Collaborative Research: RESEARCH-PGR: The genomics of host-specific response and adaptation in the parasitic agricultural pest, Cuscuta

Cuscuta (common name: dodder; Convolvulaceae) is a diverse genus of parasitic plants that causes major crop losses across the US and the globe. While dodder that are major pests attack a wide range of host species, many show host preferences, and dodder growth varies substantially across hosts. This apparent host preference suggests some dodder genotypes and populations are adapted to a particular set of hosts. Understanding the genetic mechanisms of these host preferences could help farmers in their battle against dodder. The central biological question of this project is: how do agriculturally relevant Cuscuta species successfully parasitize a wide range of hosts? The research team will study variation in DNA sequence and gene expression across diverse dodder populations across diverse host species to answer this question. Additionally, the team will pursue agronomic research, extension, and outreach as a part of broader impacts. In particular, the team will identify dodder-resistant cultivars of blueberries and determine the role of over-wintering of dodder in driving subsequent year infestations. Additionally, lessons in plant biology and research projects will be developed with blind and visually impaired and deaf and hard of hearing students. The research team will address the central question, how do agriculturally relevant Cuscuta species successfully parasitize a wide range of hosts, with three main aims: 1) profiling the diversity of trans-species miRNAs across Cuscuta populations and identifying their host mRNA targets, 2) resequencing Cuscuta genomes to characterize population genetic processes affecting miRNA diversity and host-specificity, and 3) determining how genetic variation in Cuscuta response to hosts is driven by gene expression and associated with success of attachments to hosts. The study will cover the two most common species of Cuscuta in the study region of the northeast US, C. campestris and C. gronovii. Small RNA sequencing will be used combined with host transcriptome assemblies to study the diversity of trans-species miRNAs and their targets across the region. Inference of the importance of miRNA variation will be tested using mutants in host mRNA targets. Population genetic inference will be applied to understand what evolutionary processes have shaped diversity in host-responsive genetic loci. Microscopy and RNAseq will be used to study how genetic variation in Cuscuta interacts with different host species to determine attachment success and gene expression. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.