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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: 3] [Impact Index Per Article: 3.0] [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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2
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Cai L, Comont D, MacGregor D, Lowe C, Beffa R, Neve P, Saski C. The blackgrass genome reveals patterns of non-parallel evolution of polygenic herbicide resistance. THE NEW PHYTOLOGIST 2023; 237:1891-1907. [PMID: 36457293 PMCID: PMC10108218 DOI: 10.1111/nph.18655] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 11/23/2022] [Indexed: 05/31/2023]
Abstract
Globally, weedy plants are a major constraint to sustainable crop production. Much of the success of weeds rests with their ability to rapidly adapt in the face of human-mediated management of agroecosystems. Alopecurus myosuroides (blackgrass) is a widespread and impactful weed affecting agriculture in Europe. Here we report a chromosome-scale genome assembly of blackgrass and use this reference genome to explore the genomic/genetic basis of non-target site herbicide resistance (NTSR). Based on our analysis of F2 seed families derived from two distinct blackgrass populations with the same NTSR phenotype, we demonstrate that the trait is polygenic and evolves from standing genetic variation. We present evidence that selection for NTSR has signatures of both parallel and non-parallel evolution. There are parallel and non-parallel changes at the transcriptional level of several stress- and defence-responsive gene families. At the genomic level, however, the genetic loci underpinning NTSR are different (non-parallel) between seed families. We speculate that variation in the number, regulation and function of stress- and defence-related gene families enable weedy species to rapidly evolve NTSR via exaptation of genes within large multi-functional gene families. These results provide novel insights into the potential for, and nature of plant adaptation in rapidly changing environments.
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Affiliation(s)
- Lichun Cai
- Department of Plant and Environmental SciencesClemson UniversityClemsonSC29634USA
| | - David Comont
- Protecting Crops and the EnvironmentRothamsted ResearchHarpenden, HertfordshireAL5 2JQUK
| | - Dana MacGregor
- Protecting Crops and the EnvironmentRothamsted ResearchHarpenden, HertfordshireAL5 2JQUK
| | - Claudia Lowe
- Protecting Crops and the EnvironmentRothamsted ResearchHarpenden, HertfordshireAL5 2JQUK
| | - Roland Beffa
- Bayer Crop SciencesIndustriepark Höchst65926Frankfurt am MainGermany
- Königsteiner Weg 465835LiederbachGermany
| | - Paul Neve
- Protecting Crops and the EnvironmentRothamsted ResearchHarpenden, HertfordshireAL5 2JQUK
- Department of Plant and Environmental SciencesUniversity of CopenhagenHøjbakkegård Allé 13Tåstrup2630Denmark
| | - Christopher Saski
- Department of Plant and Environmental SciencesClemson UniversityClemsonSC29634USA
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3
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Milani A, Panozzo S, Pinton S, Danielis RA, Sattin M, Scarabel L. Diversity and Spread of Acetolactate Synthase Allelic Variants at Position 574 Endowing Resistance in Amaranthus hybridus in Italy. PLANTS (BASEL, SWITZERLAND) 2023; 12:332. [PMID: 36679045 PMCID: PMC9860533 DOI: 10.3390/plants12020332] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 06/17/2023]
Abstract
Poor control of Amaranthus spp. with herbicides inhibiting acetolactate synthase (ALS) has been observed for several years in soybean fields in north-eastern Italy, but to date only a few ALS-resistant populations have been confirmed. An extensive sampling of putatively resistant Amaranthus accessions was completed in the Friuli Venezia Giulia region, across an arable land area of about 3000 km2. In total, 58 accessions were tested to confirm their resistance status, recognize the Amaranthus species, identify the mutant ALS alleles endowing the resistance and determine the efficacy of 3 pre-emergence herbicides. Most accessions resulted in cross-resistance to thifensulfuron-methyl and imazamox. Genomic DNA were extracted from single seeds with a newly developed protocol; an allele-specific PCR assay revealed the presence of the 574-leucine in 20 accessions, of the 574-methionine in 22, and of both alleles in 9 accessions. The two variants showed a different spatial distribution. All resistant populations were ascribed to A. hybridus. A. hybridus resistant to ALS herbicides is well-established in this Italian region and its resistance is due to two ALS mutant alleles. Metribuzin, clomazone and metobromuron can be used as alternative herbicides to be applied in pre-emergence and they should be integrated into the management strategies to limit the spread of resistance.
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Affiliation(s)
- Andrea Milani
- Institute for Sustainable Plant Protection (IPSP-CNR), 35020 Legnaro, Italy
| | - Silvia Panozzo
- Institute for Sustainable Plant Protection (IPSP-CNR), 35020 Legnaro, Italy
| | - Samuele Pinton
- Institute for Sustainable Plant Protection (IPSP-CNR), 35020 Legnaro, Italy
| | - Renato Antonio Danielis
- Regional Agency for Rural Development of Friuli Venezia Giulia (ERSA), 33050 Pozzuolo del Friuli, Italy
| | - Maurizio Sattin
- Institute for Sustainable Plant Protection (IPSP-CNR), 35020 Legnaro, Italy
| | - Laura Scarabel
- Institute for Sustainable Plant Protection (IPSP-CNR), 35020 Legnaro, Italy
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Spring JF, Revolinski SR, Young FL, Lyon DJ, Burke IC. Weak population differentiation and high diversity in Salsola tragus in the inland Pacific Northwest, USA. PEST MANAGEMENT SCIENCE 2022; 78:4728-4740. [PMID: 35872633 DOI: 10.1002/ps.7093] [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: 03/11/2022] [Revised: 07/13/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Salsola tragus is a widespread and problematic weed of semi-arid wheat production globally, and in the inland Pacific Northwest region of the USA. The species exhibits high levels of phenotypic diversity across its range and, at least in California USA, previous work has described cryptic diversity comprising a multi-species complex. Such cryptic diversity could suggest the potential for a differential response to management inputs between groups, and have important implications for the spread of herbicide resistance or other adaptive traits within populations. We used a genotyping-by-sequencing approach to characterize the population structure of S. tragus in the inland Pacific Northwest. RESULTS Our results indicated that the population in this region is comprised of a single, tetraploid species (S. tragus sensu latu) with weak population structure on a regional scale. Isolation-by-distance appears to be the primary pattern of structure, but an independent set of weakly differentiated clusters of unknown origin were also apparent, along with a mixed mating system and high levels of largely unstructured genetic diversity. CONCLUSIONS Despite considerable phenotypic variability within S. tragus in the region, agronomic weed managers can likely consider it as a single entity across the region, rather than a collection of cryptic subgroups with possible differential responses to management inputs or agroecosystem conditions. A lack of strong barriers to migration and gene flow mean that adaptive traits, such as herbicide resistance, can be expected to spread rapidly through populations across the region. © 2022 Society of Chemical Industry.
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Affiliation(s)
- John F Spring
- Oregon State University Central Oregon Agricultural Research and Extension Center, Madras, OR, USA
| | - Samuel R Revolinski
- Washington State University Department of Crop and Soil Sciences, Pullman, WA, USA
| | - Frank L Young
- USDA-ARS Northwest Sustainable Agroecosystems Research Unit, Pullman, WA, USA
| | - Drew J Lyon
- Washington State University Department of Crop and Soil Sciences, Pullman, WA, USA
| | - Ian C Burke
- Washington State University Department of Crop and Soil Sciences, Pullman, WA, USA
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Tsuruta SI, Srithawong S, Sakuanrungsirikul S, Ebina M, Kobayashi M, Terajima Y, Tippayawat A, Ponragdee W. Erianthus germplasm collection in Thailand: genetic structure and phylogenetic aspects of tetraploid and hexaploid accessions. BMC PLANT BIOLOGY 2022; 22:45. [PMID: 35065606 PMCID: PMC8783461 DOI: 10.1186/s12870-021-03418-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 12/24/2021] [Indexed: 06/05/2023]
Abstract
BACKGROUND The genus Erianthus, which belongs to the "Saccharum complex", includes C4 warm-season grasses. Erianthus species are widely distributed throughout Southeast Asia, East Asia and South Asia. Erianthus arundinaceus (Retz.) Jeswiet is highly adaptable to the environment, has a high percentage of dry matter, and is highly productive. Recently, this species has attracted attention as a novel bioenergy crop and as a breeding material for sugarcane improvement. Such interest in E. arundinaceus has accelerated the collection and conservation of its genetic resources, mainly in Asian countries, and also evaluation of morphological, agricultural, and cytogenetic features in germplasm collections. In Thailand, genetic resources of E. arundinaceus have been collected over the past 20 years and their phenotypic traits have been evaluated. However, the genetic differences and relatedness of the germplasms are not fully understood. RESULTS A set of 41 primer pairs for nuclear simple sequence repeats (SSRs) developed from E. arundinaceus were used to assess the genetic diversity of 121 Erianthus germplasms collected in Thailand; of these primer pairs, 28 detected a total of 316 alleles. A Bayesian clustering approach with these alleles classified the accessions into four main groups, generally corresponding to the previous classification based on phenotypic analysis. The results of principal coordinate analysis and phylogenetic analysis of the 121 accessions on the basis of the SSR markers showed the same trend as Bayesian clustering, whereas sequence variations of three non-coding regions of chloroplast DNA revealed eight haplotypes among the accessions. The analysis of genetic structure and phylogenetic relationships, however, found some accessions whose classification contradicted the results of previous phenotypic classification. CONCLUSIONS The molecular approach used in this study characterized the genetic diversity and relatedness of Erianthus germplasms collected across Thailand. This knowledge would allow efficient maintenance and conservation of the genetic resources of this grass and would help to use Erianthus species as breeding materials for development of novel bioenergy crops and sugarcane improvement.
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Affiliation(s)
- Shin-Ichi Tsuruta
- Tropical Agriculture Research Front, Japan International Research Center for Agricultural Sciences (JIRCAS), Ishigaki, Okinawa, 907-0002, Japan.
| | - Suparat Srithawong
- Department of Agriculture, Khon Kaen Field Crops Research Center (KKFCRC), Khon Kaen, 40000, Thailand
- Present address: Biotechnology Research and Development Office (BIRDO), Department of Agriculture, Pathum Thani, 12110, Thailand
| | | | - Masumi Ebina
- Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization (NARO), Nasushiobara, Tochigi, 329-2793, Japan
| | - Makoto Kobayashi
- Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization (NARO), Nasushiobara, Tochigi, 329-2793, Japan
| | - Yoshifumi Terajima
- Tropical Agriculture Research Front, Japan International Research Center for Agricultural Sciences (JIRCAS), Ishigaki, Okinawa, 907-0002, Japan
| | - Amarawan Tippayawat
- Department of Agriculture, Khon Kaen Field Crops Research Center (KKFCRC), Khon Kaen, 40000, Thailand
- Present address: Department of Agriculture, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Werapon Ponragdee
- Department of Agriculture, Khon Kaen Field Crops Research Center (KKFCRC), Khon Kaen, 40000, Thailand
- Present address: Field and Renewable Energy Crops Research Institute (FCRI), Department of Agriculture, Bangkok, 10900, Thailand
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6
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Development of simplex and multiplex RT-qPCR assays for the detection of three cryptic viruses of black-grass (Alopecurus myosuroides). J Virol Methods 2021; 300:114389. [PMID: 34848282 DOI: 10.1016/j.jviromet.2021.114389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 06/17/2021] [Accepted: 11/26/2021] [Indexed: 11/22/2022]
Abstract
Simplex and multiplex RT-qPCR assays were developed for Alopecurus myosuroides partitivirus 1 (AMPV1), Alopecurus myosuroides partitivirus 2 (AMPV2) and Alopecurus myosuroides varicosavirus 1 (AMVV1), and compared to the existing conventional PCR assays. All assays had a high specificity and their sensitivity was increased compared to the conventional RT-PCR assays. As viral quantification is an important element in comparative experiments, the effect of high- and low-temperature drying treatments, prior to RNA extraction and analysis, was studied and optimised. AMVV1 detection was reduced by both drying treatments, but particularly by the high-temperature. AMPV1 and AMPV2 detection on the other hand was not impeded by the drying treatments, and enables standardisation of plant tissue prior to extraction, in particular for quantitative analysis.
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7
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Milani A, Lutz U, Galla G, Scarabel L, Weigel D, Sattin M. Population structure and evolution of resistance to acetolactate synthase (ALS)-inhibitors in Amaranthus tuberculatus in Italy. PEST MANAGEMENT SCIENCE 2021; 77:2971-2980. [PMID: 33631029 PMCID: PMC8251816 DOI: 10.1002/ps.6336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/12/2021] [Accepted: 02/25/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Before 2010, Amaranthus tuberculatus (Moq.) J. D. Sauer was barely known to farmers and stakeholders in Italy. Since then, several populations resistant to acetolactate synthase (ALS)-inhibiting herbicides have been collected. In most populations, a known target site resistance-endowing mutation was found, a Trp to Leu substitution at position 574 of the ALS gene, but it was unclear whether they had evolved resistance independently or not. The aims of the work were (i) to elucidate the population structure of Italian ALS-resistant A. tuberculatus populations, and (ii) to analyze the ALS haplotypes of the various populations to determine whether resistance arose multiple times independently. RESULTS In order to determine the population structure of eight A. tuberculatus populations, eight previously described microsatellite loci were used. Two ancestors were found: three populations derived from one, and five from the other. In the 4-kb ALS region of the genome, including the 2-kb coding region, 389 single nucleotide polymorphisms were found. In silico haplotype estimation was used to reconstruct the sequence of three distinct haplotypes carrying the Trp574Leu mutation. In addition, no mutation was found in 83% of plants of a single population. CONCLUSIONS (i) Resistance must have arisen independently at least three times; (ii) at least one population was already resistant to ALS inhibitors when introduced in Italy; (iii) a single haplotype with a Trp574Leu mutation was shared among six populations, probably because of broad seed dispersal; and (iv) one population likely evolved nontarget site ALS inhibitors resistance. © 2021 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Andrea Milani
- Institute for Sustainable Plant Protection (IPSP‐CNR)LegnaroItaly
| | - Ulrich Lutz
- Max Planck Institute for Developmental BiologyTübingenGermany
| | | | - Laura Scarabel
- Institute for Sustainable Plant Protection (IPSP‐CNR)LegnaroItaly
| | - Detlef Weigel
- Max Planck Institute for Developmental BiologyTübingenGermany
| | - Maurizio Sattin
- Institute for Sustainable Plant Protection (IPSP‐CNR)LegnaroItaly
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8
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Dixon A, Comont D, Slavov GT, Neve P. Population genomics of selectively neutral genetic structure and herbicide resistance in UK populations of Alopecurus myosuroides. PEST MANAGEMENT SCIENCE 2021; 77:1520-1529. [PMID: 33155426 DOI: 10.1002/ps.6174] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 10/22/2020] [Accepted: 11/06/2020] [Indexed: 06/07/2023]
Abstract
BACKGROUND Alopecurus myosuroides (blackgrass) is a major weed in Europe with known resistance to multiple herbicide modes of action. In the UK, there is evidence that blackgrass has undergone a range expansion. In this paper, genotyping-by-sequencing and population-level herbicide resistance phenotypes are used to explore spatial patterns of selectively neutral genetic variation and resistance. We also perform a preliminary genome-wide association study (GWAS) and genomic prediction analysis to evaluate the potential of these approaches for investigating nontarget site herbicide resistance. RESULTS Blackgrass was collected from 47 fields across the British Isles and up to eight plants per field population (n = 369) were genotyped by Restriction site-associated DNA (RAD)-sequencing. A total of 20 426 polymorphic loci were identified and used for population genetic analyses. Phenotypic assays revealed significant variation in herbicide resistance between populations. Population structure was weak (FST = 0.024-0.048), but spatial patterns were consistent with an ongoing westward and northward range expansion. We detected strong and consistent Wahlund effects (FIS = 0.30). There were no spatial patterns of herbicide resistance or evidence for confounding with population structure. Using a combination of population-level GWAS and genomic prediction we found that the top 20, 200, and 2000 GWAS loci had higher predictive abilities for fenoxaprop resistance compared to all markers. CONCLUSION There is likely extensive human-mediated gene flow between field populations of the weed blackgrass at a national scale. The lack of confounding of adaptive and neutral genetic variation can enable future, more extensive GWAS analyses to identify the genetic architecture of evolved herbicide resistance. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Andrea Dixon
- Rothamsted Research, West Common, Harpenden, Hertfordshire, UK
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - David Comont
- Rothamsted Research, West Common, Harpenden, Hertfordshire, UK
| | - Gancho T Slavov
- Rothamsted Research, West Common, Harpenden, Hertfordshire, UK
- Scion, Rotorua, New Zealand
| | - Paul Neve
- Rothamsted Research, West Common, Harpenden, Hertfordshire, UK
- Agriculture & Horticulture Development Board, Warwickshire, UK
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Leon RG, Dunne JC, Gould F. The role of population and quantitative genetics and modern sequencing technologies to understand evolved herbicide resistance and weed fitness. PEST MANAGEMENT SCIENCE 2021; 77:12-21. [PMID: 32633005 PMCID: PMC7754128 DOI: 10.1002/ps.5988] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 06/26/2020] [Accepted: 07/06/2020] [Indexed: 05/11/2023]
Abstract
Evolution of resistance to multiple herbicides with different sites of action and of nontarget site resistance (NTSR) often involves multiple genes. Thus, single-gene analyses, typical in studies of target site resistance, are not sufficient for understanding the genetic architecture and dynamics of NTSR and multiple resistance. The genetics of weed adaptation to varied agricultural environments is also generally expected to be polygenic. Recent advances in whole-genome sequencing as well as bioinformatic and statistical tools have made it possible to use population and quantitative genetics methods to expand our understanding of how resistance and other traits important for weed adaptation are genetically controlled at the individual and population levels, and to predict responses to selection pressure by herbicides and other environmental factors. The use of tools such as quantitative trait loci mapping, genome-wide association studies, and genomic prediction will allow pest management scientists to better explain how pests adapt to control tools and how specific genotypes thrive and spread across agroecosystems and other human-disturbed systems. The challenge will be to use this knowledge in developing integrated weed management systems that inhibit broad resistance to current and future weed-control methods. © 2020 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Ramon G Leon
- Department of Crop and Soil SciencesNorth Carolina State UniversityRaleighNCUSA
| | - Jeffrey C Dunne
- Department of Crop and Soil SciencesNorth Carolina State UniversityRaleighNCUSA
| | - Fred Gould
- Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNCUSA
- Genetic Engineering and Society CenterNorth Carolina State UniversityRaleighNCUSA
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10
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Martin SL, Benedict L, Wei W, Sauder CA, Beckie HJ, Hall LM. High gene flow maintains genetic diversity following selection for high EPSPS copy number in the weed kochia (Amaranthaceae). Sci Rep 2020; 10:18864. [PMID: 33139774 PMCID: PMC7608611 DOI: 10.1038/s41598-020-75345-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 10/05/2020] [Indexed: 02/06/2023] Open
Abstract
Kochia, a major weed species, has evolved resistance to four herbicide modes of action. Herbicide resistance appears to spread quickly, which could result in diminished standing genetic variation, reducing the ability of populations to adapt further. Here we used double digest restriction enzyme associated sequencing to determine the level of gene flow among kochia populations and whether selection for glyphosate resistance reduces genetic variation. Canadian Prairie populations show little to no genetic differentiation (FST = 0.01) and no correlation between genetic and geographic distance (r2 = - 0.02 p = 0.56), indicating high gene flow and no population structure. There is some evidence that kochia populations are genetically depauperate compared to other weed species, but genetic diversity did not differ between glyphosate susceptible and resistant populations or individuals. The inbreeding coefficients suggest there are 23% fewer heterozygotes in these populations than expected with random mating, and no variation was found within the chloroplast. These results indicate that any alleles for herbicide resistance can be expected to spread quickly through kochia populations, but there is little evidence this spread will reduce the species' genetic variation or limit the species' ability to respond to further selection pressure.
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Affiliation(s)
- Sara L Martin
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON, Canada.
| | - Leshawn Benedict
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON, Canada
| | - Wei Wei
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Connie A Sauder
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON, Canada
| | - Hugh J Beckie
- Australian Herbicide Resistance Initiative, School of Agriculture and Environment, University of Western Australia, Perth, Australia
| | - Linda M Hall
- Agricultural Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
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11
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Herbicide resistance: Development of wheat production systems and current status of resistant weeds in wheat cropping systems. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.cj.2019.09.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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12
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Liu C, Scursoni JA, Moreno R, Zelaya IA, Muñoz MS, Kaundun SS. An individual-based model of seed- and rhizome-propagated perennial plant species and sustainable management of Sorghum halepense in soybean production systems in Argentina. Ecol Evol 2019; 9:10017-10028. [PMID: 31534710 PMCID: PMC6745659 DOI: 10.1002/ece3.5578] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 07/23/2019] [Accepted: 07/28/2019] [Indexed: 11/30/2022] Open
Abstract
Perennial plants which propagate through both seeds and rhizomes are common in agricultural and nonagricultural systems. Due to their multifaceted life cycle, few population models are available for studying such species. We constructed a novel individual-based model to examine the effects of ecological, evolutionary, and anthropogenic factors on the population dynamics of perennial species. To exemplify the application of the model, we presented a case study of an important weed, Sorghum halepense (L.) Pers. (Johnsongrass), in soybean productions in Argentina. The model encompasses a full perennial weed life cycle with both sexual (seeds) and asexual (rhizomes) propagations. The evolution of herbicide resistance was modeled based on either single genes or quantitative effects. Field experiments were conducted in the species' native environment in Argentina to parameterize the model. Simulation results showed that resistance conferred by single-gene mutations was predominantly affected by the initial frequency of resistance alleles and the associated fitness cost. Population dynamics were influenced by evolved resistance, soil tillage, and rhizome fecundity. Despite the pivotal role of rhizomes in driving the population dynamics of Johnsongrass, most herbicides target the aboveground biomass, and chemical solutions to control rhizomes are still very limited. To maintain effective (short-term) and sustainable (long-term) weed management, it is recommended to combine soil tillage with herbicide applications for suppressing the rhizomes and delaying the evolution of resistance. This novel model of seed- and rhizome-propagated plants will also be a useful tool for studying the evolutionary processes of other perennial weeds, cash crops, and invasive species.
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Affiliation(s)
- Chun Liu
- Herbicide BioscienceSyngenta LtdBracknellUK
| | - Julio A. Scursoni
- Departamento de Producción Vegetal, Facultad de AgronomíaUniversidad de Buenos AiresBuenos AiresArgentina
| | - Raúl Moreno
- Product BiologySyngenta ArgentinaBuenos AiresArgentina
| | - Ian A. Zelaya
- Product BiologySyngenta ColombiaSanta Fé de BogotáColombia
| | - María Sol Muñoz
- Departamento de Producción Vegetal, Facultad de AgronomíaUniversidad de Buenos AiresBuenos AiresArgentina
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Baucom RS. Evolutionary and ecological insights from herbicide-resistant weeds: what have we learned about plant adaptation, and what is left to uncover? THE NEW PHYTOLOGIST 2019; 223:68-82. [PMID: 30710343 DOI: 10.1111/nph.15723] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 01/22/2019] [Indexed: 06/09/2023]
Abstract
The evolution of herbicide resistance in crop weeds presents one of the greatest challenges to agriculture and the production of food. Herbicide resistance has been studied for more than 60 yr, in the large part by researchers seeking to design effective weed control programs. As an outcome of this work, various unique questions in plant adaptation have been addressed. Here, I collate recent research on the herbicide-resistant problem in light of key questions and themes in evolution and ecology. I highlight discoveries made on herbicide-resistant weeds in three broad areas - the genetic basis of adaptation, evolutionary constraints, experimental evolution - and similarly discuss questions left to be answered. I then develop how one would use herbicide-resistance evolution as a model for studying eco-evolutionary dynamics within a community context. My overall goals are to highlight important findings in the weed science literature that are relevant to themes in plant adaptation and to stimulate the use of herbicide-resistant plants as models for addressing key questions within ecology and evolution.
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Affiliation(s)
- Regina S Baucom
- Ecology and Evolutionary Biology Department, University of Michigan, 4034 Biological Sciences Building, Ann Arbor, MI, 48109, USA
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Vila-Aiub MM, Yu Q, Powles SB. Do plants pay a fitness cost to be resistant to glyphosate? THE NEW PHYTOLOGIST 2019; 223:532-547. [PMID: 30737790 DOI: 10.1111/nph.15733] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 01/30/2019] [Indexed: 06/09/2023]
Abstract
We reviewed the literature to understand the effects of glyphosate resistance on plant fitness at the molecular, biochemical and physiological levels. A number of correlations between enzyme characteristics and glyphosate resistance imply the existence of a plant fitness cost associated with resistance-conferring mutations in the glyphosate target enzyme, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS). These biochemical changes result in a tradeoff between the glyphosate resistance of the EPSPS enzyme and its catalytic activity. Mutations that endow the highest resistance are more likely to decrease catalytic activity by reducing the affinity of EPSPS for its natural substrate, and/or slowing the velocity of the enzyme reaction, and are thus very likely to endow a substantial plant fitness cost. Prediction of fitness costs associated with EPSPS gene amplification and overexpression can be more problematic. The validity of cost prediction based on the theory of evolution of gene expression and resource allocation has been cast into doubt by contradictory experimental evidence. Further research providing insights into the role of the EPSPS cassette in weed adaptation, and estimations of the energy budget involved in EPSPS amplification and overexpression are required to understand and predict the biochemical and physiological bases of the fitness cost of glyphosate resistance.
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Affiliation(s)
- Martin M Vila-Aiub
- Australian Herbicide Resistance Initiative (AHRI) - School of Agriculture & Environment, University of Western Australia (UWA), Crawley, 6009, Western Australia, Australia
- IFEVA - CONICET - Faculty of Agronomy, Department of Ecology, University of Buenos Aires (UBA), Buenos Aires, 1417, Argentina
| | - Qin Yu
- Australian Herbicide Resistance Initiative (AHRI) - School of Agriculture & Environment, University of Western Australia (UWA), Crawley, 6009, Western Australia, Australia
| | - Stephen B Powles
- Australian Herbicide Resistance Initiative (AHRI) - School of Agriculture & Environment, University of Western Australia (UWA), Crawley, 6009, Western Australia, Australia
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15
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Alvarado-Serrano DF, Van Etten ML, Chang SM, Baucom RS. The relative contribution of natural landscapes and human-mediated factors on the connectivity of a noxious invasive weed. Heredity (Edinb) 2018; 122:29-40. [PMID: 29967398 DOI: 10.1038/s41437-018-0106-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/16/2018] [Accepted: 05/17/2018] [Indexed: 01/20/2023] Open
Abstract
Examining how the landscape may influence gene flow is at the forefront of understanding population differentiation and adaptation. Such understanding is crucial in light of ongoing environmental changes and the elevated risk of ecosystems alteration. In particular, knowledge of how humans may influence population structure is imperative to allow for informed decisions in management and conservation as well as to gain a better understanding of anthropogenic impacts on the interplay between gene flow, genetic drift, and selection. Here, we use genome-wide molecular markers to characterize the population genetic structure and connectivity of Ipomoea purpurea (Convolvulaceae), a noxious invasive weed. We, likewise, assess the interaction between natural and human-driven influences on genetic differentiation among populations. Our analyses find that human population density is an important predictor of pairwise population differentiation, suggesting that the agricultural and/or horticultural trade may be involved in maintaining some level of connectivity across distant agricultural fields. Climatic variation appears as an additional predictor of genetic connectivity in this species. We discuss the implications of these results and highlight future research needed to disentangle the mechanistic processes underlying population connectivity of weeds.
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Affiliation(s)
- Diego F Alvarado-Serrano
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University, 2020E Biological Science Building, Ann Arbor, MI, 48109-1085, USA.
| | - Megan L Van Etten
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University, 2020E Biological Science Building, Ann Arbor, MI, 48109-1085, USA
| | - Shu-Mei Chang
- Department of Plant Biology, University of Georgia, Rm 3613; 2502 Miller Plant Sciences, Athens, GA, 30602-7271, USA
| | - Regina S Baucom
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University, 2020E Biological Science Building, Ann Arbor, MI, 48109-1085, USA
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Küpper A, Manmathan HK, Giacomini D, Patterson EL, McCloskey WB, Gaines TA. Population Genetic Structure in Glyphosate-Resistant and -Susceptible Palmer Amaranth ( Amaranthus palmeri) Populations Using Genotyping-by-sequencing (GBS). FRONTIERS IN PLANT SCIENCE 2018; 9:29. [PMID: 29422910 PMCID: PMC5788914 DOI: 10.3389/fpls.2018.00029] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 01/09/2018] [Indexed: 05/25/2023]
Abstract
Palmer amaranth (Amaranthus palmeri) is a major weed in United States cotton and soybean production systems. Originally native to the Southwest, the species has spread throughout the country. In 2004 a population of A. palmeri was identified with resistance to glyphosate, a herbicide heavily relied on in modern no-tillage and transgenic glyphosate-resistant (GR) crop systems. This project aims to determine the degree of genetic relatedness among eight different populations of GR and glyphosate-susceptible (GS) A. palmeri from various geographic regions in the United States by analyzing patterns of phylogeography and diversity to ascertain whether resistance evolved independently or spread from outside to an Arizona locality (AZ-R). Shikimic acid accumulation and EPSPS genomic copy assays confirmed resistance or susceptibility. With a set of 1,351 single nucleotide polymorphisms (SNPs), discovered by genotyping-by-sequencing (GBS), UPGMA phylogenetic analysis, principal component analysis, Bayesian model-based clustering, and pairwise comparisons of genetic distances were conducted. A GR population from Tennessee and two GS populations from Georgia and Arizona were identified as genetically distinct while the remaining GS populations from Kansas, Arizona, and Nebraska clustered together with two GR populations from Arizona and Georgia. Within the latter group, AZ-R was most closely related to the GS populations from Kansas and Arizona followed by the GR population from Georgia. GR populations from Georgia and Tennessee were genetically distinct from each other. No isolation by distance was detected and A. palmeri was revealed to be a species with high genetic diversity. The data suggest the following two possible scenarios: either glyphosate resistance was introduced to the Arizona locality from the east, or resistance evolved independently in Arizona. Glyphosate resistance in the Georgia and Tennessee localities most likely evolved separately. Thus, modern farmers need to continue to diversify weed management practices and prevent seed dispersal to mitigate herbicide resistance evolution in A. palmeri.
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Affiliation(s)
- Anita Küpper
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States
| | - Harish K. Manmathan
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States
| | - Darci Giacomini
- Department of Crop Sciences, University of Illinois at Urbana–Champaign, Urbana, IL, United States
| | - Eric L. Patterson
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States
| | | | - Todd A. Gaines
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States
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Han H, Vila-Aiub MM, Jalaludin A, Yu Q, Powles SB. A double EPSPS gene mutation endowing glyphosate resistance shows a remarkably high resistance cost. PLANT, CELL & ENVIRONMENT 2017; 40:3031-3042. [PMID: 28910491 DOI: 10.1111/pce.13067] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Revised: 08/24/2017] [Accepted: 08/28/2017] [Indexed: 05/12/2023]
Abstract
A novel glyphosate resistance double point mutation (T102I/P106S, TIPS) in the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene has been recently identified for the first time only in the weed species Eleusine indica. Quantification of plant resistance cost associated with the TIPS and the often reported glyphosate resistance single P106S mutation was performed. A significant resistance cost (50% in seed number currency) associated with the homozygous TIPS but not the homozygous P106S EPSPS variant was identified in E. indica plants. The resistance cost associated with the TIPS mutation escalated to 85% in plants under resource competition with rice crops. The resistance cost was not detected in nonhomozygous TIPS plants denoting the recessive nature of the cost associated with the TIPS allele. An excess of 11-fold more shikimate and sixfold more quinate in the shikimate pathway was detected in TIPS plants in the absence of glyphosate treatment compared to wild type, whereas no changes in these compounds were observed in P106S plants when compared to wild type. TIPS plants show altered metabolite levels in several other metabolic pathways that may account for the expression of the observed resistance cost.
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Affiliation(s)
- Heping Han
- Australian Herbicide Resistance Initiative (AHRI)-School of Agriculture and Environment, University of Western Australia (UWA), Perth, Australia
| | - Martin M Vila-Aiub
- Australian Herbicide Resistance Initiative (AHRI)-School of Agriculture and Environment, University of Western Australia (UWA), Perth, Australia
- IFEVA-CONICET-Faculty of Agronomy, Department of Ecology, University of Buenos Aires (UBA), Buenos Aires, Argentina
| | - Adam Jalaludin
- Australian Herbicide Resistance Initiative (AHRI)-School of Agriculture and Environment, University of Western Australia (UWA), Perth, Australia
| | - Qin Yu
- Australian Herbicide Resistance Initiative (AHRI)-School of Agriculture and Environment, University of Western Australia (UWA), Perth, Australia
| | - Stephen B Powles
- Australian Herbicide Resistance Initiative (AHRI)-School of Agriculture and Environment, University of Western Australia (UWA), Perth, Australia
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18
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Karn E, Jasieniuk M. Genetic diversity and structure of Lolium perenne ssp. multiflorum in California vineyards and orchards indicate potential for spread of herbicide resistance via gene flow. Evol Appl 2017; 10:616-629. [PMID: 28616068 PMCID: PMC5469165 DOI: 10.1111/eva.12478] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 03/05/2017] [Indexed: 11/28/2022] Open
Abstract
Management of agroecosystems with herbicides imposes strong selection pressures on weedy plants leading to the evolution of resistance against those herbicides. Resistance to glyphosate in populations of Lolium perenne L. ssp. multiflorum is increasingly common in California, USA, causing economic losses and the loss of effective management tools. To gain insights into the recent evolution of glyphosate resistance in L. perenne in perennial cropping systems of northwest California and to inform management, we investigated the frequency of glyphosate resistance and the genetic diversity and structure of 14 populations. The sampled populations contained frequencies of resistant plants ranging from 10% to 89%. Analyses of neutral genetic variation using microsatellite markers indicated very high genetic diversity within all populations regardless of resistance frequency. Genetic variation was distributed predominantly among individuals within populations rather than among populations or sampled counties, as would be expected for a wide-ranging outcrossing weed species. Bayesian clustering analysis provided evidence of population structuring with extensive admixture between two genetic clusters or gene pools. High genetic diversity and admixture, and low differentiation between populations, strongly suggest the potential for spread of resistance through gene flow and the need for management that limits seed and pollen dispersal in L. perenne.
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Affiliation(s)
- Elizabeth Karn
- University of California DavisDepartment of Plant SciencesDavisCAUSA
| | - Marie Jasieniuk
- University of California DavisDepartment of Plant SciencesDavisCAUSA
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19
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Tafoya-Razo JA, Núñez-Farfán J, Torres-García JR. Migration by seed dispersal of ACCase-inhibitor-resistant Avena fatua in north-western Mexico. PEST MANAGEMENT SCIENCE 2017; 73:167-173. [PMID: 27038305 DOI: 10.1002/ps.4282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 03/29/2016] [Accepted: 03/30/2016] [Indexed: 06/05/2023]
Abstract
BACKGROUND Biotypes of Avena fatua resistant to ACCase-inhibiting herbicides have been reported in the States of Baja California (BC) and Sonora (SON), Mexico. We hypothesised that resistant biotypes present in SON (Valle de Hermosillo and Valle del Yaqui) are derived from a resistant population from BC (Valle de Mexicali) via gene flow through the transport and exchange of contaminated wheat seed. This study aimed to determine (1) the resistance of A. fatua to ACCase-inhibiting herbicides in populations from BC and SON, (2) the mutation at the site of action and (3) the genetic structure and gene flow among populations. RESULTS DNA sequencing showed that all biotypes shared the same mutation (Leu × Ile at codon 1781). Microsatellites showed evidence of a genetic bottleneck in SON, and spatial analysis of molecular variance grouped one biotype from the Valle de Mexicali with two biotypes from the Valle de Hermosillo. Migration analysis suggested gene flow from the Valle de Mexicali to the Valle de Hermosillo, but not to the Valle del Yaqui. CONCLUSIONS The presence of resistant biotypes of A. fatua in the Valle de Hermosillo, SON, are likely derived from seeds from BC, possibly through the transport of contaminated wheat seeds. © 2016 Society of Chemical Industry.
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Affiliation(s)
- J Antonio Tafoya-Razo
- Departamento de Parasitología Agrícola, Universidad Autónoma Chapingo, Texcoco, State of Mexico, Mexico
| | - Juan Núñez-Farfán
- Laboratorio de Genética Ecológica y Evolución, Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Jesús R Torres-García
- Laboratorio de Genética Ecológica y Evolución, Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
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20
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Pan L, Wang Z, Cai J, Gao H, Zhao H, Dong L. High-throughput sequencing reveals differential regulation of miRNAs in fenoxaprop-P-ethyl-resistant Beckmannia syzigachne. Sci Rep 2016; 6:28725. [PMID: 27353151 PMCID: PMC4926119 DOI: 10.1038/srep28725] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 06/09/2016] [Indexed: 12/02/2022] Open
Abstract
Non-target site resistance (NTSR) to herbicides is an increasing concern for weed control. The majority of previous studies have focused on metabolic resistance mechanisms of NTSR, but no research exists on gene regulation mechanisms behind herbicide resistance, such as microRNA (miRNA). Here, we identified 3 American sloughgrass (Beckmannia syzigachne Steud.) populations containing fenoxaprop-P-ethyl-resistant plants. We then constructed small RNA libraries and subjected them to deep sequencing and bioinformatics analyses. Forty known and 36 potentially novel, predicted miRNAs were successfully identified. Of these, we identified 3 conserved, predicted candidate NTSR-determinant miRNAs and their potential corresponding target genes, as well as 4 novel potential miRNAs with high count. Target gene prediction and annotation indicated that these 7 differentially expressed miRNAs potentially play a role in regulating specific stress-responsive genes, very likely related to herbicide resistance. Expression profiles were determined with quantitative real-time PCR. The present study is a novel, large-scale characterization of weed miRNAs. The results should further our understanding of miRNA expression profiles associated with herbicide resistance, allowing for the development of more effective weed management strategies.
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Affiliation(s)
- Lang Pan
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China.,Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education, Nanjing 210095, China
| | - Zhaoyun Wang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China.,Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education, Nanjing 210095, China
| | - Jia Cai
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China.,Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education, Nanjing 210095, China
| | - Haitao Gao
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China.,Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education, Nanjing 210095, China
| | - Hongwei Zhao
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China.,Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education, Nanjing 210095, China
| | - Liyao Dong
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China.,Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education, Nanjing 210095, China
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Kuester A, Chang SM, Baucom RS. The geographic mosaic of herbicide resistance evolution in the common morning glory, Ipomoea purpurea: Evidence for resistance hotspots and low genetic differentiation across the landscape. Evol Appl 2015; 8:821-33. [PMID: 26366199 PMCID: PMC4561571 DOI: 10.1111/eva.12290] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 06/16/2015] [Indexed: 12/01/2022] Open
Abstract
Strong human-mediated selection via herbicide application in agroecosystems has repeatedly led to the evolution of resistance in weedy plants. Although resistance can occur among separate populations of a species across the landscape, the spatial scale of resistance in many weeds is often left unexamined. We assessed the potential that resistance to the herbicide glyphosate in the agricultural weed Ipomoea purpurea has evolved independently multiple times across its North American range. We examined both adaptive and neutral genetic variations in 44 populations of I. purpurea by pairing a replicated dose–response greenhouse experiment with SSR genotyping of experimental individuals. We uncovered a mosaic pattern of resistance across the landscape, with some populations exhibiting high-survival postherbicide and other populations showing high death. SSR genotyping revealed little evidence of isolation by distance and very little neutral genetic structure associated with geography. An approximate Bayesian computation (ABC) analysis uncovered evidence for migration and admixture among populations before the widespread use of glyphosate rather than the very recent contemporary gene flow. The pattern of adaptive and neutral genetic variations indicates that resistance in this mixed-mating weed species appears to have evolved in independent hotspots rather than through transmission of resistance alleles across the landscape.
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Affiliation(s)
- Adam Kuester
- Department of Ecology and Evolutionary Biology, 830 North University, University of Michigan Ann Arbor, MI, USA
| | - Shu-Mei Chang
- Plant Biology Department, University of Georgia Athens, GA, USA
| | - Regina S Baucom
- Department of Ecology and Evolutionary Biology, 830 North University, University of Michigan Ann Arbor, MI, USA
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Gardin JAC, Gouzy J, Carrère S, Délye C. ALOMYbase, a resource to investigate non-target-site-based resistance to herbicides inhibiting acetolactate-synthase (ALS) in the major grass weed Alopecurus myosuroides (black-grass). BMC Genomics 2015; 16:590. [PMID: 26265378 PMCID: PMC4534104 DOI: 10.1186/s12864-015-1804-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 07/31/2015] [Indexed: 12/29/2022] Open
Abstract
Background Herbicide resistance in agrestal weeds is a global problem threatening food security. Non-target-site resistance (NTSR) endowed by mechanisms neutralising the herbicide or compensating for its action is considered the most agronomically noxious type of resistance. Contrary to target-site resistance, NTSR mechanisms are far from being fully elucidated. A part of weed response to herbicide stress, NTSR is considered to be largely driven by gene regulation. Our purpose was to establish a transcriptome resource allowing investigation of the transcriptomic bases of NTSR in the major grass weed Alopecurus myosuroides L. (Poaceae) for which almost no genomic or transcriptomic data was available. Results RNA-Seq was performed from plants in one F2 population that were sensitive or expressing NTSR to herbicides inhibiting acetolactate-synthase. Cloned plants were sampled over seven time-points ranging from before until 73 h after herbicide application. Assembly of over 159M high-quality Illumina reads generated a transcriptomic resource (ALOMYbase) containing 65,558 potentially active contigs (N50 = 1240 nucleotides) predicted to encode 32,138 peptides with 74 % GO annotation, of which 2017 were assigned to protein families presumably involved in NTSR. Comparison with the fully sequenced grass genomes indicated good coverage and correct representation of A. myosuroides transcriptome in ALOMYbase. The part of the herbicide transcriptomic response common to the resistant and the sensitive plants was consistent with the expected effects of acetolactate-synthase inhibition, with striking similarities observed with published Arabidopsis thaliana data. A. myosuroides plants with NTSR were first affected by herbicide action like sensitive plants, but ultimately overcame it. Analysis of differences in transcriptomic herbicide response between resistant and sensitive plants did not allow identification of processes directly explaining NTSR. Five contigs associated to NTSR in the F2 population studied were tentatively identified. They were predicted to encode three cytochromes P450 (CYP71A, CYP71B and CYP81D), one peroxidase and one disease resistance protein. Conclusions Our data confirmed that gene regulation is at the root of herbicide response and of NTSR. ALOMYbase proved to be a relevant resource to support NTSR transcriptomic studies, and constitutes a valuable tool for future research aiming at elucidating gene regulations involved in NTSR in A. myosuroides. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1804-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Jérôme Gouzy
- INRA, UMR441 LIPM, F-31326, Castanet-Tolosan, France.
| | | | - Christophe Délye
- INRA, UMR1347 Agroécologie, 17 rue de Sully, F-21000, Dijon, France.
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Harter DEV, Jentsch A, Durka W. Holocene re-colonisation, central-marginal distribution and habitat specialisation shape population genetic patterns within an Atlantic European grass species. PLANT BIOLOGY (STUTTGART, GERMANY) 2015; 17:684-693. [PMID: 25266560 DOI: 10.1111/plb.12269] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 09/19/2014] [Indexed: 06/03/2023]
Abstract
Corynephorus canescens (L.) P.Beauv. is an outbreeding, short-lived and wind-dispersed grass species, highly specialised on scattered and disturbance-dependent habitats of open sandy sites. Its distribution ranges from the Iberian Peninsula over Atlantic regions of Western and Central Europe, but excludes the two other classical European glacial refuge regions on the Apennine and Balkan Peninsulas. To investigate genetic patterns of this uncommon combination of ecological and biogeographic species characteristics, we analysed AFLP variation among 49 populations throughout the European distribution range, expecting (i) patterns of SW European glacial refugia and post-glacial expansion to the NE; (ii) decreasing genetic diversity from central to marginal populations; and (iii) interacting effects of high gene flow and disturbance-driven genetic drift. Decreasing genetic diversity from SW to NE and distinct gene pool clustering imply refugia on the Iberian Peninsula and in western France, from where range expansion originated towards the NE. High genetic diversity within and moderate genetic differentiation among populations, and a significant pattern of isolation-by-distance indicate a gene flow drift equilibrium within C. canescens, probably due to its restriction to scattered and dynamic habitats and limited dispersal distances. These features, as well as the re-colonisation history, were found to affect genetic diversity gradients from central to marginal populations. Our study emphasises the need for including the specific ecology into analyses of species (re-)colonisation histories and range centre-margin analyses. To account for discontinuous distributions, new indices of marginality were tested for their suitability in studies of centre-periphery gradients.
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Affiliation(s)
- D E V Harter
- Department of Biogeography, BayCEER, University of Bayreuth, Bayreuth, Germany
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Darmency H, Menchari Y, Le Corre V, Délye C. Fitness cost due to herbicide resistance may trigger genetic background evolution. Evolution 2014; 69:271-8. [DOI: 10.1111/evo.12531] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 09/08/2014] [Indexed: 11/30/2022]
Affiliation(s)
| | - Yosra Menchari
- INRA; UMR1347 Agroécologie; Dijon 21000 France
- Current Address: Institut Supérieur de Biotechnologie de Béja; 9000 Béja Tunisia
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25
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Waselkov KE, Olsen KM. Population genetics and origin of the native North American agricultural weed waterhemp (Amaranthus tuberculatus; Amaranthaceae). AMERICAN JOURNAL OF BOTANY 2014; 101:1726-36. [PMID: 25091000 DOI: 10.3732/ajb.1400064] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
UNLABELLED • PREMISE OF THE STUDY The evolution of invasiveness has been extensively studied in natural ecosystems; however, far less is known about the evolution of agricultural invasiveness, despite the major economic impact of weeds on crop productivity. Examining the population structure of recently arisen weeds can provide insights into evolutionary avenues to invasion of agroecosystems. Weeds that originate from wild plants are the most common yet least frequently studied type of agricultural invasive. Here we address several questions about the origin of the native North American agricultural weed waterhemp (Amaranthus tuberculatus), which invaded corn and soy fields in the midwestern United States in the 20th century.• METHODS We genotyped 38 populations from across the species range with 10 microsatellite markers and used these data to assess genetic diversity and population structure within and outside the geographical region where waterhemp is agriculturally problematic.• KEY RESULTS We found evidence for two ancestral genetic lineages in our data, supporting the hypothesis that A. tuberculatus was diverging into two evolutionary lineages prior to the 20th century. However, we found no support for the hypothesis that agricultural weed populations arose from admixture of these two lineages after secondary contact. Our data suggest that eastward movement of the western genetic lineage, facilitated by changing agricultural practices, is the source of the agricultural invasion of waterhemp.• CONCLUSIONS This research demonstrates that agricultural invasion by native, wild plant species can proceed via different evolutionary trajectories from weeds related to domesticated plants, which has implications for evolutionary biology and weed control.
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Affiliation(s)
| | - Kenneth M Olsen
- Department of Biology, Washington University, St. Louis, Missouri 63130 USA
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26
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Walsh MJ, Powles SB. Management of herbicide resistance in wheat cropping systems: learning from the Australian experience. PEST MANAGEMENT SCIENCE 2014; 70:1324-1328. [PMID: 24318955 DOI: 10.1002/ps.3704] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 11/21/2013] [Accepted: 12/06/2013] [Indexed: 06/02/2023]
Abstract
Herbicide resistance continues to escalate in weed populations infesting global wheat (Triticum aestivum L.) crops, threatening grain production and thereby food supply. Conservation wheat production systems are reliant on the use of efficient herbicides providing low-cost, selective weed control in intensive cropping systems. The resistance-driven loss of herbicide resources combined with limited potential for new herbicide molecules means greater emphasis must be placed on preserving existing herbicides. For more than two decades, since the initial recognition of the dramatic consequences of herbicide resistance, the challenge of introducing additional weed control strategies into herbicide-based weed management programmes has been formidable. Throughout this period, herbicide resistance has expanded unabated across the world's wheat production regions. However, in Australia, where herbicide resources have become desperately depleted, the adoption of harvest weed seed control is evidence, at last, of a successful approach to sustainable weed management in wheat production systems. Growers routinely including strategies to target weed seeds during crop harvest, as part of herbicide-based weed management programmes, are now realising significant weed control and crop production benefits. When combined with an attitude of zero weed tolerance, there is evidence of a sustainable weed control future for wheat production systems. The hard-learned lessons of Australian growers can now be viewed by global wheat producers as an example of how to stop the continual loss of herbicide resources in productive cropping systems.
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Affiliation(s)
- Michael J Walsh
- Australian Herbicide Resistance Initiative, School of Plant Biology, University of Western Australia, Perth, WA, Australia
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Délye C, Menchari Y, Michel S, Cadet E, Le Corre V. A new insight into arable weed adaptive evolution: mutations endowing herbicide resistance also affect germination dynamics and seedling emergence. ANNALS OF BOTANY 2013; 111:681-91. [PMID: 23393095 PMCID: PMC3605953 DOI: 10.1093/aob/mct018] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 12/18/2012] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS Selective pressures exerted by agriculture on populations of arable weeds foster the evolution of adaptive traits. Germination and emergence dynamics and herbicide resistance are key adaptive traits. Herbicide resistance alleles can have pleiotropic effects on a weed's life cycle. This study investigated the pleiotropic effects of three acetyl-coenzyme A carboxylase (ACCase) alleles endowing herbicide resistance on the seed-to-plant part of the life cycle of the grass weed Alopecurus myosuroides. METHODS In each of two series of experiments, A. myosuroides populations with homogenized genetic backgrounds and segregating for Leu1781, Asn2041 or Gly2078 ACCase mutations which arose independently were used to compare germination dynamics, survival in the soil and seedling pre-emergence growth among seeds containing wild-type, heterozygous and homozygous mutant ACCase embryos. KEY RESULTS Asn2041 ACCase caused no significant effects. Gly2078 ACCase major effects were a co-dominant acceleration in seed germination (1·25- and 1·10-fold decrease in the time to reach 50 % germination (T50) for homozygous and heterozygous mutant embryos, respectively). Segregation distortion against homozygous mutant embryos or a co-dominant increase in fatal germination was observed in one series of experiments. Leu1781 ACCase major effects were a co-dominant delay in seed germination (1·41- and 1·22-fold increase in T50 for homozygous and heterozygous mutant embryos, respectively) associated with a substantial co-dominant decrease in fatal germination. CONCLUSIONS Under current agricultural systems, plants carrying Leu1781 or Gly2078 ACCase have a fitness advantage conferred by herbicide resistance that is enhanced or counterbalanced, respectively, by direct pleiotropic effects on the plant phenology. Pleiotropic effects associated with mutations endowing herbicide resistance undoubtedly play a significant role in the evolutionary dynamics of herbicide resistance in weed populations. Mutant ACCase alleles should also prove useful to investigate the role played by seed storage lipids in the control of seed dormancy and germination.
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Affiliation(s)
- Christophe Délye
- Institut National de la Recherche Agronomique, UMR1347 Agroécologie, Dijon, France.
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Délye C. Unravelling the genetic bases of non-target-site-based resistance (NTSR) to herbicides: a major challenge for weed science in the forthcoming decade. PEST MANAGEMENT SCIENCE 2013; 69:176-87. [PMID: 22614948 DOI: 10.1002/ps.3318] [Citation(s) in RCA: 229] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 01/24/2012] [Accepted: 03/15/2012] [Indexed: 05/08/2023]
Abstract
Non-target-site-based resistance (NTSR) can confer unpredictable cross-resistance to herbicides. However, the genetic determinants of NTSR remain poorly known. The current, urgent challenge for weed scientists is thus to elucidate the bases of NTSR so that detection tools are developed, the evolution of NTSR is understood, the efficacy of the shrinking herbicide portfolio is maintained and integrated weed management strategies, including fully effective herbicide applications, are designed and implemented. In this paper, the importance of NTSR in resistance to herbicides is underlined. The most likely way in which NTSR evolves-by accumulation of different mechanisms within individual plants-is described. The NTSR mechanisms, which can interfere with herbicide penetration, translocation and accumulation at the target site, and/or protect the plant against the consequences of herbicide action, are then reviewed. NTSR is a part of the plant stress response. As such, NTSR is a dynamic process unrolling over time that involves 'protectors' directly interfering with herbicide action, and also regulators controlling 'protector' expression. NTSR is thus a quantitative trait. On this basis, a three-step procedure is proposed, based on the use of the 'omics' (genomics, transcriptomics, proteomics or metabolomics), to unravel the genetic bases of NTSR.
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The red queen in the corn: agricultural weeds as models of rapid adaptive evolution. Heredity (Edinb) 2012. [PMID: 23188175 DOI: 10.1038/hdy.2012.104] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Weeds are among the greatest pests of agriculture, causing billions of dollars in crop losses each year. As crop field management practices have changed over the past 12 000 years, weeds have adapted in turn to evade human removal. This evolutionary change can be startlingly rapid, making weeds an appealing system to study evolutionary processes that occur over short periods of time. An understanding of how weeds originate and adapt is needed for successful management; however, relatively little emphasis has been placed on genetically characterizing these systems. Here, we review the current literature on agricultural weed origins and their mechanisms of adaptation. Where possible, we have included examples that have been genetically well characterized. Evidence for three possible, non-mutually exclusive weed origins (from wild species, crop-wild hybrids or directly from crops) is discussed with respect to what is known about the microevolutionary signatures that result from these processes. We also discuss what is known about the genetic basis of adaptive traits in weeds and the range of genetic mechanisms that are responsible. With a better understanding of genetic mechanisms underlying adaptation in weedy species, we can address the more general process of adaptive evolution and what can be expected as we continue to apply selective pressures in agroecosystems around the world.
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Wang T, Chen G, Zan Q, Wang C, Su YJ. AFLP genome scan to detect genetic structure and candidate loci under selection for local adaptation of the invasive weed Mikania micrantha. PLoS One 2012; 7:e41310. [PMID: 22829939 PMCID: PMC3400595 DOI: 10.1371/journal.pone.0041310] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 06/25/2012] [Indexed: 11/18/2022] Open
Abstract
Why some species become successful invaders is an important issue in invasive biology. However, limited genomic resources make it very difficult for identifying candidate genes involved in invasiveness. Mikania micrantha H.B.K. (Asteraceae), one of the world's most invasive weeds, has adapted rapidly in response to novel environments since its introduction to southern China. In its genome, we expect to find outlier loci under selection for local adaptation, critical to dissecting the molecular mechanisms of invasiveness. An explorative amplified fragment length polymorphism (AFLP) genome scan was used to detect candidate loci under selection in 28 M. micrantha populations across its entire introduced range in southern China. We also estimated population genetic parameters, bottleneck signatures, and linkage disequilibrium. In binary characters, such as presence or absence of AFLP bands, if all four character combinations are present, it is referred to as a character incompatibility. Since character incompatibility is deemed to be rare in populations with extensive asexual reproduction, a character incompatibility analysis was also performed in order to infer the predominant mating system in the introduced M. micrantha populations. Out of 483 AFLP loci examined using stringent significance criteria, 14 highly credible outlier loci were identified by Dfdist and Bayescan. Moreover, remarkable genetic variation, multiple introductions, substantial bottlenecks and character compatibility were found to occur in M. micrantha. Thus local adaptation at the genome level indeed exists in M. micrantha, and may represent a major evolutionary mechanism of successful invasion. Interactions between genetic diversity, multiple introductions, and reproductive modes contribute to increase the capacity of adaptive evolution.
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Affiliation(s)
- Ting Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Guopei Chen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qijie Zan
- Shenzhen Wildlife Rescue and Rehabilitation Center, Shenzhen, China
| | - Chunbo Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ying-juan Su
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- * E-mail:
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Abstract
Populations that have independently evolved reproductive isolation from their ancestors while remaining reproductively cohesive have undergone parallel speciation. A specific type of parallel speciation, known as parallel ecological speciation, is one of several forms of evidence for ecology's role in speciation. In this paper we search the literature for candidate examples of parallel ecological speciation in plants. We use four explicit criteria (independence, isolation, compatibility, and selection) to judge the strength of evidence for each potential case. We find that evidence for parallel ecological speciation in plants is unexpectedly scarce, especially relative to the many well-characterized systems in animals. This does not imply that ecological speciation is uncommon in plants. It only implies that evidence from parallel ecological speciation is rare. Potential explanations for the lack of convincing examples include a lack of rigorous testing and the possibility that plants are less prone to parallel ecological speciation than animals.
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Délye C, Clément JA, Pernin F, Chauvel B, Le Corre V. High gene flow promotes the genetic homogeneity of arable weed populations at the landscape level. Basic Appl Ecol 2010. [DOI: 10.1016/j.baae.2010.06.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Délye C, Michel S, Bérard A, Chauvel B, Brunel D, Guillemin JP, Dessaint F, Le Corre V. Geographical variation in resistance to acetyl-coenzyme A carboxylase-inhibiting herbicides across the range of the arable weed Alopecurus myosuroides (black-grass). THE NEW PHYTOLOGIST 2010; 186:1005-1017. [PMID: 20345631 DOI: 10.1111/j.1469-8137.2010.03233.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
*The geographical structure of resistance to herbicides inhibiting acetyl-coenzyme A carboxylase (ACCase) was investigated in the weed Alopecurus myosuroides (black-grass) across its geographical range to gain insight into the process of plant adaptation in response to anthropogenic selective pressures occurring in agricultural ecosystems. *We analysed 297 populations distributed across six countries in A. myosuroides' main area of occupancy. The frequencies of plants resistant to two broadly used ACCase inhibitors and of seven mutant, resistant ACCase alleles were assessed using bioassays and genotyping, respectively. *Most of the resistance was not endowed by mutant ACCase alleles. Resistance and ACCase allele distribution patterns were characterized by mosaicism. The prevalence of resistance and of ACCase alleles differed among countries. *Resistance clearly evolved by redundant evolution of a set of resistance alleles or genes, most of which remain unidentified. Resistance in A. myosuroides was shaped by variation in the herbicide selective pressure at both the individual field level and the national level.
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Affiliation(s)
- Christophe Délye
- INRA, UMR1210 Biologie et Gestion des Adventices, F-21000 Dijon, France
| | - Séverine Michel
- INRA, UMR1210 Biologie et Gestion des Adventices, F-21000 Dijon, France
| | - Aurélie Bérard
- INRA, UR1279 Étude du Polymorphisme des Génomes Végétaux, CEA-Institut de Génomique, Centre National de Génotypage, F-91000 Évry, France
| | - Bruno Chauvel
- INRA, UMR1210 Biologie et Gestion des Adventices, F-21000 Dijon, France
| | - Dominique Brunel
- INRA, UR1279 Étude du Polymorphisme des Génomes Végétaux, CEA-Institut de Génomique, Centre National de Génotypage, F-91000 Évry, France
| | | | - Fabrice Dessaint
- INRA, UMR1210 Biologie et Gestion des Adventices, F-21000 Dijon, France
| | - Valérie Le Corre
- INRA, UMR1210 Biologie et Gestion des Adventices, F-21000 Dijon, France
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Neve P, Vila-Aiub M, Roux F. Evolutionary-thinking in agricultural weed management. THE NEW PHYTOLOGIST 2009; 184:783-793. [PMID: 19780985 DOI: 10.1111/j.1469-8137.2009.03034.x] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Agricultural weeds evolve in response to crop cultivation. Nevertheless, the central importance of evolutionary ecology for understanding weed invasion, persistence and management in agroecosystems is not widely acknowledged. This paper calls for more evolutionarily-enlightened weed management, in which management principles are informed by evolutionary biology to prevent or minimize weed adaptation and spread. As a first step, a greater knowledge of the extent, structure and significance of genetic variation within and between weed populations is required to fully assess the potential for weed adaptation. The evolution of resistance to herbicides is a classic example of weed adaptation. Even here, most research focuses on describing the physiological and molecular basis of resistance, rather than conducting studies to better understand the evolutionary dynamics of selection for resistance. We suggest approaches to increase the application of evolutionary-thinking to herbicide resistance research. Weed population dynamics models are increasingly important tools in weed management, yet these models often ignore intrapopulation and interpopulation variability, neglecting the potential for weed adaptation in response to management. Future agricultural weed management can benefit from greater integration of ecological and evolutionary principles to predict the long-term responses of weed populations to changing weed management, agricultural environments and global climate.
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Affiliation(s)
- Paul Neve
- Warwick HRI, University of Warwick, Wellesbourne, Warwickshire, UK.
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Vila-Aiub MM, Neve P, Powles SB. Fitness costs associated with evolved herbicide resistance alleles in plants. THE NEW PHYTOLOGIST 2009; 184:751-767. [PMID: 19825013 DOI: 10.1111/j.1469-8137.2009.03055.x] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Predictions based on evolutionary theory suggest that the adaptive value of evolved herbicide resistance alleles may be compromised by the existence of fitness costs. There have been many studies quantifying the fitness costs associated with novel herbicide resistance alleles, reflecting the importance of fitness costs in determining the evolutionary dynamics of resistance. However, many of these studies have incorrectly defined resistance or used inappropriate plant material and methods to measure fitness. This review has two major objectives. First, to propose a methodological framework that establishes experimental criteria to unequivocally evaluate fitness costs. Second, to present a comprehensive analysis of the literature on fitness costs associated with herbicide resistance alleles. This analysis reveals unquestionable evidence that some herbicide resistance alleles are associated with pleiotropic effects that result in plant fitness costs. Observed costs are evident from herbicide resistance-endowing amino acid substitutions in proteins involved in amino acid, fatty acid, auxin and cellulose biosynthesis, as well as enzymes involved in herbicide metabolism. However, these resistance fitness costs are not universal and their expression depends on particular plant alleles and mutations. The findings of this review are discussed within the context of the plant defence trade-off theory and herbicide resistance evolution.
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Affiliation(s)
- Martin M Vila-Aiub
- Western Australian Herbicide Resistance Initiative (WAHRI), School of Plant Biology, The University of Western Australia, Crawley, WA 6009, Australia.
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Gressel J. Evolving understanding of the evolution of herbicide resistance. PEST MANAGEMENT SCIENCE 2009; 65:1164-73. [PMID: 19743401 DOI: 10.1002/ps.1842] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A greater number of, and more varied, modes of resistance have evolved in weeds than in other pests because the usage of herbicides is far more extensive than the usage of other pesticides, and because weed seed output is so great. The discovery and development of selective herbicides are more problematic than those of insecticides and fungicides, as these must only differentiate between plant and insect or pathogen. Herbicides are typically selective between plants, meaning that before deployment there are already some crops possessing natural herbicide resistance that weeds could evolve. The concepts of the evolution of resistance and the mechanisms of delaying resistance have evolved as nature has continually evolved new types of resistance. Major gene target-site mutations were the first types to evolve, with initial consideration devoted mainly to them, but slowly 'creeping' resistance, gradually accruing increasing levels of resistance, has become a major force owing to an incremental accumulation of genetic changes in weed populations. Weeds have evolved mechanisms unknown even in antibiotic as well as other drug and pesticide resistances. It is even possible that cases of epigenetic 'remembered' resistances may have appeared.
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Affiliation(s)
- Jonathan Gressel
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel.
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