Isolation and characterization of SSR and EST-SSR loci in Chamaecyparis formosensis (Cupressaceae)

Applications in Plant Sciences
Chiun-Jr HuangChi-Hsiang Chao

Abstract

Simple sequence repeat (SSR) and expressed sequence tag (EST)-SSR markers were developed as tools for marker-assisted selection of Chamaecyparis formosensis and for the molecular differentiation of cypress species. Based on the SSR-enriched genomic libraries and transcriptome data of C. formosensis, 300 primer pairs were selected for initial confirmation, of which 19 polymorphic SSR and eight polymorphic EST-SSR loci were chosen after testing in 92 individuals. The number of alleles observed for these 27 loci ranged from one to 17. The levels of observed and expected heterozygosity ranged from 0.000 to 1.000 and from 0.000 to 0.903, respectively. Most markers also amplified in C. obtusa var. formosana. The developed SSR and EST-SSR sequences are the first reported markers specific to C. formosensis. These markers will be useful for individual identification of C. formosensis and to distinguish cypress species such as C. obtusa var. formosana.

References

Nov 5, 1999·Methods in Molecular Biology·S Rozen, H Skaletsky
Jan 5, 2005·Trends in Biotechnology·Rajeev K VarshneyMark E Sorrells
May 4, 2005·Methods in Enzymology·Travis C Glenn, Nancy A Schable

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Datasets Mentioned

BETA
PRJNA454510
SRP145153
SRP145033

Methods Mentioned

BETA
PCR

Software Mentioned

Primer3
BLASTX
Geneious
GenAlEx
GENEPOP
Simple Sequence Repeat Identification Tool ( SSRIT
CLC Genomics Workbench
pSTR Finder

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