Coffee arabica genome sequenced for first time

For the first time, scientists have discovered the genome sequence for Coffea arabica, the species responsible for 70 per cent of the global coffee production.
"This new genome sequence for Coffea arabica contains information crucial for developing high-quality, disease-resistant coffee varieties that can adapt to the climate changes that are expected to threaten global coffee production in the next 30 years," said Juan Medrano, a geneticist at University of California, Davis (UC Davis) in the US.
"We hope that the C arabica sequence will eventually benefit everyone involved with coffee - from coffee farmers, whose livelihoods are threatened by devastating diseases like coffee leaf rust, to coffee processors and consumers around the world," said Medrano, co-researcher on the sequencing effort.

In 2014, researchers elsewhere sequenced the genome of Coffea canephora - commonly known as robusta coffee and used for making coffee blends and instant coffee.
There has been, however, no publicly accessible genome sequence for the higher-value and more genetically complex C arabica.
Working with farmer Jay Ruskey, the UC Davis researchers collected genetic material - DNA and RNA samples - from different tissues and developmental stages of 23 Geisha coffee trees.

Geisha, known for its unique aromatic qualities, is a high-value C arabica variety that originated in the mountains of western Ethiopia.
Plant material from one of the trees - UCG-17 Geisha - was used for developing the C arabica genome sequence.

C arabica is a hybrid cross derived from two other plant species: C canephora (robusta coffee), and the closely related C eugenioides.
As a result of that hybrid crossing, C arabica's complex genome has four sets of chromosomes - unlike many other plants and humans, which have only two chromosome sets.
Using sequencing technology, the researchers estimated that UCG-17 Geisha has a genome made up of 1.19 billion base pairs - about one-third that of the human genome.
The study used a combination of the latest technologies for genome sequencing and genome assembly, revealing an estimated 70,830 predicted genes.
Researchers will focus on identifying genes and molecular pathways associated with coffee quality, in hopes that these will provide a better understanding of the flavor profiles of Geisha coffee.

They have sequenced samples from 22 other Geisha coffee trees to obtain a glimpse of the genetic variation within that variety and among 13 other C arabica varieties, which will also be important for developing plants that can resist disease and cope with other environmental stresses.