Plant Genetic Resources to Create Novel Crop Varieties for...

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Plant Genetic Resources to Create

Novel Crop Varieties for Global

Warming Adaptation and against

Population Increase

Tsukasa NAGAMINE

Research Supervisor of SATREPS

Japan Science and Technology Agency

FAPESP/JST Joint Workshop 2019

Biotechnologies for Efficient and Improved

Production of Food Crops and Bioenergy

Nov. 5th 2019

Contents

1. About SATREPS

2. Rice for global warming adaptation

3. Rice for high yield

4. Wheat for global warming adaptation

5. Wild wheat for high yield

6. Use of core collection

7. Improvement of active collection

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3

Science and Technology Research Partnership

for Sustainable Development

(SATREPS)

Global

issuesEnvironment

Food security

Natural disasters

Infectious diseases

Global

challenges

by science

and

technology

New knowledge

New technology

Innovation

Economic development

International collaborative research program

Aims of SATREPS

Expecting outcomes to make a real contribution to society

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1. Enhancing cooperation in science & technology

2. New technology, new knowledge, innovations

3. Capacity development

By utilization and implementation of research outcomes

International collaborative research

MOFA,

JICA

MEXT,JST

Collaboration

Competitiveresearch

fund

Technical cooperation

Japan Counterpart country

Research institutions

Research institutions

Researchpartnership

Structure of SATREPS program

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Research areas of SATREPS

4 fields 5 areas

1) Environment and Energy

・Global-scale Environmental Issues

・Low-carbon Society/Energy

2) Bioresource Utilization

3) Disaster Prevention and Mitigation

4) Infectious Diseases Control

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In total (since 2008) : 145 projects with 51 countries:

Area Number of eligible countries Number of projects

Asia 14 countries 77 projects

Africa 21 countries 39 projects

Latin America/Caribbean 9 countries 21 projects

Other regions 7 countries 8 projects7

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SATREPS’s contribution for SDGs

17 goals and 169 targets

2015 UN General Assembly

Research contributing to sustainable production and

utilization of bioresources

Project goals

→ food security,

→ human health promotion,

→ nutrition improvement,

→ sustainable agriculture, forestry, and fisheries

Research in Bioresource utilization

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World population

increase

Plant genetic

resources

International

research

collaboration

Global warming/Climate changes

Drought

tolerance

Heat tolerance

Pest and

disease

resistance

High yield

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SATREPS projects using plant genetic resources

Crop Country Representative research institute in Japan

Main researchactivity

soybean Brazil JIRCAS GM

rice Vietnam (V) Kyushu University breeding

wheat Afghanistan (A) Yokohama City University breeding

rice Kenia (K) Nagoya University breeding

indigenous crops Mexico Tsukuba University conservation

rice Columbia (C) Tokyo University breeding

rice Madagascar (Ma) JIRCAS breeding

rice Myanmar (M) Kyushu University breeding

wheat Sudan (S) Tottori University breeding

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1. Disease resistance

・bacterial leaf blight

・blast

2. Insect resistance

・brown plant hopper

・green leaf hopper

・white-backed plant hopper

3. Flooding tolerance

4. Drought tolerance

Rice genetic resources for global warming

adaptation

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Gene (Source variety) → Country

・Gene(s) is used for the breeding.

・Source variety is a donor of the gene.

・Country where SATREPS project was conducted.

A: Afghanistan, C:Columbia, K:Kenia,

Ma: Madagascar, M:Myanmar, S:Sudan

・Genetic resources are brought into counterpart

country from Japan with each DNA marker after

signing of MTA.


adaptation

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Breeding method

Recurrent parent (RP) X Donor parent with gene(s)

F1 X RP Backcross

Bｃ１F1 X RP Backcross, MAS

Bc2F1 X RP Backcross, MAS

Bc3F1 MAS, Selfing

Bc3F2 MAS, Selfing

Bc3F3 Selfing

Lines (By Yoshimura et al.(2018))


adaptation

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adaptation

Gene Chromoso

me

Trait Gene ID

(IRGSP)

Position No. of

SNPs

detected

XA4 11 bacterial blight

resistance

R1506-S12886 27,822,819-

28.130,150

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XA7 6 ditto RM20576-

RM340

28,796,789-

29,000,232

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GN1a 1 number of

spikelets

Os01g019770

0

5,270,449-

5,275,585

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APO1 6 ditto Os01g066540

0

27,480,082-

27,481,450

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WFP 8 number of

branches

Os08g050960

0

25,274,541-

25,278,696

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Table Example of useful genes with SNP information

(By Kuroshima et al. (2016) and Yoshimura et al. (2018))

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1. Disease resistance

・bacterial leaf blight

Xa4（TKM6） → V, M

Xa5 (DZ192) → M

Xa7 (BV85) → M

Xa13 → M

Xa21（O. longistaminata) → V, M

・rice blast

Pi21 (Sensho) → K, M


adaptation

Mega-varietyKoshihikari

Blast-resistancewith Pi21

NARO Japan

Miyagi Pref. Gov.

Ibaraki Pref. Gov.

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2. Insect resistance

・brown plant hopper (BPH)BPH3 (Rathu Heenati) → M

BPH17 (ditto) → M

BPH25 (ADR52) → V

BPH26 (ditto) → V

・green leaf hopper (GLH)

GRH2 (DV85) → V

GRH4 (Lepedumai) → V

GRH6 （O. nivara) → V

・white-backed plant hopper (WBPH)

OVC (Asominori) → V

qOVA (ditto) → V


adaptation

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3. Flood tolerance


adaptation

SUB1 (floating rice) → M

SUB2 (floating rice) → M

SK1 (floating rice) → M

SK2 (floating rice) → M

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DRO1（Kinandang Patong）→ C, K

DRO2（ditto）→ C, K

DRO3（ditto）→ C, K

QRO1（ditto）→ C

QRO2（ditto）→ C

QRL6.1(ditto) → C

QFSR4(ditto) → C


adaptation

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QTLs on root architecture were introduced into

Colombian popular rice varieties (A60, FA174,

FA473, CT21375)

↓

Novel rice breeding lines having QTLs were selected

↓

The lines showed longer root length compared with

popular varieties

↓

Variety registration in Columbia, seed increase


adaptation

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Rice genetic resources for high yield

1. Grain number

Gn1a (Habataki) → V, K, M

to increase the number of spikelet per panicle

WFP (ST12) → V, K, M

to increase the number of primary branch

APO1 (Habataki) → V, K

to increase the number of spikelet per panicle

qGN8 → K

to increase the number of secondary branch

Nipponbare ST12

The Japanese Society of chemical regulation of plants

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2. Grain size

GS3 → V

to increase grain size (long grain)

GW2 → V

to increase grain size (width and weight)

GW5 → V

to increase grain size (width)

3. Tiller number

MP3 (Koshihikari) → Ma

4. Biomass production

LCSILs (O. longistaminata) → K

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4. Phosphorus uptake

Pup1 （Kasalath) → Ma

phosphorus (P) uptake

PUE11 (DJ123) → Ma

QTL for increasing dry matter production

/ amount of phosphorus uptake

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Wheat genetic resources for global warming

adaptation

Disease resistance

・rust resistance

Lr34 → A

・Stripe-rust resistance

Lr34 → A

Ibaraki Pref .Gov

Chiba Pref. Gov.

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Wheat genetic resources for global warming

adaptation


・Afghanistan indigenous varieties showed

high yield under drought condition.

・KU11209 and KU3089 showed root architecture of

growing downward.

→ A

2. Bread making quality

Glu-D1d （Norin 61 near isogenic line) → S

Good bread making quality under high temperature

(Bohain)

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Wild wheat genetic resources for high yield

Use of wild species of wheat

・drought tolerance (Aegilops tauschi) → A, S

Afghanistan improved variety X Ae. Tauschii

↓

Multiple synthetic derivative population

↓

drought tolerance

high biomass production

large panicle

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Use of core collection

Core collection

・a representative sample of the entire collection with

minimum representatives and maximum genetic

diversity of a crop species

・It contains 5 to 20% of the accessions present in

the entire collection.

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Use of core collectionCore collection in NARO Genebank

No. Collection name No. of representative

accessions

No. of total accessions

DNAmarkers

1 World rice 300 37,000 RFLP

2 Japanese local rice 50 2,000 SSR

3 Japanese local maize 86 1,300 AFLP

4 World soybean 96 4,000 SNP

5 Japanese local soybean 96 6,000 SNP

6 World sorghum 105 3,500 SNP

7 World Vigna 415 2,000 SNP

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Use of core collection

Example of use

・Variation of lipoxygenase 3 using NARO world core

collection

・New resistance varieties against Striga using NARO

world collection

・ New QTL for efficient phosphorus uptake using IRRI

core collection

Future scope of core collection

・Further use of existing collection

・Establishment of unique core collection in local

genebank

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Quantitative and qualitative improvement of

active collection in genebank

Genebank

Base collection

Active collection

Passport

data

Character

ization

data

DNAdata

Users

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Refferences

Brown, A. H. D. (1993) The core collection at the crossroads. In Core

collections of plant genetic resources.

Yoshimura, A. et al. (2018) Development of rice promising lines using

genomic technology and information in Vietnam. In Crop production

under stressful conditions –Application of cutting-edge science and

technology in developing countries. 11-26.

Kuroshima, Y. et al. (2016) Construction of versatile SNP array for

pyramiding useful genes of rice. Plant Sci. 242:131-139.

Makihara, D. et al. (2018) Development of rice breeding and cultivation

technology tailored for Kenya’s environment. In ditto. 27-48.

Okada, K. and Lopez-Galvis, L. (2018) Improving resources utilization

efficiency in rice production system with contour-levee irrigation in

Colombia. In ditto. 71-86.

Ban, T. (2018) Development of wheat breeding materials using genetic

resources in Afghanistan. In ditto. 87-110.

Tsujimoto, T. (2018) Annual Rep. of 2017 fiscal year of SATREPS

Project in Madagascar. In Japanese.

Yoshimura, A. (2019) Annual Rep. of 2018 fiscal year of SATREPS

Project in Myanmar. In Japanese.

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Thank you very much for your attention !

Muito obrigado!

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