Mining and characterizing microsatellites from citrus ESTs

Publication Overview
TitleMining and characterizing microsatellites from citrus ESTs
AuthorsChen C, Zhou P, Choi Y, Huang S, Gmitter FJ
TypeJournal Article
Journal NameTheoretical and applied genetics
Volume112
Issue7
Year2006
Page(s)1248-1257
CitationChen C, Zhou P, Choi Y, Huang S, Gmitter FJ. Mining and characterizing microsatellites from citrus ESTs. Theoretical and applied genetics. 2006; 112(7):1248-1257.

Abstract

Freely available computer programs were arranged in a pipeline to extract microsatellites from public citrus EST sequences, retrieved from the NCBI. In total, 3,278 bi- to hexa-type SSR-containing sequences were identified from 56,199 citrus ESTs. On an average, one SSR was found per 5.2 kb of EST sequence, with the tri-nucleotide motifs as the most abundant. Primer sequences flanking SSR motifs were successfully identified from 2,295 citrus ESTs. Among those, a subset (100 pairs) were synthesized and tested to determine polymorphism and heterozygosity between/within two genera, sweet orange (C. sinensis) and Poncirus (P. trifoliata), which are the parents of the citrus core mapping population selected for an international citrus genomics effort. Eighty-seven pairs of primers gave PCR amplification to the anticipated SSRs, of which 52 and 35 appear to be homozygous and heterozygous, respectively, in sweet orange, and 67 and 20, respectively, in Poncirus. By pairing the loci between the two intergeneric species, it was found that 40 are heterozygous in at least one species with two alleles (9), three alleles (28), or four alleles (3), and the remaining 47 are homozygous in both species with either one allele (31) or two alleles (16). These EST-derived SSRs can be a resource used for understanding of the citrus SSR distribution and frequency, and development of citrus EST-SSR genetic and physical maps. These SSR primer sequences are available upon request.
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Properties
Additional details for this publication include:
Property NameValue
Publication TypeJournal Article
Publication Date2006
Published Location|||
Language Abbreng
Publication Model[electronic resource].
URLhttp://dx.doi.org/10.1007/s00122-006-0226-1
KeywordsCitrus sinensis, Poncirus trifoliata, oranges, Citroncirus webberi, expressed sequence tags, microsatellite repeats, genetic markers, gene banks, computer software, bioinformatics, DNA primers, polymerase chain reaction, genetic polymorphism, heterozygosity, loci, alleles
Cross References
This publication is also available in the following databases:
DatabaseAccession
AGL: USDA National Agricultural LibraryAGL:3835494
PMID: PubMedPMID:16474971