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EST / Contigs Library

Contigs & Putative Gene

SNP Report

SSR Found in EST
SSR Found in Contigs
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Validated Cocoa EST-SSR Markers

     The cacao ( Theobroma cacao ) plant is an Neo-Tropical species whose natural habitat is the Amazon basin. Over the last 30 years there has been a considerable geographical expansion in the availability of cacao genetic resources. As a result the plant has a rich genetic diversity that exists at two levels: that of the primitive populations in the area of original distribution of the species, and that of the derived cultivated populations.     The cacao tree ( Theobroma cacao ),  which has a small genome of 390 Mb,    and   2n = 2x = 20 chromosomes, is undoubtedly one of the fruit trees whose genome has been the most studied.

     The first step of genome sequencing project is to make the EST sequence of respective organisms. ESTs are small pieces of DNA sequence (usually 200 to 500 nucleotides long) that are generated by sequencing either one or both ends of an expressed gene. The idea is to sequence bits of DNA that represent genes expressed in certain cells, tissues, or organs from different organisms and use these "tags" to fish a gene out of a portion of chromosomal DNA by matching base pairs. The challenge associated with identifying genes from genomic sequences varies among organisms and is dependent upon genome size as well as the presence or absence of introns, the intervening DNA sequences interrupting the protein coding sequence of a gene. Expressed Sequence Tags or ESTs provide researchers with a quick and inexpensive route for discovering new genes, for obtaining data on gene expression and regulation, and for constructing genome maps.

     Molecular markers are DNA sequences that can be identified by a simple electrophoretic assay, allowing the presence or absence of neighboring stretches of the genome to be inferred. The marker may be short, such as a single base-pair change (single nucleotide polymorphism) or long, such as a DNA fragment generated by a restriction digest. The marker may be identified directly, for example by DNA sequencing, or indirectly, as in the case of allozymes. EST derived molecular markers especially SSR and SNP are highly useful in developing linkage maps and markers assisted breeding programs. These markers are also transferable to related genera. Harnessing the synteny, EST resources are tissue specific and useful in studying the gene expression.

     This Database contains result of computational analysis of EST resources of Cocoa for Simple Sequence Repeats and Single Nucleotide Polymorphisms. Primers are designed by using Primer3 and SSRPrimer tool.



Riju A, Rajesh MK, Fasila Sherin PTP, Chandrasekar A, Apshara SE & Arunachalam V (2009) Mining of expressed sequence tag libraries of cacao for microsatellite markers using five computational tools - Journal of Genetics, 88 (2) 217-225