New York University Abu Dhabi maps date palm genome
Dates have been central to the diets in the Gulf for thousands of years, providing sustenance to everyone from the simple desert societies of the past through to today’s residents of shiny skyscrapers.
As well as being a treat enjoyed daily by many, they retain particular significance as the most popular food in the UAE and many other countries to break the fast during Ramadan.
So it is all the more appropriate that scientists in the Emirates are going a long way towards uncovering the genetic secrets of the date palm and its myriad types.
New York University Abu Dhabi (NYUAD) launched its 100 Dates! initiative in late 2012 with the aim of sequencing the genomes – the full set of genes – of 100 varieties of the date palm.
Less than a year-and-a-half on, the project has already carried out studies on about 60 varieties from North Africa, the Middle East and across to Pakistan, and has now set itself an even more ambitious goal: to analyse as many as 1,000 varieties.
The study involves extracting the DNA from palm fronds, cutting it into fragments and attaching short artificially synthesised stretches of DNA called adaptors. Fluorescent imaging techniques help determine the sequence of DNA “letters”, of which there are four – A, C, G and T – that make up the fragment. Using a genome analysed by researchers in Qatar as a guide, computers assemble the fragments into the plant’s genome.
The project has already uncovered fascinating detail about where date palms were originally domesticated, an issue where investigations have previously had to rely on archaeological data.
To identify the centre of origin, scientists have been looking to see where date varieties show the greatest genetic variation.
Although the researchers say their findings remain preliminary, as they are not yet published in a scientific journal, they can already say that there was probably not a single domestication event. They are also determining which species of date palms were first cultivated.
“There were multiple domestication events, not just in one place. There could be one in Iraq, one in North Africa, one somewhere else. We’re analysing this data,” said Dr Khaled Hazzouri, a postdoctoral associate in NYUAD’s Centre for Genomics and System Biology, which is running the project.
On a more practical level, a key goal of the project is to create tools that can be used to improve the yields of date palm varieties.
The researchers want to develop genetic markers that would allow beneficial characteristics such as pest resistance or variations in sugar content to be introduced into varieties through breeding programs or genetic engineering.
Creating these markers involves carrying out genome-wide association mapping, a process that involves looking at the relationship between variations in tiny sections of the date palm’s DNA, called Single Nucleotide Polymorphism (SNP) markers, and the plant’s physical characteristics. For such mapping, a vast number of varieties must be looked at.
“You cannot do genome association with 100 [varieties]. We’re [expanding] it to 300 or 400 or 1,000,” said Dr Hazzouri, who is working on the project with a fellow postdoctoral researcher, Dr Jonathan Flowers, under the direction of Professor Michael Purugganan, NYU’s Dorothy Schiff Professor of Genomics and Professor of Biology.
Sourcing all the varieties used in the project is not always straightforward. To ensure varieties have been identified accurately, samples must be collected from other universities rather than other, less well catalogued, collections. And before material can be transferred, agreements often need to be signed between the institutions. “We’re not relying on fruit markets,” said Dr Hazzour.
Published: April 16, 2014 04:00 AM