{"doi":"10.3389/fpls.2025.1627531","title":"The genetic architecture of gene expression regulation in a Citrus x Poncirus hybrid tolerant to Huanglongbing","abstract":"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 ( 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 ( C Las). To explore the genetic architecture of the early transcriptional response to Candidatus Liberibacter asiaticus ( C Las) infection in ‘US-897’, we performed transcriptomic analysis of the hybrid and its parents, ‘Cleopatra’ ( C. reticulata ) and ‘Flying Dragon’ ( P. trifoliata ). A haplotype-resolved 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 C Las were identified to explore how gene regulation associated with tolerance to HLB was rewired between Citrus and its relative Poncirus .","journal":"Frontiers in Plant Science","year":2025,"id":542238,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":2,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9559,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1431355,"name":"Omar Zayed","orcid":"0000-0003-1388-1903","position":1,"is_corresponding":false},{"id":996238,"name":"Emmanuel Ávila de Dios","orcid":"0000-0001-7914-0927","position":2,"is_corresponding":false},{"id":1431795,"name":"Claire Jiang","orcid":null,"position":3,"is_corresponding":false},{"id":492449,"name":"Kim D. Bowman","orcid":"0000-0002-5796-5626","position":4,"is_corresponding":false},{"id":996239,"name":"Danelle K. Seymour","orcid":"0000-0003-2250-8377","position":5,"is_corresponding":false},{"id":1431794,"name":"Isaac A. Diaz","orcid":null,"position":0,"is_corresponding":true}],"reference_count":73,"raw_metadata":null,"created_at":"2026-07-19T02:52:55.809501Z","pmid":"40978800","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}