conference welcome - home | ahdb potatoes report from netherlands early 1970’s most early findings...

Conference welcome

Allan Stevenson

Chairman, Potato Council

Dickeya – The GB and

Overseas Experience

Gerry Saddler

Head of Diagnostics and Analytical Services, SASA

The GB experience

Dickeya causing disease in potatoes

Where did it come from and how is it spread?

The situation in GB

Legislation can only go so far…..

What is industry doing and what can it do?

Future prospects

Causes of blackleg, soft rot, etc.

Hosts (Symptoms) Old Name New Name

Potato (blackleg, soft rot)

Erwinia carotovora subsp.

atroseptica

Pectobacterium atrosepticum

Potato & a wide range of other

crops (blackleg, soft rot)

Erwinia carotovora subsp.

carotovora

Pectobacterium carotovorum

Potato, Dianthus, tomato,

maize, chrysanthemum etc.

(blackleg, wilt, vascular

browning, soft rot)

Erwinia chrysanthemi D. chrysanthemi

D. dadantii

D. dianthicola

D. dieffenbachiae

D. paradisiaca

D. zeae

‘D. solani’

Dickeya on potatoes in Europe

First report from Netherlands early 1970’s

Most early findings across Europe identified as D. dianthicola

In 2005 and 2006 a new more aggressive Dickeya sp.,

provisionally named ‘Dickeya solani’, recognised in the

Netherlands – Originally from Scilla sp.?

Subsequent reports from Belgium, Denmark, Finland, France,

Germany, Hungary, Poland, Slovenia, Spain, Sweden and

Switzerland; more recently Czech Republic and Norway

‘D. solani’: Symptoms

‘D. solani’: Mechanisms of spread

Predominantly on seed (harvesting and grading important)

In the field; plant-to-plant spread occurs

Found on weeds and in water – significance?

Does not survive in soil (less than 3 months)

Does not survive on surfaces (less than a few days)

Very susceptible to standard disinfectants

(FAM 30, GPC8, Halamid, Jet 5, Jeye’s Fluid, V18, Vanoquat)

Scotland

Seed and Ware Stem Survey

Since 2007 13 positive findings (4 in 2009 and 9 in 2010) from 2294 samples

Current sampling rate approx. 600-800 per annum

Post-harvest and pre-planting tuber survey

Since 2006 2 positive findings (2 in 2009/10) from 1181 samples


Water sampling

Since 2006 3 positive findings (1 each in 2006, 2007 & 2008) from 467 rivers

Only 1 ‘D. solani’ positive


England and Wales

Voluntary and seed survey samples

Since 2007 59 positive findings (1 in 2007; 1, 2008; 16,

2009; 41, 2010) from voluntary testing

Since 2010 27 positive findings (17 in 2010; 5, 2011; 5,

2012) from 697 survey samples

Water sampling

Since 2009 17 positive findings (8 in 2009; 3, 2010; 6, 2011)

from 86 rivers

Only 1 ‘D. solani’ positive

From John Elphinstone, Fera

The Scottish approach

Zero tolerance for all Dickeya species in the Seed Classification Scheme

Where found, no tubers from the crop permitted for planting

All crop waste (including soil and brock) controlled to prevent further spread

Ground keepers controlled in the affected field for two years

All machinery and boxes which have been in contact with the stock to be cleaned and disinfected

In the case of infested watercourses growers in the vicinity will be informed

It is illegal to plant seed potatoes infected with Dickeya spp. in Scotland

The approach in England and Wales

No distinction made between ‘D. solani’ and P. atrosepticum

Managed by application of blackleg tolerances in English & Welsh SPCS

In 2010-11 GB imported 18,000 tonnes of seed*

Almost all of it was planted in England & Wales

At least some would be for varieties unavailable or with limited supply domestically

*, GB Potatoes: Market Intelligence 2010-11

The current state-of-play

The ‘D. solani’ clone continues to spread across Europe and beyond in a very short period of time

All findings to-date linked to non-GB origin seed ‘D. solani’ is not indigenous to GB

Pathogen has yet to crossover to domestic production

Prospect of an EU-approach to problem unlikely Now too widespread

Could non-EU seed importers drive change?

Dual-approach within GB also likely to continue for the foreseeable future Scotland near-closed system

England and Wales reliant on non-GB origin seed

What is industry doing?

Potato Council

Funding R&D and KE

Safe Haven Scheme

Sourcing Scottish seed

In 2007 there were 86 non-Scottish origin ware crops (3.4%) grown in Scotland

In 2012 there were none!

Working in partnership

Complying with irrigation advice in affected areas

Packers giving prior notification of foreign imports and discussing hygiene measures

Future Prospects

Indicators are conflicting….

Incidence dropping in continental Europe in recent years – weather related or passing wave?

Disease still spreading to other European countries

Inevitable that ‘D. solani’ will crossover into domestic production if non-GB origin seed continues to be grown

Future prospects continued

If ‘D. solani’ were to become established…

Potential end to ‘good’ blackleg years as weather would select either for P. atrosepticum or ‘D. solani’

Loss of seed export opportunities

Potatoes are susceptible to many damaging pests and diseases

There are more out there!

The measures applied and the lessons learned from ‘D. solani’ will have value for other pests and diseases in future

Industry and government need to continue to work closely together

Acknowledgments

Staff from the Rural Payments & Inspections and Agriculture & Rural Development Divisions, Scottish Government

SASA – Greig Cahill, Karen Fraser & Rachel Kelly

Fera – John Elphinstone & Neil Parkinson

JHI – Ian Toth, Sonia Humphris & Leighton Pritchard

Funding – Potato Council and Scottish Government

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Dickeya status in Israel

Leah Tsror Potato Pathologist, Head of Gilat Research Center ARO (Volcani Inst)

Potato Production in Israel

Spring

7500 ha; Avg. yield 45 t/ha; Seed tubers imported from Europe (25,000 ton) Planting: Dec-Feb Harvest: Apr-Jul Production - 300,000 ton

Autumn-Winter

8000 ha; Avg. yield 40 t/ha (baby potatoes - 20 t/ha) Domestic seed tubers (35,000 ton) Planting: Sep-Nov Harvest: Dec-Mar Production - 300,000 ton

Upper Galilee

Coast

Western Negev

Negev Heights

Southern Arava

Consumption 45kg/capita/year

Potato Production in Israel

48% 35% 11% 6%

Imported potato seed lots

Average - 25,000 ton

Erwinia chrysanthemi = Dickeya spp.

Dickeya in Israel warm&dry conditions

Erwinia chrysanthemi is considered in Israel as a quarantine pest EPPO A-2 Zero tolerance (tuber inspection)

A single report from Israel on E. chrysanthemi in potato grown from seed tubers imported from the Netherlands! (1986 - Lumb et al) Starting at 2004-5 it occur more frequent, in high intensity causing damage

Jelly

Dickeya symptoms in warm/dry conditions


Initial wilting of top leaves

Wilting of lower leaves followed with desiccation of foliage


External darkening of the stem base


Discoloration of vascular system in the stem base


In severe infections the stem or the whole plant is dried out. Symptoms are usually associated with a soft rot of the mother


Soft rot of the daughter tubers (depending on level of infection)


Rotting tubers


Disease incidence in potato fields

ton

2004-2010

Erythromycin ELISA

Production of indole

Ech

bacteria Plant material Pm

Characterization of Dickeya solani

PFGE dendogram

A 37 strains

C

B


ML tree dnaX

cvs. Nicola and Mondial

Soil or stem inoculation – 3-7 dai Maceration assay in tubers


Expression of virulence genes of D. solani strains from different climate regions

dspE - encoding type III secretion effector pelL- encoding a pectic enzyme

Europe Israel

• Sample size: 200-300 tubers • Surface sterilization • Cutting stolon-end segments from each tuber (50 tubers X 4-6 rep) • Incubation in enrichment medium for 48 h • PCR or RT-PCR analysis Plating on CVP

Detection of Dickeya in imported seed lots

Good correlation between latent seed infection & Dickeya symptoms in the field

Detection of Dickeya in IL

Dickeya in imported seed lots

Average of 2100 contaminated lots out of 25,000 ton total import

56% 80% 28% 45% 22% 21% 21%

#

# lots

Dickeya transmission to potato crop in IL (for the Fall-Winter crop)

Field trial ‘Sapphire’ seed tubers, harvested early from a heavily contaminated (30%) field in the Spring crop, were planted in a fumigated field (Halutza) in 10/2005. Disease incidence in the Fall crop was 15%. Observations in potato fields 2006 – Santana; 2007- Santé, Bellini, Romans, Vivaldi, Rosanna, Valor; 2008 – Dora

Field experiments were conducted in field plots where Dickeya-contaminated plants were observed in Spring : 1. Fall 2005, Nir Yitshak, DI in spring 30% (cv. Sapphire)

2. Fall 2009, Gilat, DI in spring 25% (cvs. Mondial, Carrera)

Clean seed tubers were used No disease symptoms appeared during the growing season! Daughter tubers were disease-free!

Survival of Dickeya in soil?

Weeds (12 species) were collected from potato plots where Dickeya was detected (Gilat, spring 2009-2010)

Cyperus rotundus, Orobanche aegyptiaca, Amaranthus spinosus, Polygonum equisetiforme, Chenopodium sp., Heliotropium sp., Centaurea iberica, Sorghum haepense, Malva nicaeensis, Cynodon dactylon, Amaranthus blitum and Solanum elaeagnifolium.

Survival of Dickeya in weeds

Dickeya solani is ‘imported’ to IL each year with seed tubers

imported from EU (NL, G, F); causing economic damage

(max DI 50%), transmitted to progeny tubers that serve

as seeds for the fall-winter season

Using free-Dickeya seed tubers is the best way to avoid

potential establishment and spread to other crops

Monitoring seed tubers for Dickeya-latent infection, using

enrichment-PCR is on-going

D. solani may spread to weeds, doesn't survive well in soil

We continue to study cultivars’ susceptibility, inoculum

threshold, environmental conditions affecting disease

expression in the field

Summary

Thanks for your attention!

Funding: Chief Scientist, Ministry of Agriculture Israeli Potato Growers Organization

“Potato Pests” free i-Phone/-Pad application

http://itunes.apple.com/il/app/potato-pests/id548936298?mt=8







Holland

France Scotland

7.9 10.4

11.7

7.5 7.7

11.8

5.6

Germany

6.8

Monitoring Powdery Scab in seed tubers

• Field inspections by the PPIS (twice a season) • Counting diseased plants in 10 randomly chosen blocks (2 rows wide, 12m long ~ 500–600 plants) • If disease incidence >10%, additional 10 blocks are checked • A sample of 15-20 diseased plants per plot is tested in lab

Detection of Dickeya in potato fields

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Breeding for the future

Iain Gordon

Chief Executive, The James Hutton Institute

Can we develop new varieties in time to meet the challenges of the 21st Century?

World Potato Production 1991-2007

Third most important global crop

Production growth second to wheat

Yield potential under exploited

More than 1 billion people eat potato

For children 100g provides 10% RDA for calories and essential vitamins (thiamine, niacin and folate) and 50% of vitamin C

Global production ~ 330 million tonnes >50% in developing countries

Intensive (reliant on chemicals and water)

Potato yield varies dramatically across the globe

Consumer Perspectives

Cost

Nutritional Quality

Safety

Choice

Today

Environmental Quality

Social Equity

Resource Use

Tomorrow

(sustainability)

+

Potato Yield Gap Analysis (Expert Panel) Yield (t/ha)

0

5

10

15

20

25

30

National Average (14.5 t/ha)

Late Blight

Clean Seed

Virus

Bacterial Wilt + 0.6 tonnes

+5.1 tonnes

+ 2.8 tonnes

+6.0 tonnes

Source:

a) Keith Fuglie. 2007. Research Priority Assessment for the CIP 2005-2015 Strategic Plan: Projecting Impacts on

Poverty, Employment, Health and Environment

b) Yearbook of China Agricultural Statistics. 2005.

Many cereals/grains with rapid multiplication e.g. Barley,Wheat, Maize, Sorghum - 2 seasons/yr 4 to 5 years Some clonal crops relatively slow (x8 to x10) multiplication e.g. Strawberry, Potato 8 to 10 years Top fruit woody perennials – clonal, slow multiplication e.g. Blueberry, Raspberry 13 to 15 years Forestry – slow growth, long time to maturity/assessment e.g. Douglas Fir 30 to 35 years

Time scales: hybridisation to National List trialling

The Potato Genome

Genetic Mapping Marker Mapping Transcriptomics & Physical Mapping

QTL Interval Mapping

Breeding Phytochemistry Biochemistry

Statistics Informatics Modelling

Transcriptomics Genetics

Genomics

Marketplace Molecular

markers to deliver new cultivars

Ch

rom

oso

me Su

perscaffo

lds

QTL

Chromosome SNP Map Gene located here

Multidisciplinary approach needed

Potato Tuber Quality Traits

Appearance

Flavour

Texture

Nutrition

Health

Safety

Impacting Factors

Abiotic – Climate change

Biotic stress

Tuberisation and dormancy (Storage performance)

The nutrient content of potatoes, based on 100 g, after boiling in skin.

Low Acrylamide Potato Figure 1

>120 OC

Cytochrome

P450

Glycidamide

Amino acid

adducts

DNA

adducts

%-a

ve

rag

e d

aily in

take

1. Asparagine accumulation in sink tissues 2. Heat-induced acrylamide formation

3. Dietary intake

40

30

20

10

0

+ glucose

O NH2

O

O NH2

Obread products coffee other

glutamine glutamate

asparagineaspartate

NO-

3NO

-

3

NO-

2NO-

2

NH+

4NH+

4

Asparaginase

Asparagine Synthetase

O

H2N

O

H2N

acrylamide

O

NH2

H2N

O

O

NH2

H2N

O

Conjugation with glutathione

(detoxification and secretion)

Cancer chemical alert over crisps & coffee as Food Standards Agency identifies 13 at-risk products.

Acrylamide is a chemical that is considered to be probably

carcinogenic (cancer causing) & which affects the nervous &

reproductive systems. A breeding goal is to therefore to lower the

reducing sugar & asparagine content of tubers.

http://www.dailymail.co.uk/

Identified a breeding population which segregates for sugar & amino acid content, & acrylamide-forming potential.

Used the genetic maps we have developed for potato to identify a region in a specific chromosome which correlates with asparagine content.

Used broad scale gene expression analysis (ca. 40,000 genes analysed) to identify genes associated with the production of asparagine tubers.

QTL

Gene

Biotic Stresses

Potato Virus Y (PVY)

Phytophthora infestans

Aphid

Potato cyst nematode (PCN)

Bacteria: Dickeya solani

Late Blight - Phytophthora infestans

One week later

Up to 20 chemical sprays

EU directive 91/414/EEC –

banning/ reducing chemicals

R1 R2 R6 R3 R5 R4 R7 R8 R10 R11

Genetic resistance introduced by

breeding has been readily defeated

Discovery pipeline for Resistance genes

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0013

490_

chr0

5

0011527_chr04

0001992_chr11

0030855_ch

r08

0001993_chr11

100

72

100

98

72

91

100

99

96

79

93

71

84

76

100

100

78

100

100

89

84

100

100

99

100

100

100

100

100

100

73

100

100

93

99

87

100

70

100

96

93

92

87

100

93

74

100

70

99

97

100

100

95

100

100

99

99

91

81

73

100

82

100

100

82

98

90

99

99

71

99

94

100

98

98

100

100

100

100

79

97

100

72

100

100

100

100

100

100

100

80

100

93

78

99

84

98

94

100

91

84

99

98

81

10076

100

100

100

100

100

97

100

98

88

93

93

0020735_ch

r06

CNL-5

CNL-6

CNL-7

CNL-8

CN

L-R

TN

L

CNL-1

CN

L-2

CN

L-3

CN

L-4

Durable Resistance

Pathogen genome

The Pathogen: Biology and genome revealing virulence proteins that are essential for late blight

The CPC: • 1800 accessions across

80 wild species • Source of resistances

that recognise our pathogen virulence proteins

Potato Genome: Revealing the resistance genes that recognise Phytophthora virulence proteins

The Pathogen: Biology and genome revealing virulence proteins that are essential for late blight

The CPC: • 1800 accessions across

80 wild species • Source of resistances

that recognise our pathogen virulence proteins

Biodiversity: The CPC

Late Blight Resistance:

The Case for Genetic modification

The pathogen is highly changeable and multiple

resistances need to be combined to be effective (durable)

Resistances from different wild relatives which don’t cross

directly with cultivated potato.

We can introduce into cultivars that have been bred for

other desirable traits required by the industry.

We are introducing potato genes into potato, and can do

so via ‘cis-genics’ (i.e. avoiding antibiotic resistance

markers etc)

Most countries lack wild relatives and thus gene flow

from the genetically modified crops is negligible.

Heat Stress in Potato

Global warming will expose the crop to high day and night temperatures

High temperature: a major abiotic stress that impacts on yield

Potato is best adapted to cool temperate zones

Commercial cultivar yield is optimal in range of 14 - 22oC

Tuber yield falls sharply above optimum temperatures

Constrains production in Asia and Sub-Saharan Africa

European production under pressure in some seasons

Challenges for the Seed Potato Industry

Scottish seed exports now exceed 100,000 tonnes per

annum

75% of exports to Egypt, Morocco and Israel

Urgent need to understand the mechanisms underlying

heat tolerance

Aim of the work is to:

Identify molecular, biochemical and physiological responses to heat stress

Identify markers for the rapid screening of germplasm resistant to temperature stress

Develop strategies to protect potato production

Screening for heat stress tolerance

TOLERANT SENSITIVE

20˚C

33˚C

Enables high throughput screening under controlled conditions

Heat stress experiment

Use comprehensive potato microarray (39,000 genes) to follow gene expression during heat stress

Leaves and tubers sampled every 4 hours

3 biological replicates

2 temperatures; 22 and 30oC

Matched GC-MS analysis of metabolites (polar and non-polar)

Cluster genes by expression patterns

Construct network using different data types gene expression, N metabolism etc)

In field image (from 8m height) Corresponding Near IR image

Using Infra-red thermography to monitor water stress

200150100500

2.0

1.6

1.2

0.8

0.4

0.0

-0.4

-0.8

-1.2

Genotypes

Te

mp

era

ture

Dif

fere

nce

Trial 4_28_06

Trial 4_05_07

Trial 4_12_07

Mean

Scatterplot of Trial 4

Rankings are highly consistent across measurement dates.

Can map effects and use genome to identify genes.

Significant yield correlation

POTATO BREEDING

There are two ways to improve on

existing cultivars:

Produce new cultivars using sexual

hybridization.

Genetic modification of existing

cultivars by transformation.

These approaches are complementary.

Research at James Hutton Institute has

dramatically improved the efficiency of

potato breeding and the quality of

parental germplasm available.

Scientific Breeding Methods The James Hutton Institute and Mylnefield Research Services are in the business of breeding new cultivars

with market relevance, based on scientific principles and its broad based germplasm.

Breeding techniques

Expensive to run breeding programmes:

Relatively Lengthy timescales

Some traits take a long time to screen for, others are

impossible to screen on a high-throughput basis

Field/glasshouse costs

Need to reduce timescale and increase efficiency

Time to potato cv. 7 to 9 years (+ 2 yrs NL trials)

Extensive phenotyping in field, glasshouse and CE

rooms

Increasingly we are able to establish the link

between genotype (genes) and phenotype

Molecular Breeding

Faster identification of genetically superior individuals in

breeding populations

Can be utilised in situations where:

Assessment in field takes a long time

Identify pathogen resistance which can be lengthy, imprecise

Assessment can only be done on mature plants over time

Quality, abiotic stresses (e.g. drought res. test in Scotland?)

Basic research development costs relatively high,

deployment costs low

No environmental effects to influence assessment

Must be reliably associated with detailed phenotyping

Eurobarometer Survey 2010

Public perceptions of cisgenics

Conclusions

Plant breeding is essential to address:

– Global issues

– Grower needs

– Consumer needs

The strong science base at the James Hutton Institute

creates competitive advantage, innovation and economic

growth

New genetic technologies are essential e.g. molecular

markers and GM

Partnerships with breeders, and rest of supply chain are

essential

Thank You

Glenn Bryan, Paul Birch, Finlay Dale, Howard Davies, Nigel Kerby, Louise Shepherd, Derek Stewart, Mark Taylor

Opportunity for questions

Morning coffee break

Please be at your Workshop

destination by 11.45

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