Soybean farmers in Brazil are losing crops to eight species of caterpillar that are evolving resistance to pesticides faster than scientists can track them. This project tackles a fundamental question in biology—whether evolution repeats itself in predictable ways when different species face the same pressures—while also solving a practical crisis in global food production. The researchers will sequence the complete genomes of five pest species (three are already done), then analyse DNA from 800 sites across Brazil collected over six years. They will look for genetic signatures of population expansion and collapse, map how pests move across the landscape, and identify which genes allow caterpillars to survive Bt toxins engineered into soybean plants. If successful, the team will produce an amplicon panel—a cheap, rapid DNA test—that Brazilian farmers and regulators can use to spot emerging insecticide resistance in real time, rather than waiting for crop failure. The genomic data will also reveal whether evolution is predictable enough to anticipate which resistance genes will appear next. This is primarily fundamental science about the repeatability of evolution, but with a direct pipeline to practical pest monitoring tools that could protect a multi-billion-dollar agricultural supply chain.
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Evolution by natural selection can occur rapidly and over short timescales, but the degree to which such short-term evolution is predictable and repeatable between populations and species remains unclear. Recent analytical advances offer the ability to address hypotheses over recent timescales from genomic data, but tracing the repeatability of selection will also require fine scale spatial and temporal sampling across multiple species. Here we explore signatures of demography and selection in a guild of species critical to global food security: the lepidopteran soybean pests of Brazil. Taking advantage of an established international collaboration with Brazilian scientists, we will study a unique collection of eight soybean pest species collected from 800 sites across Brazil over six years. The project has the following goals: Reference genome assembly for a pest guild: First, we will build reference genomes for five species, such that high quality chromosome level reference genomes are available for the entire guild of pests (three species are already sequenced). Population genomics of expanding crop pests: Next, using whole genome re-sequencing we will study the recent population history of the 8 species, to explore signatures of variation in the genome across an entire guild of species found in the same agricultural environments. These species have contrasting recent histories of expansion and contraction in response to changes in control measures, offering a unique opportunity to compare census and genetic estimates of population size across species. We will then apply novel cutting edge methods developed for humans to explore movement across the landscape, identifying connectivity and barriers. Identify the genetic basis for recent selection: We will test how often the same regions of the genome are implicated in climate and crop adaptation across species subjected to the same selection pressures. We will conduct genome wide association studies to identify genetic variants associated with climatic variables, and with transgenic crop type. This will be complimented by genome-wide selection scans, drawing a link between genotype and selection pressure. We will also take advantage of our temporal sampling to look for consistent changes in allele frequency through time to test whether allele frequency changes are repeatable across geographic space and between species. Develop an amplicon panel for cost effective genomic monitoring of pest species and insecticide resistance: Finally, we will use the genomic data acquired here to develop an amplicon panel for rapid monitoring of lepidopteran pests and their resistance to control measures. This will allow rapid acquisition of genome-scale information on pest outbreaks as they occur, greatly facilitating pest monitoring. It will also allow provide detailed temporal data for much larger sample sizes, to further test our hypotheses regarding the action of selection. Training workshop: We will run a genomics training workshop in the UK for Brazilian and UK postgraduate students. The project will explore fundamental questions about the repeatability of evolution over short timescales, as well as generating detailed knowledge of pest movement and demography, identifying genes associated with Bt resistance, and developing a tool for rapid pest monitoring. The genomic resources generated will serve as valuable tools for future research in pest biology and resistance. This project is highly relevant to BBSRC’s long-term research and innovation priorities, particularly in sustainable agriculture and crop protection and fits the BBSRC research priority “Understanding the rules of life” and strategic impact priority “Sustainable agriculture and food”.
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