marker assisted selection individuals carrying the trait of interest are selected based on a marker...
TRANSCRIPT
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
•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 Baronesse
Orca
BCD DB
BCD47 BCD12 D3-6/B23 D3-6/B61
AJO BU OPS
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+
4H
BIS
ON
5H
BIS
ON
1H+
5H
BIS
ON
4H+
5H
BIS
ON
1H+
4H+
5H
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+
4H 5H
1H+
5H
4H+
5H
1H+
4H+
5H 7H
BC
D12
BC
D47
0 2 4 6 8
10
12
14
HVM40
HVM03Bmac181
Bmac030B
GBM1071MWG2180
Bmac310
EBmac635
EST4535*k07229baal29j18HvMLO3*k03352
GBM1015
Bmag419HvSnf2
HdAmyB
1_1292 –EST4535
0 2 4 6 8
10
12
14
HVM40
HVM03Bmac181
Bmac030B
GBM1071MWG2180
Bmac310
EBmac635
EST4535*k07229baal29j18HvMLO3*k03352
GBM1015
Bmag419HvSnf2
HdAmyB
1_1292 –EST4535
1_1292 –EST45351_1292 –EST4535
EBmac701
baal29j18SSR markers used for MAS
*
BCD14340DsT-667Act8A12RbgMD18MWG837B22scind0004625ABC165C26Bmac039929GBM100730BCD09836GBM104248BG36701354Bmag021158BG36994061GBM105168ABC16073JS10C86Bmac0144A87MWG706A96KFP170101Blp111ABC261119MWG2028121KFP257B122WMC1E8130MWG912133ABG387Ascssr04163scssr08238
136
1H
DsT-10ABG0585scind026227
ABG00817
scssr1022636scssr0775939GBM106642Pox45scssr0338156scssr12344scssr02236Ebmac0684
63
BCD1434.265ABG35668GBM102371scsnp0334383vrs188Bmag012594DsT-4197MWG503102GBM1062103KFP203104MWG882A108ABG1032117ABG072124Ebmc0415137cnx1139Zeo1149GBM1019161Aglu5F3R2163MWG720165GBM1012170wst7173scssr08447179MWG949A180
2H
BCD9070
ABC171A26GBM107430scssr1055933MWG798B36Dst-2739BCD70642DsT-3958alm61Bmac020966ABC32569DsT-6773
scssr2569187ABG37789Bmag022598
Act8C121ABG499124GBM1043125
scsnp23255151ABG004155
scind02281166MWG883172
DsT-24181
HVM62190
DsT-40199
ABC172scssr25538212
DsT-35218
3H
MWG6340MWG07721HVM4024DsT-2929CDO54230CDO12231hvknox335Dhn639ABC303scssr2056941
CDO79544HVM349DST-46scind03751scssr18005
50
Tef252GBM102060Bmag035362scind1045567DsT-7974scssr14079ABG47280
GBM105983KFP22192Ebmac070194MWG652B95GBM1048101Hsh111HVM67112KFP241.1116ABG601124
4H
scssr023060MWG6186DsT-68ABC48311ABG61012
ABG39537scssr0250344scssr1807645Bmac009653NRG045A55scsnp0426056Ale58
ABC30279scind1699182scssr1533485scsnp0614490srh100
scssr05939111
RSB001A120
scsnp001771280SU-STS1134ABG003B141
scssr10148157Tef3166MWG877169BE456118A170ABG496179scsnp02109E10757A193
ABG391197JS10B198ABC622205DsT-33207Bmag0113C215MWG602A223scssr03907224scssr03906225
5H
MWG6200Bmac0316scssr093984
MWG652A31MWG602B35scind6000242JS10A45GBM102151GBM106861BG29929765HVM3168rob70Bmag0009scssr0209371
ABG47481Bmac0218C88ABG38892scsnp2122699MWG820101GBM1008122scssr05599123MWG934126scind04312b132scssr00103GBM1022135
Bmac0040143DsT-18145DsT-32B146DsT-22152DsT-28159scind60001DsT-74160
MWG514162MWG798A163DsT-71167
6H
ABG7040Bmag000714scind0069420AW98258029MWG089CDO47536
ABG38038BE60207344scssr0797057scsnp0046066ABC25568ABC165D69HvVRT273scssr1586482GBM103086scsnp22290MWG808DAK642scind00149
89
scsnp00703MWG203197
RSB001C98nud103lks2115ABC1024117Bmag0120125DsT-30126WG380B127ABC310B137Ris44139
ABG461A167WG380A171GBM1065178
HVM5196scssr04056KFP255197
ThA1199
7H
Flanking markers in each target region
Three resistance genes in chromosome 1H, 4H and 5H
THE PROBLEM
KURTFORD
•6 –rowed hooded feed barley
•Well adapted to California conditions
•Short height
•Stripe Rust Susceptible
I Bison
1H 4H 5H
Kurtford
1H 4H 5H
XF1 heterozygote at 3 BSR resistance loci
X
Kurtford
1H 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
ES
T4
47
3,
1F
/4R
, B
an
II
Bm
ag
39
9
ES
T4
53
5,
1F
/5R
, N
arI
Ba
al2
9j1
8
Ba
gs
4e
Bm
ag
22
3
Bm
ag
81
2
BM
AG
33
7
Pla
nt N
um
ber
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 Genotyping Phenotyping
Development of Prediction Model / Cross-Validation
Application of prediction modelGenotyping Genotyping
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
Tru
e V
alue
Tru
e V
alue
• 3,000 SNPs• Ridge Regression• Results of Cross Validation