The genetic architecture of gene expression regulation in a Citrus x Poncirus hybrid tolerant to Huanglongbing

Interspecific hybridization is a common and effective strategy for producing disease resilient citrus cultivars, including those with tolerance to Huanglongbing (HLB) disease. Several HLB-tolerant cultivars have been developed through hybridization of mandarins (<i>Citrus reticulata</i>) with their wild relative <i>Poncirus trifoliata</i>. One such cultivar, 'US-897', exhibits robust tolerance to the bacteria causing HLB disease, <i>Candidatus Liberibacter asiaticus</i> (<i>C</i>Las). To explore the genetic architecture of the early transcriptional response to <i>Candidatus</i> Liberibacter asiaticus (<i>C</i>Las) infection in 'US-897', we performed transcriptomic analysis of the hybrid and its parents, 'Cleopatra' (<i>C. reticulata</i>) and 'Flying Dragon' (<i>P. trifoliata</i>). A haplotype-resolved genome for 'US-897' was generated using PacBio HiFi sequencing reads to support quantification of the expression of both the <i>Citrus and Poncirus</i> alleles. By profiling gene expression in this parent-offspring trio, we were able to determine the mode of inheritance for genes differentially expressed between parents ('Cleopatra' and 'Flying Dragon') and their interspecific hybrid ('US-897'), with the majority genes exhibiting non-additive patterns of gene expression inheritance. Additionally, analysis of allele-specific expression in the hybrid 'US-897' revealed the contribution of cis- versus trans-acting regulatory variants on genes with additive and non-additive modes of inheritance. A strong correlation between differential expression between parents and allele-specific expression in 'US-897' suggests that cis-regulatory variation is a significant source of expression divergence between species. Finally, genes responsive to infection with <i>C</i>Las were identified to explore how gene regulation associated with tolerance to HLB was rewired between <i>Citrus</i> and its relative <i>Poncirus</i>.