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Analysis of expressed sequence tags from grapevine flower and fruit and development of simple sequence repeat markers

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Abstract

A total of 6,230 EST sequences were produced from 7,561 clones in a cDNA library generated from grapevine (Vitis vinifera cv. ‘Summer Black’) flower and fruit tissues in this study. After cluster and assembly analysis of the datasets, 3,582 unigenes (GenBank accession numbers GW836604–GW840185) were established, among which 381 were new grapevine EST sequences. Out of the 381 new ESTs, 289 could be mapped on the 19 grapevine chromosomes. 913 unique ESTs with known or putative functions were assigned to 11 putative cellular roles. 540 potentially workable grapevine EST-SSRs were developed from 3,582 unigenes and about 42.6% of these unigenes were identified as true-to-type SSR loci and could amplify polymorphic bands from 22 individual plants of V. vinifera L, indicating that grapevine EST datasets are a valuable source for the development of functional simple sequence repeat (SSR) markers.

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Abbreviations

EST:

Expressed sequence tag

mRNA:

Messenger RNA

cDNA:

Complementary DNA

SSR:

Simple sequence repeat

PCR:

Polymerase chain reaction

NCBI:

National center of biotechnology information

bp:

Base pair

RAPD:

Random amplified polymorphic DNA

AFLP:

Amplified fragment length polymorphism

NR:

Non-redundant sequences

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Acknowledgments

This research was supported by the Fundamental Research Funds for the Central Universities (No. KYJ200909), A Project Funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD) and the Program of NCET (No. NCET08-0796).

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Correspondence to Shen-Chun Qu or Jing-Gui Fang.

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Wang, XC., Guo, L., Shangguan, LF. et al. Analysis of expressed sequence tags from grapevine flower and fruit and development of simple sequence repeat markers. Mol Biol Rep 39, 6825–6834 (2012). https://doi.org/10.1007/s11033-012-1507-1

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  • DOI: https://doi.org/10.1007/s11033-012-1507-1

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