1 2012 Vol: 12(1):237. DOI: 10.1186/1471-2229-12-237

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

Date 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. In 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. Date 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.

Mentions
Figures
Figure 1: Distribution of EST-SSRs with various motifs across different repeat numbers Figure 2: Polymorphism detected by three EST-SSR markers among 12 date palm varltivars Figure 3: Characterization of date palm EST-SSRs by gene ontology categories
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References
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    • . . . Increased availability of these markers would aid in the genetic and genomic studies in date palm as they are better tools than RAPD markers because of their co-dominant inheritance, multi-allelic nature, and high reproducibility 5 37 38 39 40 41 . . .
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    • . . . Primers were designed using BatchPrimer3 45 with the following conditions: optimum primer length of 20 nucleotides, optimum melting temperature of 50°C, an optimum product size of 150 bp, and an optimum G/C content of 50% . . .
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    • . . . The sequences containing SSR were subjected for functional characterization using Blast2GO 46 to identify the biological process, molecular function, and cellular component ontology for these sequences . . .
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