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
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.


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.

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PMID: PubMedPMID:24711351