Large-scale identification of polymorphic microsatellites using an <Emphasis Type="Italic">in silico</Emphasis> approach |
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Authors: | Jifeng Tang Samantha J Baldwin Jeanne ME Jacobs C Gerard van der Linden Roeland E Voorrips Jack AM Leunissen Herman van Eck Ben Vosman |
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Institution: | (1) Wageningen UR Plant Breeding, PO Box 16, 6700AA Wageningen, the Netherlands;(2) Laboratory of Bioinformatics, Wageningen University, PO Box 8128, 6700ET Wageningen, the Netherlands;(3) New Zealand Institute for Crop and Food Research, Private Bag 4704, Christchurch, New Zealand |
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Abstract: | Background Simple Sequence Repeat (SSR) or microsatellite markers are valuable for genetic research. Experimental methods to develop
SSR markers are laborious, time consuming and expensive. In silico approaches have become a practicable and relatively inexpensive alternative during the last decade, although testing putative
SSR markers still is time consuming and expensive. In many species only a relatively small percentage of SSR markers turn
out to be polymorphic. This is particularly true for markers derived from expressed sequence tags (ESTs). In EST databases
a large redundancy of sequences is present, which may contain information on length-polymorphisms in the SSR they contain,
and whether they have been derived from heterozygotes or from different genotypes. Up to now, although a number of programs
have been developed to identify SSRs in EST sequences, no software can detect putatively polymorphic SSRs. |
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