Journal of Zhejiang University

Journal of Zhejiang University SCIENCE B 2014 Vol.15 No.4 P.303-312

Development of genic SSR markers from transcriptome sequencing of pear buds* #

Author(s): Xiao-yan Yue¹,Guo-qin Liu^1,2,Yu Zong¹,Yuan-wen Teng¹,Dan-ying Cai¹
Affiliation(s): 1. 1. State Agricultural Ministry Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Department of Horticulture, Zhejiang University, Hangzhou 310058, China more
Corresponding email(s): ywteng@zju.edu.cn
Key Words: Genic marker, Simple sequence repeat, Transcriptome, Genetic diversity, Pyrus

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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[J]. Journal of Zhejiang University Science B, 2014, 15(4): 303-312.

@article{title="Development of genic SSR markers from transcriptome sequencing of pear buds",
author="Xiao-yan Yue, Guo-qin Liu, Yu Zong, Yuan-wen Teng, Dan-ying Cai",
journal="Journal of Zhejiang University Science B",
volume="15",
number="4",
pages="303-312",
year="2014",
publisher="Zhejiang University Press & Springer",
doi="10.1631/jzus.B1300240"
}

%0 Journal Article
%T Development of genic SSR markers from transcriptome sequencing of pear buds
%A Xiao-yan Yue
%A Guo-qin Liu
%A Yu Zong
%A Yuan-wen Teng
%A Dan-ying Cai
%J Journal of Zhejiang University SCIENCE B
%V 15
%N 4
%P 303-312
%@ 1673-1581
%D 2014
%I Zhejiang University Press & Springer
%DOI 10.1631/jzus.B1300240

TY - JOUR
T1 - Development of genic SSR markers from transcriptome sequencing of pear buds
A1 - Xiao-yan Yue
A1 - Guo-qin Liu
A1 - Yu Zong
A1 - Yuan-wen Teng
A1 - Dan-ying Cai
J0 - Journal of Zhejiang University Science B
VL - 15
IS - 4
SP - 303
EP - 312
%@ 1673-1581
Y1 - 2014
PB - Zhejiang University Press & Springer
ER -
DOI - 10.1631/jzus.B1300240

Abstract
Chinese Summary
Academic Network
Reviewer Comment

Abstract: A total of 8375 genic simple sequence repeat (SSR) loci were discovered from a unigene set assembled from 116 282 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.

基于“酥梨”芽转录组的简单序列重复（SSR）标记开发

研究目的：基于转录组数据开发具有扩增率高和跨物种转移性的基因组编码区内的SSR（genic-SSR）标记，为梨属植物的分子系统发育关系和遗传多样性相关研究提供新的方法。
创新要点：首次利用梨属植物的转录组测序（RNA-seq）数据结合M-13荧光尾巴高效率地开发了104个genic-SSR标记，并成功将其应用于梨属植物的系统发育关系研究中。
研究方法：应用生物信息学软件从转录组测序数据中搜索SSR位点和设计相应引物，结合高效的M-13荧光尾巴的方法筛选多态性高的SSR标记。
重要结论：转录组数据能够为梨属植物分子系统发育关系和遗传多样性研究提供新的SSR标记来源。

关键词：简单序列重复（SSR）标记；转录组；遗传多样性；梨属