Mining of expressed sequence tag libraries of cacao for microsatellite markers using five computational tools

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dc.contributor.authorAikkal Riju
dc.contributor.authorRajesh, M.K.
dc.contributor.authorFasila Sherin, P.T.P.
dc.contributor.authorChandrasekhar, A.
dc.contributor.authorElain Apshara, S.
dc.contributor.authorVadivel Arunachalam
dc.date.accessioned2014-07-05T05:11:28Z
dc.date.available2014-07-05T05:11:28Z
dc.date.issued2009
dc.description.abstractExpressed sequence tags (ESTs) provide researchers with a quick and inexpensive route for discovering new genes, data on gene expression and regulation, and also provide genic markers that help in constructing genome maps. Cacao is an important perennial crop of humid tropics. Cacao EST sequences, as available in the public domain, were downloaded and made into contigs. Microsatellites were located in these ESTs and contigs using five softwares (MISA, TRA, TROLL, SSRIT and SSR primer). MISA gave maximum coverage of SSRs in cacao ESTs and contigs, although TRA was able to detect higher order (>5-mer) repeats. The frequency of SSRs was one per 26.9 kb in the known set of ESTs. One-third of the repeats in ESTcontigs were found to be trimeric. A few rare repeats like 21-mer repeat were also located. A/T repeats were most abundant among the mononucleotide repeats and the AG/GA/TC/CT type was the most frequent among dimerics. Flanking primers were designed using Primer3 program and verified experimentally for PCR amplification. The results of the study are made available freely online database (http://riju.byethost31.com/cocoa/). Seven primer pairs amplified genomic DNA isolated from leaves were used to screen a representative set of 12 accessions of cacao.en_US
dc.identifier.citationJournal of Genetics, Vol. 88, No. 2, p.217-225 August 2009en_US
dc.identifier.urihttp://hdl.handle.net/123456789/3694
dc.language.isoenen_US
dc.subjectgenomeen_US
dc.subjectin silicoen_US
dc.subjectsimple sequence repeatsen_US
dc.subjectMalvalesen_US
dc.subjectTheobroma cacao L.en_US
dc.titleMining of expressed sequence tag libraries of cacao for microsatellite markers using five computational toolsen_US
dc.typeArticleen_US

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