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Plant Diversity 2017, 39(05) 287-293 DOI:   10.1016/j.pld.2017.08.004  ISSN: 2096-2703 CN: 53-1233

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Keywords
Echinochloa phyllopogon
Polymorphic
RAD sequencing
SNP
SSR
Authors
PubMed

Identification of massive molecular markers in Echinochloa phyllopogon using a restriction-site associated DNA approach

Guoqi Chena,b, Wei Zhanga,b, Jiapeng Fanga,b, Liyao Donga,b

a College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China;
b Key Laboratory of Integrated Pest Management on Crops in East China(Nanjing Agricultural University), Ministry of Agriculture, Nanjing 210095, China

Abstract

Echinochloa phyllopogon proliferation seriously threatens rice production worldwide. We combined a restriction-site associated DNA (RAD) approach with Illumina DNA sequencing for rapid and mass discovery of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers for E. phyllopogon. RAD tags were generated from the genomic DNA of two E. phyllopogon plants, and sequenced to produce 5197.7 Mb and 5242.9 Mb high quality sequences, respectively. The GC content of E. phyllopogon was 45.8%, which is high for monocots. In total, 4710 putative SSRs were identified in 4132 contigs, which permitted the design of PCR primers for E. phyllopogon. Most repeat motifs among the SSRs identified were dinucleotide (>82%), and most of these SSRs were four motif-repeats (>75%). The most frequent motif was AT, accounting for 36.3%-37.2%, followed by AG and AC. In total, 78 putative polymorphic SSR loci were found. A total of 49,179 SNPs were discovered between the two samples of E. phyllopogon, 67.1% of which were transversions and 32.9% were transitions. We used eight SSRs to study the genetic diversity of four E. phyllopogon populations collected from rice fields in China and all eight loci tested were polymorphic.

Keywords Echinochloa phyllopogon   Polymorphic   RAD sequencing   SNP   SSR  
Received 2017-02-22 Revised 2017-08-28 Online:  
DOI: 10.1016/j.pld.2017.08.004
Fund:This research was supported by China Postdoctoral Science Foundation (2015M571763) and the Special Fund for Agroscientific Research in the Public Interest of China (201303022).We thank Kui Wu and Zhi-hui Yan (Nanjing Agricultural University,China) for providing helps on plant cultivation.Thanks are also due to the reviewers and editors for their helpful comments and English polish on earlier drafts of the manuscript.
Corresponding Authors: Liyao Dong,E-mail address:dly@njau.edu.cn
Email: dly@njau.edu.cn
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