Haplotype-resolved transcriptomics defines the inheritance and genetic architecture of response to Huanglongbing disease

Interspecific hybridization is a common and effective strategy for producing disease resilient citrus rootstocks, including those with tolerance to Huanglongbing (HLB) disease. Several HLB-tolerant rootstocks have been developed through hybridization of mandarin cultivars (Citrus reticulata) with their wild relative Poncirus trifoliata. One such cultivar, US-897, exhibits robust tolerance to the bacteria causing HLB disease, Candidatus Liberibacter asiaticus and confers improved performance of the grafted scion in production regions where HLB is endemic. To explore the basis of disease tolerance in this hybrid and to investigate the genetic architecture of gene expression regulation, we performed transcriptomic analysis of the hybrid and its parents, Cleopatra (C. reticulata) and Flying Dragon (P. trifoliata), including in response to CLas infection.