Genetic diversity and effects of stripe rust QTLs in CIMMYT Germplasm

Dr Garry Rosewarne CIMMYT, Chengdu, China g.rosewarne@cgiar.org

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