Parallel genome-wide association studies using SNP- and k-mer-based methods to identify genomics underlying variable vector acquisition phenotype in Diaphorina citri

Variable vector capacity hinders long-term solutions for vector transmitted diseases in agriculture, often leading to misaligned lab-to-field results and rapid insecticide resistance. We studied vector capacity of Diaphorina citri (Asian citrus psyllid), the hemipteran vector of a phloem-limited, unculturable bacteria "Candidatus Liberibacter asiaticus" (CLas). CLas is the causative agent of Huanglongbing (HLB), a global threat for all citrus trees, currently devastating the US citrus industry. Growers are desperate for a cure and HLB management relies on heavy insecticide and antibiotic applications to slow tree death. Prior research showed that D. citri acquires and transmits CLas in a circulative, propagative manner, and that CLas acquisition rate and mean titer is a generationally stable, population-specific phenotype. We hypothesize that the ability to acquire CLas is a heritable, quantitative trait regulated by D. citri genetics. Genome-wide association studies (GWAS) and mitochondrial haplotyping utilized 500 individuals collected from four active citrus groves in Florida, USA. Our model addressed sampling bias, grove effects, kinship, and variability, and was made possible by a high quality, chromosomal-level reference genome. We identified single-nucleotide polymorphisms, genes and loci linked to CLas acquisition, showing our phenotype comprises a polygenic, multi-locus network likely linked with an environmental component. Moving forward, functional annotation of genes and K-mer-based GWAS will clarify biological insights. Our unique application of GWAS to a qualitative phenotype in a non-model insect vector highlights the significance of high-quality reference genomes, unveils genetic architecture of an invasive agricultural pest, and opens new avenues for studying vector-pathogen-plant interactions.