Next Generation DNA Sequencing Applied to the Date Palm Tree (Phoenix dactylifera)

• Published in: Acta horticulturae no. 882; pp. 249 - 252
• Main Author: Malek, J.A
• Format: Journal Article
• Language: English
• Published: International Society for Horticultural Science 01.01.2010
• Subjects: agricultural land; arid lands; arid zones; genes; genetic markers; Phoenix dactylifera; sequence analysis; single nucleotide polymorphism; trees
• ISSN: 0567-7572
• DOI: 10.17660/ActaHortic.2010.882.27

Date Palm, a dioecious monocot with historical records of cultivation of over 5000 years, is a fruit producing tree important in agriculture and tradition in the middle east and other arid regions of the world. The date palm's ability to withstand extremely harsh conditions, while producing highly nutritious fruit with relatively minimal care, makes it a good candidate for improving arid land agriculture. Despite the importance of date palm in the agriculture of many countries, relatively little is known about its genetics. To provide the foundation for date palm genetic studies the genome of a female date palm tree was sequenced using massively parallel shotgun sequencing by synthesis technology. A de novo assembly was generated using only the shotgun reads and was annotated for both genes and parental allelic differences. To assist future studies on possible genetic differences between male and female trees, we generated light shotgun sequencing of 3 male trees and 1 additional female tree. We report large scale polymorphisms between these genomes. With this information date palm researchers will now be able to begin genetic research in earnest as they have essentially the full set of date palm genes available to them. From this they will be able to more thoroughly understand how disease affects certain varieties over others, fruit differences, and a host of other genetically based differences in date palm. We have also provided a large set of novel DNA markers (SNPs) which will allow much more accurate typing of various date palm varieties. Researchers can access the genome with ease and use it in their research.