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Max FeldmanWA/OR Potato Conference
Kennewick, WAJanuary 23rd, 2020
Genetics, Measurement, and Standardization in the Potato
Genetics Lab at USDA-ARS Prosser
Research Background
Research TechnicianUniversity of Arizona(2004-2006)
Graduate Research AssistantWashington State University(2006-2012)
Postdoctoral Research AssociateDonald Danforth Plant Science Center(2013-2018)
0
5
10
15
20
height_27_BP14
Chromosome
lod
1 2 3 4 5 6 7 8 9
[email protected]@34.9
[email protected]@78.3
Sabelli PA, .. Feldman M.. (2013) DOI: 10.1073/pnas.1304903110
Feldman MJ et al., 2015DOI: 10.1007/s00425-015-2322-4
Feldman MJ et al., 2017DOI: 10.1371/journal.pgen.1006841
Mission: Breed a More Profitable and Sustainable Potato
Mission: Breed a More Profitable and Sustainable Potato
Identify and introgress disease resistance alleles into production clones
(Guenthner 2009)
Fumigation is a major expense
Mission: Breed a More Profitable and Sustainable Potato
Identify and introgress disease resistance alleles into production clones
(Guenthner 2009)
Fumigation is a major expense
Mission: Breed a More Profitable and Sustainable Potato
Identify and introgress disease resistance alleles into production clones
Pathogens
Columbia Root Knot Nematode (CRKN)
Stubby Root Nematode (SRN)
Tobacco rattle virus (TRV)
Potato virus Y (PVY)
(Guenthner 2009)
Mission: Breed a More Profitable and Sustainable Potato
Develop specialty potato clones for fresh market and chipping industry
Yield, size, disease resistance, chemical composition, storage and skin quality are important traits
Purple Pelisse AmaRosa Yukon Nugget
Genetics
Tri-State Breeding Program
20-hills, 2 repsKlamath (SI)
Single Hills Klamath Falls (~60,000 in Field)
20-hills, 2 repsOntario
20-hills, 2 repsHermiston
4-hills (~700)Hermiston
CrossesAberdeen, ID, Prosser, WA and Oregon
Seedling tuber productionCorvallis (~60,000 in GH)
15-hills (~700)Klamath Falls (SI)
Oregon Statewide trials3 Locations
Tri-State TrialsID, OR, WA
W. Regional TrialsCA, CO, ID, OR, TX, WA
NameTri-State release, PVP
Klamath Falls (SI)
Yr. 1
Yr. 2
Yr. 3
Yr. 4-6
Yr. 6-8
Yr. 8-10
Yr. 10-12
Field Generation
Potato is a Clonal Crop
Slide credit: Sagar Sathuvalli
Tri-State Breeding Program
20-hills, 2 repsKlamath (SI)
Single Hills Klamath Falls (~60,000 in Field)
20-hills, 2 repsOntario
20-hills, 2 repsHermiston
4-hills (~700)Hermiston
CrossesAberdeen, ID, Prosser, WA and Oregon
Seedling tuber productionCorvallis (~60,000 in GH)
15-hills (~700)Klamath Falls (SI)
Oregon Statewide trials3 Locations
Tri-State TrialsID, OR, WA
W. Regional TrialsCA, CO, ID, OR, TX, WA
NameTri-State release, PVP
Klamath Falls (SI)
Yr. 1
Yr. 2
Yr. 3
Yr. 4-6
Yr. 6-8
Yr. 8-10
Yr. 10-12
Field Generation
Potato is a Clonal Crop
Slide credit: Sagar Sathuvalli
Single Hill Selection
Single Hill Selection
Tri-State Breeding Program
20-hills, 2 repsKlamath (SI)
Single Hills Klamath Falls (~60,000 in Field)
20-hills, 2 repsOntario
20-hills, 2 repsHermiston
4-hills (~700)Hermiston
CrossesAberdeen, ID, Prosser, WA and Oregon
Seedling tuber productionCorvallis (~60,000 in GH)
15-hills (~700)Klamath Falls (SI)
Oregon Statewide trials3 Locations
Tri-State TrialsID, OR, WA
W. Regional TrialsCA, CO, ID, OR, TX, WA
NameTri-State release, PVP
Klamath Falls (SI)
Yr. 1
Yr. 2
Yr. 3
Yr. 4-6
Yr. 6-8
Yr. 8-10
Yr. 10-12
Field Generation
Potato is a Clonal Crop
Slide credit: Sagar Sathuvalli
Tri-State Breeding Program
20-hills, 2 repsKlamath (SI)
Single Hills Klamath Falls (~60,000 in Field)
20-hills, 2 repsOntario
20-hills, 2 repsHermiston
4-hills (~700)Hermiston
CrossesAberdeen, ID, Prosser, WA and Oregon
Seedling tuber productionCorvallis (~60,000 in GH)
15-hills (~700)Klamath Falls (SI)
Oregon Statewide trials3 Locations
Tri-State TrialsID, OR, WA
W. Regional TrialsCA, CO, ID, OR, TX, WA
NameTri-State release, PVP
Klamath Falls (SI)
Yr. 1
Yr. 2
Yr. 3
Yr. 4-6
Yr. 6-8
Yr. 8-10
Yr. 10-12
Field Generation
Potato is a Clonal Crop
Slide credit: Sagar Sathuvalli
Can Quantitative Genetics Improve Efficiency?
Can Quantitative Genetics Improve Efficiency?
Will estimation of combining ability for important clones help us narrow our search space for cross evaluation?
Example 1: Columbia Root Knot Nematode Resistance
Columbia Root Knot Nematode (CRKN) is an Important Pathogen
Meloidogyne chitwoodi
External
InternalSlide credit: Russ Ingham (OSU)
PA99N82-4 is a CRKN Resistant Clone Developed by Our Program
Dr. Charles Brown
PA99N82-4 Still Has Not Made it to Market
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10
15
Yield Tuber_SizeTrait
Value
Data from Rosyara et al., 2016
How can we pick the best crosses to make and families to focus on?
PAN99N82-4
Female Parent
X
Male Parent
Innovator
Mountain Gem
Katahdin
Clearwater
Western
AO6084-1TE
Markies
AO2060-1TE
POR08BD1-3
Currently growing out ten F1 families (~100 clones each) for minitubers
How can we pick the best crosses to make and families to focus on?
Harvest F1s as bulk samples at 10 hill intervals
Emergence/Maturity (UAV)
Yield, Tuber Size (Potato sorter)
Specific gravity Hollow
HeartGrowth Cracks
How can we pick the best crosses to make and families to focus on?
PAN99N82-4
Female Parent
X
Male Parent
Innovator
Mountain Gem
Katahdin
Clearwater
Western
AO6084-1TE
Markies
AO2060-1TE
POR08BD1-3
Select Families Based Upon Mean
and Variance
How can we pick the best crosses to make and families to focus on?
PAN99N82-4
Female Parent
X
Male Parent
Innovator
Mountain Gem
Katahdin
Clearwater
Western
AO6084-1TE
Markies
AO2060-1TE
POR08BD1-3
Select Families Based Upon Mean
and Variance
Can Quantitative Genetics Improve Efficiency?
Can we identify genetic markers linked to important traits? What are the costs and benefits of utilizing this technology?
Example 2: Identify and deploy molecular markers to select TRV and/or PVY resistant clones
Cause of Corky Ringspot DiseaseTobacco rattle
virus (TRV)
Stubby Root Nematode
(Paratrichodorusallius)
Weeds
Crops
Why Is Corky Ringspot Disease a Problem?
Incidence of 6% renders tubers unmarketable
(Hafez and Sundararaj 2009)
25
30
35
40
45
50
−120 −100 −80Longitude
Latitude
Castle Russet: A Success of the Tri-State Breeding Program
Fusarium dry rot resistantErwinia soft rot resistantCold sweetening resistant
TRV resistantPVY resistantPMTV resistant
Long, medium-to-late russet, suitable for fresh or processing market
50%25%
12.5%
6%
X
[ ]
Can we identify QTL associated with CRS resistance?
Next step is identifying genetic markers associated with traits
Castle Russet Susceptible
Gen
oty
pes
Phen
oty
pes
Castle Russet CRS Disease Scores 2018
810.7 12.8
25.1
32.1
9.11.1
1.1
0
5
10
15
20
25
30
35
40
45
0-1 1.1-5 5.1-10 10+
Perc
ent
Average DSI
Phenotypic Evaluation of 185 Progenyusing RT-PCR to Verify Absence or Presence
of TRV
RT-PCRNegRT-PCR Pos
Extreme Resistance
Moderate Resistance
Moderate Susceptible
Susceptible
Castle Russet x Susceptible
Castle Russet
Susceptible
Richard Quick Launa Cimrhakl
Genotyped Population by Genotyping-By-Sequencing (GBS)
Heather Tuttle Laura Shannon
Library Prep and Sequencing at University of
Minnesota
Loga
rithm
of o
dds
(LO
D) s
core
Genome location
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−13
AA BBS9_6724364
wet.d13C_
BP14
S9_6724364●
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AA
BB
How Do We Find Genetic Markers?
Castle Russet
Susceptible
Jeff Endelman
Used gwaspoly to do association, will use TetraploidSNPMapand polymapR once implemented
01
23
45
ave_dsi (additive)
Chromosome
−log
10(p)
1 2 3 4 5 6 7 8 9 10 11 12
Castle Russet
Susceptible
We Detect/Verify CRS QTL on Chromosome 9!
Chr09:52647396_T/C
Sagar Sathuvalli
David Douches
NeilGudmestad
Loga
rithm
of o
dds
(LO
D) s
core
Genome location
We can apply this to more traits simultaneously[
[…
Castle Russet
Susceptible
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AA BBS9_6724364
wet.d13C_
BP14
S9_6724364●
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AA
BB
Loga
rithm
of o
dds
(LO
D) s
core
Genome location
We can apply this to more traits simultaneously[
[…
Disease Resistance
Castle Russet
Susceptible
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−13
AA BBS9_6724364
wet.d13C_
BP14
S9_6724364●
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AA
BB
Loga
rithm
of o
dds
(LO
D) s
core
Genome location
We can apply this to more traits simultaneously[
[…
Disease Resistance Yield
Castle Russet
Susceptible
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−13
AA BBS9_6724364
wet.d13C_
BP14
S9_6724364●
●
AA
BB
Loga
rithm
of o
dds
(LO
D) s
core
Genome location
We can apply this to more traits simultaneously[
[…
Disease Resistance Yield Tuber
composition
Castle Russet
Susceptible
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−13
AA BBS9_6724364
wet.d13C_
BP14
S9_6724364●
●
AA
BB
Loga
rithm
of o
dds
(LO
D) s
core
Genome location
Will Help Select Best Progeny
[
[…
Disease Resistance Yield Tuber
composition
Castle Russet
Susceptible
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−13
AA BBS9_6724364
wet.d13C_
BP14
S9_6724364●
●
AA
BB
Measurement
Need to take more measurements with less personal time
Yield Characteristics
Tuber Properties
Plant/Foliar Growth (UAV)
Digger + Bagger
Sorter
Need to take more measurements with less personal time
Yield Characteristics
Tuber Properties
Digger + Bagger
Sorter
Plant/Foliar Growth (UAV)
What size pot to use in controlled environment assays?
Four pot sizes
Two genotypes- Russet Burbank- Castle Russet
Replicated n=3
1 2 3 4
Katelyn Greeen
How much tuber mass per pot?
Weighted entire tuber lot from each pot
Strong relationship… R2 = 0.65
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200
300
400
1 2 3 4Potsize
Wei
ght Genotype
●●●●
Castle Russet
Russet Burbank
How many tubers per pot?
Harvested tubers and counted them
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1 2 3 4Potsize
Tube
r_C
ount Genotype
●●●●
Castle Russet
Russet Burbank
No significant relationship between pot size and tuber number!
What can we learn using computer vision?
Image acquisition set upPhoto booth: Havox HPB-80D (32” x 32” x 32”)Camera: Nikon D7100Tripod: KF-TM2534T
Image processing pipeline in python
Steps in image processing:
1) Crop image2) Break into sub-images3) Threshold tuber from
background4) Perform
measurements5) Write measurements
to file/object
What % of the trait mean does standard error contribute between sides
Side 1
Side 2
Relationship between Tuber Area, Tuber Number, and Weight
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4e+05
100 200 300 400Weight
Tube
r_Ar
ea Genotype●
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Russet Burbank
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Tube
r_C
ount Genotype
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Russet Burbank
Total tuber area is more reflective of weight than number of tubers
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Red Green Blue
Length Width L/W Ratio
Area Perimeter Eccentricity
1 2 3 4 1 2 3 4 1 2 3 4
1 2 3 4 1 2 3 4 1 2 3 4
1 2 3 4 1 2 3 4 1 2 3 4
0.2
0.4
0.6
0.8
1.0
1.5
2.0
2.5
40
50
60
70
80
90
500
1000
1500
2000
100
200
300
60
80
100
0
50000
100000
150000
200
400
600
80
100
120
140
160
Potsize
Valu
e
Genotype●●
●●
Castle Russet
Russet Burbank
Characteristics of 118 individual
tubers
Size of tubers increases with pot size
Can see genotypic size differences at pot size 3 but not at pot size 2
Why are RGB values so different for pot size 4?
Color spectrum: Burbank in pot 4 is rotten
Burbank Pot 3
Burbank Pot 4
Color spectrum: Burbank vs. Castle (Pot 3)
Castle Pot 3
Burbank Pot 3
Can discriminate between genotypes
Current efforts
Rich Novy and Jaebum Park
Current efforts
Quantification of disease symptoms
Current efforts
Columbia Root Knot Nematode
Quantification of disease symptoms
Current efforts
Columbia Root Knot Nematode
Quantification of disease symptoms
Powdery scab galls
Other measurements types:Hyperspectral imaging to classify genotypes and disease symptoms (Daniel Gleason & Sushma Thapa)
Other measurements types:Hyperspectral imaging to classify genotypes and disease symptoms (Daniel Gleason & Sushma Thapa)
UAV and integrated field sensors for data collection
Standardization
Electronic record keeping
Electronic record keeping
Collecting data in a consistent manner
across programs and making it publicly
accessible will make our efforts more valuable
and create larger impact
Electronic record keeping
Thank you for your attention. Questions?
Richard Quick Katelyn GreeneLauna Cimrhakl Esteban Caldron
