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ZJUS-B
Journal of Zhejiang University-SCIENCE B (Biomedicine & Biotechnology)  2014, Vol. 15 Issue (4): 303-312    DOI: 10.1631/jzus.B1300240
Articles     
Development of genic SSR markers from transcriptome sequencing of pear buds
Xiao-yan Yue, Guo-qin Liu, Yu Zong, Yuan-wen Teng, Dan-ying Cai
State Agricultural Ministry Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Department of Horticulture, Zhejiang University, Hangzhou 310058, China; College of Agriculture, Guizhou University, Guiyang 550025, China
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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 鈮?5 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.

Key words： Genic marker      Simple sequence repeat      Transcriptome      Genetic diversity      supplementary materials Table S1

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Received: 06 September 2013      Published: 06 April 2014
CLC:  S661.2  
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Xiao-yan Yue
Yuan-wen Teng
Guo-qin Liu
Yu Zong
Dan-ying Cai
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Xiao-yan Yue, Guo-qin Liu, Yu Zong, Yuan-wen Teng, Dan-ying Cai. Development of genic SSR markers from transcriptome sequencing of pear buds. Journal of Zhejiang University-SCIENCE B (Biomedicine & Biotechnology), 2014, 15(4): 303-312.

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http://www.zjujournals.com/xueshu/zjus-b/10.1631/jzus.B1300240     OR     http://www.zjujournals.com/xueshu/zjus-b/Y2014/V15/I4/303

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