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

Authors: DIAZ, ISAAC - University Of California, Riverside; ZAYED, OMAR - University Of California, Riverside; ÁVILA DE DIOS, EMMANUEL - University Of California, Riverside; JIANG, CLAIRE - University Of California, Riverside; Bowman, Kim; SEYMOUR, DANELLE - University Of California, Riverside

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/31/2025
Publication Date: 9/4/2025
Citation: Diaz, I., Zayed, O., Ávila De Dios, E., Jiang, C., Bowman, K.D., Seymour, D.K. The genetic architecture of gene expression regulation in a Citrus x Poncirus hybrid rootstock tolerant to Huanglongbing. Frontiers in Plant Science. 16:1627531. 2025. https://doi.org/10.3389/fpls.2025.1627531.
DOI: https://doi.org/10.3389/fpls.2025.1627531

Interpretive Summary: Interspecific hybridization is a common and effective strategy for producing disease-resilient crops, and this has been applied to develop citrus scions and rootstocks resilient to the devastating bacterial citrus disease, Huanglongbing (HLB). One hybrid with strong HLB-resilience is US-897, a hybrid of mandarin (Citrus reticulata) and a wild relative Poncirus trifoliata. US-897 has good characteristics for use as a citrus rootstock in an environment affected by HLB disease. Our study aimed to explore the genetic basis of tolerance to HLB in US-897, and how that tolerance was inherited from the two parents. Genes responsive to infection with the HLB disease were identified and used to explore how gene regulation associated with tolerance to HLB was rewired in hybrids between Citrus and its relative Poncirus.

Technical Abstract: 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 (CLas), 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. A phased, diploid genome for US-897 was generated using PacBio HIFI sequencing reads to support quantification of the expression of both the Citrus and Poncirus 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 CLas were identified to explore how gene regulation associated with tolerance to HLB was rewired between Citrus and its relative Poncirus.