Sustainable Coffee Production: Control of Major Diseases by Resistant Varieties

4 - 6 July, 2016

Maria do Céu Silva, Ana Cabral, Ana Paula Pereira, Ana Vieira, Diogo Silva,

Dora Batista, Helena Azinheira, Inês Diniz, Leonor Guerra-Guimarães,

Pedro Talhinhas, Vítor Várzea

Coffee is the most important agricultural commodity, worth an estimated retail valueof 70 billion USD, crucial for the economy of more than 70 countries and the main

income resource for hundreds of millions people worldwide (ICO*, 2016).

Brazil

Vietnam

Colombia

Coffee

Major coffee producingcountries:

*International Coffee Organization

There are more than 100coffee species but only two,Coffea arabica (Arabica) andCoffea canephora (Robusta),are commercially used for theproduction of coffee as abeverage

Brazil India

Coffee Leaf Rust

Coffee leaf rust (CLR) caused by the fungus Hemileia vastatrix (Hv) isthe most important disease of Arabica coffee

Hv attacks coffee leaves andcauses defoliation, weakeningthe plants and even leading todeath. Yield losses can reachup to 30 %

1861

1867

LakeVictoria

Sri Lank

a

1869

CLR was first recorded in 1861 near Lake Victoria (East Africa), but it caused the first major outbreak in 1869in Ceylon (now Sri Lanka). The disease gained a worldwide distribution, becoming practically endemic in all regions of the world where coffee is grown

Coffee Berry DiseaseCoffee Berry Disease (CBD) caused by the fungus Colletotrichumkahawae (Ck) is the the main limiting factor of Arabica coffeeproduction at high altitude, in Africa

CK infects green coffee berriescausing their mummification andpremature dropping. Yield lossescan reach up to 50-80%

In Tanzania 50% of the production costs are spent to control CLR and CBD using fungicides

CBD

Ck = Biological weapon

CBD, first reported in Kenya in 1922, isstill restricted to Africa but its dispersalto Latin America and Asia represents aserious concern

LabsGreenhouses

CIFC – Centro Inv. Ferrugens do Cafeeiro (Coffee Rusts Research Centre)

CIFC’s main objectives: To centralize and develop, at international co-operation level, the research on coffee leaf rust (and later on coffee berry disease) for the creation of resistant varieties to both diseases

More than 3.000m2 of heated greenhouses

The importance of coffee leaf rust as a threat to world production led, in 1955, the Governments of the USA and Portugal (Agreement FO-PO-5, Project D. O. A. 72-11-004), to provide for the foundation of CIFC in Portugal, where a pioneer work on this disease had been initiated by Prof. Branquinho d’ Oliveira.

CIFC activities were included in LEAF (January 2015), while still being a research unit of IICT

CIFC was integrated in the Instituto Superior de Agronomia/UL in August, 2015

CIFC was created in 1955 as part of Junta de Investigações Científicas do Ultramar (JICU), laterInstituto de Investigação Científica Tropical (IICT).

As Portugal is not a coffee growing country and the pathogens are specific of coffee plants, their introduction poses no danger to national agriculture

Oeiras

CIFC Research Lines

H. vastatrix (Hv), C. kahawae (Ck) and coffee unique world collections

Pathogen Genetic Diversity

and EvolutionPopulation and evolutionary

genetics and genomics

Coffee Resistance & Fungal Effectors

Microscopy, biochemistry/proteomics,

transcriptomics and gene expression analysis

Screening of Disease Resistance

Spectrum of coffee resistance to CIFC’s

Hv races and Ck isolates

Pathogenicity Surveys

Hv on leaves of coffee differentials

Ck on coffee green fruits and hypocothyls

A decisive step forward in the researchprogramme of the CIFC was the discovery,in the late 1950´s, of the Timor Hybrid(HDT), a spontaneous natural hybridbetween Arabica and Robusta

Pathogenicity Surveys & Screening of Disease Resistance

Some HDTs , with resistance to all known

rust races, were used as sources of

resistance in the breeding programmes

More than 50 H. vastatrix races(from different coffee growingcountries) were characterized

C. kahawae isolates (from several African regions) were characterized (aggressiveness, vegetative compatibility, isoenzymes and molecular polymorphism)

The screening tests allowed to select coffeegenotypes with different levels of resistanceto C. kahawae to be used in the breedingprogrammes

Honduras

IHCAFE 90

LEMPIRA 98

India

CHANDRAGIRI

CAUVERY

Costa Rica

COSTA RICA 95

SARCHIMOR

Guatemala

CATIMOR

Kenya

RUIRU 11

CATIMOR 88

Colombia

COLOMBIA

TABI

CASTILLO

Mexico

ORO AZTECA

Papua New Guinea

CATIMOR

Vietnam

CATIMOR

China

CATIMOR

Panamá

MIDA 96

Thailand

CATIMOR

Philippines

CATIMOR

Tanzania

CATIMOR

Malawi

CATIMOR

Zimbabwe

CATIMOR

Brazil

IBC-PALMA 1 e 2

CANÁRIO

SABIÁ

OEIRAS

OBATÃ

TUPI

IAPAR 59

IPR 97

IPR 98

IPR 99

IPR 104

IPR 107

IPR 108

SARCHIMOR

CATIMOR

More than 90% of Arabica coffee varieties resistant to rust grown in differentcoffee growing countries were created from studies carried out at CIFC

Pathogenicity Surveys & Screening of Disease Resistance

HDT

Pathogen Genetic Diversity and Evolution

Main goals: Understand population genetic structure and dynamics, host adaptation and virulence evolution in H. vastatrix and C. kahawae, and identify molecular markers associated with specific pathotypes.

• Identification of a geographically related genetic structuring in Ck and its centre of origin, and proposal of a new hypothesis of speciation through host-jump• Uncovering of host-related genetic variation and evidences of introgression in Hv

Coffee ResistanceMain goal: Understanding coffee resistance mechanisms to H. vastatrix and C. kahawae to find putatively linked biomarkers to be used in the breeding programmes

Early plant responses associated: HR, accumulation of

phenolic-like compounds and up-regulation of genes

and proteins putatively involved in plant defenses

Fungal Effectors

Main goal: To understand H. vastatrix and C. kahawae infection mechanisms and to identify fungal effectors and coffee targets, for marker assisted selection

•Genome sizes: Ck (79,5 Mbp) ; Hv (797 Mbp) •Identification of minichromosome profiles of Ck isolates with different aggressiveness•Activation of genes encoding putative effectors at different stages of the infection process in susceptible and resistant coffee plants

R & D Projects (2011-2016)

FCT Projects2016-2018. A new paradigm on fungal nuclear cycles? An investigation to the widespread occurrence of diploid nuclei throughout the life cycle of rust fungi and comparison with other Pucciniomycotina . PTDC/BIA-MIC/1716/2014Institutions: ISA/UL , CFE/FCT/Universidade de Coimbra, UIC/IGC, UCIBIO/FCT/UNLCoordination: Pedro Talhinhas

2012-2016. Population genomics of virulence adaptation in coffee leaf rust (Hemileia vastatrix). PTDC/AGR-GPL/119943/2010 Institutions: CIFC/IICT, FC/UL (Centro de Biologia Ambiental), IBET (Forest Biotech Group) (Portugal)Coordination: Dora Batista

2011-2014. Unravelling defence mechanisms underlying coffee resistance to Colletotrichum kahawae. PTDC/AGR-GPL/112217/2009 Institutions: CIFC/IICT - Coordinator, BioFIG/FCUL (Portugal), CRF (Kenya)Coordination: Maria do Céu Silva

2011-2014. Search for candidate protein biomarkers of Coffea arabica resistance to Hemileia vastatrix (leaf rust) -PTDC/AGR-GPL/109990/2009Institutions: CIFC/IICT, ITQB/UNL (Plant Cell Biology Lab.), IHMT (Instituto de Higiene e Medicina Tropical) (Portugal)Coordinaton : Leonor Guerra-Guimarães

2011- 2014. The pathogen’s perspective of molecular plant-microbe interactions: genes expressed during theinfection process of coffee leaf rust - Hemileia vastatrix - PTDC/AGR-GPL/114949/2009Institutions: CIFC/IICT, ITQB/UNL (Plant Cell Biology Lab.) (Portugal), University of Konstanz (Germany)Coordinaton: Pedro Talhinhas

International Cooperation (2011-2016)

2014-2017. Pathogenic, cytological and epidemiological studies to achieve coffee varieties withdurable resistance to leaf rust at Yunnan Province. Financed by FCT and the State Administration ofForeign Experts AffairsInstitutions: CIFC/ISA , DTARI - Dehong Tropical Agriculture Research Institute of Yunnan (China)Coordination: Vitor Várzea, Li Jinhong

2013-2014. Caracterização funcional e citológica de genes de Hemileia vastatrix expressos durante oprocesso de infeção do cafeeiro. Financed by DAADInstitutions : CIFC/IICT, Universidade de Hohenheim (Germany)Coordination: Pedro Talhinhas, Ralp Voegele

2010-2012. “Factores de virulência de Hemileia vastatrix, agente causal da ferrugem alaranjada docafeeiro”. Programa Pessoa. Financed by FCT and EGIDEInstitutions: CIFC/IICT, IRD (Montpellier, France), INRA (Nancy, France)Coordination: Maria do Céu Silva, Diana Fernandez

2010-2012. Análise transcricional e proteómica da interacção Coffea arabica-Hemileia vastatrix.Financed by FCT and CAPESInstitutions : CIFC/IICT, Universidade Federal de Viçosa (Brazil)Coordination: Leonor Guerra-Guimarães, Laércio Zambolim

Since 2016. Memorandum of understanding for technical and scientific cooperation CIFC/ISA/UL- Instituto del Café de Chiapas (México). Coordination: Vítor Várzea

2016-2018. Research Agreement CIFC/ISA/UL - FAO/AIEA Division (JointFAO/International Atomic Energy Agency ) Identification and characterization of the resistance to leaf rust in coffee mutants in the scope of the Project” EfficientScreening Techniques to Identify Mutant Plants with Resistance to Disease”Chief Scientific Investigator (CSI): Vítor Várzea

2011-2014. “Protocolo de Cooperação entre o IPAD - Instituto Português de Apoio ao Desenvolvimento (now Instituto Camões) - IICT/CIFC . Programa de Extensão Rural (PER) em Timor-Leste”Financed by Ministério dos Negócios Estrangeiros, PortugalInstitutions: CIFC/IICT, Ministério da Agricultura e Pescas de Timor-LesteCoordination: Vítor Várzea

1973 – 2014. Agreement CIFC/IICT - CENICAFÉ - Centro Nacional de Investigaciones de Café (Colômbia) Characterization of coffee resistance to Colletotrichum kahawaeFinanced by Federcafé - Federación Nacional de Cafeteros (Colombia)Instituições participantes: CIFC/IICTCoordination: Vítor Várzea

Agreements (last 5 years)

Since 1955, several hundreds of researchers and technicians received training at CIFC.

2009: Brazil (1); CABI Africa - Zimbabwé (1); India (2)

2010: Brazil (2); CABI Africa - Rwanda, Kenya, Uganda (3)

2011: Brazil (1)

2012: Brazil (1); Timor (2)

2013: Brazil (2)

2014: Brazil (1); China (2)

2015: China (2)

2016: China (2)

Training and CapacitationTraining of Researchers, Technicians, Students from Coffee Growing Countries

(2013 – 2017) Ana Vieira - (SFRH/BD/89397/2012). FCUL. Supervisors: Dora Batista; Octávio S. Paulo

(2013 – 2017) Diogo Silva (SFRH/BD/86736/2012). FCUL. Supervisors: Dora Batista; Octávio S. Paulo

(2013 – 2017) Inês Diniz (SFRH/BD/84188/2012). ISA/UL. Supervisors: Maria do Céu Silva, Helena

Oliveira, Leonor Guerra-Guimarães

BD Grants

Interaction with the community

“Ocupação Científica deJovens nas Férias”European Researchers’ NightFascination of Plants Day“Visitas de Estudo”“Dia Aberto”

Recent Collaborations - Coffee Growing CountriesOver the past 60 years, CIFC has played a central role in the development of an InternationalResearch Network of more than 40 coffee growing countries on CLR and on CBD

MEXICO(IC Chiapas)

COLOMBIA (CENICAFÉ)

BRAZIL

(EMBRAPA–Café, INCT Café

UFV, UFLA, UFES, UFPel)

KENYA(KALRO)

TANZANIA

(TaCri)

CHINA (DTARY)

INDIA

(CCRI)

TIMOR LOROSAE(MAP)

UGANDA, RWANDA, ZIMBABWE(CABI-Africa)

THAILAND(DOA)

Recent Collaborations - Europe

FRANCEIRD, INRA, CIRAD

GERMANY UNIVERSITIES of Rostock,Konstanz and Hohenheim

AUSTRIAFAO/AIEA

LUXEMBOURGLIST

PORTUGALUniversities: Universidade de Lisboa (FCUL), Universidade NOVA de Lisboa (ITQB, IHMT),

Universidade de Coimbra (UC)

Research Institutes: IBET, INIAV, IGC

Conclusions and Perspectives

The gradual loss of resistance in some varieties due to theappearance of new and more virulent Hv races, as well asthe current epidemics in Central America is leadingresearch institutions from coffee growing countries tocontinuously seek CIFC´s support for the discovery andcharacterization of new sources of resistance

To answer these requests, CIFC is giving priority to the re-evaluation of resistant coffeegenotypes (CIFC ’s collection and from international partners) with the new rust races.This strategy also includes the joint research approach for better understanding thecoffee resistance mechanisms along with the characterization of pathogen effectors andgenetic variability, as an informed base to breed efficiently for durable resistance