light on their involvement in the mechanisms of MHR.
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Affiliation(s)
- Elisavet Ioannou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, 11855 Athens, Greece;
| | | | - Nikolaos E. Labrou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, 11855 Athens, Greece;
- Correspondence:
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Pro-197-Ser Mutation and Cytochrome P450-Mediated Metabolism Conferring Resistance to Flucarbazone-Sodium in Bromus japonicus. PLANTS 2022; 11:plants11131641. [PMID: 35807593 PMCID: PMC9269166 DOI: 10.3390/plants11131641] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/15/2022] [Accepted: 06/20/2022] [Indexed: 11/17/2022]
Abstract
In crop fields, resistance to acetolactate synthase (ALS)-inhibiting herbicides found in many troublesome weed species, including Bromus japonicus Thunb, is a worldwide problem. In particular, the development of herbicide resistance in B. japonicus is a severe threat to wheat production in China. The purpose of this research was to investigate the physiological and molecular basis of B. japonicus resistance to flucarbazone-sodium. Dose-response analysis demonstrated that, compared with the susceptible B. japonicus (S) population, the resistant (R) population exhibited a 120-fold increase in flucarbazone-sodium resistance. Nucleotide sequence alignment of the ALS gene indicated that the Pro-197-Ser mutation in ALS was associated with resistance to flucarbazone-sodium in the R population. The results of a malathion pretreatment study showed that B. japonicus might also have remarkable cytochrome P450 monooxygenase (P450)-mediated metabolic resistance. This is the first report of a Pro-197-Ser mutation and P450-mediated metabolism conferring resistance to flucarbazone-sodium in B. japonicus.
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Identification of the most suitable reference gene for gene expression studies with development and abiotic stress response in Bromus sterilis. Sci Rep 2021; 11:13393. [PMID: 34183710 PMCID: PMC8238991 DOI: 10.1038/s41598-021-92780-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 06/11/2021] [Indexed: 01/15/2023] Open
Abstract
Bromus sterilis is an annual weedy grass, causing high yield losses in winter cereals. Frequent use of herbicides had led to the evolution of herbicide resistance in this species. Mechanisms underlying herbicide resistance in B. sterilis must be uncovered because this problem is becoming a global threat. qRT-PCR and the next-generation sequencing technologies can elucidate the resistance mechanisms. Although qRT-PCR can calculate precise fold changes, its preciseness depends on the expression of reference genes. Regardless of stable expression in any given condition, no gene can act as a universal reference gene. Hence, it is necessary to identify the suitable reference gene for each species. To our knowledge, there are no reports on the suitable reference gene in any brome species so far. Thus, in this paper, the stability of eight genes was evaluated using qRT-PCR experiments followed by expression stability ranking via five most commonly used software for reference gene selection. Our findings suggest using a combination of 18S rRNA and ACCase to normalise the qRT-PCR data in B. sterilis. Besides, reference genes are also recommended for different experimental conditions. The present study outcomes will facilitate future molecular work in B. sterilis and other related grass species.
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Sen MK, Hamouzová K, Mikulka J, Bharati R, Košnarová P, Hamouz P, Roy A, Soukup J. Enhanced metabolism and target gene overexpression confer resistance against acetolactate synthase-inhibiting herbicides in Bromus sterilis. PEST MANAGEMENT SCIENCE 2021; 77:2122-2128. [PMID: 33332713 DOI: 10.1002/ps.6241] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/14/2020] [Accepted: 12/17/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND Intensive application of acetolactate synthase (ALS)-inhibiting herbicides has resulted in herbicide-resistance in many weeds, including Bromus sterilis. The present study was conducted to identify the mechanisms conferring resistance to ALS-inhibiting herbicides in a Bromus sterilis biotype. RESULTS Dose-response studies revealed the resistant biotype to be 288 times less sensitive to pyroxsulam than the susceptible biotype. Furthermore, experiment with a single-dose, proved this biotype was also cross-resistant to propoxycarbazone, iodosulfuron plus mesosulfuron and sulfosulfuron. Prior treatment with malathion, a known inhibitor of cytochrome P450s, reduced the level of resistance to pyroxsulam. No mutations were detected from the partial ALS gene sequencing. Flow cytometry and chromosome counting rejected ploidy level variation between the susceptible and resistant biotypes. Relative copy number variation ruled out gene amplification. Quantitative real-time polymerase chain reaction (PCR) detected a significant difference in ALS gene expression between the susceptible and resistant biotypes. CONCLUSIONS Target gene overexpression and enhanced metabolism by cytochrome P450s are likely mechanisms of resistance to pyroxsulam in Bromus sterilis. The current findings highlight the need to monitor additional brome populations for herbicide resistance in Europe and endorse the need for alternate herbicides in integrated weed management to delay the possible evolution of herbicide resistance in these species. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Madhab Kumar Sen
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Katerina Hamouzová
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Jakub Mikulka
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Rohit Bharati
- Department of Crop Sciences and Agroforestry, The Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Pavlina Košnarová
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Pavel Hamouz
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Amit Roy
- Excellent Team for Mitigation (ETM), Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Josef Soukup
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
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No fitness cost associated with Asn-2041-Ile mutation in winter wild oat (Avena ludoviciana) seed germination under various environmental conditions. Sci Rep 2021; 11:1572. [PMID: 33452441 PMCID: PMC7810857 DOI: 10.1038/s41598-021-81310-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 01/04/2021] [Indexed: 11/21/2022] Open
Abstract
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.
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Scarabel L, Panozzo S, Loddo D, Mathiassen SK, Kristensen M, Kudsk P, Gitsopoulos T, Travlos I, Tani E, Chachalis D, Sattin M. Diversified Resistance Mechanisms in Multi-Resistant Lolium spp. in Three European Countries. FRONTIERS IN PLANT SCIENCE 2020; 11:608845. [PMID: 33384707 PMCID: PMC7769757 DOI: 10.3389/fpls.2020.608845] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/20/2020] [Indexed: 06/12/2023]
Abstract
Annual ryegrass species (Lolium spp.) infest cereal crops worldwide. Ryegrass populations with multiple resistance to the acetyl coenzyme A carboxylase (ACCase) and acetolactate synthase (ALS) inhibitors are an increasing problem in several European countries. We investigated the resistance pattern and level of resistance in ryegrass populations collected in Denmark, Greece and Italy and studied the diversity of mechanisms endowing resistance, both target-site and metabolism based. All populations showed high resistance indexes (RI) to the ALS inhibitors, iodosufuron-methyl-sodium + mesosulfuron-methyl (RI from 8 to 70), whereas the responses to the two ACCase inhibitors, clodinafop-propargyl and pinoxaden, differed. The Greek and Italian populations were moderately to highly resistant to clodinafop (RI > 8) and showed low to moderate resistance to pinoxaden (RI ranged from 3 to 13) except for one Italian population. In contrast, the Danish Lolium populations showed low to moderate resistance to clodinafop (RI ranged from 2 to 7) and only one population was resistant to pinoxaden. Different mutant ACCase alleles (Leu1781, Cys2027, Asn2041, Val2041, Gly2078, Arg2088, Ala2096) and ALS alleles (Gly122, Ala197, Gln197, Leu197, Ser197, Thr197, Val205, Asn376, Glu376, Leu574) endowing resistance were detected in the Greek and Italian populations. In several plants, no mutated ALS and ACCase alleles were found showing a great heterogeneity within and among the Greek and Italian populations. Conversely, no mutant ACCase alleles were identified in the four Danish populations and only one mutant ALS allele (Leu574) was detected in two Danish populations. The expression level of nitronate monooxygenase (NMO), glutathione S-transferase (GST) and cytochrome P450s (CYP72A1 and CYP72A2) varied broadly among populations and individual plants within the populations. Constitutive up-regulation of GST, CYP72A1 and CYP72A2 was detected in resistant plants respect to susceptible plants in one Danish and one Italian population. It appears that the mechanisms underlying resistance are rather complex and diversified among Lolium spp. populations from the three countries, coevolution of both target-site resistance and metabolic based herbicide resistance appears to be a common feature in Denmark and Italy. This must be considered and carefully evaluated in adopting resistance management strategies to control Lolium spp. in cereal crops.
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Affiliation(s)
- Laura Scarabel
- Institute for Sustainable Plant Protection (IPSP-CNR), National Research Council of Italy, Padua, Italy
| | - Silvia Panozzo
- Institute for Sustainable Plant Protection (IPSP-CNR), National Research Council of Italy, Padua, Italy
| | - Donato Loddo
- Institute for Sustainable Plant Protection (IPSP-CNR), National Research Council of Italy, Padua, Italy
| | | | | | - Per Kudsk
- Department of Agroecology, Aarhus University, Flakkebjerg, Denmark
| | - Thomas Gitsopoulos
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization-Demeter, Thessaloniki, Greece
| | - Ilias Travlos
- Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Eleni Tani
- Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | | | - Maurizio Sattin
- Institute for Sustainable Plant Protection (IPSP-CNR), National Research Council of Italy, Padua, Italy
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Yu X, Tang W, Yang Y, Zhang J, Lu Y. Comparative Transcriptome Analysis Revealing the Different Germination Process in Aryloxyphenoxypropionate-Resistant and APP-Susceptible Asia Minor Bluegrass ( Polypogon fugax). PLANTS 2020; 9:plants9091191. [PMID: 32932586 PMCID: PMC7569813 DOI: 10.3390/plants9091191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/08/2020] [Accepted: 09/08/2020] [Indexed: 11/25/2022]
Abstract
Herbicide-resistant mutations are predicted to exhibit fitness cost under herbicide-free conditions. Asia minor bluegrass (Polypogon fugax) is a common weed species in the winter crops. Our previous study established a P. fugax accession (LR) resistant to aryloxyphenoxypropionate (APP) herbicides, which also exhibited germination delay relative to the susceptible accession (LS). A comparative transcriptome was conducted to analyze the gene expression profile of LS and LR at two germination time points. A total of 11,856 and 23,123 differentially expressed genes (DEGs) were respectively identified in LS and LR. Most DEGs were involved in lipid metabolism, carbohydrate metabolism, amino acid metabolism, and secondary metabolites biosynthesis. Twenty-four genes involved in carbohydrate and fatty acid metabolism had higher relative expression levels in LS than LR during germination. Nine genes involved in gibberellin (GA) and abscisic acid (ABA) signal transduction showed different expression patterns in LS and LR, consistent with their different sensitivity to exogenous hormones treatments. This study first provided insight into transcriptional changes and interaction in the seed germination process of P. fugax. It compared the differential expression profile between APP herbicides resistance and susceptible accessions during germination, which contributed to understanding the association between herbicide resistance and fitness cost.
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