genetics, measurement, and standardization in the potato
TRANSCRIPT
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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
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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
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Mission: Breed a More Profitable and Sustainable Potato
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Mission: Breed a More Profitable and Sustainable Potato
Identify and introgress disease resistance alleles into production clones
(Guenthner 2009)
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Fumigation is a major expense
Mission: Breed a More Profitable and Sustainable Potato
Identify and introgress disease resistance alleles into production clones
(Guenthner 2009)
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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)
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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
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Genetics
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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
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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
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Single Hill Selection
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Single Hill Selection
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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
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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
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Can Quantitative Genetics Improve Efficiency?
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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
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Columbia Root Knot Nematode (CRKN) is an Important Pathogen
Meloidogyne chitwoodi
External
InternalSlide credit: Russ Ingham (OSU)
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PA99N82-4 is a CRKN Resistant Clone Developed by Our Program
Dr. Charles Brown
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PA99N82-4 Still Has Not Made it to Market
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5
10
15
Yield Tuber_SizeTrait
Value
Data from Rosyara et al., 2016
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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
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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
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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
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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
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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
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Cause of Corky Ringspot DiseaseTobacco rattle
virus (TRV)
Stubby Root Nematode
(Paratrichodorusallius)
Weeds
Crops
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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
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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%
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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
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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
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Genotyped Population by Genotyping-By-Sequencing (GBS)
Heather Tuttle Laura Shannon
Library Prep and Sequencing at University of
Minnesota
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Loga
rithm
of o
dds
(LO
D) s
core
Genome location
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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
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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
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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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−14
−13
AA BBS9_6724364
wet.d13C_
BP14
S9_6724364●
●
AA
BB
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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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−14
−13
AA BBS9_6724364
wet.d13C_
BP14
S9_6724364●
●
AA
BB
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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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−14
−13
AA BBS9_6724364
wet.d13C_
BP14
S9_6724364●
●
AA
BB
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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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−14
−13
AA BBS9_6724364
wet.d13C_
BP14
S9_6724364●
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AA
BB
![Page 37: Genetics, Measurement, and Standardization in the Potato](https://reader034.vdocuments.site/reader034/viewer/2022042405/625dd55e3beb5c3d91526b5b/html5/thumbnails/37.jpg)
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●
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AA
BB
![Page 38: Genetics, Measurement, and Standardization in the Potato](https://reader034.vdocuments.site/reader034/viewer/2022042405/625dd55e3beb5c3d91526b5b/html5/thumbnails/38.jpg)
Measurement
![Page 39: Genetics, Measurement, and Standardization in the Potato](https://reader034.vdocuments.site/reader034/viewer/2022042405/625dd55e3beb5c3d91526b5b/html5/thumbnails/39.jpg)
Need to take more measurements with less personal time
Yield Characteristics
Tuber Properties
Plant/Foliar Growth (UAV)
Digger + Bagger
Sorter
![Page 40: Genetics, Measurement, and Standardization in the Potato](https://reader034.vdocuments.site/reader034/viewer/2022042405/625dd55e3beb5c3d91526b5b/html5/thumbnails/40.jpg)
Need to take more measurements with less personal time
Yield Characteristics
Tuber Properties
Digger + Bagger
Sorter
Plant/Foliar Growth (UAV)
![Page 41: Genetics, Measurement, and Standardization in the Potato](https://reader034.vdocuments.site/reader034/viewer/2022042405/625dd55e3beb5c3d91526b5b/html5/thumbnails/41.jpg)
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
![Page 42: Genetics, Measurement, and Standardization in the Potato](https://reader034.vdocuments.site/reader034/viewer/2022042405/625dd55e3beb5c3d91526b5b/html5/thumbnails/42.jpg)
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
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Castle Russet
Russet Burbank
![Page 43: Genetics, Measurement, and Standardization in the Potato](https://reader034.vdocuments.site/reader034/viewer/2022042405/625dd55e3beb5c3d91526b5b/html5/thumbnails/43.jpg)
How many tubers per pot?
Harvested tubers and counted them
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1 2 3 4Potsize
Tube
r_C
ount Genotype
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Castle Russet
Russet Burbank
No significant relationship between pot size and tuber number!
![Page 44: Genetics, Measurement, and Standardization in the Potato](https://reader034.vdocuments.site/reader034/viewer/2022042405/625dd55e3beb5c3d91526b5b/html5/thumbnails/44.jpg)
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
![Page 45: Genetics, Measurement, and Standardization in the Potato](https://reader034.vdocuments.site/reader034/viewer/2022042405/625dd55e3beb5c3d91526b5b/html5/thumbnails/45.jpg)
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
![Page 46: Genetics, Measurement, and Standardization in the Potato](https://reader034.vdocuments.site/reader034/viewer/2022042405/625dd55e3beb5c3d91526b5b/html5/thumbnails/46.jpg)
What % of the trait mean does standard error contribute between sides
Side 1
Side 2
![Page 47: Genetics, Measurement, and Standardization in the Potato](https://reader034.vdocuments.site/reader034/viewer/2022042405/625dd55e3beb5c3d91526b5b/html5/thumbnails/47.jpg)
Relationship between Tuber Area, Tuber Number, and Weight
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1e+05
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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
![Page 48: Genetics, Measurement, and Standardization in the Potato](https://reader034.vdocuments.site/reader034/viewer/2022042405/625dd55e3beb5c3d91526b5b/html5/thumbnails/48.jpg)
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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
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2.5
40
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Potsize
Valu
e
Genotype●●
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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?
![Page 49: Genetics, Measurement, and Standardization in the Potato](https://reader034.vdocuments.site/reader034/viewer/2022042405/625dd55e3beb5c3d91526b5b/html5/thumbnails/49.jpg)
Color spectrum: Burbank in pot 4 is rotten
Burbank Pot 3
Burbank Pot 4
![Page 50: Genetics, Measurement, and Standardization in the Potato](https://reader034.vdocuments.site/reader034/viewer/2022042405/625dd55e3beb5c3d91526b5b/html5/thumbnails/50.jpg)
Color spectrum: Burbank vs. Castle (Pot 3)
Castle Pot 3
Burbank Pot 3
Can discriminate between genotypes
![Page 51: Genetics, Measurement, and Standardization in the Potato](https://reader034.vdocuments.site/reader034/viewer/2022042405/625dd55e3beb5c3d91526b5b/html5/thumbnails/51.jpg)
Current efforts
Rich Novy and Jaebum Park
![Page 52: Genetics, Measurement, and Standardization in the Potato](https://reader034.vdocuments.site/reader034/viewer/2022042405/625dd55e3beb5c3d91526b5b/html5/thumbnails/52.jpg)
Current efforts
Quantification of disease symptoms
![Page 53: Genetics, Measurement, and Standardization in the Potato](https://reader034.vdocuments.site/reader034/viewer/2022042405/625dd55e3beb5c3d91526b5b/html5/thumbnails/53.jpg)
Current efforts
Columbia Root Knot Nematode
Quantification of disease symptoms
![Page 54: Genetics, Measurement, and Standardization in the Potato](https://reader034.vdocuments.site/reader034/viewer/2022042405/625dd55e3beb5c3d91526b5b/html5/thumbnails/54.jpg)
Current efforts
Columbia Root Knot Nematode
Quantification of disease symptoms
Powdery scab galls
![Page 55: Genetics, Measurement, and Standardization in the Potato](https://reader034.vdocuments.site/reader034/viewer/2022042405/625dd55e3beb5c3d91526b5b/html5/thumbnails/55.jpg)
Other measurements types:Hyperspectral imaging to classify genotypes and disease symptoms (Daniel Gleason & Sushma Thapa)
![Page 56: Genetics, Measurement, and Standardization in the Potato](https://reader034.vdocuments.site/reader034/viewer/2022042405/625dd55e3beb5c3d91526b5b/html5/thumbnails/56.jpg)
Other measurements types:Hyperspectral imaging to classify genotypes and disease symptoms (Daniel Gleason & Sushma Thapa)
UAV and integrated field sensors for data collection
![Page 57: Genetics, Measurement, and Standardization in the Potato](https://reader034.vdocuments.site/reader034/viewer/2022042405/625dd55e3beb5c3d91526b5b/html5/thumbnails/57.jpg)
Standardization
![Page 58: Genetics, Measurement, and Standardization in the Potato](https://reader034.vdocuments.site/reader034/viewer/2022042405/625dd55e3beb5c3d91526b5b/html5/thumbnails/58.jpg)
Electronic record keeping
![Page 59: Genetics, Measurement, and Standardization in the Potato](https://reader034.vdocuments.site/reader034/viewer/2022042405/625dd55e3beb5c3d91526b5b/html5/thumbnails/59.jpg)
Electronic record keeping
![Page 60: Genetics, Measurement, and Standardization in the Potato](https://reader034.vdocuments.site/reader034/viewer/2022042405/625dd55e3beb5c3d91526b5b/html5/thumbnails/60.jpg)
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
![Page 61: Genetics, Measurement, and Standardization in the Potato](https://reader034.vdocuments.site/reader034/viewer/2022042405/625dd55e3beb5c3d91526b5b/html5/thumbnails/61.jpg)
Thank you for your attention. Questions?
Richard Quick Katelyn GreeneLauna Cimrhakl Esteban Caldron