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Coffee Botany 101: Genetics, Varieties, and
Physiology
Emma Sage
SCA Coffee Science Manager
About ME
• Coffee Scientist = ??
• A botanist
• A plant physiologist
• Studied climate change
• Coffee groupie
• SCAA Science Manager
DISCLAIMER
SCIENCE = Privilege
• System
• Infrastructure
• Monetary investment
• Professors & Students
• Stability
Use science to address threats to coffee • Understanding the plant
= Understanding the problem
= Solutions
Part 1. Botanical Tidbits
Botanic Taxonomy
Linnaean Classification:
• Family
• Genus
• Species
• Sub-Species/Variety
For Coffee:
• Rubiaceae• Coffea (>120 species)
• arabica L.
Linneaus!
Coffea Diversity120+ Species
Images courtesy of Dr. Aaron Davis
Species
• Individuals that can breed with each other to produce viable offspring
• Coffea arabica
• Coffea canephora
• Coffea eugenioides
Cultivar
• Definition:
Cultivated variants of a species originating through human influence, distinct group of plants that has stable characteristics
Variety
• To a Botanist:
• A measureable variant of a species that can interbreed with other varieties
• To a Plant Breeder:
• A stable and quantifiable line that can be legally protected by intellectual property laws
Cultivar
• To a Botanist:
• Cultivated variants of a species originating through human influence
• To a Plant Breeder:
• A distinct group of plants that has stable characteristics which are retained in successive generations
Plant Breeding Terminology
• Interbreeding of species, races, varieties, and so on among plants or animals. • Some consider ONLY crosses between species hybrids
(more strict definition)
• Many use the term more loosely to describe a cross between very different individuals
Hybrid Vigor?Superior qualities arising from the crossbreeding of genetically different plants or animals
Hybrid
F1 Hybrid
• F1 = “First Filial” generation• MEANS: The first seeds/plant
offspring resulting from a cross mating of distinctly different parents.
• IN THE COFFEE INDUSTRY• Breeders have colloquialized:
• MEANS: the first cross between a normal cultivar and a wild Ethiopian coffee
Landrace (“Traditional/Wild Variety”)
• A locally cultivated plant species which as developed largely by natural processes, often named for the geographic region they are confined to.
This is DIFFERENT than wild plants!
• Used to describe some coffees that have come from different regions in Ethiopia• Gesha, Zeghie, Gimma Kaffa, Sudan Rumé
“Heirloom Variety” ?!
•Refers to old cultivars, bred once, then fell out of popularity/favor
•Not the same thing as landrace or wild coffee
Heirloom coffee?
Part 2: Genetics Determine Everything
The Plant Cell & DNA
Image: http://faculty.kutztown.edu/friehauf/science_outreach/cells.html
Courtesy: National Human Genome Research Institute.
How DNA Codes for Life
• Transcription
• Translation
• Protein Synthesis
– The building blocks of life
• DNA codes for the expression of TRAITS
Courtesy: National Institutes of General Medical Sciences
Transcription & Translation:
Reading DNA & forming proteins
Traits
• Measureable physical or behavioral characteristics of an organism, determined by DNA• Leaf color, Fruit Color
• Height, distance between leaves
• Leaf shape
• Rooting pattern
• Phenology (timing of events like flowering, budding, fruiting, etc)
Genetic Diversity
• The amount of differences in the genetic makeup of a population or species. • An important
mechanism for populations to adapt to changing environments
Climate Change & Genetic Diversity
• Diversity = a tool box
• Climate change = challenges• Increased weather variability
• Warming of many regions
• Water insecurity
• Outbreaks of pests & pathogens
Genetic Variation
• A measure of genetic differences in or between populations, species, or larger units, such as ecosystems
• Often, genetic markers are used
Coffea Diversity120+ Species
Images courtesy of Dr. Aaron Davis
Coffea labatiiCoffea ambongensis
Coffeaarabica
Images courtesy of Dr. Aaron Davis
Traits: Coffea arabica
Phenotypes & Genotypes
•Phenotypes• The observable traits
that manifest from an organisms genotype
•Genotypes• The genetic
constitution of an organism
genotype expressed differently in different environments
Phenotypic Plasticity
Trai
t Ex
pre
sse
d
Environment
No Phenotypic Plasticity
Genotype 1
Genotype 2
Genotype 3
Trai
t Ex
pre
sse
d
Environment
High Phenotypic Plasticity
Genotype 1
Genotype 2
Genotype 3
Losses of Genetic Variation
• Can occur through:• Population sub-
division
• Migration
• Bottleneck/Founder Effect
• Inbreeding
• ARTIFICIAL SELECTION
Inbreeding
Image: Franklin et al., 2010. Introduction to Conservation Genetics
F = inbreeding
coefficient,
where 1 =
completely
Self pollination = inbreeding
Artificial Selection: Plant Breeding
Tanksley and McCouch, 1997
A Note on Plant Health
• Seed development affects the chemical precursors to coffee – taste!
The Tasty Seed
Marraccini P, Allard C, M.-L. A, C. C, Gaborit C, Lacoste N, Meunier A, Michaux S, Petit V, Priyono P, Rogers JW, Deshayes A. 2001. Update on Coffee Biochemical Compounds, Protein, and Gene Expression during Bean Maturation and in other Tissues. Proc. 19th ASIC. Trieste.
The story of C. arabicacoffees
PART 3:
What about Coffee?
• Artificial selection ≠ adaptation• Selections
• Breeding
• De Cleu and the population bottleneck
Image: Ukers, 1909. All About Coffee
Anthony et al., 2002. The origin of cultivated Coffea arabica L varieties revealed by AFLP and SSR Markers. Theor ApplGenet.
History of Coffee Genetic Restriction
Figure 1. From Teressa et al., 2010.
Genetic Diversity of Arabica coffee
(Coffea arabica L.) collections.
PCA
Analysis
Cultivated
= 53% of
wild alleles
found
similar
similar
The Timeline
• Wild Coffee
• Local coffee cultivation in Ethiopia
• Brought to Yemen• Yemen to Java
• Yemen to Bourbon
Image: Ukers, 1909. All About Coffee
The Journey of C. arabica
Yemen –India?- to Java (Typica)
• Arrive ~1690’s
• Spread around Indonesia
• Brought to Amsterdam botanic garden ~1710
• 1 plant given to France (shortly after 1710)
• Dutch brought to Surinam ~1720’s
• France brought to Martinique ~1718
• Spread around Central/South America from there
Yemen to Bourbon (Bourbon)
• Arrive ~1718
• Late 1800’s• Brazil (Rio)• Kenya• Tanzania
• Early 1900’s• West Africa
• Spread around South/Central America & world from there
Typica
• A general group of coffee cultivars• Originally brought to java via Yemen & India• In early 1700’s was brought to Amsterdam B.G.• 1720’s brought to Martinique, C. America via France• Brought to Brazil in ~1760s from India
• Coffees:• Blue mountain• Guatemala• Sumatra• Java• Pache• Kona
Bourbon
• A general group of coffee cultivars
• Originally brought to Ile Bourbon via Yemen by the French
• Brought to Brazil in early 1800s
• Brought to Kenya, Tanzania in late 1800s
Typica Mutations
• Maragogype• Found in Brazil, 1870
• Large fruits
• Long seeds, with characteristic twist
• Lower yield
Image:
Kaldiscoffee.com
Bourbon Mutations
• Pacas: • Dwarf mutation
• Found in 1949 in El Salvador
• One parent of Pacamara
• Bourbon Pointu• Dwarf “Christmas tree”
mutation
• Described in 1947 on Reunion Island
• Caturra
• Dwarf mutant, very productive
• Found in 1937 in Brazil
• Pure-Line
• Villa Sarchi• Dwarf mutant
• Found in Costa Rica, 1957
Crosses
• Mundo Novo• Tall cultivar
• Sumatra Typica X red Broubon cross
• Developed in 1940s in Brazil
• Pacamara• Maragogype (typica mut) X Pacas (bourbon mut) cross
• Released in 1984
• Less stable cultivar
• Catuai• Pure line cultivar, dwarf
• Mundo Novo X yellow Caturra cross
• Developed in Brazil, released 1968
Hybrids
• Timor Hybrid• Natural cross
• originated in Timor, thought to have occurred on one occasion
• C. canephora X C. arabica (Typica)
• Good resistance characteristics
• Catimor• A group of pure-line cultivars
• Timor Hybrid X Caturra (Bourbon) bred in 1980s
• Some resistance to rust and coffee berry disease• CR 95: 1995
• Sarchimor• A group of pure-line cultivars
• Villa Sarchi (Bourbon) X Timor Hybrid
• Some resistance to rust
Coffea arabica
Questions?