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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?