Coffee

4 - 6 July, 2016
Sustainable Coffee Production: Control of Major
Diseases by Resistant Varieties
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
 Coffee is the most important agricultural commodity, worth an estimated retail value
of 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).
There are more than 100
coffee species but only two,
Coffea arabica (Arabica) and
Coffea canephora (Robusta),
are commercially used for the
production of coffee as a
beverage
Major coffee producing
countries:
Brazil
Vietnam
Colombia
*International Coffee Organization
Brazil
India
Coffee Leaf Rust
Coffee leaf rust (CLR) caused by the fungus Hemileia vastatrix (Hv) is
the most important disease of Arabica coffee
1867
1861
Lake
Victoria
Hv attacks coffee leaves and
causes defoliation, weakening
the plants and even leading to
death. Yield losses can reach
up to 30 %
1869
Sri
Lank
a
CLR was first recorded in 1861 near Lake Victoria (East
Africa), but it caused the first major outbreak in 1869
in 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 Disease
Coffee Berry Disease (CBD) caused by the fungus Colletotrichum
kahawae (Ck) is the the main limiting factor of Arabica coffee
production at high altitude, in Africa
CBD
Ck = Biological weapon
CK infects green coffee berries
causing their mummification and
premature dropping. Yield losses
can reach up to 50-80%
CBD, first reported in Kenya in 1922, is
still restricted to Africa but its dispersal
to Latin America and Asia represents a
serious concern
In Tanzania 50% of the production costs are spent to control CLR and CBD using fungicides
CIFC – Centro Inv. Ferrugens do Cafeeiro (Coffee Rusts Research Centre)
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.
Labs
Greenhouses
More than 3.000m2 of heated greenhouses
Oeiras
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
As Portugal is not a coffee growing country and the pathogens are specific of
coffee plants, their introduction poses no danger to national agriculture
CIFC was created in 1955 as part of Junta de Investigações Científicas do Ultramar (JICU), later
Instituto de Investigação Científica Tropical (IICT).
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 Research Lines
Pathogenicity Surveys
Screening of Disease Resistance
Hv on leaves of coffee differentials
Spectrum of coffee resistance to CIFC’s
Ck on coffee green fruits and hypocothyls
Hv races and Ck isolates
H. vastatrix (Hv), C. kahawae (Ck) and coffee unique world collections
Pathogen Genetic Diversity
and Evolution
Coffee Resistance & Fungal Effectors
Population and evolutionary
genetics and genomics
transcriptomics and gene expression analysis
Microscopy, biochemistry/proteomics,
Pathogenicity Surveys & Screening of Disease Resistance
C. kahawae isolates (from several African
regions) were characterized (aggressiveness,
vegetative compatibility, isoenzymes and
molecular polymorphism)
The screening tests allowed to select coffee
genotypes with different levels of resistance
to C. kahawae to be used in the breeding
programmes
A decisive step forward in the research
programme of the CIFC was the discovery,
in the late 1950´s, of the Timor Hybrid
(HDT), a spontaneous natural hybrid
between Arabica and Robusta
More than 50 H. vastatrix races
(from different coffee growing
countries) were characterized
Some HDTs , with resistance to all known
rust races, were used as sources of
resistance in the breeding programmes
Pathogenicity Surveys & Screening of Disease Resistance
More than 90% of Arabica coffee varieties resistant to rust grown in different
coffee growing countries were created from studies carried out at CIFC
Brazil
Colombia
IAPAR 59
COLOMBIA
CANÁRIO
OEIRAS
IPR 98
SARCHIMOR
IBC-PALMA 1 e 2
IPR 104
CASTILLO
Honduras
IPR 107
SABIÁ
OBATÃ
IPR 99
CATIMOR
Mexico
IPR 97
ORO AZTECA
TUPI
IPR 108
China
TABI
IHCAFE 90
CATIMOR
LEMPIRA 98
Costa Rica
Guatemala
SARCHIMOR
CATIMOR
COSTA RICA 95
Papua New Guinea
Panamá
MIDA 96
CATIMOR
Zimbabwe
Vietnam
HDT
CATIMOR
CATIMOR
Kenya
Thailand
Tanzania
Malawi
India
CATIMOR
RUIRU 11
CAUVERY
CATIMOR 88
CATIMOR
CATIMOR
Philippines
CHANDRAGIRI
CATIMOR
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 Resistance
Main 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 Projects
2016-2018. 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/1716/2014
Institutions: ISA/UL , CFE/FCT/Universidade de Coimbra, UIC/IGC, UCIBIO/FCT/UNL
Coordination: Pedro Talhinhas
2012-2016. Population genomics of virulence adaptation in coffee leaf rust (Hemileia vastatrix). PTDC/AGRGPL/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/AGRGPL/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/109990/2009
Institutions: 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 the
infection process of coffee leaf rust - Hemileia vastatrix - PTDC/AGR-GPL/114949/2009
Institutions: 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 with
durable resistance to leaf rust at Yunnan Province. Financed by FCT and the State Administration of
Foreign Experts Affairs
Institutions: 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 o
processo de infeção do cafeeiro. Financed by DAAD
Institutions : CIFC/IICT, Universidade de Hohenheim (Germany)
Coordination: Pedro Talhinhas, Ralp Voegele
2010-2012. “Factores de virulência de Hemileia vastatrix, agente causal da ferrugem alaranjada do
cafeeiro”. Programa Pessoa. Financed by FCT and EGIDE
Institutions: 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 CAPES
Institutions : CIFC/IICT, Universidade Federal de Viçosa (Brazil)
Coordination: Leonor Guerra-Guimarães, Laércio Zambolim
Agreements (last 5 years)
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 (Joint
FAO/International Atomic Energy Agency ) Identification and characterization of the
resistance to leaf rust in coffee mutants in the scope of the Project” Efficient
Screening 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, Portugal
Institutions: CIFC/IICT, Ministério da Agricultura e Pescas de Timor-Leste
Coordination: Vítor Várzea
1973 – 2014. Agreement CIFC/IICT - CENICAFÉ - Centro Nacional de
Investigaciones de Café (Colômbia)
Characterization of coffee resistance to Colletotrichum kahawae
Financed by Federcafé - Federación Nacional de Cafeteros (Colombia)
Instituições participantes: CIFC/IICT
Coordination: Vítor Várzea
Training and Capacitation
Training of Researchers, Technicians, Students from Coffee Growing Countries
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)
BD Grants
(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
Interaction with the community
“Ocupação Científica de
Jovens nas Férias”
European Researchers’ Night
Fascination of Plants Day
“Visitas de Estudo”
“Dia Aberto”
Recent Collaborations - Coffee Growing Countries
Over the past 60 years, CIFC has played a central role in the development of an International
Research Network of more than 40 coffee growing countries on CLR and on CBD
BRAZIL
(EMBRAPA–Café, INCT Café
UFV, UFLA, UFES, UFPel)
COLOMBIA
(CENICAFÉ)
UGANDA, RWANDA, ZIMBABWE
(CABI-Africa)
CHINA
(DTARY)
INDIA
(CCRI)
KENYA
(KALRO)
TIMOR LOROSAE
(MAP)
MEXICO
(IC Chiapas)
TANZANIA
(TaCri)
THAILAND
(DOA)
Recent Collaborations - Europe
AUSTRIA
FAO/AIEA
FRANCE
IRD, INRA, CIRAD
GERMANY
UNIVERSITIES of Rostock,
Konstanz and Hohenheim
LUXEMBOURG
LIST
PORTUGAL
Universities: 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 the
appearance of new and more virulent Hv races, as well as
the current epidemics in Central America is leading
research institutions from coffee growing countries to
continuously seek CIFC´s support for the discovery and
characterization of new sources of resistance
To answer these requests, CIFC is giving priority to the re-evaluation of resistant coffee
genotypes (CIFC ’s collection and from international partners) with the new rust races.
This strategy also includes the joint research approach for better understanding the
coffee resistance mechanisms along with the characterization of pathogen effectors and
genetic variability, as an informed base to breed efficiently for durable resistance