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United States Department of Agriculture

Agricultural Research Service

Research Project: GENETICS AND GENETIC IMPROVEMENT OF DISEASE RESISTANCE AND QUALITY TRAITS IN WATERMELON, BROCCOLI, AND LEAFY GREEN BRASSICAS Title: A Glance at Microsatellite Motifs from 454 Sequencing Reads of Watermelon Genomic DNA

Authors
item Nimmakayala, P -
item Levi, Amnon
item Ponniah, S -
item Tomason, Y -
item Nepal, N -
item Wechter, William
item Reddy, U -

Submitted to: Cucurbitaceae Proceedings
Publication Type: Proceedings
Publication Acceptance Date: July 30, 2010
Publication Date: November 14, 2010
Citation: Nimmakayala, P., Levi, A., Ponniah, S., Tomason, Y., Nepal, N., Wechter, W.P., Reddy, U. 2010. A Glance at Microsatellite Motifs from 454 Sequencing Reads of Watermelon Genomic DNA. Cucurbitaceae Proceedings. p. 91-94. Thies, J.A., Kousik, C., and Levi, A. (Eds).

Technical Abstract: A single 454 (Life Sciences Sequencing Technology) run of Charleston Gray watermelon (Citrullus lanatus var. lanatus) genomic DNA was performed and sequence data were assembled. A large scale identification of simple sequence repeat (SSR) was performed and SSR sequence data were used for the development of primers used for marker development. We have characterized a total of 2143 contigs that contain a total of 2727 SSRs from a pool of 13,176 contigs of 454 sequencing reads. We identified 587 SSR motifs that could be used as potential molecular markers based on their longer repeat lengths and quality of flanking sequence for primer design. We further calculated the proportions of di, tri, tetra, penta and hexa nucleotide repeats in the total repeat pool. A subset of 24 primer pairs from the database of 587 pairs was randomly picked for amplification. Experiments with eight reference samples, representing Citrullus lanatus, Citrullus citroides, Citrullus colocynthis, Lagenaria siceraria, Cucumis melo, Cucumis sativus and Cucurbita pepo, revealed sizable degree of transferability of repeat motifs across the Cucurbitaceous family.

Last Modified: 12/22/2014
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