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Team Reports on Findings from Date Palm Genome

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – In Nature Biotechnology online yesterday, an international research group led by investigators at Weill Cornell Medical College in Qatar presented findings from their effort to sequence and characterize the date palm genome.

The researchers used high-throughput sequencing to tackle the genome of a female date palm, Phoenix dactylifera, belonging to the Khalas variety. By comparing this draft genome to sequences for another eight female and backcrossed male cultivars from three other date palm varieties, the group was able to gain new insights into the plant's biology — in particular, it's system for gender inheritance and genetic regions controlling this process.

That result is of interest to date palm producers, the team explained, because female plants produce fruit and male plants do not. Despite this key difference, though, male and female plants are indistinguishable from one another until plants reach maturity, which can take between five and eight years.

Comparative analyses between date palm sequences also yielded genetic markers that may be useful for classifying date palm plants based on gender, variety, and more.

"Our results lay the foundation for future date palm research at the genomic level by providing the first genome-wide gene set, the first genome-wide multi-variety polymorphism set, and the first gender-linked regions for this species," corresponding author Joel Malek, director of WCMC-Q's genomics laboratory, and co-authors wrote.

Malek and co-workers announced that they had completed a draft version of the date palm genome in 2009. In the current study, they present findings from this and subsequent sequencing efforts and analyses.

Date palms have been cultivated for thousands of years, the researchers noted, and are an especially important crop in some locales with hot, arid climates. Despite its long history of domestication, there are still quirks involved in farming the plant, prompting interest in genetic and other strategies for improving date palm production.

"[D]ate palm biotechnology faces many challenges, including long generation times, the inability to simply distinguish between the many varieties of date palm, and the inability to distinguish female from male trees at an early stage," the authors explained.

"Especially because date palm orchards, which primarily comprise fruit-bearing female trees, can be rapidly ravished by disease," they added, "the ability to quickly replant orchards from seeds or seedlings known to be female would be of great benefit."

The researchers used the Illumina GAIIx to do massively parallel paired-end sequencing of DNA isolated from a female Khalas cultivar. In the process, they generated 381 million bases of sequence representing some 60 percent of the date palm genome and about 90 percent of the plant's genes.

Their subsequent analyses uncovered 28,890 predicted protein-coding genes. Of these, more than 25,000 appear to code for proteins resembling those in the NCBI database.

Tens of thousands of sequences in the genome correspond to transposable element sequences, researchers noted, including 2,949 predicted gene models and almost 2,100 of the protein-coding genes. Even so, they explained, there are likely many more, yet undetected transposable elements in the genome.

The team also tracked down some 1.7 million SNPs in the draft genome. That list of polymorphisms grew substantially when they incorporated data on another eight plants that they sequenced to a range of coverage levels.

The additional cultivars included both female and male backcrossed plants, they explained, and represented two commercially important date palm varieties as well as a non-commercial variety called AlrijalF.

Comparisons between all nine plants revealed nearly 10,400 copy number variations affecting gene regions, along with more than 3.5 million SNPs. Among them: 32 SNPs that could be used to distinguish between date palm varieties included in the study.

"We have sequenced three of the top date palm varieties that are important in three regions of date palm production: Khalas, favored in Arabia; Deglet Noor, favored in North Africa; and Medjool, increasingly favored in California," the researchers wrote. "This resource will allow future comparisons of traits, such as fruit quality and ripening time, which vary among these favored varieties."

Another 1,605 SNP corresponded to gender, they reported, and the genetic patterns they observed were consistent with an XY-type gender determination system in which males typically carried a heterozygous genotype while females were homozygous for most variants found in a gender related region of the genome.

Together, the findings indicate that it should be possible to genetically discern productive female from fruitless male plants, researchers explained, noting that the "capacity to use genetics to differentiate between cultivars and predict the gender of immature trees are perhaps the two most immediate challenges in applying biotechnology to date palm cultivation and improvement."

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