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

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.

Transcriptome analysis of potential simple sequence repeat markers in Ammopiptanthus mongolicus

“…Based on the results of the GO functional analysis, the majority of transcripts were assigned "cell" in the cellular component category, involved in "binding" in the molecular function category, and involved in "metabolic activity" in the biological process in A. mongolicus. Similar results were reported in date palm (Zhao et al, 2012) and citrus (Palmieri et al, 2007).…”

Rediscovering Medicinal Plants' Potential with OMICS: Microsatellite Survey in Expressed Sequence Tags of Eleven Traditional Plants with Potent Antidiabetic Properties

“…Not only is the in silico approach time-and cost effective, but also it allows for the discovery of SSRs from ESTs that represent only the coding region in the genome (Scott et al, 2000;Kantety et al, 2002;Varshney et al, 2002). Recent trends in marker development and studies in plants are more towards gene-specific markers rather than random DNA markers, and microsatellite markers are of great importance in identification of genes (Zhao et al, 2012). Additionally, bioinformatics tools also supplement existing approaches by automating the task of SSR identification from available DNA sequences.…”

Identification of a non-redundant set of 202 in silico SSR markers and applicability of a select set in chickpea (Cicer arietinum L.)

“…We also evaluated and proved the authenticity of 25 in silico identified genic SSRs. Similar work was also reported in castor bean (Qiu et al 2010), pepper (Kong et al 2012) and date palm (Zhao et al 2012), where the available EST sequences were used for identification of genic polymorphic SSRs followed by validation of some of these markers. In this study, 44 chickpea genotypes of kabuli, desi and wild type representing cultivated chickpea breeding lines, wild relatives and parents of mapping populations were exploited for diversity study using 25 genic SSR markers.…”