Huanglongbing (HLB), or citrus greening disease, caused by the phloem-limited bacterium Candidatus Liberibacter asiaticus (CaLas), poses a significant threat to citrus production worldwide. Identifying and developing HLB-tolerant cultivars has become necessary to mitigate its devastating impact. In Lake County, Florida, several Hamlin-type citrus trees, that’s are generally susceptible to HLB exhibited significant tolerance to the disease. The CaLas bacterial titer for most of the surviving trees was comparable to that of the susceptible control trees, and the qPCR Ct values ranged from 28 to 37. The visually tolerant citrus trees had increased chlorophyll and carotenoid content compared to the susceptible control trees. Juice quality assessments indicated a brix-to-acid ratio of 15-25, with other juice parameters meeting current U.S. Grade A standards. Interestingly, despite being labeled as Hamlin cultivars, several of these trees displayed variations in seed count, some aligning more with Parson Brown cultivars. To investigate their genetic origin, whole-genome DNA sequencing was performed on these trees, as well as on several Hamlin and Parson Brown clones. Genomic analysis revealed that the escape trees were genetically diverse; most were either likely Parson Brown types or Hamlin clones. Among them, two promising lines, R20-T30 (Parson Brown-type) and R21-T36 (Hamlin-type) were identified as superior and included in the 2024 Citrus Research and Field Trials (CRAFT) program. Both cultivars have demonstrated excellent yield and juice quality. Hamlin types, such as Hamlin 1-4-1 and Hamlin R21-T36, and Parson Brown types, such as Parson Brown F-56-2 and Parson Brown R20-T30, also displayed differences at the genomic level. Whole genome sequencing of the root DNA from these escape trees identified nucellar or zygotic Swingle as the predominant rootstock among escape trees with others similar to Carrizo and Poncirus trifoliata rootstocks. These findings underscore the role of genetic analysis in identifying HLB-tolerant cultivars, establishing a foundation for targeted breeding strategies aimed at improving citrus resilience to HLB.
