Efforts intensify to decode cassava “alphabet soup”

12 February, 2013 by (comments)

Imagine having to write a story, using a pile of several billion letters.

First the letters have to be arranged into words, the words into sentences and paragraphs to produce a coherent, accurate chapter. There are 18,000 chapters in each book, and 5,000 books make the full story.

The story is the complete genetic history of cassava.

NP Cassava Genome

Making biological sense of that pile of letters – otherwise known as sequencing the cassava genome – might seem like a daunting prospect, but the result should be a precise genetic fingerprint of the plant and all its known variations. It promises to accelerate the development of improved varieties by helping scientists home-in on the genes responsible for increasing yields, boosting starch or protein content, and improving resistance to notorious pests like whitefly, diseases like brown streak.

“Genome sequencing generates an enormous amount of data – at the moment we just have an ‘alphabet soup’ of information that we need to arrange into the right order,” explained CIAT cassava geneticist Luis Augusto Becerra. “But once all those letters are in order, it means we will really, truly understand cassava.

The first draft of the cassava genome was completed in 2009, by the U.S. Department of Energy Joint Genome Institute (DOE JGI), and 454 Life Sciences. While it only sequenced one cassava variety – the equivalent of one single book in the set – it was enough to help scientists isolate the gene responsible for “waxy” roots, a major breakthrough for the development of high-value cassava for industrial use.

Crucially, the first draft also provides a firm foundation for speeding up subsequent sequencing, since many cassava varieties contain similar characteristics to the draft, with only small variations in the sequence responsible for particular characteristics. In just three years, the first draft has enabled a further 200 varieties to be quickly decoded.

RTB East Africa1-107

Using cassava varieties conserved in genebanks around the world – including domesticated “landraces” and undomesticated wild relatives – a further 1,000 varieties will be sequenced in 2013, funded by CGIAR’s Roots, Tubers and Bananas research program. The aim is for all 5,000 cassava varieties – representing 95% of the crop’s global genetic diversity – to be sequenced by 2017.

Launched in mid-2012, The Global Cassava Genome Initiative, jointly coordinated by CIAT and the Beijing Genomics Institute (BGI), with support from the International Institute of Tropical Agriculture (IITA), RIKEN, DOE JGI and the Chinese Academy of Tropical Agricultural Sciences (CATAS), will pool the expertise of scientists and the technical capacity of participating institutions around the world to try and put speed up the process of putting the pieces of the puzzle together.

“This initiative will really help to accelerate the work to decode cassava,” continued Becerra. “So it’s not a matter if we’re going to find, say, the gene responsible for resistance to whitefly, or increasing yields – it’s a matter of when. That makes the process tremendously exciting; it could be cassava’s Green Revolution, both as a cash crop and a food crop.”

Once the cassava genome is fully decoded, scientists will be able to breed cassava in silico (on the computer) to establish the most effective combinations of parent plants to produce offspring with the most valuable traits.

It could enable them to help cassava fulfill its enormous potential as both a food security crop and an industrial crop – in a fraction of the time required by conventional breeding methods.

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