Identification and characterization of gene-based SSR markers in date palm (Phoenix dactylifera L.).

Yongli Zhao,C S Prakash,Guohao He,Roxanne Williams

doi:10.1186/1471-2229-12-237

Abstract

BackgroundDate palm (Phoenix dactylifera L.) is an important tree in the Middle East and North Africa due to the nutritional value of its fruit. Molecular Breeding would accelerate genetic improvement of fruit tree through marker assisted selection. However, the lack of molecular markers in date palm restricts the application of molecular breeding.ResultsIn this study, we analyzed 28,889 EST sequences from the date palm genome database to identify simple-sequence repeats (SSRs) and to develop gene-based markers, i.e. expressed sequence tag-SSRs (EST-SSRs). We identified 4,609 ESTs as containing SSRs, among which, trinucleotide motifs (69.7%) were the most common, followed by tetranucleotide (10.4%) and dinucleotide motifs (9.6%). The motif AG (85.7%) was most abundant in dinucleotides, while motifs AGG (26.8%), AAG (19.3%), and AGC (16.1%) were most common among trinucleotides. A total of 4,967 primer pairs were designed for EST-SSR markers from the computational data. In a follow up laboratory study, we tested a sample of 20 random selected primer pairs for amplification and polymorphism detection using genomic DNA from date palm cultivars. Nearly one-third of these primer pairs detected DNA polymorphism to differentiate the twelve date palm cultivars used. Functional categorization of EST sequences containing SSRs revealed that 3,108 (67.4%) of such ESTs had homology with known proteins.ConclusionDate palm EST sequences exhibits a good resource for developing gene-based markers. These genic markers identified in our study may provide a valuable genetic and genomic tool for further genetic research and varietal development in date palm, such as diversity study, QTL mapping, and molecular breeding.

Highlights

Date palm (Phoenix dactylifera L.) is an important tree in the Middle East and North Africa due to the nutritional value of its fruit
Because some Expressed Sequence Tags (EST) sequences harbored more than one motif, a total of 5,981 various motifs were found from these simple-sequence repeats (SSRs) (Table 1)
The gene ontology categorization of date palm EST sequences containing SSRs using Blast2GO in our study revealed that 52% of them classified as involved in biological process for “cellular process” and “metabolic process”

Summary

Introduction

Date palm (Phoenix dactylifera L.) is an important tree in the Middle East and North Africa due to the nutritional value of its fruit. Date palm (Phoenix dactylifera L.) is a dioecious, perennial, monocotyledonous fruit tree belonging to the family Arecaceae, originated in Mesopotamia [1]. Date palm is one of the world’s first cultivated fruit trees representing an ancient group of fruit trees including olive and fig [2]. It is cultivated across the tropical and subtropical areas of South Asia and Africa. As with many other plants, genetic diversity of date palm in its center of origin is threatened by habitat loss due to deforestation, population pressure, and clearance for agriculture development [3]. Preservation and evaluation of genetic diversity are critical and timely concerns in the conservation of date palm germplasm [3]

Objectives

Methods

Results

Discussion

Conclusion