Pulse Crop Root Rot Workshop

Aphanomyces root rot of pea :
disease management
and genetics of resistance
Marie-Laure PILET-NAYEL1, Anne MOUSSART1,2
1 INRA,
UMR IGEPP, 2 Terres Inovia
Le Rheu F-35653, France
photo: UNIP
photo: INRA Rennes
Pulse Crop Root Rot Workshop
Niagara Falls (CA),
November 7th 2015
Aphanomyces root rot (Aphanomyces euteiches):
a major disease of pea in France
600
Area (Mha)
55
Aphanomyces
root rot
700
55
50
50 500
400
45 300
45
40
40 200
100
35
0
(Source: FAO)
Area harvested (mHa)
2012
2010
2008
2006
2004
2002
2000
1998
1996
1994
1992
1990
1988
1986
1984
1982
35
1980
30
Yield (Qx/ha)
60 800
Yield (Qx/Ha)
Decrease and yield instability of pea
cultivated areas in France
No methods of control of
Aphanomyces root rot,
except for avoidance of heavily
infested fields and long rotations
Symptoms on pea
Research for an integrated disease management
Inoculum potential
Rotations (Legumes or other species)
Sowing date, tillage
Pea resistant varieties
Photo: INRA Rennes
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Pilet-Nayel and Moussart
Pulse Crop Root Rot Workshop
th 2015
November
July 10
7th
2014
Avoidance of heavily infested fields
• A biological test allows to determine the Inoculum
Potential (IP) of the field and disease risk. It is used by
French pea growers to identify fields suitable for pea
crops.
Moussart et al (2009) EJPP
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Pilet-Nayel and Moussart
Pulse Crop Root Rot Workshop
th 2015
November
July 10
7th
2014
Choice of Legumes species/variety of the
rotation
Lentil
• Four categories among the legume species/cultivars
tested (one isolate)
(1) susceptible species : lentil, alfalfa, French bean
(2) legume species including susceptible genotypes and
genotypes with high levels of resistance :common
vetch, faba bean and clover
(3) species with a very high level of resistance : chickpea
(4) Species displaying no symptoms (non-host?): lupin
Faba bean
→ Choice of Legumes species/variety according to IP of the field
Moussart et al (2008) EJPP
Chickpea
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Pilet-Nayel and Moussart
Pulse Crop Root Rot Workshop
th 2015
November
July 10
7th
2014
Choice of Legumes species/variety of the
rotation
• Growing resistant legume species/variety do not
increase IP of the field
Moussart et al (2012) Plant Pathol.
Resistant faba bean is cultivated in heavily infested field or in rotation
with pea in healthy or weakly infested fields
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Pilet-Nayel and Moussart
Pulse Crop Root Rot Workshop
th 2015
November
July 10
7th
2014
Genetics of partial resistance in pea
LGI
LGII
LGIII
LGIV
LGV
R
Ae-Ps3.1
R²=5-30%
A
Ae-Ps4.1
R²=5-25%
Ae-Ps5.1
(=Aph2)
R²=6-38%
LGVII
RIL pop
Puget x 90-2079 A
DSP x 90-2131 A
Baccara x PI180693 B
Baccara x 552 B
SSRs genetic maps
Pops from USDAA, INRAB
Ae-Ps2.2
R²=6-27%
af, A, R: genes of
morphological traits
af
Ae-Ps1.2
(=Aph3)
R²=5-20%
Ae-Ps4.5
(=Aph1)
R²=5-44%
Ae-Ps7.6
R²=5-60%
Few sources of partial resistance in pea
7 main meta-QTL with large intervals (/23 QTL)
Pilet-Nayel et al. (2002) TAG (2005) Phytopathol.; Hamon et al. (2011) TAG (2013) BMC Plant Biol.
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Pilet-Nayel and Moussart
Pulse Crop Root Rot Workshop
th 2015
November
July 10
7th
2014
Back-cross Assisted Selection in pea
#
RIL 847-50 ●
RIL 831-08
RIL BAP8.70
RIL BAP8.195
Resistant
(DSP*90-2131) (Baccara*PI180693) (Baccara*PI180693)
(Puget*90-2079)
line
Ae-Ps4.5
Years
2008
Ae-Ps5.1 + 7.6
Ae-Ps4.1 + 7.6
Ae-Ps1.2 + 2.2 + 3.1
Recipient line BB
552 X •Reference line
Ae-Ps2.2 +
DSP
3.1 + 7.6
or Puget
or Baccara
X
• Dry pea cultivars
Isard : Winter
Eden : Spring
Enduro●: Winter
one chromosomal pair
2009
F1 X
BC1 X
2010
BC2 X
BC3 X
seven chromosomes
BC4 X
2011
a
# AA: Resistant parental line
(90-2131,90-2079, 552 or PI180693).
BC5
2012
a McGee
b
et al. 2012
Near Isogenic Lines
2013
BC5 X
BC5S1*
BC6
BC5S2
BC6S1*
BC5S3
BC6S2
16 Set of NILs
Lavaud et al (2015) TAG
2014
157 pea NILsb fixed at 0, 1, 2 or 3 of the 7 main resistance QTL
NILs fingerprinted
(10k SNPs, GenoPea Infinium®BeadChip, Tayeh et al., in press)
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Pilet-Nayel and Moussart
Pulse Crop Root Rot Workshop
th 2015
November
July 10
7th
2014
NILs resistance in controlled conditions
Validation of major and some minor QTL effects in NILs
RB84 Strain (Pathotype I)
RB84 strain (Pathotype I)
Ae109 strain (Pathotype III)
The major QTL Ae-Ps7.6 and Ae-Ps4.5 and the minor QTL Ae-Ps5.1
individually reduce disease severity
The effect of the major QTL Ae-Ps7.6 is increased i)- when combined
with QTL Ae-Ps5.1 or Ae-Ps4.1, ii)- in the winter variety Isard
Validate QTL effects in NILs on resistance in the field
Lavaud et al. (2015) TAG
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Pilet-Nayel and Moussart
Pulse Crop Root Rot Workshop
th 2015
November
July 10
7th
2014
Genome-wide association mapping
Panel of 175 pea lines enriched in sources of resistance to A. euteiches
Evaluation for resistance in field infested nurseries (9 FR-US environments) and in
climatic chamber (2 strains)
Genotyping with 13,204 SNPs from GenoPea Infinium® BeadChip (Tayeh et al., in press)
52 QTL small size-intervals identified with high resolution (0-5.2cM)
• Confirmation of 6 of the 7 main previous QTL
• Identification of 11 new resistance loci
• Identification of marker haplotypes at 14
consistent QTL regions Accumulation of
best haplotypes in the most resistant lines
Desgroux et al. (accepted) BMC Genomics
• Numerous putative candidate genes
underlying QTL
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Pilet-Nayel and Moussart
Pulse Crop Root Rot Workshop
th 2015
November
July 10
7th
2014
Conclusion
The integration of non-host or resistant legume species in rotations
limits the increase of soil inoculum potential
Resistance genetic loci identified and validated, and closely linked
associated markers, will be useful for marker-assisted-selection of
resistant varieties QTL combination strategies ?
Combining prophylactic, cultural and genetic methods
key strategy for durable disease management
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Pilet-Nayel and Moussart
Pulse Crop Root Rot Workshop
th 2015
November
July 10
7th
2014
Acknowledgments
IGEPP, INRA Rennes, France
Terres-Inovia, France
A. Baranger, B. Tivoli
C. Onfroy, M-N. Even
G. Boutet, J-P. Rivière, P. Vetel, I. Glory,
C. Piriou, G. Le Roy, H. Miteul, G. Morin, M. Hervé
R. Delourme, M. Manzanares-Dauleux
PhD Students: C. Hamon, C. Lavaud, A. desgroux
Temporary engineers: A. Lesné, V. L’Anthoëne
Master Students: M. Bavière, B. Fopa Fomeju
Agroécologie, INRA Dijon, France
USDA-ARS, Pullman (WA), USA
G. Aubert, N. Tayeh, V. Bourion, J. Burstin
C.J. Coyne, R.J. McGee
GSP breeders, France
Experimental Unit-Epoisses, INRA Dijon, France
Experimental Unit and greenhouse group-Le Rheu, INRA Rennes, France
Genotyping plat-form INRA Clermont, France
UNILET, France