Date with destiny for palm DNA

Their place at the heart of UAE culture is beyond question. As a source of food and shelter, Emiratis have relied on the date palm for millennia.

And yet much about them remains a mystery.

"Almost nothing is known about date palms in terms of their genetic diversity and what the varieties look like genetically," says Michael Purugganan, a professor of genomics at New York University.

He is helping a new Dh3.6 million effort by scientists at NYU Abu Dhabi's laboratory in Mussafah to unravel the secrets of the date palm through its DNA. The project, called 100 Dates!, aims to sequence the genomes of 100 dates species initially. Once that is done, the researchers hope to extend the project to include every type of date palm on the planet.

After extracting the DNA from date palm leaves, the team chop it into small pieces, which are put through a sequencer - the only one of its kind in the UAE.

They are stained with a fluorescent marker, and then photographed, in a process that can take up to 10 days. That results a DNA code sequence - made up of the nucleotide "letters" A, T, G and C - for each short fragment of DNA.

Those DNA fragments then have to be assembled into a whole genome. It is, says Jonathan Flowers, one of the project's scientists, "like a 200 million-piece puzzle", and takes about three days.

Five years ago, that would have taken years and cost millions, if not hundreds of millions, of dirhams.

The result is a long string of letters. In date palms, that string is around 600 million letters long; the human genome is five times that.

The technology being used at NYUAD cannot quite assemble all of that, as there are substantial "junk" sections that resist attempts to order them.

It is, however, good enough to put together a "draft" genome that describes the order of around two thirds of the letters - around 400 million bases.

The next question is what those letters mean. The scientists have to work out where the genes - the bits that actually represent proteins produced within the date palms' cells - are.

Most of these genes are functionally the same in all date palms. But there are many more subtle differences - some 3.5 million of the 400 million letters in the draft vary between varieties. And while many of those nucleotide-level variations are in "junk" DNA, or make no functional difference, some contribute to each variety's unique characteristics.

"We have ways of predicting which words should do something by comparing [them] to other organisms where you know something about certain sequences," said Mr Flowers. "That's called phenotyping."

He gives the example of bananas, which of the species that have been closely studied are the date's nearest relative. Dates and bananas diverged around 100 million years ago.

So far, they have sequenced two date varieties - halawi and khisab, both of which originate from Iraq.

They are now proceeding in batches of 15 varieties, with the process taking between two and four weeks for each batch.

By early 2014, they hope to have a detailed map of the genes that vary between all 100 varieties.

"It's those genetic differences that help breeders breed new varieties," said Mr Purugganan. "We're trying to get genes from different [dates] and mix together a new variety."

Understanding those differences is key because date palms encounter difficulties that farmers are sometimes unable to address. Those include infestations such as the date palm weevil, which can destroy entire plantations.

"We also need date palms with different qualities such as taste," said Mr Purugganan. "All that is included in the genes so by sequencing the genome and understanding what [each variety] looks like at a genetic level, we can help farmers build better varieties in the future."

Once the scientists work out which genes confer resistance to such pests, farmers will be able to target them in breeding or plant resistant varieties.

"They have to wait three to seven years before getting yield so they have to make those choices far in advance," said Mr Purugganan.

With conventional breeding, that is a slow process. "It could take 30 years because it's six years before the date palm can make a fruit from its seed," said Mr Flowers. "After one generation, you have to cross again and again, five or six times to have the gene replaced."

Once they have described the various genomes in detail, they hope to be able to pick and mix useful genes to engineer better species - a process that would be far quicker than breeding.

Beyond the purely practical, the scientists hope to learn something of the date palm's history.

"These mutations that you find in date palms are the result of thousands of years of their evolution," said Mr Purugganan.

"There are a lot of questions about date palms - we don't know where they come from, their origin, how they spread, how they adapted to the very different climates in North Africa, the Gulf, Pakistan, and which wild species gave rise to [them]."

By sampling varieties from all over North Africa and the Middle East, the team will be able to identify the region with the most genetic diversity - and that, says Mr Flowers, is likely to be where they originated.

UAE University will also lend a helping hand by providing the lab with 50 different varieties from around the UAE. "We started working with a group of dates that were fairly common," said Mr Flowers.

The Ministry of Environment and Water will also provide around 120 local varieties, such as Al Khalas and Al Khanezi.

"We need as many varieties as possible," said Mr Purugganan. "Just sequencing a few is not enough, 100 dates is the minimum before we can get meaningful information."

The team hopes to have 50 varieties sequenced in the next six months, with the other half soon after that. Its aim is eventually to sequence the DNA of every date palm variety available.

"I think that this project can become the centre for the study of genetic diversity," said Mr Purugganan.

"We really think we can do a thousand and what's limiting us right now is can we get our hands on a thousand? We want to become the central clearing house for date palm diversity, looking at the genomic level."