Genetic diversity and effects of stripe rust QTLs in CIMMYT Germplasm
Dr Garry Rosewarne CIMMYT, Chengdu, China [email protected]
Introduction
● Development of near-immune lines by breeding for
partial resistance (Singh et al 2000)
● Crossing moderately resistant by moderately resistant
and looking for transgressive segregants
● Many elite lines with multi-genic resistance
● QTL mapping to “deconstruct” wheat lines to identify
genetic loci contributing to resistance
● Ensure stable resistance moving into the future
QTL Analysis of CIMMYT Germplasm
Avocet x Attila •148 RILs •Bulked segregant analysis •Stripe rust screening in Mexico •Rosewarne et al TAG 2008
Avocet x Pastor •148 RILs for phenotyping, 84 RILs for mapping •DArT Map •Stripe rust in Mexico •Rosewarne et al TAG 2012
Avocet x Chapio •DArT Map of 137 RILs • BSA of 277 RILs •Stripe rust phenotyping in Mexico and China on 277 RILs •Yang et al, Submitted to TAG 2012
Avocet x Pavon 76 •William et al Genome 2006
Avocet x Saar Avocet x Parula
•Lillemo et al TAG 2008, BGRI 2011
Attila QTLs Phenotypic Explained Variance
Markers Chromosome 2000 2002 2004
LTN 1BL 12.5 12.1 15.0
XP32/M62-XP88/M64 2BS 4.7 9.3 5.5
XP32/M59-Xgwm344 7BL 3.1 3.1 3.1
XP33/M550.0
XP35/M5511.3
LTN20.1
XP84/M7825.9XP86/M6728.5
XP33/M5940.8
1BL
Xwmc100.0
Xgwm3447.2
XP32/M5919.2
Xgwm14631.0
Xwmc27351.5
Xgwm57759.1
Attila 7BL
Xwmc2570.0
Xwmc15420.8
Xgwm68240.9
XP32/M6263.2
XP88/M6482.7
Xgwm120108.1
Xgwm501122.2XP84/M68131.1
Attila 2BS
1BL 7BL 2BS
Pastor QTLs
Location Flanking Markers LOD PEV
2000
PEV
2002
PEV
2009a
PEV
2009b
1AL wPT6005 4.9 4.1 1.5* 3.6 0.0*
1BS wPT8168-wPT6240 6.6 5.1 5.0 2.1* 1.7*
1BL Lr46/Yr29-Xgwm818 23 15.1 16.4 16.3 22.1
2BS wPT6278-Yr31 60 17.9 13.8 15.2 8.2
3BS wPT2458-wPT0036 16.2 4.6 5.8 3.8 0.2*
4DS wPT6880 11.8 4.9 1.9* 2.8 1.5*
5AL wPT3257 13.2 3.9 6.6 2.8* 1.6*
6BL wPT6329-wPT5176 5.6 0.5* 3.9 2.3 4.4
7BL wPT3190-wPT1475 25.8 6.3 7.8 5.4 4.2
Pastor QTLs: Known Genes
Location Flanking Markers LOD PEV
2000
PEV
2002
PEV
2009a
PEV
2009b
1AL wPT6005 4.9 4.1 1.5* 3.6 0.0*
1BS wPT8168-wPT6240 6.6 5.1 5.0 2.1* 1.7*
1BL Lr46/Yr29 23 15.1 16.4 16.3 22.1
2BS Yr31 60 17.9 13.8 15.2 8.2
3BS Sr2/Yr30 16.2 4.6 5.8 3.8 0.2*
4DS wPT6880 11.8 4.9 1.9* 2.8 1.5*
5AL wPT3257 13.2 3.9 6.6 2.8* 1.6*
6BL wPT6329-wPT5176 5.6 0.5* 3.9 2.3 4.4
7BL wPT3190-wPT1475
(Lr68) 25.8 6.3 7.8 5.4 4.2
Chapio QTLs
Locus Toluca
2004
Toluca
2005
Toluca
2009a
Toluca
2009b
Wenjiang
2009
Wenjiang
2010
Dayi
2010
Xindu
2010
1BL (Lr46/Yr29) - - - - - - - -
2BS 5.2 7.8 3.3 - - - - -
3BS (Sr2/Yr30) 4.4 5.8 3.8 - 18.0 16.0 10.8 9.4
3D - - - 8.0 - 3.2 - 4.4
5BL - - - - 4.5 4.3 3.6 10.3
7DS (Lr34/Yr18) 9.3 6.7 15.8 26.2 36.6 41.7 51.1 44.5
Mexico China
LOD Scores
Main Stripe Rust Loci in CIMMYT Germplasm
Locus Attila Pastor Chapio Saar* Parula* Pavon 76**
Lr34/Yr18 - - + + + +
Lr46/Yr29 + + + + + -
Sr2/Yr30 - (?) + + + + +
1AL - + - - - -
1BS - + - - - -
2BS (Yr31) + +(Yr31) +(Yr31) - - -
2DS - - - + - -
3AS - - - + - -
3D - - + - - -
4DS - + - - - -
5AL - + - - - -
5BL ? ? + - ? ?
6BL - + - - - -
7BL + + - - -? -
* Lillemo et al (2011) ** William et al (2006)
Main Stripe Rust Loci in CIMMYT Germplasm
Locus Attila Pastor Chapio Saar* Parula* Pavon 76**
Lr34/Yr18 - - + + + +
Lr46/Yr29 + + + + + -
Sr2/Yr30 - (?) + + + + +
1AL - + - - - -
1BS - + - - - -
2BS (Yr31) + +(Yr31) +(Yr31) - - -
2DS - - - + - -
3AS - - - + - -
3D - - + - - -
4DS - + - - - -
5AL - + - - - -
5BL ? ? + - ? ?
6BL - + - - - -
7BL + + - - -? -
* Lillemo et al (2011) ** William et al (2006)
Interaction of Yr18 and Yr29
Suenaga et al (2003) Fukuho-komugi x Oligoculm Lr34/Yr18 effective against both leaf and stripe rust Lr46/Yr29 only effective against leaf rust
0
10
20
30
40
50
60
70
Parula Saar
None
Yr29
Yr18
Yr29+Yr18
Lillemo et al (2011)
Avera
ge D
isease
Severity
Yr29 and Yr18 in Chapio
0
20
40
60
80
100
Fin
al D
ise
ase
Sev
eri
ty
None
Yr29
Yr18
Yr29+Yr18
7BL and Lr68
Xwmc10 0.0
Xgwm344 7.2
XP32/M59 19.2
Xgwm146 31.0
Xwmc273 51.5
Xgwm577 59.1
Attila 7BL
wPT-98130.0wPT-71084.0wPT-50697.0wPT-108511.0wPT-147516.0wPT-319024.0wPT-393932.0wPT-892148.0wPT-434251.0
wPT-760273.0wPT-765379.0
wPT-7318101.0
Pastor 7BL
Xgwm1460.0Lr680.6Psy-1-11.1cs7BLNLRR1.4csGS1.8Xcfa22572.5Xwmc2322.7Xbarc1823.3
Xwmc2736.7
Xgwm57711.3
Parula 7B
Parula Lr68 Attila 7BL Pastor 7BL
Summary
● Deconstruction of CIMMYT near-immune lines show
resistance is often based upon varying combinations
Lr34/Yr18, Lr46/Yr29, Sr2/Yr30
● Many other minor loci are important in supporting these
resistances – achieved through a long term breeding
approach based on avoidance of major resistance
genes and strong phenotypic selection
● Yr18 and Yr29 interact epistatically such that Yr18 has
a stronger effect which masks any effect of Yr29
● Yr29 is an important locus but may be ineffective in
certain environments
Leaf and Yellow Rust QTL
Start0.0Xpsr94943.0Centromere45.1Xgwm60454.4Xgwm18a55.3Xgwm1160.8Xgwm27361.7glk48363.2Xgwm13168.5Xgwm268117.4Xwmc44159.5Xgwm793173.0
Start0.0
Xgwm49769.7XksuH9c70.4XksuG34b72.5
End131.4
start0.0Xwmc1474.8
Centromere99.5
End204.0
Xgwm2106.4Xbarc12414.9Xwmc154a28.5Xgwm148b61.2Xbarc1884.5Xwg99687.0Xglk40087.8Xbarc13b88.8Centromere95.6Xwmc245b98.1Xpsr92499.7Xbarc124a101.3Xbarc230103.6Xbarc167105.0Xgwm120112.7Xpsr540117.0XwPt-6278121.9Xwmc175b126.5Xwmc332134.2End172.2
Start Xwmc1110.0Xgwm2619.1Xcfd5310.0Centromere22.0Xgwm10229.2Xwmc19043.9XwPt-372852.2Xgwm53953.9
Xgwm34983.6Xgwm30192.0Xgwm320 End95.0
Start0.0Xcfd3630.3Xgwm359b52.2Xgwm122a56.3Centromere88.4Xcfa2263102.7Xsfr.BE590525a133.1Xwmc170152.1
End213.5
Start0.0XwPt-78902.9Xbarc31023.0Centromere49.3Xpsr59854.0Xpsr57058.4Xpsr54360.9
End170.1
Start0.0Xgwm389a2.4Xgwm533a7.6Xgwm493a20.0Xpsr91991.5Xpsr110195.5Xgwm383a150.8Xgwm131b179.7XwPt-0036198.4Xbcd131212.6Xgwm299c270.4Xgwm340301.1End306.4
Start0.0
Xfba9189.4Xfba24190.0Xbcd1532104.1XksuA6109.3Xbarc125121.4Xgwm456133.1Centromere156.4End226.6
Start0.0
Centromere29.2
gwm742 gwm83288.2gwm16088.9End103.2
Start0.0Centromere9.0gwm54010.1wmc23811.9gwm49517.0gwm16519.9gwm36822.1gwm14923.0
End70.7
Start0.0
gwm16530.0Centromere30.5gwm19231.3
End84.1
Start0.0
glk42459.1Centromere60.9barc15185.3Vrn197.2Xfbb209.1105.0Xabg391110.0gwm126117.7End133.5
Start0.0Centromere34.5gwm63955.3wmc415a56.8gwm49959.6
End158.5
Start0.0Centromere23.4
End268.0
Start gwm4590.0gwm3343.8
wPt-095942.5Centromere45.7wPt-706358.8wmc256b69.9barc377.4gwm617107.7gwm427111.2End112.0
Start0.0
gwm13233.0Centromere48.0barc10155.0barc13656.8gwm19361.0gwm36163.0gwm62676.6gwm21992.7End104.5
Start0.0
Centromere75.0
bcd1510120.4ksuD27134.8End149.5
Start Xgwm4710.0wPt-8149 wPt-41727.0gwm66618.2fba12751.8Xwmc28375.7barc17485.5cfa217491.2Xbarc10899.9Centromere104.1
End207.0
Start0.0gwm935c57.0gwm57357.9gwm4661.6gwm4367.5Centromere69.0psr35086.8psr129a88.3pwir23297.4psr59398.1gwm131103.0wmc273a106.4ksuD2116.3gwm146a119.8gwm146b133.0wmc273b134.4psr680b136.9gwm344b142.8barc182143.5gwm577156.6End190.7
Start0.0Xcfd6626.9XwPt-332841.7Xgwm29552.2Xgwm13055.0XcsLV3456.4Xbcd143859.1Xgwm1002a59.5Xwmc405b79.2Xgwm1002b80.3Centromere97.9
End227.0
Chromosome 1A
Chromosome 7D Chromosome 6D Chromosome 5D Chromosome 4D Chromosome 3D
Chromosome 7B Chromosome 6B Chromosome 5B Chromosome 4B Chromosome 3B Chromosome 2B
Chromosome 7A Chromosome 6A Chromosome 5A Chromosome 4A Chromosome 3A
Chromosome 2D
Chromosome 2A
Chromosome 1D
Chromosome 1B
叶锈和条锈病的QTL
Acknowledgements ● CIMMYT
Dr Ravi Singh
Dr Julio Huerta-Espino
Dr Sybil Herrera-Foessel
Dr Garry Rosewarne
● Sichuan Academy Agricultural Sciences
Dr Yang Ennian
● Chinese Academy of Agricultural Sciences
Dr Xia Xianchun
● Norwegian University of Life Sciences
Morten Lillemo
● DuPont
Dr Manilal William
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