Development of genic SSR markers from transcriptome sequencing of pear buds

Publication Overview
TitleDevelopment of genic SSR markers from transcriptome sequencing of pear buds
AuthorsYue XY, Liu GQ, Zong Y, Teng YW, Cai DY
TypeJournal Article
Journal NameJournal of Zhejiang University. Science. B
Volume15
Issue4
Year2014
Page(s)303-12
CitationYue XY, Liu GQ, Zong Y, Teng YW, Cai DY. Development of genic SSR markers from transcriptome sequencing of pear buds. Journal of Zhejiang University. Science. B. 2014 Apr; 15(4):303-12.

Abstract

A total of 8375 genic simple sequence repeat (SSR) loci were discovered from a unigene set assembled from 116282 transcriptomic unigenes in this study. Dinucleotide repeat motifs were the most common with a frequency of 65.11%, followed by trinucleotide (32.81%). A total of 4100 primer pairs were designed from the SSR loci. Of these, 343 primer pairs (repeat length ≥15 bp) were synthesized with an M13 tail and tested for stable amplification and polymorphism in four Pyrus accessions. After the preliminary test, 104 polymorphic genic SSR markers were developed; dinucleotide and trinucleotide repeats represented 97.11% (101) of these. Twenty-eight polymorphic genic SSR markers were selected randomly to further validate genetic diversity among 28 Pyrus accessions. These markers displayed a high level of polymorphism. The number of alleles at these SSR loci ranged from 2 to 17, with a mean of 9.43 alleles per locus, and the polymorphism information content (PIC) values ranged from 0.26 to 0.91. The UPGMA (unweighted pair-group method with arithmetic average) cluster analysis grouped the 28 Pyrus accessions into two groups: Oriental pears and Occidental pears, which are congruent to the traditional taxonomy, demonstrating their effectiveness in analyzing Pyrus phylogenetic relationships, enriching rare Pyrus EST-SSR resources, and confirming the potential value of a pear transcriptome database for the development of new SSR markers.

Features
This publication contains information about 104 features:
Feature NameUniquenameType
TXY1TXY1genetic_marker
TXY2TXY2genetic_marker
TXY4TXY4genetic_marker
TXY5TXY5genetic_marker
TXY8TXY8genetic_marker
TXY11TXY11genetic_marker
TXY12TXY12genetic_marker
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TXY16TXY16genetic_marker
TXY19TXY19genetic_marker
TXY20TXY20genetic_marker
TXY23TXY23genetic_marker
TXY25TXY25genetic_marker
TXY29TXY29genetic_marker
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TXY40TXY40genetic_marker
TXY45TXY45genetic_marker
TXY47TXY47genetic_marker
TXY48TXY48genetic_marker
TXY49TXY49genetic_marker
TXY51TXY51genetic_marker
TXY53TXY53genetic_marker
TXY61TXY61genetic_marker
TXY62TXY62genetic_marker
TXY63TXY63genetic_marker

Pages

Properties
Additional details for this publication include:
Property NameValue
Publication ModelPrint
ISSN1862-1783
eISSN1862-1783
Publication Date2014 Apr
Journal AbbreviationJ Zhejiang Univ Sci B
DOI10.1631/jzus.B1300240
Elocation10.1631/jzus.B1300240
LanguageEnglish
Language Abbreng
Publication TypeJournal Article
Journal CountryChina
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DatabaseAccession
PMID: PubMedPMID:24711351