Molecular Methods for Distinguishing Between Wild and ...€¦ · Citrus health response programs...
Transcript of Molecular Methods for Distinguishing Between Wild and ...€¦ · Citrus health response programs...
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Molecular Methods for Distinguishing Between Wild and Commercial Cotton Variants of
Anthonomus grandis
Raul Ruiz-Arce
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USDA APHIS PPQ Mission Lab (ML)
Molecular methods development at ML
TW/BW diagnostics at ML ◦ Description & performance of three methods
◦ Summary for captures 2011-2015
Recent advancements and future work
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Overview of Facilities, Expertise, and Diagnostics at USDA APHIS
Mission Lab - Edinburg, TX
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4 Molecular Scientists
3 Entomologists
1 GIS Specialist
3 Biologists
1 Plant Pathologist
18 Technicians
3 Office Administration
1 IT specialist
2 Interns
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Citrus health response programs ◦ Detection and ID citrus pests
◦ Citrus greening biocontrol
Mexican fruit fly SIT support ◦ Strain development & QC
◦ Colony health
Molecular diagnostics – Conventional/NGS* ◦ *Fruit flies – ID, Source estimation
◦ BW/TW – variant ID
◦ Helicoverpa – ID methods Old/New World Bollworm
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Organelles
Membranes
DNAs
Their importance
to molecular work
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DNA molecule
Sample preservation
Contaminants
Harvesting DNA
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Why: Pest$ take a big bite We’re a small world Quality food is important
What do they tell us: Confirm ID Differences among species Where pests originate History and movement Speciation
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3 temperature ◦ Denaturing
◦ Annealing
◦ Extension
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Indigenous to C America/S Mexico
Found in Cuba & Haiti in the 1800s
First reported in Texas 1892
S America (1949-1990s)
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Morphological - Burke (1968) and Burke et al (1986)
Molecular ◦ Roehrdanz (2001) ◦ ML RAPD-PCR 1990s – 2000s
Southeastern boll weevil (BW) ◦ Host – commercial cotton (Gossypium hirsutum)
Thurberia weevil (TW) Host – wild cotton (G. thurberi), occurs in N Mexico &
SW US
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Captures ◦ Trapped weevils initiate response
Challenge in using older methods ◦ Morphology (Burke, 1968)
◦ Molecular (Roehrdanz, 2001)
Opportunity for Improving management ◦ ID source of infestation
◦ Helps in decision for management
◦ Reduction to resources
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Molecular Methods (Barr et al., 2013)
Sequencing COI Barcode (Folmer et al 1994)
SCAR (seq characterized amplified region)
Classical Taxonomy (perf by C. Reuter)
Morphometrics (Burke, 1968)
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n=158 weevils 30 sample sites 10 Wild cotton 20 Comm cotton
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503 base pair fragment
Reference database (n=158), 31 unique seqs
◦ N=84, 14 sites in 7 MX states
◦ N=74, 16 sites in 4 US States
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AN2 T C A A C G C G T C A C A C T G G A A A A G T T G T A A A A A C G C A A A T A C T T A T A A A A
AN3 . . . . . . . . . . G . . . . A . . . . . . . . . . . . . . . . . A . . . . . . . . . . . . . .
AN4 . . G . . . . . . . G . . . . . . G . . . . . . . . . . . . . . . A . . . . . . . . . . . . . .
AN6 . . G . . A . . . . G . . . . . . . . . . . . . . . . . . . . . . A . . . . . . . . . . . . . .
AN7 . . G . . . . . . . G . . . . . . G . . . . . . . . . . . . . . . . . . . . . . C . . . T . . .
AN8 . . G . . . . . . . G . . . . . . . . . . . . . . . . . . . . . . A . . G . . . . . . . . . . .
AN14 . . G . . . . . . . G . . . . . . G . . . . . . . . . . . . . . . A G . . . . . . . . . . . . .
AN15 . . . . . . . . . . G . . . . . . . G . . . . . . . . . . . . . A . . . . . . . . C . . . . . .
AN16 . . G . T . . . . . G . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
AN17 . . G . . . . . . . G . . . . . . . . . . . . . . . . . . . . . A . . . . . . . . . . . . . . .
AN18 . . G . . . . . . . G . . . C . . . . . . . . . . . . . . . . . . A . . G . . . . . . . . . . .
AN19 . . G . . . . . . . G . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
AN20 . . . . . . . . . . G . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
AN21 . . G . . . . . . . G . . . . . . . . . . . . . . . . . . . . . A . . . . . . . . . . . . . . .
AN22 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . G . . . . . . . . . . . .
AN23 . . G . . . . A . . G . . . . . . . . . . . . . . . . . . . . . . A . . . . . . . . . . . . . .
AN24 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A . . . . . . . . . . . . . . .
AN26 . T G . . . . . . . G . . . C . . . . . . . . . . . . . . . . . . A . . G . . . . . . . . . . .
AN5 C T G . . . T . C T . . . T . . . . . . . . C C A . . . . . . . . . . . . . . T . . . . . . . T
AN1 G . . G . A . . . T G A . . . A A . . . . . . . A C . C . . G . . . . . . . T . C . . . . G G .
AN9 G . . G . A . . . T . A . . . A . . . . G . . . A C G C . G G T . . . G . C T . C . . C . G . .
AN10 G . . G . A . . . T G A . . . A . . . G . . . . A C G C G . G . . . . . . . T . C . . . . G G .
AN11 G . . G . C . . . T . A . . . A . . . . . . . . A C G C . . G . . . . G . . T . C . . C . G . .
AN12 G . . G . A . . . T . A . . . A . . . . . . . . A C G C . . G . . . . G . . T . C . . C . G . .
AN13 A . . G . A . . . T G A . . . A . . . . . . . . A C G C G . G . . . . . . . T . C . . C . G G .
AN25 G . . G . A . . . T . A . . . A . . . . . . . . A C . C . . G . . . . G . . T . C . . C . G . .
AN27 G . . G . A . . . T . A . . . A . . . . G . . . A C G C . G G T A . . G . C T . C . . C . G . .
AN28 G . . . . A . . . T . A G . . A . . . . . . . . A C G C G . . . . . . . . . T . C . G C . G G .
AN29 G . . G . A . . . T G A . . . A . . . . . . . . A C G C G . G . . . . . . . T . C . . . . G G .
AN30 G . . G . A . . . T G A . . . A . . . G . A . . A C G C G . G . . . . . . . T . C . . . . G G .
AN31 G . . G . A . . . T G A . . . A . . . . . . . . A C . C G . G . . . . . . . T . C . . . . G G .
443
The list of variable nucleotide positions for the 31 COI haplotypes recovered from the Anthonomus spp. specimens. The diagnostic positions distinguishing Thurberia and boll weevil highlighted.
SNPs consistent with boll weevil
TW
BW
* Sonora, Chihuahua, Coahuila, Durango, AZ
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Developed from excised band fixed to BW
- = not BW
+ = BW
Neg C
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Femur Ratio (length:width) (Burke, 1968) ◦ 3.0-3.4 TW
◦ 3.6-4.0 BW
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ID
Morphometrics
SCAR
COI profile
Correct*
89.4%
82.9%
94.3%
Identification results for n=158 with different methods (Barr
et al 2013).
*considered correct when the results agreed w/host
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C. Reuter (Phoenix, Az) Morp ID then,
Shipped to ML
Day 1
• Intake
• DNA Isolation – minimally invasive
Day 2 PCR/Electrophoresis
Day 3 Send off for sequencing
Day 5+ Interpret data/complete report
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Capture Date
n Collection Site
Reported ID
March 2011 30 Ojinaga, Chihuahua
BW
March 2011 30 Delicias, Chihuahua
BW
10 May 2012 3 Sonoyta, Sonora
TW
1 Oct 2014 3 Caborca, Sonora
TW
22 Oct 2014 8 Caborca, Sonora
TW
7 July 2015 1 Delicias, Chihuahua
NOT A. grandis
16 July 2015 2 Nuevo San Lucas, Chi
NOT A. grandis
17 July 2015 1 Delicias, Chihuahua
NOT A. grandis
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Provides early warning ◦ Results to managers within ~5-7days
Helps improve management strategies ◦ Identifies hot spots/feedback
Reduction to resources ◦ TW ID = no spraying, trade is not impacts, etc
◦ BW ID = target only problematic areas
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1. Sequence and assemble the CBW genome
2. Resolve the population genomic structure of A. grandis in northern Mexico
3. Infer movement/dispersal of CBW in northern Mexico and southern Texas
4. Identify source populations of potential reintroductions in southern Texas
5. Additional marker development
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Mediterranean fruit fly (Ceratitis capitata)
• Frequent US infestations (captures)
• Identified informative markers (conserved & fine scale)
• Informative reference database
• Results: Effective tool for determining the source of introductions
• Improve pest management strategies
• Minimize future infestations
• Identify hot-spots
*
*Photograph by: Scott Bauer, USDA
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DNA Marker set A
DNA marker set B
GEO DIST =
=
=
Source = “Below Regional-level”
Source = “Regional-level”