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Sequencing Study Uncovers Date Palm Population Structure, History, Links to Traits

NEW YORK (GenomeWeb) – Using data generated for the "100 Dates!" genome sequencing project, researchers from the US, the United Arab Emirates, and elsewhere have detected signs of at least two separate domestication events for the date palm plant, Phoenix dactylifera.

In a study published online today in Nature Communications, the team reported that it has already generated genome sequencing data for more than five dozen date palm varieties grown in 12 North African, Middle Eastern, and South Asian countries, and has used the millions of SNPs identified in the plants to begin delving into date palm population structure.

The researchers also narrowed in on 56 parts of the genome that appear to have undergone selective pressure during adaptation to various environments, along with genes showing potential ties to fruit traits such as color, texture, and ripening patterns.

"The data on diversity in the genomes helps us to identify genes that may help develop better date palms," senior author Michael Purugganan, a biology, genomics, and systems biology researcher at New York University Abu Dhabi, said in a statement. "It also tells us how date palms evolve, and provides clues as to where date palms came from."

The original date palm genome — generated with DNA from a female date palm of the Khalas variety — was described in Nature Biotechnology in 2012 by a team led by researchers at the Weill Cornell Medical College in Qatar.

Comparisons between re-sequenced female and male cultivars done for that study offered a peek at some potential genetic markers in date palm, a perennial plant that is widely grown in dry areas in North Africa, the Middle East, and beyond.

For the new analysis, Purugganan and colleagues sought clues to date palm population structure, domestication origins, and more, using paired-end Illumina sequencing to assess the genomes of three dozen Middle Eastern date palm varieties, 17 varieties grown in North Africa, and nine South Asian varieties.

After generating almost 21-fold average coverage for each of the varieties and aligning the reads to the date palm reference genome, they identified almost 7.2 million SNPs, including more than 5.2 million intergenic SNPs.

The team's look at relationships between the plants pointed to two clusters of date palm populations, one made up of North African varieties and another containing populations from the Middle East and South Asia, with some admixture between populations in the Middle East and North Africa.

Together with diversity patterns in the populations, such results suggest that the North African varieties belong to a lineage that split from the lineage leading to Middle Eastern and South Asian varieties prior to domestication.

In a search for genomic changes contributing to adaptations to various environments, the researchers uncovered 20 regions of the date palm genome showing signs of positive selection in North African populations. Three dozen more regions appeared to be under positive selection in date palm populations from the Middle East.

For example, their results hint that selection on parts of the genome containing a pectin lyase enzyme may have led to softer fruit texture in dates from more than three quarters of Middle Eastern and South Asian varieties.

The team also began tapping the population sequence data to search for candidate contributors to other fruit and plant traits — from flowering time to disease resistance. The group is continuing to add date palm genomes to their collection in the hopes of characterizing genomic features that could improve future varieties of the plant.