1. Identification and evaluation of QTL
for adult plant resistance to stripe
rust in the US PNW winter wheat
Yukiko Naruoka
Washington State University
4/29/2014
2. 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
3. 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
4. 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
5. 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
1947
1960
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
John
BatumMalcolm
1988 Madsen
1986 Oveson
Eltan1990 Kmor
Macvicar
Bonneville1991
1992 Rod
1993 Rohde
1994 Lambert
1998 HillerCodaWeatherford
1997 Boundary
2001 Bruehl
Basin
FinchChukar
Cappelle Desprez
GaryBrundage 96
2002 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
Year
release 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
JohnJohn
BatumBatumMalcolmMalcolm
1988 MadsenMadsen
1986 OvesonOveson
EltanEltan1990 KmorKmor
MacvicarMacvicar
BonnevilleBonneville1991
1992 RodRod
1993 RohdeRohde
1994 LambertLambert
1998 HillerHillerCodaCodaWeatherfordWeatherford
1997 Boundary
2001 BruehlBruehl
BasinBasin
FinchFinchChukarChukar
Cappelle DesprezCappelle Desprez
GaryGaryBrundage 96Brundage 96
2002 TubbsTubbs
2000 HubbardHubbard
2004 MasamiMasami
EdwinEdwin
2005 MDMMDM BauermeisterBauermeister
2007 XerphaXerpha
Nord
Desprez
Nord
Desprez
2006 DarwinDarwin
AlpowaAlpowa
1979 WalladayWalladay
WawawaiWawawai
ExpressExpress
FrontanaFrontana
LouiseLouise
1987 WakanzWakanzSpillmanSpillman
OtisOtis
Year
release Wheat cultivars and their possible source of HTAP resistance
Dr. Orville Vogel
Photo courtesy: WSU
CAHNRS
6. 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
7. 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
8. Significant QTL for strip rust reactions
through GWAS
1B
10.7
22.6
cM
26.3
11.6
18.1
1D
15.5
cM
2D
0
cM
154.8
IT DS
2B
15.1
37.9
cM IT DS
4A
cM
65.7
IT DS
4B
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. 2014
Vazquez et al. 2012
2A
9.6
11.1
IT DS
gwm359
29.2
243.8
cM
Yr17Ventriup/LN2
QYrst.orr-2AS
9. 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
10. The effect of APR pyramiding
0
2
4
6
8
10
0 1 2 3 4 5 6 7 8 9 10 11 12 13
y= -0.40 X + 6.94
R2 = 0.37
0
20
40
60
80
100
0 1 2 3 4 5 6 7 8 9 10 11 12 13
y= -6.05 X + 67.63
R2 = 0.49
# of Resistant allele # of Resistant allele
IT
DS
• Significant linear regression (p≤0.0001) was found for
both IT and DS
11. 0
2
4
6
8
10
0 1 2 3 4 5 6 7 8 9 10 11 12 13
IT
# of Resistant allele
AP700CL
Stephens
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
12. The effect of APR pyramiding to yield
Resistant
combination
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 3.2
Days > 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)
13. 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
14. Acknowledgement
Arron Carter
Kim Campbell
Mike Pumphrey
Xianming Chen
Deven 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 #5238
National Research Initiative Competitive Grants CAP project 2011-68002-30029
from the USDA National Institute of Food and Agriculture
