Successfully reported this slideshow.
We use your LinkedIn profile and activity data to personalize ads and to show you more relevant ads. You can change your ad preferences anytime.
Ancient host adaptation modulated the actual resistance-breaking ability of the  Rice yellow mottle virus Directeur :  Den...
Kenya 1966 Rice yellow mottle disease <ul><li>Emerging disease in Africa </li></ul><ul><li>Induced yield losses 20-100% </...
Rice yellow mottle virus <ul><li>Genus  Sobemovirus </li></ul><ul><li>(+) ssRNA   (4,4kb) </li></ul><ul><li>Host range res...
High resistance of rice toward RYMV Khush G.S. 1997 ~500.000 years safe inoculated safe infected Resistant  plants Suscept...
Breakdown of the resistance alleles  rymv1-2   ( O. sativa indica )   rymv1-3   ( O. glaberrima ) Resistance breakdown ( R...
Traore et al, unpublished Pinel-Galzi et al, 2007 Breakdown of the resistance alleles  rymv 1-2  ( O. sativa indica ) S3 S...
<ul><li>dN/dS < 1 : codon under  conservative  selection </li></ul><ul><li>dN/dS = 1 : codon under  neutral  selection </l...
Pinel-Galzi et al 2007 Genetic signatures VPg East-Africa S5-S6 100 90 84 100 99 West-Africa Central -Africa S2-S3 Sa S1 S...
S2/S3 T S1 T / E S4 E S5 E Traore et al, unpublished Pinel-Galzi et al, 2007 Breakdown of the resistance alleles  rymv 1-2...
Portères R. , 1951 Semon et al. 2005 Traore et al. 2010 Geographic distribution of  Oryzae glaberrima   and polymorphism a...
Molecular signatures of adaptations <ul><li>dN/dS > 1  :  diversifying  selection in all RYMV genome </li></ul>T49   =   u...
<ul><li>Competitions of isolates polymorphic at codon 49 in  susceptible plants </li></ul><ul><li>- 3 cultivars  O. sativa...
<ul><li>Validation by  mutagenesis  : CIa*T 49E </li></ul>T49 = signature of the adaptation to  O. glaberrima O. glaberrim...
<ul><li>CIa ( 49T ) and CIa*T 49E  inoculated at the  same concentration  to resistant  O. sativa indica   ( rymv 1-2 ) </...
Ancient host adaptation and actual resistance-breaking ability of RYMV <ul><li>domestication of  O. glaberrima : ~ 3.500 y...
Conclusion <ul><li>Role of  T49  in the adaptation of  O. glaberrima   ? </li></ul><ul><li>- interaction VPg / eIF(iso)4G ...
Denis Fargette Eugénie Hébrard Agnès Pinel-Galzi Jamel Aribi Nils Poulicard Christelle Lirette Stelly Mississipi UMR  Rési...
 
Histoire évolutive du RYMV Fargette et al, 2004 Fargette et al, 2008 <ul><li>Emergence : ~ 150 ans </li></ul>R = 0.77 0 2 ...
Contrasted  rymv 1-2  resistance-breaking ability Pinel-Galzi et al, 2007 VPg 48 E49 Why CIa is not able to overcome the  ...
Antagonistic epistasis between T49 and  rymv1-2  RB mutations <ul><li>*48G is lethal in CIa isolate.  Influence of T49 ? <...
viral RNA copies / mg of leaves a b b c CI4 *48 I *48 G *48 E Capacités de contournement contrastées entre souches CI4 E C...
Polymorphism at codon 49 and resistance-breaking <ul><li>H52Y mutation involved in the resistance-breaking of  rymv 1-2  a...
Effet de la mutation A303D dans eIFiso4G d’O. glaberrima O. glaberrima O. sativa susceptible susceptible MIF4G A303D E360 ...
viral RNA copies / mg of leaves CI4 *48 I *48 G *48 E a b c d Évaluation de la multiplication virale sur plantes sensibles...
pGBK VPg pGAD iso4G No interaction No transcription of the reporter gene  yeast death VPg Trp 4G Leu Yeast double hybrid a...
Upcoming SlideShare
Loading in …5
×

Nils Poulicard - Relations entre histoire évolutive et capacité d'adaptation à des hotes résistants chez le Rice yellow mottle virus

1,279 views

Published on

Published in: Technology, Business
  • Be the first to comment

  • Be the first to like this

Nils Poulicard - Relations entre histoire évolutive et capacité d'adaptation à des hotes résistants chez le Rice yellow mottle virus

  1. 1. Ancient host adaptation modulated the actual resistance-breaking ability of the Rice yellow mottle virus Directeur : Denis FARGETTE Co-directeur : Eugénie HEBRARD UMR RPB Directeur : Michel NICOLE Équipe Durabilité des Résistances Nils POULICARD
  2. 2. Kenya 1966 Rice yellow mottle disease <ul><li>Emerging disease in Africa </li></ul><ul><li>Induced yield losses 20-100% </li></ul>
  3. 3. Rice yellow mottle virus <ul><li>Genus Sobemovirus </li></ul><ul><li>(+) ssRNA (4,4kb) </li></ul><ul><li>Host range restricted to Oryzae species </li></ul><ul><li>Mechanical transmission (insects and human) </li></ul><ul><li>Non-transmitted by seeds </li></ul><ul><li>Molecular-dating : Emergence = ~ 150 years ago </li></ul>Fargette et al, 2004 Fargette et al, 2008 S3 S2 S1 S4 S5 S2/S3 S1 S4 S5 <ul><li>Emergence in East Africa </li></ul><ul><li>Dissemination to the rest of Africa </li></ul>5' 3' VPg ORF1 ORF2b ORF2a ORF4
  4. 4. High resistance of rice toward RYMV Khush G.S. 1997 ~500.000 years safe inoculated safe infected Resistant plants Susceptible plants <ul><li>Recessive resistance </li></ul><ul><li>High resistance : no symptoms , no multiplication </li></ul><ul><li>Resistance gene Rymv 1 = translation initiation factor eIF(iso)4G </li></ul>Albar et al, 2006 E309K rymv1-2 N-terminal domain Δ 322-324 rymv1-3 C-terminal domain eIF(iso)4G rymv1-2 rymv1-3
  5. 5. Breakdown of the resistance alleles rymv1-2 ( O. sativa indica ) rymv1-3 ( O. glaberrima ) Resistance breakdown ( RB ) <ul><li>Direct interaction between VPg and eIF(iso)4G </li></ul>VPg eIF(iso)4G Hébrard et al. 2010 Traore et al, unpublished <ul><li>Interaction strongly affected by resistance mutations </li></ul>* X * <ul><li>Interaction restored by resistance-breaking mutations </li></ul>* Infected susceptible plant mechanical inoculation Resistant plant SPFEIYGKFR EANSEEYDES LRHGVQYAEY DFSGDTIRAS S NTWVRE R ER Y H AEERRKSG QPSWADRFGD DSGEDVDIE 52 41 48 5' 3' VPg ORF1 ORF2b ORF2a ORF4 Hébrard et al. 2006 Pinel-Galzi et al, 2007 Traore et al, unpublished
  6. 6. Traore et al, unpublished Pinel-Galzi et al, 2007 Breakdown of the resistance alleles rymv 1-2 ( O. sativa indica ) S3 S2 S1 S4 S5 S2/S3 S1 S4 S5 rymv 1-2 : + / - rymv 1-2 : + / - rymv 1-2 : ++ rymv 1-2 : ++ O. sativa rymv 1-2 rymv 1-3 : ++ rymv 1-3 : + / - rymv 1-3 : - - rymv 1-3 : - - O. glaberrima rymv 1-3 rymv 1-3 ( O. glaberrima )
  7. 7. <ul><li>dN/dS < 1 : codon under conservative selection </li></ul><ul><li>dN/dS = 1 : codon under neutral selection </li></ul><ul><li>dN/dS > 1 : codon under diversifying selection ( positive selection) </li></ul>Genetic signatures Codon 49 is under strong diversifying selection dN/dS 1 + 26 + 49 + 62 codon Pinel-Galzi et al 2007 VPg
  8. 8. Pinel-Galzi et al 2007 Genetic signatures VPg East-Africa S5-S6 100 90 84 100 99 West-Africa Central -Africa S2-S3 Sa S1 S4 S1-ca 99 100 98 91 100 99 99 100 90 100 83 86 49
  9. 9. S2/S3 T S1 T / E S4 E S5 E Traore et al, unpublished Pinel-Galzi et al, 2007 Breakdown of the resistance alleles rymv 1-2 ( O. sativa indica ) rymv 1-2 : - - rymv 1-2 : + / - rymv 1-2 : ++ rymv 1-2 : ++ rymv 1-3 : ++ rymv 1-3 : + / - rymv 1-3 : - - rymv 1-3 : - - rymv 1-3 ( O. glaberrima )
  10. 10. Portères R. , 1951 Semon et al. 2005 Traore et al. 2010 Geographic distribution of Oryzae glaberrima and polymorphism at codon 49 T49 = adaptation to O. glaberrima ? T49 E49 <ul><li>Correlation between T49 and repartition area of O. glaberrima </li></ul>
  11. 11. Molecular signatures of adaptations <ul><li>dN/dS > 1 : diversifying selection in all RYMV genome </li></ul>T49 = unique signature of adaptation to O. glaberrima ? VPg ORF1 ORF2b ORF2a ORF4 P1 IFEL 55 79 165 191 192 REL 55 66 79 104 125 162 165 191 192 214 Coat Protein Sel 55 79 81 116 165 191 216 218 IFEL 21 66 110 REL 26 45 54 66 85 99 110 Sel 12 26 42 45 47 53 54 66 74 79 81 85 101 110 IFEL REL Sel 45 203 226 Protease VPg IFEL 49 REL 49 Sel 21 26 49 50 62 Polymerase IFEL 114 237 REL 114 123 134 136 186 187 190 233 237 370 389 400 437 441 Sel 114 174 179 324 <ul><li>signature of co-variations in RYMV genome? </li></ul>no co-variation between codon 49 of the VPg and the others positions under diversifying selection
  12. 12. <ul><li>Competitions of isolates polymorphic at codon 49 in susceptible plants </li></ul><ul><li>- 3 cultivars O. sativa indica </li></ul><ul><li>- 3 cultivars O. glaberrima </li></ul>West Africa Central Africa East Africa T T T T T T E E T E E E T E E E E E E E E E E E E E E E T49 = signature of the adaptation to O. glaberrima Ni1 ( T ) Ni1 ( T ) Tz8 / Ni1 BF5 ( T ) BF5 ( T ) CI4 / BF5 BF1 ( T ) BF1 ( T ) Ma10 / BF1 BF5 ( T ) BF5 ( T ) Tz209 / BF5 BF5 ( T ) Mg16 ( E ) Mg16 / BF5 BF1 ( T ) BF1 ( T ) Tz8 / BF1 CIa ( T ) CI4 ( E ) CI4 / CIa CIa ( T ) Mg16 ( E ) Mg16 / CIa CIa ( T ) CIa ( T ) Tz209 / CIa O. glaberrima O. sativa indica Competitions
  13. 13. <ul><li>Validation by mutagenesis : CIa*T 49E </li></ul>T49 = signature of the adaptation to O. glaberrima O. glaberrima O. sativa indica Competition CIa ( T ) CIa*T 49E ( E ) CIa*T 49E / CIa E49 T49 viral ARN copies / mg of leaves a a a a real time-PCR CIa CIa*T 49E O. sat. O. glab. O. sat. O. glab. T49 = adaptation signature to O. glaberrima
  14. 14. <ul><li>CIa ( 49T ) and CIa*T 49E inoculated at the same concentration to resistant O. sativa indica ( rymv 1-2 ) </li></ul><ul><li> O. glaberrima ( rymv 1-3 ) </li></ul>Polymorphism at codon 49 and resistance-breaking 0 % 40 % 100% CIa*T 49E 95 % 5 % 100% CIa ( T49 ) O. glaberrima rymv1-3 O. sativa indica rymv1-2 IR64 (susceptible) DAS-ELISA + 42 dpi Codon 49 influence the resistance-breaking of rymv 1-2 and rymv 1-3
  15. 15. Ancient host adaptation and actual resistance-breaking ability of RYMV <ul><li>domestication of O. glaberrima : ~ 3.500 years ago </li></ul><ul><li>intensification of O. sativa cultivation: since XIX th centuries </li></ul><ul><li>introduction of O. sativa : VII-X th centuries in East Africa </li></ul><ul><li> XV th century in West Africa </li></ul>+++ - - - + / - +++ O. sativa indica rymv1-2 O. glaberrima rymv1-3 T49 T49 O. glaberrima O. sativa indica East Africa West Africa E49 E49
  16. 16. Conclusion <ul><li>Role of T49 in the adaptation of O. glaberrima ? </li></ul><ul><li>- interaction VPg / eIF(iso)4G ? </li></ul><ul><li>Role of the host genetic background ? </li></ul><ul><li>- introgression of the rymv1-3 resistance allele in O. sativa indica genetic background)? </li></ul>Evolutionary history of RYMV could influence the adaptation to resistant plants Ancient host adaptation could modulate the actual adaptation ability of pathogens Perspectives <ul><li>Competitions in susceptible plants O. sativa indica / O. glaberrima </li></ul><ul><li>- 3 phylogenetic branches of T49 </li></ul><ul><li>- competitions with enclosed-isolates </li></ul>
  17. 17. Denis Fargette Eugénie Hébrard Agnès Pinel-Galzi Jamel Aribi Nils Poulicard Christelle Lirette Stelly Mississipi UMR Résistance des Plantes aux Bioagresseurs Équipe Durabilité des Résistances Rémy Froissart Thierry Michon Benoît Moury Michel Nicole UMR Génome et Développement des Plantes Équipe Génomique appliquée au Riz Alain Ghesquière Laurence Albar Florence Vignol Deless Thiemele Gnissa Konate Oumar Traoré Drissa Sérémé Burkina-Faso Côte d’Ivoire Madagascar Séré Yacouba Fatogoma Sorho Sissi Rakotomalala Tanzanie Zakaria Kanyeka Emmanuel Sangu
  18. 19. Histoire évolutive du RYMV Fargette et al, 2004 Fargette et al, 2008 <ul><li>Emergence : ~ 150 ans </li></ul>R = 0.77 0 2 4 6 8 10 12 2.00 2.50 3.00 3.50 4.00 Distance Geographique (log) Génome entier Distance Génétiques (%nt) S3 S2 S1 S4 S5 Afrique de l’Est Afrique de l’Ouest 0 2 4 6 8 10 Afrique Centrale Diversité nucleotidique (%nt) Nombre total de sites S5 S4 S1AC S1AO S2 S3 <ul><li>Propagation d’Est en Ouest </li></ul><ul><li>Emergence en Afrique de l’Est </li></ul>
  19. 20. Contrasted rymv 1-2 resistance-breaking ability Pinel-Galzi et al, 2007 VPg 48 E49 Why CIa is not able to overcome the rymv 1-2 resistance allele ? <ul><li>inoculation CIa ( 49T ) no emergence of resistance-breaking (RB) mutations </li></ul>T49 T49 X *48 G is lethal in CIa X <ul><li>directed mutagenesis CIa validation of 48 E RB mutations </li></ul>
  20. 21. Antagonistic epistasis between T49 and rymv1-2 RB mutations <ul><li>*48G is lethal in CIa isolate. Influence of T49 ? </li></ul>Directed mutagenesis: Substitution of T49 to E49 : 0 1 2 CIa*48G *48G49E CIa*48G *48G49E 0 1.0 2.0 CIa*48G ( 49T ) CIa*48G * 49E CIa*48G ( 49T ) CIa*48G * 49E O. sativa indica (susceptible) O. sativa indica rymv1-2 OD (405nm) DAS-ELISA 30 dpi T49 X T49 strongly limits the emergence of rymv1-2 RB mutations
  21. 22. viral RNA copies / mg of leaves a b b c CI4 *48 I *48 G *48 E Capacités de contournement contrastées entre souches CI4 E CIa T viral RNA copies / mg of leaves CIa *48 I *48 E a b c VPg *48I*49 T VPg *48G*49 T VPg *48E*49 T dilution Interaction test (two hybrid assay) VPg *48I*49 E VPg *48G*49 E VPg *48E*49 E eIF(iso)4G rymv1-2
  22. 23. Polymorphism at codon 49 and resistance-breaking <ul><li>H52Y mutation involved in the resistance-breaking of rymv 1-2 and rymv 1-3 </li></ul><ul><li>Influence of the polymorphism at codon 49? </li></ul><ul><li>Validation by mutagenesis: - CIa( 49T )*52Y </li></ul><ul><li> - CIa* 49E *52Y </li></ul>T49 *52Y RB rymv 1-3 O. glaberrima E49 RB rymv 1-2 O. sativa indica RB rymv 1-2 O. sativa indica X RB rymv 1-3 O. glaberrima No antagonism between E49 and *52Y RB mutation 0 1 2 CIa*52Y CIa*49E*52Y CIa*52Y CIa*49E*52Y CIa*52Y ( 49T ) CIa*52Y * 49E CIa*52Y ( 49T ) CIa*52Y * 49E O. sativa indica rymv1-2 O. glaberrima rymv1-3 0 1.0 2.0 OD (405nm) Influence of the host genetic background ? E49 X O. glaberrima
  23. 24. Effet de la mutation A303D dans eIFiso4G d’O. glaberrima O. glaberrima O. sativa susceptible susceptible MIF4G A303D E360 5.5 A° A303 E360 D303
  24. 25. viral RNA copies / mg of leaves CI4 *48 I *48 G *48 E a b c d Évaluation de la multiplication virale sur plantes sensibles <ul><li>le WT a la meilleure multiplication </li></ul><ul><li>*48E est le plus contre-sélectionné </li></ul>réversion CI4*48E en CI4*48G (et non mutations compensatoires) CI4 S1 30dpi VPg VPg *48 I VPg *48 G VPg *48 E dilution dilution eIF(iso)4G HUM UM HUAM dilution Growth control Interaction assay
  25. 26. pGBK VPg pGAD iso4G No interaction No transcription of the reporter gene yeast death VPg Trp 4G Leu Yeast double hybrid assay DBD AD Promotor Histidine VPg DBD Yeast strain leu- trp- his- Transformation (-leu-trp) Interaction test (-His) pGBK VPg pGAD iso4G 4G Leu AD VPg Trp DBD iso4G AD Interaction Transcription of the reporter gene yeast growth Promotor Histidine VPg DBD iso4G AD

×