Loci under selection and markers associated with host plant and host-related strains shape the genetic structure of Brazilian populations of Spodoptera frugiperda (Lepidoptera, Noctuidae)

PLoS One. 2018 May 22;13(5):e0197378. doi: 10.1371/journal.pone.0197378. eCollection 2018.

Abstract

We applied the ddRAD genotyping-by-sequencing technique to investigate the genetic distinctiveness of Brazilian populations of the noctuid moth Spodoptera frugiperda, the fall armyworm (FAW), and the role of host-plant association as a source of genetic diversification. By strain-genotyping all field-collected individuals we found that populations collected from corn were composed primarily of corn-strain individuals, while the population collected from rice was composed almost entirely of rice-strain individuals. Outlier analyses indicated 1,184 loci putatively under selection (ca. 15% of the total) related to 194 different Gene Ontologies (GOs); the most numerous GOs were nucleotide binding, ATP binding, metal-ion binding and nucleic-acid binding. The association analyses indicated 326 loci associated with the host plant, and 216 loci associated with the individual strain, including functions related to Bacillus thuringiensis and insecticide resistance. The genetic-structure analyses indicated a moderate level of differentiation among all populations, and lower genetic structure among populations collected exclusively from corn, which suggests that the population collected from rice has a strong influence on the overall genetic structure. Populations of S. frugiperda are structured partially due to the host plant, and pairs of populations using the same host plant are more genetically similar than pairs using different hosts. Loci putatively under selection are the main factors responsible for the genetic structure of these populations, which indicates that adaptive selection on important traits, including the response to control tactics, is acting in the genetic differentiation of FAW populations in Brazil.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Triphosphate / chemistry
  • Alleles
  • Animals
  • Bacillus thuringiensis / genetics*
  • Bayes Theorem
  • Brazil
  • Ecology
  • Gene Library
  • Gene Ontology
  • Genetic Markers*
  • Genetics, Population*
  • Genotype
  • Geography
  • Insecticide Resistance / genetics*
  • Oryza / genetics
  • Plant Diseases / genetics
  • Polymorphism, Single Nucleotide
  • Principal Component Analysis
  • Protein Binding
  • Selection, Genetic*
  • Sequence Analysis, DNA
  • Spodoptera / genetics*
  • Transcriptome
  • Zea mays / genetics

Substances

  • Genetic Markers
  • Adenosine Triphosphate

Grants and funding

This work was supported by Fundação de Amparo à Pesquisa do Estado de São Paulo (http://www.fapesp.br); Fapesp, process 2012/16266-7 (Study design, data collection and analysis). This was a fellowship to KLSB. This work was also supported by the Fundação de Amparo à Pesquisa do Estado de São Paulo (http://www.fapesp.br); Fapesp, process 2011/00417-3 to MMB (Data collection and analysis was performed in the Thunder Computer Cluster). This work was also supported by Conselho Nacional de Desenvolvimento Científico e Tecnológico (http://www.cnpq.br); CNPq process # 403851/2013-0 to CO (Decision to publish.). Monsanto do Brasil Ltda. provided support in the form of salaries for RAC and in collecting field samples, and Instituto Phytus provided support in the form of salaries for JRF and in collecting field samples. The two companies did not have any additional role in the study design and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section.