Mining of repeat elements from Pongamia for marker development

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Pongamia pinnata is a species of tree in Leguminosae family that grows over the different agro-climatic condition of India, Southeast Asia, Australia and Pacific islands. The tree is a source of seeds containing non-edible oil for biodiesel preparation and industrial uses. However, very little is known about the genetic and genomic organisation of Pongamia. Repetitive elements in eukaryotes occupy a significant portion of the nuclear and organellar genome. In the present investigation, reverse transcriptase (RT) fragment of copia, gypsy and long interspersed nuclear element (LINE) was identified in Pongamia genome. The annotation of Pongamia EST libraries yielded more than 400 TEs, confirming that some class of transposons are still transcriptionally active. With a view to understand the contribution of transposable elements (TEs) distribution and insertional orientation in Pongamia transcriptome, unigenes were screened with the RepeatMasker program. Analysis revealed that most of the unigenes were found with TE insertions, with an average of 1.42 insertions per unigene. The significant population of identified TE insertions were from retrotransposons and less with DNA transposons. Along with TEs, simple sequence repeats (SSRs) were successfully mined from transcriptome libraries of Pongamia. Among isolated repeats, dinucleotide repeat SSRs were abundant in Pongamia. Primers were successfully designed and amplified to expected size of amplicons in 14 accessions of Pongamia. All the amplified SSRs showed transferability among different families of plants. The newly designed SSR markers were found to be helpful in diversity analysis, as they successfully differentiated the accessions of Pongamia
Supervisor: Latha Rangan