Genetics revealed

The human genome is made of more than six billion genetic letters that comprise our own unique DNA order. Understanding the human genome has aided scientists with the knowledge and tools to develop treatments, cures and preventatives of diseases over the years. But what if the same was done to coffee to help generate disease-resistant varieties adaptable to climate change?

Well, that’s exactly what researchers in the United States have done, revealing an estimated 70,830 predicted genes in Coffea arabica.

The result is thanks to a collaboration between geneticist Dr. Juan Medrano, plant scientist Dr. Allen Van Deynze and genomics specialist Dr. Dario Cantu, postdoctoral research scholar Dr. Amanda Hulse-Kemp – all from University of California Davis – and farming expertise from Jay Ruskey. Together, they tackled this “ambitious project” to sequence the genome for C. arabica as part of the effort to combat the effects of climate change on global coffee production.

“The genome sequence is the genetic blueprint to base hypothesis-driven breeding (improvement) for coffee, leveraging the latest technologies available to crops,” says Allen, Director of Research at the UC Davis Seed Biotechnology Centre and Associate Director of the UC Davis Plant Breeding Centre.

In October 2015, researchers first collected DNA and RNA (ribonucleic acid) samples from different tissues and developmental stages of 23 Geisha coffee trees growing at Good Land Organics farm in California, which is growing the first commercial coffee plants in the continental US. Samples of UCG-17 Geisha and its plant tissue were then used for developing the C. arabica genome sequence.

Allen says Geisha was preferential because it’s considered the highest quality coffee variety worldwide, and is “complementary” to other ongoing genomic programs. It is also the variety being grown in California as the key foundation variety for the budding local industry.

The study then used a combination of the latest technologies for genome sequencing and genome assembly.

“The key to a genomic sequence is to extract high quality genomic DNA and to use a combination of technologies including long sequence reads from Pacific BioSciences of Menlo Park, California, and Dovetail Genomics of Santa Cruz,” Allen says. “Being in the heart of innovation technologies of California was critical to accessing the latest technology and completing a high-quality product in record time.”

No experiment is without its challenges, and in the case of this genome sequencing, Allen says it was working out the parameters to assemble a complex genome like C. Arabica, which is a hybrid cross derived from C. canephora (robusta coffee), and C. eugenioides. As a result, it has four sets of every chromosome rather than two chromosome sets like humans and many other plants. As a result, all genes were duplicated and separated in order to record an accurate genome.

“This involved developing new analyses to ensure we correctly separated each of these copies. The experience we had in similar species such as cotton with Dr. Amanda Hulse-Kemp on the project, was critical,” Allen says. “We were pleasantly surprised how well and good the quality [of the genome sequence] is.”

Allen and his UC Davis collaborators (Juan, Amanda, and Dario) have worked on dozens of genomics projects including cattle, fungi, and spinach. As such, he says previous studies have helped learn the importance of combining simple things like the quality of DNA to complex analyses, and technologies to yield the best assemblies.

Genome sequencing is no cheap affair. Japan’s Suntory Group funded this project, but Allen says the availability of technologies to cost-effectively achieve long reads (sequences) are one of the main considerations why this project hasn’t been undertaken sooner.

“Compared to the human genome and the first plant species such as Arabidopsis which ran into the billions of dollars, the few hundreds of thousands of dollars spent on the coffee genome was actually relatively small with an equal or better result in a fraction of the time,” he says.

With today’s use of advantaged genome sequencing technologies, Allen says he never doubted his team of researchers would be able to assemble the genome sequence of C. arabica. However, he enforces that the sequence is not yet complete, nor perfect, and needs further refinement.

“Not even the human sequence is complete,” Allen says. “The next stage for us is to use [the genome sequence] to define genotypes [varieties] that can help combine high yield, disease resistance, and flavour. It’s a long road.”

Although early in its development stages, Allen and his team of scientists have been able to uniquely predict and separate 70,000 genes, which he says is “twice as many as expected for the diploid progenitor species”.

“It allows us to take advantage of all that we have learnt in other crops, as DNA is the common language of genetics,” Allen says. “We are proud to be part of the beginning of sustainable coffee production for small holder farmers.”

This is not the first instance a coffee genome has been sequenced, with C. cenephora, first sequenced in 2014, but it is the first time the C. arabica genome data has been made publicly available.

“This [information] is critical to coffee improvement as it allows all researchers to improve coffee,” Allen says.

The full article features in the April 2017 edition of BeanScene Magazine.

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