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Sehgal D, Oliveira C, Mathioni S, Widdison S, Plumb W, Campos B, Kaundun SS. Genomic characterisation and dissection of the onset of resistance to acetyl CoA carboxylase-inhibiting herbicides in a large collection of Digitaria insularis from Brazil. Front Genet 2024; 15:1340852. [PMID: 38440194 PMCID: PMC10910277 DOI: 10.3389/fgene.2024.1340852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 01/19/2024] [Indexed: 03/06/2024] Open
Abstract
An in-depth genotypic characterisation of a diverse collection of Digitaria insularis was undertaken to explore the neutral genetic variation across the natural expansion range of this weed species in Brazil. With the exception of Minas Gerais, populations from all other states showed high estimates of expected heterozygosity (HE > 0.60) and genetic diversity. There was a lack of population structure based on geographic origin and a low population differentiation between populations across the landscape as evidenced by average Fst value of 0.02. On combining haloxyfop [acetyl CoA carboxylase (ACCase)-inhibiting herbicide] efficacy data with neutral genetic variation, we found evidence of presence of two scenarios of resistance evolution in this weed species. Whilst populations originating from north-eastern region demonstrated an active role of gene flow, populations from the mid-western region displayed multiple, independent resistance evolution as the major evolutionary mechanism. A target-site mutation (Trp2027Cys) in the ACCase gene, observed in less than 1% of resistant populations, could not explain the reduced sensitivity of 15% of the populations to haloxyfop. The genetic architecture of resistance to ACCase-inhibiting herbicides was dissected using a genome wide association study (GWAS) approach. GWAS revealed association of three SNPs with reduced sensitivity to haloxyfop and clethodim. In silico analysis of these SNPs revealed important non-target site genes belonging to families involved in herbicide detoxification, including UDPGT91C1 and GT2, and genes involved in vacuolar sequestration-based degradation pathway. Exploration of five genomic prediction models revealed that the highest prediction power (≥0.80) was achieved with the models Bayes A and RKHS, incorporating SNPs with additive effects and epistatic interactions, respectively.
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Affiliation(s)
- Deepmala Sehgal
- Syngenta Ltd., Jealott’s Hill International Research Centre, Bracknell, United Kingdom
| | - Claudia Oliveira
- Syngenta Crop Protection, Holambra Research and Development Center, São Paulo, Brazil
| | - Sandra Mathioni
- Syngenta Crop Protection, Holambra Research and Development Center, São Paulo, Brazil
| | - Stephanie Widdison
- Syngenta Ltd., Jealott’s Hill International Research Centre, Bracknell, United Kingdom
| | - Will Plumb
- Syngenta Ltd., Jealott’s Hill International Research Centre, Bracknell, United Kingdom
| | - Breno Campos
- Syngenta Ltd., Jealott’s Hill International Research Centre, Bracknell, United Kingdom
| | - Shiv Shankhar Kaundun
- Syngenta Ltd., Jealott’s Hill International Research Centre, Bracknell, United Kingdom
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Brunharo CACG, Tranel PJ. Repeated evolution of herbicide resistance in Lolium multiflorum revealed by haplotype-resolved analysis of acetyl-CoA carboxylase. Evol Appl 2023; 16:1969-1981. [PMID: 38143902 PMCID: PMC10739073 DOI: 10.1111/eva.13615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/27/2023] [Accepted: 10/24/2023] [Indexed: 12/26/2023] Open
Abstract
Herbicide resistance in weeds is one of the greatest challenges in modern food production. The grass species Lolium multiflorum is an excellent model species to investigate evolution under similar selection pressure because populations have repeatedly evolved resistance to many herbicides, utilizing a multitude of mechanisms to neutralize herbicide damage. In this work, we investigated the gene that encodes acetyl-CoA carboxylase (ACCase), the target site of the most successful herbicide group available for grass weed control. We sampled L. multiflorum populations from agricultural fields with history of intense herbicide use, and studied their response to three ACCase-inhibiting herbicides. To elucidate the mechanisms of herbicide resistance and the genetic relationship among populations, we resolved the haplotypes of 97 resistant and susceptible individuals by sequencing ACCase amplicons using long-read DNA sequencing technologies. Our dose-response data indicated the existence of many, often unpredictable, resistance patterns to ACCase-inhibiting herbicides, where populations exhibited as much as 37-fold reduction in herbicide response. The majority of the populations exhibited resistance to all three herbicides studied. Phylogenetic and molecular genetic analyses revealed multiple evolutionary origins of resistance-endowing ACCase haplotypes, as well as widespread admixture in the region regardless of cropping system. The amplicons generated were diverse, with haplotypes exhibiting 26-110 polymorphisms. Polymorphisms included insertions and deletions 1-31 bp in length, none of which were associated with the resistance phenotype based on an association analysis. We also found evidence that some populations have multiple mechanisms of resistance. Our results highlight the astounding genetic diversity in L. multiflorum populations, and the potential for repeated evolution of herbicide resistance across the landscape that challenges weed management approaches and jeopardizes sustainable weed control practices. We provide an in-depth discussion of the evolutionary and practical implications of our results.
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Affiliation(s)
- Caio A. C. G. Brunharo
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
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3
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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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Yu W, Xue Z, Zhao X, Zhang R, Liu J, Guo S. Glyphosate-induced GhAG2 is involved in resistance to salt stress in cotton. PLANT CELL REPORTS 2022; 41:1131-1145. [PMID: 35243542 DOI: 10.1007/s00299-022-02844-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 02/05/2022] [Indexed: 06/14/2023]
Abstract
KEY MESSAGE The transcription of GhAG2 was strongly enhanced by glyphosate treatment. Overexpression of GhAG2 could improve plant tolerance to salt and salicylic acid stress. Although glyphosate has been widely used as an herbicide over the past decade owing to its high efficacy on weed controls and worldwide commercialization of glyphosate-resistant crops, little is known about the glyphosate-induced responses and transcriptional changes in cotton plants. Here, we report the identification of 26 differentially expressed genes after glyphosate treatment, among which, six highly up-regulated sequences share homology to cotton expressed sequence tags (ESTs) responsive to abiotic stresses. In addition, we cloned GhAG2, a gene whose transcription was strongly enhanced by glyphosate treatment and other abiotic stresses. Transgenic GhAG2 plants showed improved tolerance to salt, and salicylic acid (SA) stress. The results could open the door to exploring the function of the GhAG2 proteins, the glyphosate-induced transcriptional profiles, and the physiological biochemical responses in cotton and other crops. GhAG2 could also be used to improve salt stress tolerance through breeding and biotechnology in crops. Furthermore, these results could provide guidelines to develop a glyphosate-inducible system for controlled expression of targeted genes in plants.
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Affiliation(s)
- Wancong Yu
- Biotechnology Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, 300384, China
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhaohui Xue
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Xianzheng Zhao
- Biotechnology Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, 300384, China
| | - Rui Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Jiping Liu
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture, Agricultural Research Service, Ithaca, NY, 14853, USA.
| | - Sandui Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Gonçalves Netto A, Cordeiro EMG, Nicolai M, de Carvalho SJP, Ovejero RFL, Brunharo CACG, Zucchi MI, Christoffoleti PJ. Population genomics of Digitaria insularis from soybean areas in Brazil. PEST MANAGEMENT SCIENCE 2021; 77:5375-5381. [PMID: 34302709 PMCID: PMC9291757 DOI: 10.1002/ps.6577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 07/24/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Digitaria insularis is a weed species that has gained considerable importance in Brazil's soybean production areas that rely on glyphosate-resistant cultivars. Herbicide-resistant weed populations of this species have been reported in many regions in Brazil, first in the south, followed by later reports in the north. We hypothesized that the spread of herbicide-resistant D. insularis is facilitated by movement of agricultural machinery from the southern regions of Brazil. RESULTS Population genomics revealed a weak or no genetic structure (FST = [0; 0.16]), moderate expected heterozygosity (HE = 0.15; 0.44) and low inbreeding (FIS = [-0.1; 0.1]) in D. insularis populations. Our data supported the hypothesis that herbicide resistance gene flow predominantly occurred in a south-to-north direction based on a migration analysis. We also found evidence of local adaptation of resistant populations in the northern soybean-growing regions of Brazil. CONCLUSION Evidence in our work suggests that gene flow of glyphosate-resistant D. insularis is associated with movement of agricultural machinery, although local selection pressure seems to play an important role in the evolution of herbicide resistance throughout the country. Our results suggest preventive practices such as equipment sanitation should be implemented to limit the spread of herbicide resistant D. insularis. © 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)
- Acácio Gonçalves Netto
- Crop Science DepartmentLuiz de Queiroz College of Agriculture, University of São PauloPiracicabaBrazil
| | - Erick MG Cordeiro
- Crop Science DepartmentLuiz de Queiroz College of Agriculture, University of São PauloPiracicabaBrazil
| | - Marcelo Nicolai
- Agro do Mato Consulting, Santa Barbara D'OesteSão PauloBrazil
| | - Saul JP de Carvalho
- Federal Institute of Education, Science and Technology of the South of Minas GeraisMachadoMinas GeraisBrazil
| | | | - Caio ACG Brunharo
- Department of Crop and Soil ScienceOregon State UniversityCorvallisORUSA
| | - Maria I Zucchi
- Secretariat of Agriculture and Food Supply of Sao Paulo StatePiracicabaBrazil
| | - Pedro J Christoffoleti
- Crop Science DepartmentLuiz de Queiroz College of Agriculture, University of São PauloPiracicabaBrazil
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Matzrafi M, Preston C, Brunharo CA. Review: evolutionary drivers of agricultural adaptation in Lolium spp. PEST MANAGEMENT SCIENCE 2021; 77:2209-2218. [PMID: 33300265 PMCID: PMC8048627 DOI: 10.1002/ps.6219] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 12/05/2020] [Accepted: 12/09/2020] [Indexed: 05/11/2023]
Abstract
The genus Lolium comprises many species, of which L. perenne ssp. multiflorum, L. perenne ssp. perenne, and L. rigidum are of worldwide agricultural importance as both pasture crops and as weeds. These three species are inter-fertile, obligate out-crossers with a self-incompatible reproduction system. This combination contributes to high genetic diversity that supplies new variants during expansion to new natural areas and agricultural environments. Human dispersal, de-domestication and crop-weed hybridization events between Lolium spp., or with others such as Festuca spp., are likely associated with their distinct weediness abilities. Furthermore, new introductions followed by introgression may hasten adaptation to new environments. Most Lolium-related weed science studies have focused on adaptation leading to herbicide resistance, but other forms of adaptation may also occur. In this review, we explore how the wide genetic variation among Lolium species and hybridization with other species may contribute to range expansion, and adaptation to both new agricultural practices and future predicted climate change scenarios. © 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)
- Maor Matzrafi
- Department of Plant Pathology and Weed ResearchAgricultural Research Organization (ARO), Newe Ya'ar Research CenterRamat YishayIsrael
| | - Christopher Preston
- School of Agriculture, Food & WineUniversity of AdelaideGlen OsmondSAAustralia
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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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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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9
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Li FF, Gong L, Li JS, Liu XY, Zhao CY. Low genetic differentiation yet high phenotypic variation in the invasive populations of Spartina alterniflora in Guangxi, China. PLoS One 2019; 14:e0222646. [PMID: 31527890 PMCID: PMC6748429 DOI: 10.1371/journal.pone.0222646] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 09/03/2019] [Indexed: 11/18/2022] Open
Abstract
Genetic variation and population structure may reflect important information for invasion success of exotic plant species and thus help improve management of invasive plants. Spartina alterniflora is an invasive plant that is a major threat to the economy and environment of the coastal regions in China. We analyzed the genetic structure and diversity of six populations of S. alterniflora differing in invasion histories in Guangxi, China. A total of 176 individuals from the six populations produced 348 AFLP fragments. The average heterozygosity was significantly lower than in the native population. And genetic bottlenecks were also detected in most populations. Standardized FST statistics (Φpt = 0.015) and AMOVA results indicated weak genetic differentiation. Genetic admixture and obviously isolation by distance indicated populations in Guangxi come from a pre-admixed population by a single introduction. High phenotypic variations of S. alterniflora in Guangxi influenced by soil salinity and temperature might be an important reason for the successful invasion.
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Affiliation(s)
- Fei-Fei Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, P.R. China
| | - Lu Gong
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, P.R. China
| | - Jun-Sheng Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, P.R. China
| | - Xiao-Yan Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, P.R. China
| | - Cai-Yun Zhao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, P.R. China
- * E-mail: ,
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Li F, van Kleunen M, Li J, Liu X, Gao K, Zhu J, Zhao X, Zhao C, Li J. Patterns of genetic variation reflect multiple introductions and pre-admixture sources of common ragweed (Ambrosia artemisiifolia) in China. Biol Invasions 2019. [DOI: 10.1007/s10530-019-01966-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Kim J, Ni G, Kim T, Chun J, Kern EMA, Park J. Phylogeography of the highly invasive sugar beet nematode, Heterodera schachtii (Schmidt, 1871), based on microsatellites. Evol Appl 2019; 12:324-336. [PMID: 30697343 PMCID: PMC6346664 DOI: 10.1111/eva.12719] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 07/18/2018] [Accepted: 09/04/2018] [Indexed: 12/31/2022] Open
Abstract
Plant-parasitic nematodes (PPNs) threaten crop production worldwide. Yet few studies have examined their intraspecific genetic diversity or patterns of invasion, critical data for managing the spread of these cryptic pests. The sugar beet nematode Heterodera schachtii, a global invader that parasitizes over 200 plant species, represents a model for addressing important questions about the invasion genetics of PPNs. Here, a phylogeographic study using 15 microsatellite markers was conducted on 231 H. schachtii individuals sampled from four continents, and invasion history was reconstructed through an approximate Bayesian computation approach, with emphasis on the origin of newly discovered populations in Korea. Multiple analyses confirmed the existence of cryptic lineages within this species, with the Korean populations comprising one group (group 1) and the populations from Europe, Australia, North America, and western Asia comprising another (group 2). No multilocus genotypes were shared between the two groups, and large genetic distance was inferred between them. Population subdivision was also revealed among the populations of group 2 in both population comparison and STRUCTURE analyses, mostly due to different divergent times between invasive and source populations. The Korean populations showed substantial genetic homogeneity and likely originated from a single invasion event. However, none of the other studied populations were implicated as the source. Further studies with additional populations are needed to better describe the distribution of the potential source population for the East Asian lineage.
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Affiliation(s)
- Jiyeon Kim
- Division of EcoScienceEwha Womans UniversitySeoulKorea
- Freshwater Biodiversity Research DivisionNakdonggang National Institute of Biological ResourcesSangjuKorea
| | - Gang Ni
- Division of EcoScienceEwha Womans UniversitySeoulKorea
| | - Taeho Kim
- Division of EcoScienceEwha Womans UniversitySeoulKorea
| | | | | | - Joong‐Ki Park
- Division of EcoScienceEwha Womans UniversitySeoulKorea
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12
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Peterson MA, Collavo A, Ovejero R, Shivrain V, Walsh MJ. The challenge of herbicide resistance around the world: a current summary. PEST MANAGEMENT SCIENCE 2018; 74:2246-2259. [PMID: 29222931 DOI: 10.1002/ps.4821] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 12/02/2017] [Accepted: 12/04/2017] [Indexed: 05/23/2023]
Abstract
Herbicide-resistant weeds have been observed since the early years of synthetic herbicide development in the 1950s and 1960s. Since that time there has been a consistent increase in the number of cases of herbicide resistance and the impact of herbicide-resistant weeds. Although the nature of crop production varies widely around the world, herbicides have become a primary tool for weed control in most areas. Dependence on herbicides continues to increase as global populations migrate away from rural areas to cities and the agricultural labor force declines. This increased use of herbicides and the concurrent selection pressure have resulted in a rise in cases of multiple resistance, leaving some farmers with few or no herbicide options for certain weed infestations. Global population and economic forces drive many farmer choices regarding crop production and weed control. The challenge is how to insert best management practices into the decision-making process while addressing various economic and regulatory needs. This review endeavors to provide a current overview of herbicide resistance challenges in the major crop production areas of the world and discusses some research initiatives designed to address portions of the problem. © 2017 Society of Chemical Industry.
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Affiliation(s)
| | | | | | | | - Michael J Walsh
- School of Life and Environmental Sciences, University of Sydney, Narrabri, Australia
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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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14
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Karn E, Jasieniuk M. Nucleotide Diversity at Site 106 of EPSPS in Lolium perenne L. ssp. multiflorum from California Indicates Multiple Evolutionary Origins of Herbicide Resistance. FRONTIERS IN PLANT SCIENCE 2017; 8:777. [PMID: 28536598 PMCID: PMC5423406 DOI: 10.3389/fpls.2017.00777] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 04/25/2017] [Indexed: 05/15/2023]
Abstract
The repeated evolution of herbicide resistance in weeds is an ongoing problem in agricultural regions across the world, and presents a unique system in which to study the origins and spread of adaptive traits across heterogeneous landscapes. Lolium perenne ssp. multiflorum (Lam.) (Italian ryegrass) is a widespread grass weed of agricultural crops that has repeatedly evolved resistance to herbicides across the world. In California, resistance to glyphosate has become increasingly common. To identify the mechanisms conferring glyphosate resistance in California populations of L. perenne and to gain insights into the evolutionary origins and spread of resistance in the region, we investigated the frequency of target-site mutations conferring resistance to glyphosate combined with the frequency of resistant individuals in 14 populations. A region of 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) was sequenced in 401 individuals to assay for target site mutations. Seven unique alleles were detected at codon site 106, four of which have been previously shown to confer target-site-based resistance to glyphosate. Four different resistance alleles were detected, indicating that resistance to glyphosate has evolved multiple times in the region. In two populations, no EPSPS mutations were detected despite the presence of resistant plants, strongly suggesting that non-target-site-based mechanisms confer resistance to glyphosate in these populations. It is likely that resistance to glyphosate in these 14 California populations of L. perenne derives from at least five evolutionary origins, indicating that adaptive traits can evolve repeatedly over agricultural landscapes.
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