TS6-PP6 Identification of EST-SSRs in coconut (Cocos nucifera L.) by deep transcriptome sequencing Preethi P., Rajesh M.K., Naganeeswaran S., Shafeeq Rahman and Anitha Karun ICAR-Central Plantation Crops Research Institute, Kasaragod 671124, Kerala Email:
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Microsatellites or simple sequence repeats (SSRs) are stretches of DNA containing tandem repeats of mono, di-, tri-, tetra- and above nucleotide units ubiquitously distributed throughout the genome. Desirable features such as co-dominant nature, highly polymorphic nature and repeatability make them markers of choice to evaluate genetic resources. Coconut (Cocos nucifera L.) is an important palm which sustains the livelihood of millions of families in coastal regions of the tropics. However, opportunities for molecular breeding are limited by lack of comprehensive genomic resources. Coconut transcriptome from leaf tissue of Chowghat Green Dwarf cultivar was sequenced using Illumina paired-end sequencing technology. The cleaned raw reads were assembled into a total of 130942 unigenes with an average length of 658 bp. To further evaluate the assembly quality and develop new molecular markers, the 130942 unigenes generated in the study were used to mine potential SSRs. Using MISA tool, a total of 318528 potential SSRs were identified. The number of SSR containing sequences was 89820. The number of sequences containing more than one SSR was 57578. Dinucleotide SSRs were the dominant repeat motif followed by trinucleotide and tetranucleotide repeats. Eighty EST-SSRs were randomly selected to validate amplification and to determine the degree of polymorphism in the coconut genomic DNA pools. All the primer pairs successfully amplified coconut DNA fragments and many of these primers could detect significant amounts of polymorphism among the coconut accessions.
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National Seminar on ‘New Horizons and Challenges in Biotechnology and Bioinformatics’, 9‐10 October 2014, CPCRI, Kasaragod, Kerala, India.
