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ARS Home » Northeast Area » Kearneysville, West Virginia » Appalachian Fruit Research Laboratory » Innovative Fruit Production, Improvement, and Protection » Research » Publications at this Location » Publication #419742
Research Project: Superior Fruit Tree Cultivars for Orchard Resilience, Sustainability, and Consumer Appeal

Location: Innovative Fruit Production, Improvement, and Protection

Title: Comparative genomic analysis of R-genes reveals similarities and polymorphisms between HLB-resistant wild Australian limes and susceptible cultivated citrus

Author
item LIU, JIANYANG - Oak Ridge Institute For Science And Education (ORISE)
item SINGH, KHUSHWANT - University Of California, Riverside
item HUFF, MATTHEW - University Of Tennessee
item Gottschalk, Christopher
item Do, Michael
item STATON, MARGARET - University Of Tennessee
item Keremane, Manjunath
item Krueger, Robert
item RAMADUGU, CHANDRIKA - University Of California, Riverside
item Dardick, Christopher

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/23/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary: Huanglongbing (HLB) is a highly destructive disease in citrus and has caused tremendous economic losses in many citrus production regions worldwide. The long-term solution to defend HLB is to breed HLB resistant varieties. This can be achieved by using wild citrus varieties that have natural resistance to HLB, such as some wild Australian limes. In this study, we examined the resistance genes, which are responsible for disease detection, in three HLB resistant Australian limes, in comparison with two HLB susceptible citrus cultivars. Our results showed high similarity in the structure of resistance genes in each species. We also identified some genes that were different between the wild and cultivated citrus, and these genes can serve as potential targets for breeding HLB resistant citrus varieties.

Technical Abstract: Huanglongbing (HLB) is a devastating citrus disease that globally threatens the citrus industry. HLB is associated with the bacteria Candidatus Liberibacter asiaticus (CLas) and lacks tools for economically viable disease management. Previous field evaluation of citrus germplasm identified Australian wild limes as naturally tolerant/resistant to HLB. The resistance was hypothesized to be conferred by resistance genes (R-genes), the products of which mediate pathogen-specific defense responses. To gain insight into the mechanisms underlying HLB-resistance, we annotated and categorized the R-genes of three Australian limes (Citrus australasica, C. inodora, and C. glauca) using a R-gene specific pipeline FindPlantNLRs and compared the identified R-genes with two cultivated Citrus species (C. clementina and C. sinensis). This pipeline produced comprehensive R-gene annotation, revealing many novel R-genes in each species. Based on analysis of a subset of syntenic R-genes common to all the five taxa studied, the species clustered according to their HLB-resistance patterns. However, the domain structures of the R-genes exhibited substantial similarities between wild Australian limes and cultivated Citrus species. Investigation of chromosomal sites underlying resistance-differentiating genes revealed diversifying selection signatures on several regions of chromosomes. This study may lead to the development of tools for genome-assisted breeding for HLB-resistant varieties.