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Further Information
 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 Diversity
120+ 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
 Plant Breeding Terminology
Variety Cultivar

• To a Botanist: • To a Botanist:
• A measureable variant of a • Cultivated variants of a species
species that can interbreed with originating through human
other varieties influence

• To a Plant Breeder: • To a Plant Breeder:

• A stable and quantifiable line • A distinct group of plants that has
that can be legally protected by stable characteristics which are
intellectual property laws retained in successive
generations
 Hybrid

• 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
 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/s
cience_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

 Transcription & Translation:
Reading DNA & forming proteins

Courtesy: National Institutes of General Medical Sciences

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 Diversity
120+ Species

Images courtesy of Dr. Aaron Davis

Coffea Coffea Coffea labatii
ambongensis arabica

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
Phenotypic Plasticity
genotype expressed differently in different environments
 No Phenotypic Plasticity High Phenotypic Plasticity
Trait Expressed

Trait Expressed
Genotype 1 Genotype 1
Genotype 2 Genotype 2
Genotype 3 Genotype 3

Environment Environment
Losses of Genetic Variation
• Can occur through:
• Population sub-
division
• Migration
• Bottleneck/Founder
Effect
• Inbreeding

• ARTIFICIAL
SELECTION
Inbreeding

F = inbreeding
coefficient,
where 1 =
completely

Self pollination = inbreeding

Image: Franklin et al., 2010. Introduction to Conservation Genetics
Artificial Selection: Plant Breeding

Tanksley and McCouch, 1997

A Note on
Plant Health
 The Tasty Seed

• Seed development affects the chemical

precursors to coffee – taste!

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.
PART 3:

The story of C. arabica

coffees
 What about Coffee?
• Artificial selection ≠
adaptation
• Selections
• Breeding

• De Cleu and the

population
bottleneck

Image: Ukers, 1909. All About Coffee

 History of Coffee
Genetic Restriction

Anthony et al., 2002. The origin

of cultivated Coffea arabica L
varieties revealed by AFLP
and SSR Markers. Theor Appl
Genet.
similar
PCA
Analysis

Cultivated
= 53% of
similar
wild alleles
found

Figure 1. From
Teressa et al., 2010.
Genetic Diversity of
Arabica coffee
(Coffea arabica L.)
collections.
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) Yemen to Bourbon (Bourbon)

• Arrive ~1690’s • Arrive ~1718

• Spread around Indonesia • Late 1800’s
• Brought to Amsterdam • Brazil (Rio)
botanic garden ~1710
• 1 plant given to France • Kenya
(shortly after 1710) • Tanzania
• Dutch brought to Surinam • Early 1900’s
~1720’s • West Africa
• France brought to
Martinique ~1718 • Spread around
• Spread around Central/South South/Central America &
America from there 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 mutant, very
• Dwarf mutation productive
• Found in 1949 in El • Found in 1937 in Brazil
Salvador • Pure-Line
• One parent of Pacamara • Villa Sarchi
• Bourbon Pointu • Dwarf mutant
• Dwarf “Christmas tree” • Found in Costa Rica, 1957
mutation
• Described in 1947 on
Reunion Island

• Caturra
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?