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
TXY195TXY195genetic_marker
TXY210TXY210genetic_marker
TXY213TXY213genetic_marker
TXY214TXY214genetic_marker
TXY215TXY215genetic_marker
TXY219TXY219genetic_marker
TXY222TXY222genetic_marker
TXY223TXY223genetic_marker
TXY224TXY224genetic_marker
TXY236TXY236genetic_marker
TXY238TXY238genetic_marker
TXY257TXY257genetic_marker
TXY260TXY260genetic_marker
TXY263TXY263genetic_marker
TXY267TXY267genetic_marker
TXY268TXY268genetic_marker
TXY270TXY270genetic_marker
TXY276TXY276genetic_marker
TXY277TXY277genetic_marker
TXY280TXY280genetic_marker
TXY281TXY281genetic_marker
TXY282TXY282genetic_marker
TXY283TXY283genetic_marker
TXY284TXY284genetic_marker
TXY285TXY285genetic_marker

Pages

Cross References
This publication is also available in the following databases:
DatabaseAccession
PMID: PubMedPMID:24711351