Gene tests for female date palm bear fruit

Scientists are making progress in their quest to find a DNA test that can identify fruitless male plants and thus help farmers increase yields.

DOHA // Scientists in Doha hope they are getting closer to developing a genetic test to distinguish between male and female date palms. The work, funded by the government's Qatar Foundation, could prove valuable to farmers because there are now no such tests and only female trees produce dates. The same team of scientists at Weill Cornell Medical College in Qatar announced in April they had sequenced the date palm genome.

Since then, they have been carrying out large-scale genetic analysis of male and female date palms with the aim of finding consistent differences between them. The first genetic map was produced using a female date palm. Subsequently, the researchers have carried out tests on one more female and three males using broad brush "light sequencing" techniques. Testing each tree takes just a few days using equipment that automates the process.

The five trees looked at so far come from four varieties of date palm, a species that has the Latin name Phoenix dactylifera and has been cultivated for eight millennia. The geneticists are looking for differences in the sequences of what are known as base pairs in the strands of deoxyribonucleic acid or DNA, which are bundled together into chromosomes, structures that reside in the nucleus of cells.

Stretches of base-pair sequences make up genes, which in turn code for proteins, the molecules that control the biochemistry of organisms. "In the first project, our goal was to decode every single letter, but in later sequencing, we're not going after every single letter difference, we're going after regional differences," said Joel Malek, an instructor in genetic medicine and director of the genomics laboratory where the work is being carried out.

"We're looking at regions of say 4,000 letters at a time. With light sequencing, you can tell if one genome is missing a gene or has two copies." Results so far indicate "a huge amount of variability" between the trees. One variety tested, for example, has several genes missing, but multiple copies of a different type of gene. This genetic variability is not surprising, according to Mr Malek, because other plants such as rice show similar characteristics.

The scientists have found differences shared by the three male plants analysed, but turning that into a genetic test to sex plants could prove difficult. Firstly, differences between male and female date palms will have to be repeated in several dozen plants to ensure they are not just the consequence of variability between varieties rather than the sexes. Also, Mr Malek said sourcing date palms where the sex could be identified definitively was not easy.

"There are hermaphrodite trees that can be male or female depending on the season," he said. "We're waiting until we've got a source of males and females that have been looked at for years and have been confirmed to be always male or always female and not to jump back and forth." The first few trees the team has looked at were not hermaphrodites, having come from a government farm and farms in the Doha area where the trees are well known. The scientists now have to source other trees where the sex is known not to change. "We have to be cautious [in forming conclusions so far] because at present there is no high-quality genetic resource for the date palm. We'd like trees that have been very vigorously validated," Mr Malek said.

"Plenty of farmers can give us good quality trees from a farming perspective, but what we're looking for is well-documented trees. "These are ones that have been propagated for many years in a scientific environment where they understand exactly where they came from and who their parents are, that they're stable that way [with regard to being male or female]. "We're waiting for some high-quality [trees] before we continue the testing." The trees themselves have not been near the Weill Cornell Medical College's laboratories at Education City, the government-funded complex on the outskirts of Doha that hosts branch campuses of six US institutions.

Instead, just small portions of leaf from each tree are used to extract the DNA and run the tests. A genetic test to distinguish between male and female plants would prove useful because it is not possible to tell the sexes apart by looking at the chromosomes under the microscope, unlike the case with many other species. This means that once date seeds have germinated, the plants must be grown for several years before it can be determined whether they will yield dates. Cuttings from female plants can be grown instead, although this is labour intensive.

The initial sequence information on the date palm genome has been made available online, and the scientists hope to publish a fuller set of results in a peer-reviewed scientific journal. [e-mail]