Skip to main content

ORIGINAL RESEARCH article

Front. Plant Sci.
Sec. Plant Bioinformatics
Volume 15 - 2024 | doi: 10.3389/fpls.2024.1503030
This article is part of the Research Topic Precision Exploration of Plant Germplasm Resources: Breakthroughs and Applications in Telomere-to-Telomere (T2T) Genomics View all 4 articles

Deep R-Gene Discovery in HLB Resistant Wild Australian Limes Uncovers Evolutionary Features and Potentially Important Loci for Hybrid Breeding

Provisionally accepted
Jianyang Liu Jianyang Liu 1Khushwant Singh Khushwant Singh 2Matthew Huff Matthew Huff 3Christopher Gottschalk Christopher Gottschalk 1Michael Do Michael Do 1Margaret Staton Margaret Staton 3Manjunath Keremane Manjunath Keremane 4Robert Krueger Robert Krueger 4Chandrika Ramadugu Chandrika Ramadugu 2Chris Dardick Chris Dardick 1*
  • 1 Innovative Fruit Production, Improvement, and Protection, Agricultural Research Service (USDA), Kearneysville, West Virginia, United States
  • 2 Department of Botany and Plant Sciences, College of Natural and Agricultural Sciences, University of California, Riverside, Riverside, California, United States
  • 3 Department of Entomology and Plant Pathology, Herbert College of Agriculture, The University of Tennessee, Knoxville, Knoxville, Tennessee, United States
  • 4 National Clonal Germplasm Repository for Citrus, Agricultural Research Service (USDA), Riverside, California, United States

The final, formatted version of the article will be published soon.

    Huanglongbing (HLB) is a devastating citrus disease that threatens the citrus industry globally.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 HLBresistance at the genomic level, we annotated and characterized the R-genes in the genomes of five citrus species with different HLB-resistance levels. Among these species, three were wild Australian limes rated as HLB-resistant (Citrus glauca) and HLB-tolerant (C. australasica and C. inodora), and two were cultivated species (C. clementina and C. sinensis) both rated as susceptible. Using a R-gene specific pipeline, we found that up to 70% of the R-genes were unannotated in the original genomes of each species, largely due to the methods used that do not account for impacts of masking. Surprisingly, the two cultivated species harbored 15.8 to 104% more R-genes than the Australian limes. In all species, over 75% of the R-genes occurred in clusters and nearly 80% were concentrated in three chromosomes (Chr3, 5 and 7). The syntenic R-gene based phylogenic classification grouped the five species according to their HLBresistance levels, reflecting the association between these R-genes and their distinct Australian origins. Domain structure analysis revealed substantial similarities in the R-genes between wild Australian limes and cultivated citrus. Investigation of chromosomal sites underlying Australianspecific R genes revealed diversifying selection signatures on several chromosomal regions. The findings in this study will aid in the development of tools for genome-assisted breeding for HLBresistant varieties.

    Keywords: Citrus, Honglongbing (HLB), R-genes, Australian limes, Resistance

    Received: 27 Sep 2024; Accepted: 23 Dec 2024.

    Copyright: © 2024 Liu, Singh, Huff, Gottschalk, Do, Staton, Keremane, Krueger, Ramadugu and Dardick. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Chris Dardick, Innovative Fruit Production, Improvement, and Protection, Agricultural Research Service (USDA), Kearneysville, 25430, West Virginia, United States

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.