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United States Department of Agriculture

Agricultural Research Service

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Research Project: Development of SSR Markers for Detection, Genotyping, Phenotyping and Genetic Diversity Assessment of CA. Liberibacter Strains in Florida

Location: Crop Diseases, Pests and Genetics

2011 Annual Report


1a.Objectives (from AD-416)
1. Perform genome-wide sequence analysis to identify Simple Sequence Repeat (SSR) loci. 2. Genotyping and phenotyping of CLas strains, characterizing virulent strains, host pathogen interactions; adaptation, selection and strain – strain competition. 3. Analyzing CLas population structures, assessing genetic diversity of CLas in Florida populations.


1b.Approach (from AD-416)
1. Complete genome gaps from current draft genome using long distance PCR and genomic walking techniques. 2. PCR and fragment analyses of asiaticus isolates collected from Florida populations. 3. Conduct molecular variance analysis to assess hierarchical structures of pathogen population in Florida. Documents Trust with Florida Citrus Production Research Advisory Council. Log 43636.


3.Progress Report

This Trust Agreement supports Objective 1.B of the parent project. The overall goal of the project is to investigate the genetic diversity and structure of global populations of “Candidatus Liberibacter asiaticus’ (Las) strains associated with citrus huanglongbing (HLB) disease. A panel of 7 simple sequence repeat (SSR) molecular markers was developed to construct genotypic profiles for nearly 300 Las strains collected from the US, China, India, Brazil, Cambodia, Vietnam, Taiwan, Thailand, and Japan. Analysis of SSR genotype profiles identified three major clonal complexes of Las associated with HLB: one clonal complex is composed of strains from India, two additional clonal complexes are composed of strains from other regions. Genetic analyses further revealed that recent outbreaks of huanglongbing in Florida were likely caused by Las strains introduced from China and Brazil. The multilocus SSR genotype system developed in this study provides improved resolution for strain discrimination, tracking movement of strains and assessing genetic diversity of HLB-associated Las populations.


Last Modified: 4/18/2014
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