Insights into the Huanglongbing defense responses in the Australasian citrus species

Citrus production has declined substantially due to Huanglongbing (HLB), a bacterial disease that has caused severe economic losses worldwide. Long-term field studies indicate that citrus species differ in their tolerance to HLB, underscoring the importance of incorporating disease-tolerant traits to sustain the citrus industry. This study investigates phylogenetic relationships and genetic diversity among citrus accessions to support their effective use in breeding programs. Thirty-two citrus accessions representing diverse groups were analyzed using phylogenetic analysis, homozygosity-by-descent analysis, and principal component analysis (PCA). PCA separated the cultivars into two distinct groups, explaining 73.3% of the total genetic variation. This clustering revealed unique genetic diversity within Australasian citrus, underscoring its value for conservation and future research. Australasian accessions, classified as HLB-resistant or HLB-tolerant, were further compared with the susceptible cultivar Citrus sinensis L. Osbeck (Hamlin 1-4-1) to identify potential defense mechanisms using diagnostic variants (DVs). Annotation of transposable elements in these DVs revealed insertions within genes, suggesting potential effects on gene regulation during defense responses. Functional annotation of DVs, based on sequence comparisons shared between resistant and tolerant groups, identified an amino acid substitution present only in susceptible cultivars that may compromise HLB defense. No such substitutions occurred in the Australasian citrus species. The affected genes are associated with key components of plant defense, including signaling pathways, phytohormone regulation, and secondary metabolite biosynthesis. Overall, this study highlights valuable genetic diversity in citrus germplasm for combating HLB.