Crop Advantage Series 2011

Soybean Sudden Death Syndrome: Research Update

Leonor Leandro, Dept. Plant Pathology, ISULinda Kull, National Soybean Research Laboratory, IUCU

Outline

• Overview of SDS symptoms and impact• New knowledge about the pathogen

– Toxins and pathogenicity genes• Conditions that favor SDS

– Moisture – Microbial interactions

• Disease Management – New genetics– Cultural practices

SDS Leaf Symptoms

• Yellow and brown spots or streaks between the veins

• Defoliation leaving petioles attached to the stems

SDS Root Symptoms

• Reddish-brown to gray rot in internal tap root tissue

• Poor lateral root growth• Blue spore masses may be

visible on root surface

SDS distribution and yield loss in US (2006-2008)

(Raw data provided by A. Wrather)

IA(1993)

AR(1971) Estimated yield

Loss (Mbu)

SDS in 2010 Yield loss estimate: 28 MBu

• Soilborne fungus• Species: Fusarium virguliforme• Produces sickle-shaped spores

that are blue in mass • Produces round-shaped survival

spores called chlamydospores

The SDS Pathogen

SDS Disease Cycle

Spores infect roots of young plants

Cool soil temperatureHigh moisture

Overwinters in soil, plant debris, and SCN cysts

Toxins moved to leavesSymptoms

develop

High soil moisture

Fungus colonizes

roots

Plants die

When do infections occur?

• Can occur as early as seed germination• Older seedlings are more resistant

17 23 290

500

1000

1500

2000

2500

0 DAP

3 DAP

7 DAP

13 DAP

Temperature (°F)

Root

Rot

Sev

erity

(AU

DPC

) Seedling age at inoculation

63 73 84

Source: Gongora-Canul and Leandro, ISU

Does infection time affect leaf symptoms?

• Seedlings infected at older ages develop less foliar symptoms

0

500

1000

1500

2000

0 DAP3 DAP7 DAP13 DAP

Temperature (F)

Folia

r sev

erity

(AU

DPC

)

Seedling age at inoculation

63 73 84

Source: Gongora-Canul and Leandro, ISU

Why are older seedlings less susceptible to SDS?

Infected 3 days after planting

Infected 14 days after plating

Cortex

Xylem

Source: Gongora-Canul and Leandro, ISU

Madan Bhattacharyya, ISU

Approaches to Identify Candidate Pathogenicity Genes

• Transcriptomic: Based differential expression of genes in infected tissues vs. mycelia and germinating spores.

• Proteomics: Proteome of the xylem sap of infected soybean seedlings

• Metabolomics: Metabolites of diseased and healthy soybean leaves

Source: Bhattacharyya, ISU

Detected transcripts for 97.5% of the14,845 F. virguliforme genes . Less than 100 genes expressed

in infected tissues only

Spore

Myc

elia

Early

infe

ctio

n

Late

infe

ctio

n

Only

Infe

ctio

n

Total E

xpre

ssed

0%

10%20%30%40%50%60%70%80%90%

100%

Not expressed

Expressed

Source: B. Sahu and M. Bhattacharyya, ISU

Elastinolytic metalloproteinase Mep Monooxygenase FAD-binding proteinPisatin demethylase Pectate lyase Serine protease inhibitor Endo-1,4-beta-xylanase Exopolygalacturonase GlycosyltransferaseLignostilbene dioxygenaseGibberellin 3-beta hydroxylase

Cellulase Fungal cellulose binding domain protein

25 of the gene transcripts detected only in the F. virguliforme infected soybean roots are:

Stress responsive A/B barrel domain proteinFAD binding domain-containing protein MFS transporterFAD binding domain-containing proteinHypothetical protein FOXB_14311Hypothetical protein FOXB_02038

Hypothetical protein FOXB_05665 Hypothetical protein FOXB_10278Hypothetical protein FOXB_09766 Hypothetical protein FOXB_10941 Predicted protein Hypothetical protein FOXB_13583Hypothetical protein FOXB_09991Hypothetical protein FOXB_10941

12 genes encode enzymatic functions 13 have unknown functions.

Source: B. Sahu and M. Bhattacharyya, ISU

Source: Fakhoury & Bond, SIUC

15

Identification of fungal genes and pathways involved in the development of SDS

• Genes involved in early events in pathogenesis – Hydrolases (Fvsnf1,…)

• Genes facilitating the colonization of host tissue – Kinases (Fvfsr1, Fvpmk1,…)

• Genes involved in tolerance of antimicrobial compounds produced by the host (Fvgrx2, Fvtrx1,…) S. Mansouri

Source: Fakhoury & Bond, SIUC

16

0

1

2

3

4

5

Mean(A

mount of D

NA

in

ng)

Forest

0

1

2

3

4

5

Mean(A

mount of D

NA

in

ng)

Spencer

Varie

ty

Mont-1 Control F14

TreatmentsSpencer (Susceptible soybean cultivar)

Disruption of Fvfsr1 in F. virguliforme affects the aggressiveness of the pathogen

(Mont-1 (WT), F14 (ΔFvfsr1) and control (no fungus) four weeks after planting

F. virguliforme level in infected soybean roots of wild type (Mont-1), ΔFvfsr1 (F14) and control (no fungus)

ΔFvfsr1WTControlBA

Folia

r rati

ngs (

ds)

-1

0

1

2

3

4

5

6

7

8

9

10

Control F14 Mont-1

Treatments

Each Pair

Student's t

0.05

Folia

r rati

ngs (

ds)

-1

0

1

2

3

4

5

6

7

8

Control F14 Mont-1

Treatments

Each Pair

Student's t

0.05

DC

Forest (Resistant soybean cultivar )

Fakhoury & Bond, SIUC Source: Fakhoury & Bond, SIUC

Favorable Conditions for SDS

• High soil moisture • Cool temperatures • Soil compaction • Plant stress - SCN

Does high soil moisture favor SDS?

SDS Total Precipitation (inches)

Year Incidence Apr May Jun Jul Aug2007 Low 4.3 5.3 3.5 3.1 9.12008 High 5.6 5.5 8.9 5.5 1.72010 Very high 3.8 4.6 10.3 8.1 4.52011 Low 3.0 4.5 4.9 3.5 1.7

Mean High 4.3 4.9 8.7 6.9 4.5Mean Low 3.4 5.9 4.1 3.3 5.1Mean 30-year 3.0 4.1 4.6 3.8 3.8

• SDS epidemic years are usually wetter, especially in June

Source: Robertson, Mueller, and Leandro, ISU

When is soil moisture most important?

Susceptible Resistant0

10

20

30

40

50

V5-R6R1-R6R3-R6No irrigation

SDS

Seve

rity

(%)

Irrigation field trial, Ames, 2011

Soybean Variety

47.6

55

50.2

46.2 bu/ac

Source: Leandro, ISU

Are cool seasons more favorable for SDS?

SDS Soil Temperature oC (F)

Incidence Apr May Jun Jul Aug

High SDS 9.0 (48.2)

16.1(61)

21.1(70)

24.7(76.4)

24.1(75.4)

Low SDS 11.1(51.8)

17.4(63.3)

23.3(73.9)

26.9(80.4)

25.1(77.2)

30-year 9.8(49.6)

16.3(61.3)

22.1(71.8)

25.1(77.2)

24.1(75.4)

• SDS epidemic years are generally cooler

• No consistent trend for cool temperatures at planting

Source: Robertson, Mueller, and Leandro, ISU

Do other soil microbes interact with SDS?

• Soybean Cyst Nematode (SCN)• SDS appears earlier and is

more severe with SCN• Pathogens may spread

together

What soil factors lead to SDS hotspots?

• No differences between hotspots and healthy spots:– Soil abiotic properties (N, P, K, org. matter, texture, etc)– SCN density

• Differences found in microbial populations– F. virguliforme density in soil– Diversity of fungal communities– Diversity of nematode communities

Source: Fakhoury (SIU)

Fakhoury and Bond (SIU), Malvick (UMN), Leandro (ISU)

Cultured independent approaches-PCR DGGE (IL)

Soil samples

DGGE

Isolate DNA

Species Identification by sequencing

DGGE was used to screen for polymorphism in banding patterns between samples:

Fungal ITS DGGE fingerprint for IL soil

Source: Fakhoury, SIU

What soil factors lead to SDS hotspots?

Soybean Resistance to SDS

• Controlled by many genes • Quantitative/partial resistance

– No soybean variety is immune to SDS• Two independent resistance mechanisms

– Root resistance / foliar resistance

Is there foliar resistance to pathogen toxins?

• Tested with pathogen culture filtrate assay

Source: Leandro, ISU

Some soybean lines have resistance to toxins

Source: Leandro, ISU

Identification of soybean resistance genes using VIGS

Whitham, Hill, Leandro (ISU); Radwan, Clough (UIUC)

LSD=9.6

0

5

10

15

20

25

30

3C12-1

3D7-1

3D10-1

3F5-5

Jar-1

Coi-1

H-92

Mock-V2

SD

S s

ever

ity

(%)

a

b

b

b

b b

bb

Inoculate with virus vector containing gene of interest

Radwan, UIUC

Radwan, UIUC

Expose plants to F. virguliforme culture filtrates

Can we expect better resistance in the future?

• Yes.• Breeders are searching

for new sources of SDS resistance

• Incorporating resistance genes into earlier MG

Germ release AR10SDS MGI (early)

AR10SDS: Ripley x IA1008- Ripley MG IV; IA1008 MG I

Line DI Field

DI Gh

SCN IDC Yield

HGT7R3

HGT 2.5.7 R1

bu/a

AR10SDS 2 1 R NR 2-4 51

IA1008 3-4 52

MN 1606 10 2

Suscept. 20 10

Silvia Cianzio, ISU

Germ release AR11SDS MG IIAR11SDS: Ripley x IA2036 - Ripley MGIV, IA2036 MGII

Line DI Field

DI Gh

SCN IDC Yield

HGT7R3

HGT 2.5.7

R1

bu/a

AR11 SDS 0 R LR 2-3 58

Dwight 1 R MR 3 59

SDS Res. 5

SDS Susc. 15

Silvia Cianzio, ISU

New populations for developing resistant lines Populati

on IDSusceptible parent

Resistant parent

# Sub-popul

.

# of RIL

AX19286 A95-684043*

LS94-3207**

11 391

AX19287 A95-684043

LS98-0582**

10 435

AX19288 A95-684043

LS99-2235**

1 392

AX19289 IA1006***

LS94-3207

4 446

AX19290 IA1006 LS98-0582

3 471

AX19291 IA1006 LS99-2235

1 85

AX19294 IA2050 LS94-3207

8 461

*- SCN resistant ; ** - SDS resistant ; ***- BSR resistant

Screened: SDS, SCN, and molecular screening

AX19286 (A95-684043 X LS94-3207): o 20 highly SDS

resistant (3 protocols)

o 15 also are highly resistant to SCN

Cianzio and Bhattacharyya, ISU

Does tillage help reduce SDS?Year, tillage

Foliar AUDPC

Root colonization (%)

Yield(Kg/ha)

2000Disk 47 a 49 a 2850 bNo-till 39 a 48 a 2973 b Chisel 24 b 61 b 3258 a2001Disk 149 b 61 b 3324 a No-till 329 a 67 a 3081 bChisel 185 b 71 a 3244 a

Vick et al. (2006)

Effects of planting date and tillage

Wrather et al, 1995*** *** NS

***

NS

NS

Effects of planting date and tillage

Wrather et al, 1995*** *** NS

***

NS

NS

Effects of planting date and tillage

Wrather et al, 1995*** *** NS

***

NS

NS

Crop Advantage Series 2010

Should planting be delayed to manage SDS?

• No! Delayed planting can risk yield potential • Plant fields with history of SDS last

Palle Pedersen, ISU

Planting Date

Do seed treatments work against SDS?

• No• Commercially available seed treatments are

currently not effective• New products are being tested

How about rotation with other crops? • Previous research is inconclusive• Current research at ISU shows promise

Photo courtesy of L. Miller

3-year rotation / 2-year rotation

M. Liebman, L. Leandro, A. Robertson, C. Chase, D. Mueller

Crop rotation study (ISU, 2010)

Leandro, Liebman, Robertson, Mueller, Chase, ISU

Rotation TreatmentsS2 corn-soybeanS3 corn-soybean-oat/red cloverS4 corn-soybean-oat/alfalfa - alfalfa

S2 S3 S40

102030405060708090

100SDS Severity

K287RRK2918

SDS

Seve

rity

(%)

A

BB

b b

a

S2 S3 S40

102030405060708090

100SDS Incidence

K287RRK2918

SDS

inci

denc

e (%

)

a

A

b BBb

YIELD (Bu/Acre)Rotation K-287RR K-2918

S2 42 22S3 54 55S4 55 53

Funding sources

Questions?