Genomic patterns of strain-specific genetic structure, linkage, and selection across fall armyworm populations
Abstract Background Molecular genetic approaches have become vital to understanding the evolutionary processes that act on insect pest populations. From mapping the development of resistance to monitoring and predicting pest movement, genomic tools can inform and enhance pest management programs. He...
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2025-02-01
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| Online Access: | https://doi.org/10.1186/s12864-025-11214-8 |
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| author | Ashley E. Tessnow Rodney N. Nagoshi Robert L. Meagher Todd M. Gilligan Ben M. Sadd Yves Carrière Holly N. Davis Shelby J. Fleischer Kelly Richers John C. Palumbo Patrick Porter Jose Carlos Verle Rodrigues Gregory A. Sword |
| author_facet | Ashley E. Tessnow Rodney N. Nagoshi Robert L. Meagher Todd M. Gilligan Ben M. Sadd Yves Carrière Holly N. Davis Shelby J. Fleischer Kelly Richers John C. Palumbo Patrick Porter Jose Carlos Verle Rodrigues Gregory A. Sword |
| author_sort | Ashley E. Tessnow |
| collection | DOAJ |
| description | Abstract Background Molecular genetic approaches have become vital to understanding the evolutionary processes that act on insect pest populations. From mapping the development of resistance to monitoring and predicting pest movement, genomic tools can inform and enhance pest management programs. Here, we used whole genome sequencing population genomics to unravel novel patterns of population structure, linkage, and selection across the genome of a notorious agricultural pest, the fall armyworm. Results Our data strongly support the existence of two genetically distinct strains of fall armyworm in North America, which have previously been referred to as the C-strain and the R-strain. Although these strains have diverged genetically, we find that differentiation is not uniform across the genome. The Z-chromosome appears to drive divergence between strains with high levels of linkage observed across this chromosome. We also show that a region of the Z-chromosome containing a circadian clock gene implicated in allochronic reproductive isolation is under strain-specific selection. Our data indicates that strains differ in their geographic distributions and exhibit distinct patterns of geographic sub-structuring indicative of unique dispersal patterns. We provide the first evidence for nuclear genomic differentiation between the two major overwintering populations of fall armyworm in the US. Finally, our data reveal population-specific patterns of selection on genomic regions containing putative insecticide resistance alleles, which could relate to their biogeography. Conclusions Our results support the existence of the fall armyworm as a pest dyad in the US, with genetically-distinct strains differing in their population structure, dispersal patterns, and genomic signatures of selection on regions likely involved reproductive isolation and insecticide resistance. These differences should be considered when devising and implementing management strategies. |
| format | Article |
| id | doaj-art-1b85eaf91937467494bc18d910c66e1a |
| institution | Kabale University |
| issn | 1471-2164 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj-art-1b85eaf91937467494bc18d910c66e1a2025-02-09T12:13:54ZengBMCBMC Genomics1471-21642025-02-0126111610.1186/s12864-025-11214-8Genomic patterns of strain-specific genetic structure, linkage, and selection across fall armyworm populationsAshley E. Tessnow0Rodney N. Nagoshi1Robert L. Meagher2Todd M. Gilligan3Ben M. Sadd4Yves Carrière5Holly N. Davis6Shelby J. Fleischer7Kelly Richers8John C. Palumbo9Patrick Porter10Jose Carlos Verle Rodrigues11Gregory A. Sword12Department of Entomology, Texas A&M UniversityCenter for Medical, Agricultural and Veterinary Entomology, Department of Agriculture-Agricultural Research ServiceCenter for Medical, Agricultural and Veterinary Entomology, Department of Agriculture-Agricultural Research ServiceDepartment of Agricultural Biology, Colorado State UniversitySchool of Biological Sciences, Illinois State UniversityDepartment of Entomology, University of ArizonaTexas A&M AgriLife Research and ExtensionDepartment of Entomology, The Pennsylvania State UniversityThe Wedge Entomological Research FoundationDepartment of Entomology, University of ArizonaTexas A&M AgriLife Research and ExtensionInsect Management and Molecular Diagnostics Lab, Department of Agriculture - Animal and Plant Health Inspection ServiceDepartment of Entomology, Texas A&M UniversityAbstract Background Molecular genetic approaches have become vital to understanding the evolutionary processes that act on insect pest populations. From mapping the development of resistance to monitoring and predicting pest movement, genomic tools can inform and enhance pest management programs. Here, we used whole genome sequencing population genomics to unravel novel patterns of population structure, linkage, and selection across the genome of a notorious agricultural pest, the fall armyworm. Results Our data strongly support the existence of two genetically distinct strains of fall armyworm in North America, which have previously been referred to as the C-strain and the R-strain. Although these strains have diverged genetically, we find that differentiation is not uniform across the genome. The Z-chromosome appears to drive divergence between strains with high levels of linkage observed across this chromosome. We also show that a region of the Z-chromosome containing a circadian clock gene implicated in allochronic reproductive isolation is under strain-specific selection. Our data indicates that strains differ in their geographic distributions and exhibit distinct patterns of geographic sub-structuring indicative of unique dispersal patterns. We provide the first evidence for nuclear genomic differentiation between the two major overwintering populations of fall armyworm in the US. Finally, our data reveal population-specific patterns of selection on genomic regions containing putative insecticide resistance alleles, which could relate to their biogeography. Conclusions Our results support the existence of the fall armyworm as a pest dyad in the US, with genetically-distinct strains differing in their population structure, dispersal patterns, and genomic signatures of selection on regions likely involved reproductive isolation and insecticide resistance. These differences should be considered when devising and implementing management strategies.https://doi.org/10.1186/s12864-025-11214-8Spodoptera frugiperdaPopulation genomicsStrain divergenceZ-chromosome |
| spellingShingle | Ashley E. Tessnow Rodney N. Nagoshi Robert L. Meagher Todd M. Gilligan Ben M. Sadd Yves Carrière Holly N. Davis Shelby J. Fleischer Kelly Richers John C. Palumbo Patrick Porter Jose Carlos Verle Rodrigues Gregory A. Sword Genomic patterns of strain-specific genetic structure, linkage, and selection across fall armyworm populations BMC Genomics Spodoptera frugiperda Population genomics Strain divergence Z-chromosome |
| title | Genomic patterns of strain-specific genetic structure, linkage, and selection across fall armyworm populations |
| title_full | Genomic patterns of strain-specific genetic structure, linkage, and selection across fall armyworm populations |
| title_fullStr | Genomic patterns of strain-specific genetic structure, linkage, and selection across fall armyworm populations |
| title_full_unstemmed | Genomic patterns of strain-specific genetic structure, linkage, and selection across fall armyworm populations |
| title_short | Genomic patterns of strain-specific genetic structure, linkage, and selection across fall armyworm populations |
| title_sort | genomic patterns of strain specific genetic structure linkage and selection across fall armyworm populations |
| topic | Spodoptera frugiperda Population genomics Strain divergence Z-chromosome |
| url | https://doi.org/10.1186/s12864-025-11214-8 |
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