A Simple Sequence Repeat- and Single-Nucleotide Polymorphism-Based Genetic Linkage Map of the Brown Planthopper, Nilaparvata lugens

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Abstract

In this study, we developed the first genetic linkage map for the major rice insect pest, the brown planthopper (BPH, Nilaparvata lugens). The linkage map was constructed by integrating linkage data from two backcross populations derived from three inbred BPH strains. The consensus map consists of 474 simple sequence repeats, 43 single-nucleotide polymorphisms, and 1 sequence-tagged site, for a total of 518 markers at 472 unique positions in 17 linkage groups. The linkage groups cover 1093.9 cM, with an average distance of 2.3 cM between loci. The average number of marker loci per linkage group was 27.8. The sex-linkage group was identified by exploiting X-linked and Y-specific markers. Our linkage map and the newly developed markers used to create it constitute an essential resource and a useful framework for future genetic analyses in BPH.

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Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplification.

F. B. Dean, J R Nelson, T L Giesler … (2001)

We describe a simple method of using rolling circle amplification to amplify vector DNA such as M13 or plasmid DNA from single colonies or plaques. Using random primers and phi29 DNA polymerase, circular DNA templates can be amplified 10,000-fold in a few hours. This procedure removes the need for lengthy growth periods and traditional DNA isolation methods. Reaction products can be used directly for DNA sequencing after phosphatase treatment to inactivate unincorporated nucleotides. Amplified products can also be used for in vitro cloning, library construction, and other molecular biology applications.

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L Zane, L Bargelloni, T Patarnello (2002)

In the last few years microsatellites have become one of the most popular molecular markers used with applications in many different fields. High polymorphism and the relative ease of scoring represent the two major features that make microsatellites of large interest for many genetic studies. The major drawback of microsatellites is that they need to be isolated de novo from species that are being examined for the first time. The aim of the present paper is to review the various methods of microsatellite isolation described in the literature with the purpose of providing useful guidelines in making appropriate choices among the large number of currently available options. In addition, we propose a fast and easy protocol which is a combination of different published methods.

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Is Open Access

Aggressive assembly of pyrosequencing reads with mates

Jason R. Miller, Arthur L. Delcher, Sergey Koren … (2008)

Motivation: DNA sequence reads from Sanger and pyrosequencing platforms differ in cost, accuracy, typical coverage, average read length and the variety of available paired-end protocols. Both read types can complement one another in a ‘hybrid’ approach to whole-genome shotgun sequencing projects, but assembly software must be modified to accommodate their different characteristics. This is true even of pyrosequencing mated and unmated read combinations. Without special modifications, assemblers tuned for homogeneous sequence data may perform poorly on hybrid data. Results: Celera Assembler was modified for combinations of ABI 3730 and 454 FLX reads. The revised pipeline called CABOG (Celera Assembler with the Best Overlap Graph) is robust to homopolymer run length uncertainty, high read coverage and heterogeneous read lengths. In tests on four genomes, it generated the longest contigs among all assemblers tested. It exploited the mate constraints provided by paired-end reads from either platform to build larger contigs and scaffolds, which were validated by comparison to a finished reference sequence. A low rate of contig mis-assembly was detected in some CABOG assemblies, but this was reduced in the presence of sufficient mate pair data. Availability: The software is freely available as open-source from http://wgs-assembler.sf.net under the GNU Public License. Contact: jmiller@jcvi.org Supplementary information: Supplementary data are available at Bioinformatics online.

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Author and article information

Journal

Journal ID (nlm-ta): DNA Res

Journal ID (iso-abbrev): DNA Res

Journal ID (publisher-id): dnares

Journal ID (hwp): dnares

Title: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes

Publisher: Oxford University Press

ISSN (Print): 1340-2838

ISSN (Electronic): 1756-1663

Publication date (Print): February 2013

Publication date (Electronic): 29 November 2012

Publication date PMC-release: 29 November 2012

Volume: 20

Issue: 1

Pages: 17-30

Affiliations

[1 ]Ubon Ratchathani Rice Research Center , PO Box 65, Muang, Ubon Ratchathani 34000, Thailand

[2 ]Plant Breeding Laboratory, Graduate School, Faculty of Agriculture,Kyushu University , 6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan

[3 ]National Institute of Agrobiological Sciences , 1-2, O-washi, Tsukuba, Ibaraki 305-8634, Japan

[4 ]Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization , Kumamoto 861-1192, Japan

[5 ]Laboratory of Molecular Gene Technology, Division of Molecular Biosciences, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University , 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan

Author notes

[* ]To whom correspondence should be addressed. Tel. +81 92-642-2821. Fax. +81 92-642-2822. Email: hyasui@ 123456agr.kyushu-u.ac.jp

[†]

These authors contributed equally to this work.

Article

Publisher ID: dss030

DOI: 10.1093/dnares/dss030

PMC ID: 3576655

PubMed ID: 23204257

SO-VID: d2e0fce2-5a23-44cd-821d-862cc09cebb3

License:

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

History

Date received : 1 September 2012

Date accepted : 28 October 2012

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A Simple Sequence Repeat- and Single-Nucleotide Polymorphism-Based Genetic Linkage Map of the Brown Planthopper, Nilaparvata lugens

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Genome Integrity

Most cited references 77

Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplification.

Strategies for microsatellite isolation: a review.

Aggressive assembly of pyrosequencing reads with mates

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