diversity studies on blast race and resistance … studies on blast race and resistance of rice...

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







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).

diversity studies on blast race and resistance … studies on blast race and resistance of rice...

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