Citrus genomic resources unravel putative genetic determinants of Huanglongbing, a pathogen-triggered immune disease

Abstract

Citrus is one of the most important tree crops worldwide and citrus production is threatened by Huanglongbing (HLB), a devasting citrus disease caused by Candidatus Liberibacter. HLB is a pathogen-triggered immune disease, in which the pathogen initiates systemic and chronic immune responses including the excessive production of reactive oxidative species, which subsequently lead to cell death of phloem tissues and HLB disease symptoms. Here, we identified putative genetic determinants of HLB pathogenicity by integrating citrus genomic resources to characterize the pan-genome of accessions that differ in their response to HLB. Genome-wide association mapping and analysis of allele-specific expression between susceptible, tolerant, and resistant accessions further refined candidates underlying the response to HLB. To enable these analyses we first developed a phased diploid assembly of Citrus sinensis Newhall genome and produced resequencing data for 91 citrus accessions that differ in their response to HLB. These data were combined with previous resequencing data from 356 sequenced accessions for genome-wide association mapping of the HLB response. Genes with HLB pathogenicity were associated with the host immune response, ROS production, and antioxidants. Overall, this study has provided a significant recourse of citrus genomic data and we have identified candidate genes to be further explored to understand the genetic determinants of HLB pathogenicity and to generate HLB resistant/tolerant citrus varieties.