Identification and evaluation of QTL for adult plant resistance to stripe rust in the US PNW

winter wheat

Yukiko NaruokaWashington State University

4/29/2014

SWW

HRW

HRW

HRS

SRW

Wheat production area and stripe rust epidemics

http://www.ers.usda.gov

• Pacific Northwest is a major winter wheat production area• Major stripe epidemic regions are the Pacific and Central and

Southern plains

Top 5 PST races in WA Top 5 PSTv races in PNW

Prevalence rank 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012

1 100 100 115 114 114 114 139 11 11 37

2 98 102 100 100 116 116 140 41 14 48

3 80 92 102 35 115 100 114 14 4 11

4 97 101 114 117 111 127 116 37 43 53

5 25 114 116 115 98 54 127 17 17 4

# new races 6 2 5 1 6 1 1 (16) 6 2

Race frequencies and transitions in PNW

http://striperust.wsu.edu/index.html

• Rust virulence is changing fast and new races arise every year

Durable rust resistance in PNW

• Incorporating only single race-specific seedling resistance is not reliable

• Adult plant resistance (APR) may be inadequate under cool wet summers (effective typically >25C°)

• Accumulation of effective resistance for both seedling and APR in a cultivar seems to be the best strategy for durable rust resistance in PNW

PNW wheat and their possible source of APR

• Historically APR have been incorporated in PNW winter wheat breeding programs from Brevor and multiple other sources

Chen 2013

19471960

1970

1980

1990

2000

Brevor

Nugaines

Luke

1949

1960

1965

1970

1977 Stephens

Hyslop1971

1976 Raeder Daws

Lewjain1982

McDermid

Hill 811983

Dusty1985

Sprague1972

1984

Gaines

JohnBatumMalcolm

1988 Madsen

1986 Oveson

Eltan1990 Kmor

MacvicarBonneville1991

1992 Rod1993 Rohde

1994 Lambert

1998 HillerCodaWeatherford1997 Boundary

2001 Bruehl

Basin

FinchChukar

Cappelle Desprez

GaryBrundage 962002 Tubbs

2000 Hubbard

2004 Masami

Edwin

2005 MDM Bauermeister

2007 Xerpha

Nord Desprez

2006 Darwin

Alpowa

1979 Walladay

Wawawai

Express

Frontana

Louise

1987 WakanzSpillman

Otis

Yearrelease Wheat cultivars and their possible source of HTAP resistance

BrevorBrevor

NugainesNugaines

Luke

1949

1960

1965

1970

1977 StephensStephens

HyslopHyslop1971

1976 RaederRaeder DawsDaws

LewjainLewjain1982

McDermidMcDermid

Hill 81Hill 811983

DustyDusty1985

SpragueSprague1972

1984

GainesGaines

JohnJohnBatumBatumMalcolmMalcolm

1988 MadsenMadsen

1986 OvesonOveson

EltanEltan1990 KmorKmor

MacvicarMacvicarBonnevilleBonneville1991

1992 RodRod1993 RohdeRohde

1994 LambertLambert

1998 HillerHillerCodaCodaWeatherfordWeatherford1997 Boundary

2001 BruehlBruehl

BasinBasin

FinchFinchChukarChukar

Cappelle DesprezCappelle Desprez

GaryGaryBrundage 96Brundage 962002 TubbsTubbs

2000 HubbardHubbard

2004 MasamiMasami

EdwinEdwin

2005 MDMMDM BauermeisterBauermeister

2007 XerphaXerpha

Nord DesprezNord Desprez

2006 DarwinDarwin

AlpowaAlpowa

1979 WalladayWalladay

WawawaiWawawai

ExpressExpress

FrontanaFrontana

LouiseLouise

1987 WakanzWakanzSpillmanSpillman

OtisOtis

Yearrelease Wheat cultivars and their possible source of HTAP resistance

Dr. Orville VogelPhoto courtesy: WSU

CAHNRS

Objective

• Identifying QTL and molecular markers linked to those stripe rust resistances by genome wide association mapping (GWAS)

• Evaluate the effect of APR pyramiding in PNW winter wheat germplasm

QTL identification

• Germplasm: – 402 accessions consisted of club and common winter wheat adapted to

PNW selected from 17 breeding programs

• Phenotyping: – Field evaluation: 3 sites for two years in WA– Greenhouse evaluation: Pstv-11 and Pstv-37 (predominant), and Pstv-51

(new)

• Genotyping: – 9K Illumina SNP array (5,777SNP used) and 12 SSRs and STS linked to known

genes and QTL

• Association analysis: – MLM with Q (PC) and K (kinship) matrices performed by TASSEL v.3.0– Qvalue (FDR=0.1) was used for significant test– QTL were determined based on cM and LD between significant markers and

other information from marker-trait association

Significant QTL for strip rust reactions through GWAS

1B10.7

22.6

cM

26.3

11.6

18.1

1D

15.5

cM2D

0cM

154.8

IT DS2B

15.1

37.9

cM IT DS

4AcM

65.7

IT DS4B

cM IT DS

68.3

105.6

110.6

6BcM IT DS

112.3

150.0

:Pul1-2012:Pul2-2012

:CF-2012

:Pul1-2013:CF-2013

:MV-2013

:Pstv-37:Pstv-51

:Pstv-11

QYrst.orr-2B.2

QYrco.wpg-1B.1

Case et al. 2014Vazquez et al. 2012

2A

9.6

11.1

IT DS

gwm359

29.2

243.8

cM

Yr17Ventriup/LN2

QYrst.orr-2AS

Selection of genotypes carrying only APR

• 366 Genotypes carrying at least one seedling gene or QTL; Yr17, the 1BS and 1DS QTL

• The rest of the 36 genotypes were evaluated for the effect of APR accumulation by linear regression analysis

• IT and DS averaged over all environment were used for the analysis

The effect of APR pyramiding

0 1 2 3 4 5 6 7 8 9 10 11 12 130123456789

y= -0.40 X + 6.94R2 = 0.37

1 2 3 4 5 6 7 8 9 10 11 12 130

102030405060708090

y= -6.05 X + 67.63R2 = 0.49

# of Resistant allele # of Resistant allele

IT DS

• Significant linear regression (p≤0.0001) was found for both IT and DS

0 1 2 3 4 5 6 7 8 9 10 11 12 130

2

4

6

8

10

IT

# of Resistant allele

AP700CLStephens

ORCF-103

The effect of APR pyramiding to yield

• Dr. Xianming Chen (USDA ARS) has conducted an experiment to estimate yield loss due to stripe rust by spraying fungicide since 2002

• Yield loss (%) =(yield w/ fungicide - yield w/o fungicide)/ yield w/ fungicide x 100

The effect of APR pyramiding to yield

Resistantcombination Cultivar # of APR

% of yield loss by stripe rust

2011 2012 2013

APRonly AP700CL 12 9.0* 3.3 -4.7

APRonly Stephens 6 12.6 14.0* 5.3

APRonly ORCF-103 5 32.5* 21.3* 24.0*

-APR+Seedling

PS279 (0) 89.8* 57.5* 34.2*

Madsen 7+1 -1.2 2.2 3.2Days > 25C° May-July 21 32 45

http://striperust.wsu.edu/index.html

• Increased number of APR correlated with decreased yield loss by stripe rust.

• Under the high inoculum and cool, wet summer (2011), APR alone did not seem to give enough resistance (9% yield loss = $85million)

*: p<0.05 for yield difference between control (w/o fungicide) and treatment (w/ fungicide)

Summary

• Multiple QTL associated with stripe rust response were identified through GWAS

• Pyramiding APR alleles showed significant effect on stripe rust response and decrease of yield loss by stripe rust

• Under cool, wet environments, a cultivar carrying both seedling resistance and APR showed no yield loss

• Pyramiding effective seedling and APR using molecular markers would facilitate durable rust-resistant winter wheat cultivar development

Acknowledgement

Arron CarterKim CampbellMike PumphreyXianming ChenDeven See

All staff in winter wheat and spring wheat genetics lab and USDA wheat genetics, quality physiology and disease research group

Funding:Washington Grain Commission Project #5238National Research Initiative Competitive Grants CAP project 2011-68002-30029 from the USDA National Institute of Food and Agriculture

Thank you for your attention!