diversity studies on blast race and resistance … studies on blast race and resistance of rice...
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Diversity Studies on Blast Race and Resistance of
Rice Germplasm in Indonesia
“Blast Research Network for Stable Rice Production”
Biological Resource Division, JIRCAS
JIRCAS Fellow : Santoso
Host Scientist : Dr. Y. Fukuta
Contribution of different lands to national rice area and
production
Rice cultivation area Rice production
Total rice area: 12 million Ha
Total rice production: 57 million tons per year
Upland 9%Swampy land 7%
Upland 5%
Swampy land 5%
Lowland 90%Lowland 84%
Upland rice area :
• Traditional rice varieties in Indonesian upland
area was dominant
• Major constraints of upland production are
diseases (blast, brown spot) and soil problems
(acidity, drought)
Rice blast disease
Neck /Panicle blastLeaf blast Collar blast Node blast
• Fungus “Pyricularia grisea”
• Attack from the early vegetative until generative stage.
• The yield loss was varied from 1%, even can be 100% or
died.
• Differential varieties : are used characterization
of pathogen and identification of resistance genes
• Indonesia:
• Before 1991, International (8 varieties) and
Japan (12 varieties), differential varieties were
used but not adaptable in Indonesia.
• Mogi et al. (1991) selected the Indonesian
differential varieties (7 varieties), but not
identify the resistance genes and not harbor
only single gene in each genetic background
•Through collaborative research project between
IRRI and Japan, a new set of international
standard blast differential varieties based on
monogenic lines has been developed.
•Monogenic lines as the differential varieties are
carrying different 23 resistance genes
(Kobayashi et al. 2007)
New designation system for blast races based on the reaction of monogenic lines (Hayashi and Fukuta, 2009)
GroupGroupGroupGroup IIII IIIIIIII IIIIIIIIIIII IVIVIVIV VVVV
LocusLocusLocusLocus ---- PiiPiiPiiPii PikPikPikPik PizPizPizPiz PitaPitaPitaPita
Resistance Resistance Resistance Resistance genegenegenegene
PishPishPishPish ++++ PiiPiiPiiPii PikPikPikPik----ssss PikPikPikPik----mmmm PikPikPikPik Pi9 Pi9 Pi9 Pi9 (t)(t)(t)(t) PizPizPizPiz PitaPitaPitaPita----2222 PitaPitaPitaPita Pi19Pi19Pi19Pi19
PibPibPibPib PiaPiaPiaPia Pi3Pi3Pi3Pi3 ---- Pi1Pi1Pi1Pi1 PikPikPikPik----pppp ---- PizPizPizPiz----5555 PitaPitaPitaPita----2222 PitaPitaPitaPita Pi20 Pi20 Pi20 Pi20 (t)(t)(t)(t)
PitPitPitPit ---- ---- Pi5 Pi5 Pi5 Pi5 (t)(t)(t)(t) ---- ---- PikPikPikPik----hhhh Pi7 Pi7 Pi7 Pi7 (t)(t)(t)(t) ---- ---- PizPizPizPiz----tttt ---- Pi12 Pi12 Pi12 Pi12 (t)(t)(t)(t) ---- ----
Monogenic Monogenic Monogenic Monogenic lines (IRBL)lines (IRBL)lines (IRBL)lines (IRBL)
shshshsh----SSSS LTHLTHLTHLTH iiii----F5F5F5F5 ksksksks----SSSS kmkmkmkm----TsTsTsTs kkkk----KaKaKaKa 9999----WWWW zzzz----FuFuFuFu ta2ta2ta2ta2----PiPiPiPi tatatata----K1K1K1K1 19191919----AAAA
bbbb----BBBB aaaa----AAAA 3333----CP4CP4CP4CP4 ---- 1111----CLCLCLCL kpkpkpkp----K60K60K60K60 ---- z5z5z5z5----CACACACA ta2ta2ta2ta2----ReReReRe tatatata----CP1CP1CP1CP1 20202020----IR24IR24IR24IR24
tttt----K59K59K59K59 ---- ---- 5555----MMMM ---- ---- KhKhKhKh----K3K3K3K3 7777----MMMM ---- ---- ztztztzt----TTTT ---- 12121212----MMMM ---- ----
CodeCodeCodeCode
1111 1111 1111 1111 1111 1111 1111 1111 1111 1111 1111
2222 2222 2222 ---- 2222 2222 ---- 2222 2222 2222 2222
4444 ---- ---- 4444 ---- ---- 4444 4444 ---- ---- 4444 ---- 4444 ---- ----
7777
Ex. 1 Race AEx. 1 Race AEx. 1 Race AEx. 1 Race A
SSSS SSSS SSSS SSSS SSSS SSSS SSSS SSSS SSSS SSSS SSSS
SSSS SSSS SSSS ---- SSSS SSSS ---- SSSS SSSS SSSS SSSS
SSSS ---- SSSS ---- SSSS SSSS ---- SSSS SSSS ---- ----
7777 3333 ---- 7777 ---- 1111 7777 7777 ---- 1111 7777 ---- 7777 3333 3333
U73U73U73U73----i7i7i7i7----k177k177k177k177----z17z17z17z17----ta733ta733ta733ta733
Ex. 2 Race BEx. 2 Race BEx. 2 Race BEx. 2 Race B
RRRR SSSS RRRR RRRR RRRR RRRR RRRR RRRR RRRR RRRR RRRR
RRRR RRRR RRRR ---- RRRR RRRR ---- RRRR RRRR RRRR RRRR
RRRR ---- RRRR ---- RRRR RRRR ---- RRRR RRRR ---- ----
0000 1111 ---- 0000 ---- 0000 0000 0000 ---- 0000 0000 ---- 0000 0000 0000
U01U01U01U01----i0i0i0i0----k000k000k000k000----z00z00z00z00----ta000ta000ta000ta000
3
65
Lowland
Upland
Swampy
Blast race Rice varieties
1. Collection of blast isolates
2. Pathogenicity of blast isolates to monogenic lines
3. Selection of standard differential blast isolates
Development of differential system
Selection of representative rice varieties
Classification by DNA markers
Classification by phenol test, and alkali digestion
4. Characterization of blast resistance
Relationships among blast race, rice varieties, and eco-
systems
Research subjects for diversity studies on blast race and resistance of rice germplasm in Indonesia
Ecosystem
I. Clarification for the pathogenicities of blast isolates from
Indonesia using monogenic lines as differential varieties
Materials:
• 279 blast isolates (Upland: 110, Lowland: 116, and Swampy: 53)
• 25 monogenic lines (Kobayashi, et al., 2007)
• LTH and US2 (Susceptible controls)
Method:
• Inoculation and evaluation of resistance was done by method IRRI
SES (1996)
• The judge of resistant and susceptible were done following the
method of Hayashi and Fukuta (2009)
• Classification and grouping of blast isolates was carried out based
on the reaction pattern to monogenic lines (Cluster analysis)
1.Collection of blast isolates from Indonesia
IndonesiaSumatera Selatan= 28
Lampung = 97
West Java = 100
Bali = 29
Kalimantan = 25
Sum = 279
Jawa Barat
Sukabumi = 53
Indramayu = 29
Kuningan = 18
Sum = 100
Bali
Tabanan= 29
Sum = 29
Sumatera Selatan
Kayu Agung = 23
Kota Daro II = 5
Sum = 28
Kalimantan
Kalimantan Selatan= 20
Kalimantan Tengah= 5
Sum = 25
No. of blast isolates collection
Lampung
Tamanbogo = 25
Rumbia = 14
Pekalongan = 19
Karang Endah = 19
Tulang Bawang = 20
Sum = 97
Blast isolates from Indonesia
SiteSiteSiteSite
No. of blast isolates in each No. of blast isolates in each No. of blast isolates in each No. of blast isolates in each
ecosystemecosystemecosystemecosystem
TotalTotalTotalTotal
UplandUplandUplandUpland LowlandLowlandLowlandLowland SwampySwampySwampySwampy
Sumatera Selatan 0 0 28 28
Kalimantan 0 0 25 25
Lampung 58 39 0 97
Jawa Barat 52 48 0 100
Bali 0 29 0 29
Total 110 116 53 279
Infection types of rice blast disease and the scale used in
this study
0 1 2 3 4 50 1 2 3 4 5
Hayashi and Fukuta (2009)
Avirulent VirulentMonogenic lines:
Almost all:
IRBLshS, IRBLta2Pi,
IRBLta-K1 :
IRBL5-M: :
Frequencies of virulent blast isolates (%)
Classification and grouping of blast isolates
27.7
86.6
I II III
Frequencies of blast isolates for each ecosystems (%)
Group I (n=102) II (n=66) III (n=111)
Sub group1
(n=59)2
(n=43)1
(n=31)2
(n=35)1
(n=30)2
(n=31)3
(n=50)
Upland 90 46 0 6 50 29 22
Lowland 10 54 100 86 13 3 42
Swampy land 0 0 0 8 37 68 36
1 2 1 2 1 2 3
Characterization of blast isolates group based on reaction pattern to monogenic lines
Resistance gene
Characterization of blast isolates subgroup I based on reaction pattern to monogenic lines
Resistance gene
Characterization of blast isolates subgroup II based on reaction pattern to monogenic lines
Resistance gene
Characterization of blast isolates subgroup III based on reaction pattern to monogenic lines
Resistance gene
Variation of blast pathotypes based on cluster analysis in each site of Indonesia
Blast isolate groups by cluster analysis
Blast raceBlast raceBlast raceBlast race No. of blast isolateNo. of blast isolateNo. of blast isolateNo. of blast isolate
U23U23U23U23----i0i0i0i0----k000k000k000k000----z00z00z00z00----ta700ta700ta700ta700 12121212
U63U63U63U63----i7i7i7i7----k100k100k100k100----z00z00z00z00----ta413ta413ta413ta413 5555
U73U73U73U73----i4i4i4i4----k100k100k100k100----z04z04z04z04----ta402ta402ta402ta402 4444
U73U73U73U73----i4i4i4i4----k100k100k100k100----z04z04z04z04----ta403ta403ta403ta403 5555
U73U73U73U73----i4i4i4i4----k100k100k100k100----z06z06z06z06----ta402ta402ta402ta402 4444
U73U73U73U73----i7i7i7i7----k100k100k100k100----z03z03z03z03----ta431ta431ta431ta431 7777
U73U73U73U73----i7i7i7i7----k100k100k100k100----z04z04z04z04----ta431ta431ta431ta431 5555
sumsumsumsum 42424242
Pathogenic Variability of blast isolates
A total of 279 blast isolates were classified into 202 blast races.
3. The standard differential blast isolates from Indonesia
II. Characterization of Indonesian Rice Germplasm
for blast resistance
Materials:
• 190 Indonesian rice varieties (upland:151, lowland:23, swampy:16)
• Nipponbare and Kasalath
• LTH and US2 (susceptible control varieties)
• 14 standard differential blast isolates from Indonesia
Method:
• Inoculation and evaluation of resistance was done by method IRRI
SES (1996)
• The judge of resistant and susceptible were done following the
method of Hayashi and Fukuta (2009)
• Classification of rice varieties based on the reaction pattern to blast
isolates
4. C
las
sific
atio
n o
f rice v
arie
ties b
as
ed
on
the re
ac
tion
pa
ttern
to b
last is
ola
tes
Gogo Limpok
Ase Buline
Baso-Baso
Baraya
Barisih
Pulut Krimpang
Lenggong
Mojang
Sri Makmur
Mirah Rempah
Seri Kuning
Gadagung
ProgoPute Iteng
Dusel
Baronaja
Bandang Sigadis
IRAT 13
IR54
IAC 25
Gajih
Aceh - Aceh
Gampai
CAN 2903
Krowal-2
Krowal-1
Mayang
Nippon blas
Grogol
Mutu
Gajah Mungkur
Cirad
Malio
B12644E-MR-1 (BM 2)
Batutugi
BP585F-5-23-3
Renah Pulang
Padi Merah
Padi Padang
Sapper
Ramos
Siam Kayuagung
PanceSiputih
Siam Astambul
Siam Wol
Gadis Kuning
Genjah Batu
Americana
Jemadi
Anak Daro
Pasir Honje
Hawara Batu
Padi Hitam
Cingri
Mantri
Bintang Ladang
Omas
Ketan Nangka
Ketan Ulis
Banda A
Huma Pasir
Gombang
Betonan
Kompal Coklat
Beureum
Pulut Canting
Dayang Rindu
Hitam 120 Hari
Siam Salaka
Cenggong
Ketan Mayang
Cumpo Siam
Ketan Bulu
Mangkar
Kasumba
P. Mandailing
Ketan Banjar
Jaluniung
Selegreng
Jalu Arimit
Lio Gading
Leci A
Ketan Hitam
Ampek Panjang
Beras Merah sleman
Marahmay
Jawa Wangi Sleman
Jaran Mas
Lampuyangan
Ketan Baburak
Makapi A
Katik Taram
Seni Gungu
Baluyan
Kuriak Kasambik
Segon Nyonya
Jamudin
Pare Tambang
Morin Kalawar
Deli
Ketan Rangen
Parosi
Mentik Sleman
Siawak
Serai
Ketan Huma
Cempo Turi
Pajar
Dompet Terong
Rantau Mudih
Ketan Jalupang
Sunting Bringin
Sayap
Sawa Duku
Ramces
Ketik Ana
Grogol
Simariti
Pangraman A
Sipola
Margasari
Banyuasin
Dendang
Lambur
Sei Lilin
Martapura
IR42
Cisantana
Ciujung
Bio12-MR-1-4-PN-26
B10214F-TB-7-2-3
Kal 9418
BP360E-MR-79-PN-2
BP138F-KN-23
B9852E-KA-66
B9833E-KA-14
Dewa Wakat
Limboto
Sagi (ungu)
Salumpikit
Pandanwangi
Rojolele
Memberamo
Cimelati
Situ Patenggang
B11007E-MR-3-2-PN-2-1
B10533F-KN-11-1
Selegreng-234
Klemas-363
B11577E-MR-B-12-1
B11598C-TB-2-1-B-7
TB409B-TB-14-3
B11593F-MR-11-B-2-8
TB490C-TB-1-2-1-MR-4-29
B10553E-KN-68-1-1
TB356B-47-3
TB490C-TB-1-2-1-MR-1-1
B10580-KN-28-1-1
TB368B-TB-25-MR-2
B11604E-TB-2-3
B11576F-MR-5-1
BP1351D-2-PK-3-1
IR60080-23
B11577E-MR-13-1-1-5-5
BP1976B-2-3-7-TB-1-1
TB356B-TB-18-3
BIO511B-5-12-5-1
Fatmawati
Gilirang
Ciherang
BP205
Asahan
Cisokan
IR 64Krueng Aceh
Cisanggarung
Cisadane
Kencana BaliLTH
US-2
Nipponbare
Kasalath
IRBLsh-S
IRBLb-B
IRBLt-K59
IRBLa-A
IRBLi-F5
IRBL3-CP4
IRBL5-M[US]
IRBLks-F5
IRBLkm-TsIRBL1-CLIRBLkh-K3[LT]IRBLk-K[LT]
IRBLkp-K60
IRBL7-MIRBL9-WIRBLz-FuIRBLz5-CA
IRBLzt-T
IRBLta2-Pi
IRBLta2-Re
IRBL12-M
IRBLta-K1
IRBLta-CP1
IRBL19-A
IRBL20-IR24
樹形図樹形図樹形図樹形図
ab
cd
24
.3
Distance between clusters
•LT
H (N
on
)
•US
2 (N
on
)
•Ke
nca
na
Bali (S
)
•Ka
sala
th
•Piz-t
•Pis
h
•Pi1
2(t)
•Pit
•Pik
-s
•Pia
•Pib
•Ga
mp
ai
•Gro
go
l
•Pik
•Pik
-p
•Pik
-m
•Pik
-h
•Pita
-2 R
e
•Pi1
•Pi7
(t)
•Pi9
(t)
•Piz
•Piz-5
•Pa
di la
da
ng
•Cis
oka
n
•Pi2
0(t)
•Ro
jole
le
•La
mp
uya
ng
an
•Nip
po
nb
are
•Pi1
•Pi3
•Pi5
(t)
•Pi1
9
•Pita
K1
•Pita
CP
1
•Pita
-2 P
i
Characterization of variety group based on the reaction
pattern to 14 standard differential blast isolates
Selected blast isolates from Indonesia
Selected durable resistant rice varieties in Indonesia
Varieties
Standard differential blast isolates from Indonesia
Other
ID52 ID96 ID11 ID132 ID21 ID104 ID112 ID261 ID135 ID133 ID36 ID89 ID142 ID146
Dendang R R R R R R R R R R R R R RImproved-Indica
typeBP585F-5-23-3 R R R R R R R R R R R R R R
P. Mandailing R R R R R R R R R R R R R RLandrace-
Japonica typeGampai R R R R R R R R R R R R R R
IR54
(Pita, Pib)*R R R R R R R R R R R R R R IRRI line
IRBLb-B S S S S S S S S S S R R S S
Monogenic line
IRBLta-CP1 R S S R R R S S R R R S R R
LTH S S S S S S S S S S S S S SSusceptible
controlUS2 S S S S S S S S S S S S S S
R=Resistant; S=Susceptible
*Fukuta et al. (2007)
Conclusion
• The pathogenic variation of Indonesian blast
isolates were corresponded with ecosystem of rice
cultivation
• The resistance of rice varieties from Indonesia was
varied widely according to the diversity of blast
races
Upland
LowlandSwampy
Blast
Ecosystems Resistance
genes Landrace
Improved
Pathotype /race
Diversity triangle
Recent impact and future program
• The standard differential blast isolates can be used to
estimate resistance gene in rice varieties.
• Their stability and virulence will be investigated
continuously.
• The genetic mechanism of broad resistant varieties, P.
Mandailing and Gampai, will be clarified.
Publications
1. Santoso, A. Hairmansis, Anggiani, E. Lubis, B. Kustianto. Sobrizal,
Suwarno, Y. Fukuta. 2009. Genetic diversity of upland rice varieties
in Indonesia. Poster presented in 115th Japanese Society of Breeding
Meeting. 27-28 March 2009. Tsukuba University. Japan.
2. Santoso, A. Nasution, Suwarno, A. Kawasaki, T. Noda, S. S. Namai, N. Hayashi, Y. Fukuta. 2009. Genetic diversity of rice blast isolates from Indonesia based on the reactions to monogenic lines. Poster will be presented in 6th International Rice Genetics Symposium. 16-19 November 2009. Manila Philippines.
3. A. Hairmansis, Santoso, Suwarno, A. Nasution, E. Lubis, B. Kustianto, Sobrizal, S.S. Namai, Y. Fukuta. 2009. Genetic diversity analysis of Indonesian upland rice varieties using microsatellite markers. Poster will be presented in 6th International Rice Genetics Symposium. 16-19 November 2009. Manila Philippines.
Acknowledgements
Thank YouThank You
Sesungguhnya Allah Ta’ala menurunkan penyakit dan obatnya, dan menjadikan setiap penyakit pasti ada obatnya. Maka
berobatlah kalian, tapi jangan dengan yang haram.”
(HR. Abu Dawud).
[Qs.Al-Imran :190-191] :
• 190. Sesungguhnya dalam penciptaan langit dan bumi, dan silih bergantinya malam dan siang terdapat tanda-tanda bagi
orang-orang yang berakal,
• 191. (yaitu) orang-orang yang mengingat Allah sambil berdiri
atau duduk atau dalam keadan berbaring dan mereka memikirkan tentang penciptaan langit dan bumi (seraya
berkata): "Ya Tuhan kami, tiadalah Engkau menciptakan ini dengan sia-sia, Maha Suci Engkau, maka peliharalah kami dari siksa neraka
Gambar 2. Spesies padi liar dan budi daya.
A = Oryza glaberrima;
B = O. rhizomatis;
C = O. alta;
D = IR64 (O. sativa);
E = O. latifolia;
F = O. australiensis.
Gambar 1. Spora P. grisea
banyak gen dari wild species yang telah berhasil diintrogresikan ke dalam padi budi daya, seperti
• gen ketahanan terhadap virus kerdil rumput dari O. nivara
(Khush et al. 1977),
• hama wereng coklat dari O. australiensis (Jena and Khush
1990), dan O. officinalis (Multani et al. 1994),
• hawar daun bakteri dari O. longistaminata (Khush et al. 1990),O.minuta (Amante-Bordeos et al. 1992; Mariam et al.
1996; Abdullah et al. 2001),
• penyakit blas dari O.minuta (Amante-Bordeos et al. 1992),
dan O. rufipogon (Utami et al. 2000).