germplasm screening remote sensing sathuvalli...Ø high throughput phenotyping has potential in...

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Application of High Throughput Phenotyping Tools for Germplasm Screening in Potato

Ryan Graebner, Sindhuja Sankaran, Lav Khot, Vidyasagar Sathuvalli

Hermiston Agricultural Research & Extension Center, Hermiston, OR

OverviewØTri-State Potato Breeding and Variety Development

Ø Screening Germplasm for Resistance to Verticillium Wilt

ØAerial Imaging Applications for Disease Tolerance Screening

ØVolatile Organic Compounds Profiling as a tool for Germplasm Screening

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Ø Started in 1985Ø USDA/ARS breeding programs develop germplasm needs for the

industry and will be evaluated by state land grant universities of ID, OR and WA

Ø Original intent of the stake holders:• Create a collaborative variety development program that would

allow ARS scientists to concentrate on basic genetics and germplasm development, while instituting an applied research effort for smooth delivery of new varieties to the PNW potato industry

30 years of strong and successful collaboration

Tri-State History

USDA-ARS / OSU Research Geneticists, Breeders

Land Grant State Universities Breeders, Agronomists, physiologists pathologists,

entomologists, extension specialists

Potato Commissions – ID, OR, WA

Industry – growers, processors, packers

Potato Variety Management Institute (PVMI)Commercialization

Management Guidelines

Release

Evaluation

Selection

Breeding

USDA-ARS

Tri-State Approach

Slide adapted from Knowles et al (2010)

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Year 1

Year 2

Year 3

Year 4

Yrs 4-6

Yrs 5-8

Yrs 12-15

Yrs 9-11

eye-

inde

xing

...

60,000 TPS seedling tuber production at Corvallis, OR

Wild species germplasm from Prosser, WA,

Hermiston, OR

Germplasm from genetic studies, hybridization strategies

Aberdeen, ID, Prosser, WA, Hermiston, OR

Exotic Germplasm from other CountriesCommercial varietiesParents from other breeders

Parents from the Plant Introduction Station at Sturgeon Bay, Wisconsin

Greenhouse Greenhouse100,000 TPS seedling tuber production

at Aberdeen, ID

Tubers from seedlings. Planted at Klamath Falls and Hermiston, OR

Tubers from disease resistant and specialty crosses. Prosser, WA

Tubers from seedlings. Planted at Aberdeen and Tetonia, ID

Field Field

700-1,200 clones planted at Hermiston and Klamath Falls (SI), OR

2,500 clones planted at Aberdeen, and Tetonia, ID

Disease trials in Corvallis, Aberdeen, Kimberly, Hermiston, Prosser, Rexburg

Breeder seed increasesAberdeen and Tetonia, ID, Klamath

Falls, OR

Limited generation Foundation seed

productionUI

Limited generation seed productionSeed Growers

Tri-State Trials(OR, ID, WA)

Western Regional Trials8-10 locations (OR,ID,WA,CA,TX,CO)

Name and release

Cultural management

studies &Industry trials

Lab and Greenhouses

Exchange of seeds and tubers with other States

Greenhouse CrossesAberdeen, ID, Prosser, WA

Hermiston, OR

Breeder seed increase

Klamath Falls

PVMI Promotion & Marketing

PVMIPromotion and

MarketingDeve

lopm

ent o

f a T

ri-St

ate

Pota

to V

arie

ty

ID State wide TrialsOR State wide Trials

Parti

cipat

ory b

reed

ing

Oregon Potato Breeding and Variety Development 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

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Payette Russet

ØDevelop new russet potatoes◦ Dual purpose russet varieties (ID)◦ Individual market oriented russet varieties (OR)

ØBreeding for resistance to major pests and diseases◦ PVY, Verticillium wilt, Zebra Chip, TRV, PMTV, CRKN, Scab etc.

ØBreeding of specialty potatoes◦ Reds/yellows/purples ◦ High anthocyanins, minerals, carotenoids, Nutrients, Flavor

ØBreeding for cold sweetening resistance and high nutrient efficiency◦ Low acrylamide, low N input

Breeding Objectives

Overall GoalRelease & commercialize new potato varieties that will directly benefit all segments of the PNW potato industry

Image Sources:PNW HandbookUniversity of Minnesota Extension

Verticillium Wilt (Verticillium species)

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Accession Species Ploidy # Clones # Clones Alive # Clones RetainedPI 498148 S. andreanum 2x 4 2 2PI473361 S. boliviense 2x 1 0 0PI265861 S. boliviense 2x 4 0 0PI545912 S. brevicaule 2x 4 0 0PI243508 S. bulbocastanum 2x 4 0 0PI243512 S. bulbocastanum 2x 4 2 0PI275187 S. bulbocastanum 2x 4 0 0PI498011 S. bulbocastanum 2x 4 2 1PI652828 S. guerreroense 6x 4 0 0PI239423 S. hougasii 6x 4 2 1PI283107 S. hougasii 6x 4 2 1PI275182 S. iopetalum 6x 4 3 2PI597682 S. iopetalum 6x 3 1 0PI498249 S. iopetalum 6x 1 0 0PI275181 S. iopetalum 6x 4 4 1PI498022 S. iopetalum 6x 4 0 0PI498024 S. iopetalum 6x 3 0 0PI275183 S. iopetalum 6x 4 1 0PI320265 S. stenophyllidium 2x 4 0 0PI545815 S. stenophyllidium 2x 4 0 0PI643997 S. stoloniferum 4x 4 0 0PI632334 S. stoloniferum 4x 4 0 0Russet Burbank S. tuberosum 4x 8 3 -

Verticillium dahliae Resistance Screening

1 to 4 seedlings per Plant Introduction


Ø 30,000,000 Conidia VCG4AØ Most aggressive isolate in the

Columbia basin of OR-WA

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Ø Inoculated plants evaluated for their survival up to 12 weeks


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Screening for New Sources of Resistance to VWAccession Species Ploidy # Clones # Clones Alive # Clones RetainedPI 498148 S. andreanum 2x 4 2 2PI473361 S. boliviense 2x 1 0 0PI265861 S. boliviense 2x 4 0 0PI545912 S. brevicaule 2x 4 0 0PI243508 S. bulbocastanum 2x 4 0 0PI243512 S. bulbocastanum 2x 4 2 0PI275187 S. bulbocastanum 2x 4 0 0PI498011 S. bulbocastanum 2x 4 2 1PI652828 S. guerreroense 6x 4 0 0PI239423 S. hougasii 6x 4 2 1PI283107 S. hougasii 6x 4 2 1PI275182 S. iopetalum 6x 4 3 2PI597682 S. iopetalum 6x 3 1 0PI498249 S. iopetalum 6x 1 0 0PI275181 S. iopetalum 6x 4 4 1PI498022 S. iopetalum 6x 4 0 0PI498024 S. iopetalum 6x 3 0 0PI275183 S. iopetalum 6x 4 1 0PI320265 S. stenophyllidium 2x 4 0 0PI545815 S. stenophyllidium 2x 4 0 0PI643997 S. stoloniferum 4x 4 0 0PI632334 S. stoloniferum 4x 4 0 0Russet Burbank S. tuberosum 4x 8 3 -

Ø80 seedlings from 22 wild potato accessions

Ø8 seedlings survived initial screening

Initial Screening Results

Species PI # Clones SurvivedS. andreanum 498148 2S. bulbocastanum 498011 1

S. hougasii 239423 1


S. iopetalum 275181 1


VW Initial Screening Results

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Replicated Screening for Verticillium Resistance

Chlorosis rating

Imaging

Plating

qPCR


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S. iopetalum PI 275182

Control VCG 4B VCG 4A

G/R = 1.316 G/R = - G/R = -

Replicated Screening for Verticillium ResistanceControl VCG 4B VCG 4A

S. hougasii PI 283107

G/R = 1.295 G/R = - G/R = 1.079

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S. bulbocastanum PI 498011

G/R = 1.135 G/R = 1.365 G/R = 1.251


S. andreanum PI 498148-1

Control VCG 4B VCG 4A

G/R = 1.215 G/R = 1.277 G/R = 1.223

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S. andreanum PI 498148-2

G/R = 1.167 G/R = 1.158 G/R = 1.212

Species PI # Clones Survived

S. andreanum 498148 2S. bulbocastanum 498011 1






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Aerial Imaging applications in Potato Breeding: Biotic Stress Screening

20 40 60 80 10025

50

75

100

125

150

Canopy Vigor (x 100 Total Number of Pixels)Yi

eld

(x 1

000

kg/h

a)

r = 0.58

Early Die field screening

NDVI Imaging 40 DAP

False Color Imaging 40 DAP

Potato virus Y field screening

120 140 160 180 200 220 240

50

75

100

125

150

Canopy Vigor (x 100 Total Number of Pixels)

Yiel

d (x

100

0 kg

/ha)

r = 0.80

NDVI Imaging – 40 DAP


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Potato virus Y field screening

Psuedocolor Imaging

NDVI and GNDVI values of potato plants grown from PVY infected and PVY free seed pieces


Profiling Volatile Organic Compounds

Columbia Root Knot Nematode Screening

Ø Profiling VOC emissions has potential in germplasm screening

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Conclusion

Ø High Throughput Phenotyping has potential in Germplasm Screening

Ø Once validated – remote sensing tools can add value in potato breeding

• Field screening for pest/disease

• Nitrogen and water use efficiency

• Quality

Ø Aerial imaging has potential applications in Potato Seed Industry

• PVY rouging

Ø VOCs have potential use in screening for soil borne pathogens like Nematodes

• Can it replace tedious nematode screening..

Funding Sources

ØPotato Commissions of OR, WA, IDØUSDA-NIFA Special Grant

ØCooperative Research Agreements USDA/ARS

germplasm screening remote sensing sathuvalli...Ø high throughput phenotyping has potential in...

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