MARKER ASSISTED SELECTION•Individuals carrying the trait of

interest are selected based on a marker which is linked to the trait and not on the trait itself.

•Indirect selection.•Useful when the trait is difficult to

measure, and/or is evident only at late developmental stages.

Winter Facult. Spring

Kom

polti

Nure

OSU

11

Strider

Igri

Dicktoo

88Ab5

36

Tremois

Morex

Harring

ton

ZCCT-H

HvSnf2

Trium

ph

BARLEY STRIPE RUST

www.barleyworld.org

BARLEY STRIPE RUST•Caused by fungus Puccinia striiformis

f. sp. hordei •Common in Mexico and South

America but usually not in Oregon.•It first appeared in the US in 1991 •When infection is severe, losses of

50% are common

BARLEY STRIPE RUST•Resistant cultivars are available •It is necessary to develop resistant

cultivars adapted to different barley growing areas

•Resistance to the disease is a quantitative trait (non-Mendelian inheritance)

•Three Quantitative Trait Loci (QTL) for stripe rust resistance have been mapped and their effects validated.

•There are molecular markers located in the target regions of the three QTL

Cali-sib x BowmanShyri x Galena CI10587 x Galena

BSR-45 D1-72 D3-6

Harrington BaronesseOrca

BCD DB

BCD47 BCD12 D3-6/B23 D3-6/B61

AJO BU OPS

iBISON and BISON

Disease severity of barley stripe rust resistance QTL isolines. 2006

Accession Huancayo, Peru

Toluca, Mexico

Corvallis, USA

Mean ± std. error

1H 20 45 20 28 ± 8.3 4H 5 1 20 9 ± 5.8 5H 40 60 50 50 ± 5.8 7H 0 1 1 1 ± 0.3 1H + 4H 10 1 20 10 ± 5.5 1H + 5H 50 20 40 37 ± 8.8 4H + 5H 15 33 70 39 ± 16.2 1H + 4H + 5H 0 1 0 0.3 ± 0.3 BCD12 (1H) 15 1 15 10 ± 4.7 BCD 47 (4H + 5H) 15 25 15 18 ± 3.3 Baronesse 50 80 80 70 ± 10 CI10587 (7H) 10 1 5 5 ± 2.6

P-O

PA

1 +

2 m

ap

ch cM BA

RO

NE

SS

E

BIS

ON

1H

BIS

ON

4H

BIS

ON

1H+4

H

BIS

ON

5H

BIS

ON

1H+5

H

BIS

ON

4H+5

H

BIS

ON

1H+4

H+5

H

BIS

ON

7H

BC

D12

BC

D47

1_1513 4H 71.250 a a a a a a a a a a a2_0207 4H 75.671 a a a a a a a a a a a1_0309 4H 75.671 a a a a a a a a a a b2_1332 4H 79.006 a a a a a a a a a a b1_0170 4H 81.204 a a a a a a a a a a a1_1526 4H 82.291 a a a a a a a a a a a1_1213 4H 83.378 a a a a a a a a a a a2_0765 4H 84.465 a a a a a a b a a a b1_1398 4H 84.465 a a a a a a a a a a a2_0732 4H 91.373 a a a b a a b a a b b1_1168 4H 92.460 a a a a a a a a a a a1_0785 4H 93.547 a a a a a a a a a a a

EBmac701 4H 95.786

1_1292 4H 96.854 a a b b a a b b a a b2_0838 4H 96.854 a a a a a a a a a a a2_0454 4H 99.052 a a a a a a a a a a a

baal29j181_1194 4H 104.585 a a a a a a a a a a a1_0712 4H 109.082 a a a a a a a a a a a1_1235 4H 110.169 a a a a a a a a a a a2_0883 4H 111.256 a a a a a a a a a a a1_0697 4H 112.343 a a a a a a a a a a a2_0224 4H 113.430 a a a a a a a a a a a2_0760 4H 114.517 a a a a a a a a a a a2_0007 4H 115.604 a a a a a a a a a a a1_0610 4H 115.604 a a a a a a a a a b b2_0932 4H 116.685 a a a a a a a a a a a

OWB

Chr. 4H

ORO

DEFD

FEF

BB

A

DEDE

C

A

010203040506070

Bar

ones

se 1H 4H

1H+4

H 5H

1H+5

H

4H+5

H

1H+4

H+5

H 7H

BC

D12

BC

D47

0 2 4 6 8 10 12 14

HVM40

HVM03Bmac181Bmac030B

GBM1071MWG2180

Bmac310

EBmac635

EST4535*k07229baal29j18HvMLO3*k03352

GBM1015

Bmag419HvSnf2HdAmyB

1_1292 –EST4535

0 2 4 6 8 10 12 14

HVM40

HVM03Bmac181Bmac030B

GBM1071MWG2180

Bmac310

EBmac635

EST4535*k07229baal29j18HvMLO3*k03352

GBM1015

Bmag419HvSnf2HdAmyB

1_1292 –EST4535

1_1292 –EST45351_1292 –EST4535

EBmac701

baal29j18SSR markers used for MAS

*

BCD14340DsT-667Act8A12RbgMD18MWG837B22scind0004625ABC165C26Bmac039929GBM100730BCD09836GBM104248BG36701354Bmag021158BG36994061GBM105168ABC16073JS10C86Bmac0144A87MWG706A96KFP170101Blp111ABC261119MWG2028121KFP257B122WMC1E8130MWG912133ABG387Ascssr04163scssr08238

136

1H

DsT-10ABG0585scind026227ABG00817

scssr1022636scssr0775939GBM106642Pox45scssr0338156scssr12344scssr02236Ebmac0684

63

BCD1434.265ABG35668GBM102371scsnp0334383vrs188Bmag012594DsT-4197MWG503102GBM1062103KFP203104MWG882A108ABG1032117ABG072124Ebmc0415137cnx1139Zeo1149GBM1019161Aglu5F3R2163MWG720165GBM1012170wst7173scssr08447179MWG949A180

2H

BCD9070

ABC171A26GBM107430scssr1055933MWG798B36Dst-2739BCD70642DsT-3958alm61Bmac020966ABC32569DsT-6773scssr2569187ABG37789Bmag022598

Act8C121ABG499124GBM1043125

scsnp23255151ABG004155

scind02281166MWG883172

DsT-24181

HVM62190

DsT-40199

ABC172scssr25538212DsT-35218

3H

MWG6340MWG07721HVM4024DsT-2929CDO54230CDO12231hvknox335Dhn639ABC303scssr2056941CDO79544HVM349DST-46scind03751scssr18005

50

Tef252GBM102060Bmag035362scind1045567DsT-7974scssr14079ABG47280GBM105983KFP22192Ebmac070194MWG652B95GBM1048101Hsh111HVM67112KFP241.1116ABG601124

4H

scssr023060MWG6186DsT-68ABC48311ABG61012

ABG39537scssr0250344scssr1807645Bmac009653NRG045A55scsnp0426056Ale58

ABC30279scind1699182scssr1533485scsnp0614490srh100

scssr05939111

RSB001A120scsnp001771280SU-STS1134ABG003B141

scssr10148157Tef3166MWG877169BE456118A170ABG496179scsnp02109E10757A193ABG391197JS10B198ABC622205DsT-33207Bmag0113C215MWG602A223scssr03907224scssr03906225

5H

MWG6200Bmac0316scssr093984MWG652A31MWG602B35scind6000242JS10A45GBM102151GBM106861BG29929765HVM3168rob70Bmag0009scssr0209371ABG47481Bmac0218C88ABG38892scsnp2122699MWG820101GBM1008122scssr05599123MWG934126scind04312b132scssr00103GBM1022135Bmac0040143DsT-18145DsT-32B146DsT-22152DsT-28159scind60001DsT-74160MWG514162MWG798A163DsT-71167

6H

ABG7040Bmag000714scind0069420AW98258029MWG089CDO47536ABG38038BE60207344scssr0797057scsnp0046066ABC25568ABC165D69HvVRT273scssr1586482GBM103086scsnp22290MWG808DAK642scind00149

89

scsnp00703MWG203197RSB001C98nud103lks2115ABC1024117Bmag0120125DsT-30126WG380B127ABC310B137Ris44139

ABG461A167WG380A171GBM1065178

HVM5196scssr04056KFP255197ThA1199

7H

Flanking markers in each target region

Three resistance genes in chromosome 1H, 4H and 5H

THE PROBLEMKURTFORD •6 –rowed hooded feed barley •Well adapted to California conditions•Short height

•Stripe Rust Susceptible

iBISON 1H+4H+5H

• Resistance alleles for the three genes

• 2–rowed awned barley; short height

I Bison 1H 4H 5H

Kurtford1H 4H 5H

XF1 heterozygote at 3 BSR resistance loci

X

Kurtford1H 4H 5H

BC1F1 12.5% of plants expected

to be heterozygote at 3 BSR resistance loci.

Year 1

RR RR RR SS SS SS

RS RS RS SS SS SS

Segregation in each locus:½ RS½ SS

SOLUTION: The Kurtford Conversion

We have 589 BC1F1 seeds and we expect to find around 74 target heterozygotes at the 3 BSR resistance loci.We need:

-Confirm choice of markers-DNA extraction for 589 plants-Genotyping for the 3 BSR resistance regions-Selection of targeted genotypes

Bmag399

EST4473

EST4535

Baal29j18

. Bags 4e

Bmag337

Bmag223

Bmag812

1H 4H 5H

Summer – Fall 2007

MAS1

Kurtford iBison 1H+4H+5H

I I I K I K I I K

EST4

473,

1F/

4R, B

anII

Bm

ag39

9

EST4

535,

1F/

5R, N

arI

Baa

l29j

18

Bag

s 4e

Bm

ag22

3

Bm

ag81

2

BM

AG

337

Pla

nt N

umbe

r

1H 1H 4H 4H

4H

5H 5H 5H

1 I I K K K I I K2 K K K K K I I K3 K K I I I K K K4 I I K K K K K I5 I I I I I I I I6 I I I I I K K I7 K K K K K I K K8 K K I I I I I I9 K K K K K I I K

10 I K K K K I I K11 K K I I I I I I12 I I K K K I K I13 I I I I I I I K14 I I I I I I I I15 I I I I I K K K16 K K K K K I I K17 K K I I I K K K18 K K K K K I I19 I I I I I I I I20 I K I I I I I K

1. Selection of heterozygotes (~74) 2. 10 seeds per selected plant ~ 740 BC1F2 plants.3. Grow out and genotype

We expect 25% of the BC1F2 to be homozygous for AT LEAST the 4H region (~ 185). Of these:

~ 104 homozygote only for 4H~ 35 homozygote for 4H and 1H~ 35 homozygote for 4H and 5H~ 11 homozygote for 1H, 4H and 5H

25/64 (~ 38%) of the resistant plants will be homozygous hooded

Winter 2008

MAS2BC1F2 plants segregating in each locus:¼ RR ½ RS ¼ SS

Winter 2008/2009 – seed increase

Summer 2009 – validate resistance

~ 70 homozygous hooded, BSR resistant plantsField test

Genomic Selection (GS)

•A method to estimate breeding values for individuals based on many markers distributed across the genome. •Breeding values are derived from marker effects that are estimated from a training population for which both marker and phenotypic data exist.• The primary benefits of GS are that selection can be imposed for quantitative traits very early in the breeding process, thus substantially reducing breeding cycle time. 

In a Breeding Population individuals are genotyped but not phenotyped• A genomic estimated breeding value (GEBV) for each individual is obtained

by summing the marker effects for that genotype

• Prediction model can be used to impose multiple generations of selection

A Training Population is genotyped with a large number of markers and phenotyped for important traits• Genome-wide markers are considered to be random effects and all marker

effects on the phenotype are estimated simultaneously in a single model

• One or more markers are assumed to be in LD with each QTL affecting trait

• Prediction model attempts to captures the total additive genetic variance to estimate breeding value of individuals based on sum of all marker effects

Genomic Selection Methodology

Training population(Breeding lines)Genotyping Phenotyping

Development of Prediction Model / Cross-Validation

Application of prediction modelGenotyping

Genomic estimation of breeding values (GEBV)

Selection Intermate and next cycle of GS

GENOMIC SELECTION

Marker Allele A Allele B Morex Steptoe Harrington Strider Morex Steptoe Harrington Strider3_0969 -0.003 0.003 3_0969 A A B A -0.003 -0.003 0.003 -0.0031_0895 0.004 -0.004 1_0895 A A A B 0.004 0.004 0.004 -0.0041_1223 -0.016 0.016 1_1223 A A B A -0.016 -0.016 0.016 -0.0162_1354 0.040 -0.040 2_1354 B B B B -0.040 -0.040 -0.040 -0.0402_1067 -0.037 0.037 2_1067 A B A B -0.037 0.037 -0.037 0.0372_0502 -0.035 0.035 2_0502 B A B A 0.035 -0.035 0.035 -0.0353_0715 -0.016 0.016 3_0715 B B A B 0.016 0.016 -0.016 0.0161_0419 -0.028 0.028 1_0419 A B A B -0.028 0.028 -0.028 0.0283_1144 -0.037 0.037 3_1144 B A A B 0.037 -0.037 -0.037 0.0373_0820 0.075 -0.075 3_0820 B B B B -0.075 -0.075 -0.075 -0.0751_1011 -0.006 0.006 1_1011 B B A A 0.006 0.006 -0.006 -0.0063_0933 -0.037 0.037 3_0933 B B B B 0.037 0.037 0.037 0.0371_0716 -0.008 0.008 1_0716 A A B B -0.008 -0.008 0.008 0.0082_1174 0.019 -0.019 2_1174 B B A A -0.019 -0.019 0.019 0.0192_1226 0.027 -0.027 2_1226 A A B B 0.027 0.027 -0.027 -0.0273_1149 -0.006 0.006 3_1149 B A B B 0.006 -0.006 0.006 0.0063_0918 -0.028 0.028 3_0918 A A B B -0.028 -0.028 0.028 0.0283_0951 0.007 -0.007 3_0951 B A B A -0.007 0.007 -0.007 0.0073_0950 1.976 -1.976 3_0950 A A A B 1.976 1.976 1.976 -1.9761_0332 0.075 -0.075 1_0332 A A A B 0.075 0.075 0.075 -0.0753_0955 0.017 -0.017 3_0955 B B A B -0.017 -0.017 0.017 -0.0171_0775 -0.027 0.027 1_0775 B B B A 0.027 0.027 0.027 -0.0272_0749 -0.023 0.023 2_0749 A A A B -0.023 -0.023 -0.023 0.0233_0948 0.001 -0.001 3_0948 B B B B -0.001 -0.001 -0.001 -0.0011_0030 0.029 -0.029 1_0030 B B B B -0.029 -0.029 -0.029 -0.0292_0371 -0.018 0.018 2_0371 B B A B 0.018 0.018 -0.018 0.0182_0712 0.031 -0.031 2_0712 A B B A 0.031 -0.031 -0.031 0.0313_0241 0.004 -0.004 3_0241 B A B A -0.004 0.004 -0.004 0.0041_0186 -0.009 0.009 1_0186 A B B A -0.009 0.009 0.009 -0.009

1.952 1.901 1.881 -2.041

BLUPs for each marker

Genomic Estimated Breeding Value (GEBV):

R² = 0.4996

-40.00

-20.00

0.00

20.00

40.00

60.00

80.00

100.00

0 50 100 150 200 250 300

DP_CR2004_GEBV R² = 0.7313

-40.00

-30.00

-20.00

-10.00

0.00

10.00

20.00

30.00

40.00

50.00

60.00

0 50 100 150 200

DP_SD2005_GEBV

GEBV GEBV

True

Val

ue

True

Val

ue

• 3,000 SNPs• Ridge Regression• Results of Cross Validation