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Gunn JC, Christensen BM, Bueno EM, Cohen ZP, Kissonergis AS, Chen YH. Agricultural insect pests as models for studying stress-induced evolutionary processes. INSECT MOLECULAR BIOLOGY 2024. [PMID: 38655882 DOI: 10.1111/imb.12915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 04/14/2024] [Indexed: 04/26/2024]
Abstract
Agricultural insect pests (AIPs) are widely successful in adapting to natural and anthropogenic stressors, repeatedly overcoming population bottlenecks and acquiring resistance to intensive management practices. Although they have been largely overlooked in evolutionary studies, AIPs are ideal systems for understanding rapid adaptation under novel environmental conditions. Researchers have identified several genomic mechanisms that likely contribute to adaptive stress responses, including positive selection on de novo mutations, polygenic selection on standing allelic variation and phenotypic plasticity (e.g., hormesis). However, new theory suggests that stress itself may induce epigenetic modifications, which may confer heritable physiological changes (i.e., stress-resistant phenotypes). In this perspective, we discuss how environmental stress from agricultural management generates the epigenetic and genetic modifications that are associated with rapid adaptation in AIPs. We summarise existing evidence for stress-induced evolutionary processes in the context of insecticide resistance. Ultimately, we propose that studying AIPs offers new opportunities and resources for advancing our knowledge of stress-induced evolution.
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Affiliation(s)
- Joe C Gunn
- Department of Plant and Soil Science, University of Vermont, Burlington, Vermont, USA
| | - Blair M Christensen
- Department of Plant and Soil Science, University of Vermont, Burlington, Vermont, USA
| | - Erika M Bueno
- Department of Plant and Soil Science, University of Vermont, Burlington, Vermont, USA
| | - Zachary P Cohen
- Insect Control and Cotton Disease Research, USDA ARS, College Station, Texas, USA
| | | | - Yolanda H Chen
- Department of Plant and Soil Science, University of Vermont, Burlington, Vermont, USA
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2
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Jin M, Peng Y, Peng J, Zhang H, Shan Y, Liu K, Xiao Y. Transcriptional regulation and overexpression of GST cluster enhances pesticide resistance in the cotton bollworm, Helicoverpa armigera (Lepidoptera: Noctuidae). Commun Biol 2023; 6:1064. [PMID: 37857697 PMCID: PMC10587110 DOI: 10.1038/s42003-023-05447-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 10/11/2023] [Indexed: 10/21/2023] Open
Abstract
The rapid evolution of resistance in agricultural pest poses a serious threat to global food security. However, the mechanisms of resistance through metabolic regulation are largely unknown. Here, we found that a GST gene cluster was strongly selected in North China (NTC) population, and it was significantly genetically-linked to lambda-cyhalothrin resistance. Knockout of the GST cluster using CRISPR/Cas9 significantly increased the sensitivity of the knockout strain to lambda-cyhalothrin. Haplotype analysis revealed no non-synonymous mutations or structural variations in the GST cluster, whereas GST_119 and GST_121 were significantly overexpressed in the NTC population. Silencing of GST_119 or co-silencing of GST_119 and GST_121 with RNAi significantly increased larval sensitivity to lambda-cyhalothrin. We also identified additional GATAe transcription factor binding sites in the promoter of NTC_GST_119. Transient expression of GATAe in Hi5 cells activated NTC_GST_119 and Xinjiang (XJ)_GST_119 transcription, but the transcriptional activity of NTC_GST_119 was significantly higher than that of XJ_GST_119. These results demonstrate that variations in the regulatory region result in complex expression changes in the GST cluster, which enhances lambda-cyhalothrin resistance in field-populations. This study deepens our knowledge of the evolutionary mechanism of pest adaptation under environmental stress and provides potential targets for monitoring pest resistance and integrated management.
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Affiliation(s)
- Minghui Jin
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yan Peng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jie Peng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Huihui Zhang
- Institute of Entomology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Yinxue Shan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Kaiyu Liu
- Institute of Entomology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Yutao Xiao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
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3
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Cohen ZP, François O, Schoville SD. Museum Genomics of an Agricultural Super-Pest, the Colorado Potato Beetle, Leptinotarsa decemlineata (Chrysomelidae), Provides Evidence of Adaptation from Standing Variation. Integr Comp Biol 2022; 62:1827-1837. [PMID: 36036479 DOI: 10.1093/icb/icac137] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/12/2022] [Accepted: 08/14/2022] [Indexed: 01/05/2023] Open
Abstract
Despite extensive research on agricultural pests, our knowledge about their evolutionary history is often limited. A mechanistic understanding of the demographic changes and modes of adaptation remains an important goal, as it improves our understanding of organismal responses to environmental change and our ability to sustainably manage pest populations. Emerging genomic datasets now allow for characterization of demographic and adaptive processes, but face limits when they are drawn from contemporary samples, especially in the context of strong demographic change, repeated selection, or adaptation involving modest shifts in allele frequency at many loci. Temporal sampling, however, can improve our ability to reconstruct evolutionary events. Here, we leverage museum samples to examine whether population genomic diversity and structure has changed over time, and to identify genomic regions that appear to be under selection. We focus on the Colorado potato beetle (CPB), Leptinotarsa decemlineata (Say 1824; Coleoptera: Chrysomelidae), which is widely regarded as a super-pest due to its rapid, and repeated, evolution to insecticides. By combining whole genome resequencing data from 78 museum samples with modern sampling, we demonstrate that CPB expanded rapidly in the 19th century, leading to a reduction in diversity and limited genetic structure from the Midwest to Northeast United States. Temporal genome scans provide extensive evidence for selection acting in resistant field populations in Wisconsin and New York, including numerous known insecticide resistance genes. We also validate these results by showing that known selective sweeps in modern populations are identified by our genome scan. Perhaps most importantly, temporal analysis indicates selection on standing genetic variation, as we find evidence for parallel evolution in the two geographical regions. Parallel evolution involves a range of phenotypic traits not previously identified as under selection in CPB, such as reproductive and morphological functional pathways that might be important for adaptation to agricultural habitats.
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Affiliation(s)
- Zachary P Cohen
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA.,Insect Control and Cotton Disease Research Unit, USDA, Agricultural Research Service, College Station, TX, USA
| | | | - Sean D Schoville
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
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Bras A, Roy A, Heckel DG, Anderson P, Karlsson Green K. Pesticide resistance in arthropods: Ecology matters too. Ecol Lett 2022; 25:1746-1759. [PMID: 35726578 PMCID: PMC9542861 DOI: 10.1111/ele.14030] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/12/2022] [Accepted: 05/03/2022] [Indexed: 12/22/2022]
Abstract
Pesticide resistance development is an example of rapid contemporary evolution that poses immense challenges for agriculture. It typically evolves due to the strong directional selection that pesticide treatments exert on herbivorous arthropods. However, recent research suggests that some species are more prone to evolve pesticide resistance than others due to their evolutionary history and standing genetic variation. Generalist species might develop pesticide resistance especially rapidly due to pre‐adaptation to handle a wide array of plant allelochemicals. Moreover, research has shown that adaptation to novel host plants could lead to increased pesticide resistance. Exploring such cross‐resistance between host plant range evolution and pesticide resistance development from an ecological perspective is needed to understand its causes and consequences better. Much research has, however, been devoted to the molecular mechanisms underlying pesticide resistance while both the ecological contexts that could facilitate resistance evolution and the ecological consequences of cross‐resistance have been under‐studied. Here, we take an eco‐evolutionary approach and discuss circumstances that may facilitate cross‐resistance in arthropods and the consequences cross‐resistance may have for plant–arthropod interactions in both target and non‐target species and species interactions. Furthermore, we suggest future research avenues and practical implications of an increased ecological understanding of pesticide resistance evolution.
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Affiliation(s)
- Audrey Bras
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden.,Faculty of Forestry and Wood Sciences, EXTEMIT-K and EVA.4.0 Unit, Czech University of Life Sciences, Suchdol, Czech Republic
| | - Amit Roy
- Faculty of Forestry and Wood Sciences, EXTEMIT-K and EVA.4.0 Unit, Czech University of Life Sciences, Suchdol, Czech Republic
| | - David G Heckel
- Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Peter Anderson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Kristina Karlsson Green
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
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Pélissié B, Chen YH, Cohen ZP, Crossley MS, Hawthorne DJ, Izzo V, Schoville SD. Genome resequencing reveals rapid, repeated evolution in the Colorado potato beetle. Mol Biol Evol 2022; 39:6511499. [PMID: 35044459 PMCID: PMC8826761 DOI: 10.1093/molbev/msac016] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Insecticide resistance and rapid pest evolution threatens food security and the development of sustainable agricultural practices, yet the evolutionary mechanisms that allow pests to rapidly adapt to control tactics remains unclear. Here we examine how a global super-pest, the Colorado potato beetle (CPB), Leptinotarsa decemlineata, rapidly evolves resistance to insecticides. Using whole genome resequencing and transcriptomic data focused on its ancestral and pest range in North America, we assess evidence for three, non-mutually exclusive models of rapid evolution: pervasive selection on novel mutations, rapid regulatory evolution, and repeated selection on standing genetic variation. Population genomic analysis demonstrates that CPB is geographically structured, even among recently established pest populations. Pest populations exhibit similar levels of nucleotide diversity, relative to non-pest populations, and show evidence of recent expansion. Genome scans provide clear signatures of repeated adaptation across CPB populations, with especially strong evidence of selection on insecticide resistance genes in different populations. Analyses of gene expression show that constitutive upregulation of candidate insecticide resistance genes drives distinctive population patterns. CPB evolves insecticide resistance repeatedly across agricultural regions, leveraging similar genetic pathways but different genes, demonstrating a polygenic trait architecture for insecticide resistance that can evolve from standing genetic variation. Despite expectations, we do not find support for strong selection on novel mutations, or rapid evolution from selection on regulatory genes. These results suggest that integrated pest management practices must mitigate the evolution of polygenic resistance phenotypes among local pest populations, in order to maintain the efficacy and sustainability of novel control techniques.
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Affiliation(s)
- Benjamin Pélissié
- Department of Entomology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yolanda H Chen
- Department of Plant and Soil Science, University of Vermont, Burlington, VT 05405, USA
| | - Zachary P Cohen
- Department of Entomology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Michael S Crossley
- Department of Entomology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - David J Hawthorne
- Department of Entomology, University of Maryland, College Park, MD 20742, USA
| | - Victor Izzo
- Department of Plant and Soil Science, University of Vermont, Burlington, VT 05405, USA
| | - Sean D Schoville
- Department of Entomology, University of Wisconsin-Madison, Madison, WI 53706, USA
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Cohen ZP, Brevik K, Chen YH, Hawthorne DJ, Weibel BD, Schoville SD. Elevated rates of positive selection drive the evolution of pestiferousness in the Colorado potato beetle (Leptinotarsa decemlineata, Say). Mol Ecol 2020; 30:237-254. [PMID: 33095936 DOI: 10.1111/mec.15703] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 09/28/2020] [Accepted: 10/15/2020] [Indexed: 12/16/2022]
Abstract
Contextualizing evolutionary history and identifying genomic features of an insect that might contribute to its pest status is important in developing early detection and control tactics. In order to understand the evolution of pestiferousness, which we define as the accumulation of traits that contribute to an insect population's success in an agroecosystem, we tested the importance of known genomic properties associated with rapid adaptation in the Colorado potato beetle (CPB), Leptinotarsa decemlineata Say. Within the leaf beetle genus Leptinotarsa, only CPB, and a few populations therein, has risen to pest status on cultivated nightshades, Solanum. Using whole genomes from ten closely related Leptinotarsa species native to the United States, we reconstructed a high-quality species tree and used this phylogenetic framework to assess evolutionary patterns in four genomic features of rapid adaptation: standing genetic variation, gene family expansion and contraction, transposable element abundance and location, and positive selection at protein-coding genes. Throughout approximately 20 million years of history, Leptinotarsa species show little evidence of gene family turnover and transposable element variation. However, there is a clear pattern of CPB experiencing higher rates of positive selection on protein-coding genes. We determine that these rates are associated with greater standing genetic variation due to larger effective population size, which supports the theory that the demographic history contributes to rates of protein evolution. Furthermore, we identify a suite of coding genes under positive selection that are putatively associated with pestiferousness in the Colorado potato beetle lineage. They are involved in the biological processes of xenobiotic detoxification, chemosensation and hormone function.
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Affiliation(s)
- Zachary P Cohen
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
| | - Kristian Brevik
- Department of Plant and Soil Sciences, University of Vermont, Burlington, VT, USA
| | - Yolanda H Chen
- Department of Plant and Soil Sciences, University of Vermont, Burlington, VT, USA
| | - David J Hawthorne
- Department of Entomology, University of Maryland, College Park, MD, USA
| | - Benjamin D Weibel
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
| | - Sean D Schoville
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
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Fontes-Puebla AA, Bernal JS. Resistance and Tolerance to Root Herbivory in Maize Were Mediated by Domestication, Spread, and Breeding. FRONTIERS IN PLANT SCIENCE 2020; 11:223. [PMID: 32174953 PMCID: PMC7056747 DOI: 10.3389/fpls.2020.00223] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 02/12/2020] [Indexed: 05/17/2023]
Abstract
Plants may defend against herbivory and disease through various means. Plant defensive strategies against herbivores include resistance and tolerance, which may have metabolic costs that affect plant growth and reproduction. Thus, expression of these strategies may be mediated by a variety of factors, such as resource availability, herbivory pressure, and plant genetic variation, among others. Additionally, artificial selection by farmers and systematic breeding by scientists may mediate the expression of resistance and tolerance in crop plants. In this study, we tested whether maize defense against Western corn rootworm (WCR) was mediated by the crop's domestication, spread, and modern breeding. We expected to find a trend of decreasing resistance to WCR with maize domestication, spread, and breeding, and a trend of increasing tolerance with decreasing resistance. To test our expectations, we compared resistance and tolerance among four Zea plants spanning those processes: Balsas teosinte, Mexican landrace maize, US landrace maize, and US inbred maize. We measured the performance of WCR larvae as a proxy for plant resistance, and plant growth as affected by WCR feeding as a proxy for plant tolerance. Our results showed that domestication and spread decreased maize resistance to WCR, as expected, whereas breeding increased maize resistance to WCR, contrary to expected. Our results also showed that maize resistance and tolerance to WCR are negatively correlated, as expected. We discussed our findings in relation to ecological-evolutionary hypotheses seeking to explain defense strategy evolution in the contexts of plant resistance-productivity trade-offs, plant tolerance-resistance trade-offs, and varying resource availability vis-à-vis plant physiological stress and herbivory pressure. Finally, we suggested that defense strategy evolution in maize, from domestication to the present, is predicted by those ecological-evolutionary hypotheses.
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Hlaoui A, Boukhris-Bouhachem S, Sepúlveda DA, Correa MCG, Briones LM, Souissi R, Figueroa CC. Spatial and Temporal Genetic Diversity of the Peach Potato Aphid Myzus persicae (Sulzer) in Tunisia. INSECTS 2019; 10:insects10100330. [PMID: 31581571 PMCID: PMC6835240 DOI: 10.3390/insects10100330] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/24/2019] [Accepted: 09/26/2019] [Indexed: 11/20/2022]
Abstract
The peach potato aphid, Myzus persicae (Sulzer), is a worldwide pest of many crops, and the most important aphid pest of peach and potato crops in Tunisia, mainly due to virus transmission, for which insecticides are frequently applied. We studied the genetic structure of M. persicae populations in Tunisia, in order to further our understanding of the biotic and abiotic factors shaping populations and to predict their evolutionary responses to the present management practices. We monitored peach orchards and seed potato crops in different seasons and regions from 2011–2013 and in 2016 (19 populations), assessing the genetic diversity of M. persicae at six microsatellite loci. Temporal and spatial changes in the frequency and distribution of 397 genotypes in 548 sampled aphids were studied. Only 37 genotypes were found more than once (clonal amplification), as most genotypes were found only once (91.60% in peach; 88.73% in potato crops). A similarly high genetic diversity was observed in aphids sampled from peach (G/N = 0.76; Ho = 0.617) and potato (G/N = 0.70; Ho = 0.641). Only a weak genetic differentiation among populations was found, mainly between geographic locations. Clustering analysis revealed genotypes to be grouped mainly according to host plant. The availability of the primary host, high proportion of unique genotypes, high genetic diversity and lack of structuring suggest that the aphid reproduces mainly through cyclical parthenogenesis in Tunisia. On the other hand, we provide a farm-scale study that shows how easily M. persicae can colonize different areas and hosts, which may have important implications in relation to plant virus vectoring.
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Affiliation(s)
- Amen Hlaoui
- Laboratoire de Protection des Végétaux, Institut National de Recherche Agronomique de Tunisie INRAT, Rue Hédi Karray, Ariana 2049, Tunisia.
- Département Santé Végétale et Environnement, Institut National Agronomique de Tunisie INAT, Université de Carthage, 43 Avenue Charles Nicolle, Cité Mahrajène Tunis 1082, Tunisia.
| | - Sonia Boukhris-Bouhachem
- Laboratoire de Protection des Végétaux, Institut National de Recherche Agronomique de Tunisie INRAT, Rue Hédi Karray, Ariana 2049, Tunisia.
| | - Daniela A Sepúlveda
- Centre for Molecular and Functional Ecology in Agroecosystems, Universidad de Talca, Talca 3460000, Chile.
- Facultad de Ciencias Agrarias, Universidad de Talca, Talca 3460000, Chile.
| | - Margarita C G Correa
- Centre for Molecular and Functional Ecology in Agroecosystems, Universidad de Talca, Talca 3460000, Chile.
- Institut National de la Recherche Agronomique INRA, CNRS, ISA, Université Côte d'Azur, 06903 Sophia Antipolis, France.
| | - Lucía M Briones
- Centre for Molecular and Functional Ecology in Agroecosystems, Universidad de Talca, Talca 3460000, Chile.
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca 3460000, Chile.
| | - Rebha Souissi
- Laboratoire de Protection des Végétaux, Institut National de Recherche Agronomique de Tunisie INRAT, Rue Hédi Karray, Ariana 2049, Tunisia.
| | - Christian C Figueroa
- Centre for Molecular and Functional Ecology in Agroecosystems, Universidad de Talca, Talca 3460000, Chile.
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca 3460000, Chile.
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