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

doi:10.1016/j.pld.2017.08.004

Plant Diversity ›› 2017, Vol. 39 ›› Issue (05): 287-293.DOI: 10.1016/j.pld.2017.08.004

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

Guoqi Chen^a,b, Wei Zhang^a,b, Jiapeng Fang^a,b, Liyao Dong^a,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

收稿日期:2017-02-22 修回日期:2017-08-28 出版日期:2017-10-25 发布日期:2021-11-05
通讯作者: Liyao Dong
基金资助:
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.

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

Guoqi Chen^a,b, Wei Zhang^a,b, Jiapeng Fang^a,b, Liyao Dong^a,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

Received:2017-02-22 Revised:2017-08-28 Online:2017-10-25 Published:2021-11-05
Contact: Liyao Dong
Supported by:
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.

摘要/Abstract

摘要： 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.

关键词: Echinochloa phyllopogon, Polymorphic, RAD sequencing, SNP, SSR

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.

Key words: Echinochloa phyllopogon, Polymorphic, RAD sequencing, SNP, SSR

Guoqi Chen, Wei Zhang, Jiapeng Fang, Liyao Dong. Identification of massive molecular markers in Echinochloa phyllopogon using a restriction-site associated DNA approach[J]. Plant Diversity, 2017, 39(05): 287-293.

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

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

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