Post on 16-May-2015
Departement Biochemie ● Department of Biochemistry
Potato virus Y in South Africa: Isolate characterization and
assessment of potato cultivar resistance
Chris Visser and Dirk BellstedtDepartment of BiochemistryUniversity of Stellenbosch
Introduction
• Only PVYN and PVYO with classic symptoms and yield losses occurred in South Africa before 1995
• After 1995 mosaic leaf symptoms became less prominent
• Tuber necrosis (PTNRD) observed for the first time in 2005 - associated with severe yield and quality losses for the potato producer
Changes in symptom development
Mild mosaic symptoms PTNRD
Project goals
• Characterize South African PVY isolates to understand changed symptom expression
• Establish speed of spread and PTNRD symptom development in local cultivars in order to assess cultivar resistance to PVY infection
Approach for strain characterization
• Use CP gene sequencing and differential RT-PCR for strain identification - 2004 to 2008
• Use whole genome sequencing of representative PVY strains for full characterization - 2009 to 2011
Results of CP gene sequencing and differential RT-PCR
133 PVY isolates characterized:• PVYO isolates (7.5%)
– 10 PVYO strains
• PVYN isolates (20.3%)– 22 PVYN strains
– 4 PVYNE-11 from China
– 1 SASA-61 from Scotland
• Recombinant strains (72.2%)– 34 PVYN-Wilga strain (25.6%)(1 PTNRD phenotype)
– 62 PVYNTN strain (46.6%)(20 PTNRD phenotype)
Approach for strain characterization
• Use CP gene sequencing and differential RT-PCR for strain identification - 2004 to 2008
• Use whole genome sequencing of representative PVY strains for full characterization - 2009 to 2011
Whole genome sequencing results
4 PVYN
1 SASA-61
1 PVYNE-11
15 PVYNTN
4 PVYN-Wilga
2 PVYO
Diagram showing recombination patternsNo of isolates
Whole genome sequencing results
Phylogenetic analysis of the whole genome sequence data indicates that some PVYNTN
and PVYN-Wilga were imported via tissue culture material from Europe:
Project goals
• Characterize South African PVY isolates to understand changed symptom expression
• Establish speed of spread and PTNRD symptom development in local cultivars in order to assess cultivar resistance to PVY infection
Biological characterization • Small scale greenhouse trial• 4 cultivars, 7 isolates• Mechanical infection• Viral spread monitored by
qRT-PCR• Tubers inspected for
PTNRD
Point of mechanical
infection
Monitored byqRT-PCR
here
Isolate
Cultivar
Z001 Z16 SS607 31 Z14 NTN OVS GP
Hermes
Sifra
Mondial
Fabula
0
1
2
1 2 3 4 50
1
2
1 2 3 4 50
1
2
1 2 3 4 50
1
2
1 2 3 4 50
1
2
1 2 3 4 50
1
2
1 2 3 4 5
** *
Number of weeks Number of weeks Number of weeks Number of weeks Number of weeks Number of weeks
Num
ber o
f pla
nts
Num
ber o
f pla
nts
Num
ber o
f pla
nts
Num
ber o
f pla
nts
Num
ber o
f pla
nts
Num
ber o
f pla
nts
0
1
2
1 2 3 4 50
1
2
1 2 3 4 50
1
2
1 2 3 4 50
1
2
1 2 3 4 50
1
2
1 2 3 4 50
1
2
1 2 3 4 5
* * *Num
ber o
f pla
nts
Num
ber o
f pla
nts
Num
ber o
f pla
nts
Num
ber o
f pla
nts
Num
ber o
f pla
nts
Num
ber o
f pla
nts
Number of weeks Number of weeks Number of weeks Number of weeks Number of weeks Number of weeks
0
1
2
1 2 3 4 50
1
2
1 2 3 4 50
1
2
1 2 3 4 50
1
2
1 2 3 4 50
1
2
1 2 3 4 50
1
2
1 2 3 4 5Number of weeks Number of weeks Number of weeks Number of weeks Number of weeks Number of weeks
Num
ber o
f pla
nts
Num
ber o
f pla
nts
Num
ber o
f pla
nts
Num
ber o
f pla
nts
Num
ber o
f pla
nts
Num
ber o
f pla
nts
0
1
2
1 2 3 4 50
1
2
1 2 3 4 50
1
2
1 2 3 4 50
1
2
1 2 3 4 50
1
2
1 2 3 4 5
* *
0
1
2
1 2 3 4 5
*
** * *
Number of weeks Number of weeks Number of weeks Number of weeks Number of weeks Number of weeks
Num
ber o
f pla
nts
Num
ber o
f pla
nts
Num
ber o
f pla
nts
Num
ber o
f pla
nts
Num
ber o
f pla
nts
Num
ber o
f pla
nts
Spread rate of PVYNTN isolates in 4 cultivars
Z001
NTN-OVS
Z14
SS607(31) Z16 GP
00: No symptoms observedND: Not done
Z001 Z16 SS607 31 Z14 NTN-OVS GPHermes 100.00 80.00 26.47 25.00 2.73 0.00
0.00
10.00
20.00
30.00
40.00
50.00
60.00
70.00
80.00
90.00
100.00
% T
uber
s di
spla
ying
PTN
RD
Hermes
Tuber necrosis assessment
Z001
NTN-OVS
Z14
SS607(31) Z16 GP
0
0: No symptoms observedND: Not done
Z001 Z16 SS607 31 Z14 NTN-OVS GPSifra 33.33 40.63 5.56 13.64 0.00 5.66
0.00
10.00
20.00
30.00
40.00
50.00
60.00
70.00
80.00
90.00
100.00
% T
uber
s di
spla
ying
PTN
RD
Sifra
Tuber necrosis assessment
Z001
NTN-OVS
Z14
SS607(31) Z16 GP
0
0: No symptoms observedND: Not done
Z001 Z16 SS607 31 Z14 NTN-OVS GPMondial 16.95 2.54 14.00 8.57 0.00 20.00
0.00
10.00
20.00
30.00
40.00
50.00
60.00
70.00
80.00
90.00
100.00
% T
uber
s di
spla
ying
PTN
RD
Mondial
Tuber necrosis assessment
Z001
NTN-OVS
Z14
SS607(31) Z16 GP
0
0
0
0: No symptoms observedND: Not done
Z001 Z16 SS607 31 Z14 NTN-OVS GPFabula 0.00 4.88 6.58 0.00 0.00 9.68
0.00
10.00
20.00
30.00
40.00
50.00
60.00
70.00
80.00
90.00
100.00
% T
uber
s di
spla
ying
PTN
RD
Fabula
Tuber necrosis assessment
Conclusions
• PVYN and PVYO have been replaced with PVYNTN and PVYN-Wilga strains
• Some virus isolates spread rapidly in the potato plant and induce tuber necrosis
• Some potato cultivars only allow slower viral spread and exhibit less tuber necrosis
• Together viral spread and ability to induce tuber necrosis give an indication of potato cultivar resistance
Future work• Assess rate of viral spread and tuber
necrosis formation in 20 of the most planted cultivars in South Africa
• Use rate of viral spread and PTNRD symptom development data to establish the levels of PVY resistance in cultivars planted in South Africa
• Advise farmers to plant resistant cultivars to improve yields
Acknowledgements• APA 2013 conference organizers
• Coral de Villiers, Wiets Roos, University of Stellenbosch
• Anel Espach, Potato Certification Services
• Dr Ben Pieterse, former research manager, Potatoes South Africa
• Dr Fienie Niederwieser, research manager, Potatoes South Africa
• Potatoes SA for funding
Thank you for your attention