Grant Information

AN NGS-BASED SYSTEM FOR UNAMBIGUOUS DETECTION OF HLB PATHOGEN

Sponsoring Institution Agricultural Research Service/USDA
Status ACTIVE
Funding Source USDA INHOUSE
Reporting Frequency Annual
Project Director CHEN J
Accession Number 433822
Project Number 2034-22000-014-001R
Dates 2017-10-01 - 2021-09-30
Recipient Organization AGRICULTURAL RESEARCH SERVICE

PARLIER,CA 93648
Keywords asiaticus
candidatus
generation
high
hlb
huanglongbing
liberibacter
next
sequencing
throughput
Research Effort Applied (30%)
Basic (60%)
Developmental (10%)
Classification Parameters
Knowledge AreaSubject of InvestigationField of SciencePercent
212 - Pathogens and Nematodes Affecting Plants 999 - Citrus, general/other 1040 - Molecular biology 70%
212 - Pathogens and Nematodes Affecting Plants 1131 - Wine grapes 1040 - Molecular biology 10%
215 - Biological Control of Pests Affecting Plants 1130 - Table grapes 1040 - Molecular biology 10%
215 - Biological Control of Pests Affecting Plants 1139 - Grapes, general/other 1040 - Molecular biology 10%
Goals / Objectives

The aim is to develop a detection system that can unambiguously identify "Candidatus Liberibacter asiaticus", an unculturable bacterium associated with Huanglongbing (HLB), when the bacterial concentration is very low and current polymerase chain reaction (PCR) techniques could not make a clear conclusion. There are three objectives:

  1. Effective enrichment of low titer CLas DNA from HLB suspected sample
  2. Identify a cost-effective protocol for sample sequencing
  3. Evaluate and finalize an analytical pipeline for accurate and sensitive detection of CLas.
Methods (unparsed)

The system will make direct identification of sequences of PCR template using the up-to-date next generation sequencing/high throughput sequencing technology. Sequence data will be compared to signature sequences of "Candidatus Liberibacter asiaticus" of taxonomic authority. The detection result will be either a yes (matched) or a no (un-matched), without ambiguity.

Methods
The system will make direct identification of sequences of PCR template using the up-to-date next generation sequencing/high throughput sequencing technology. Sequence data will be compared to signature sequences of "Candidatus Liberibacter asiaticus" of taxonomic authority. The detection result will be either a yes (matched) or a no (un-matched), without ambiguity.