Please use this identifier to cite or link to this item:
https://hdl.handle.net/2440/76121
Citations | ||
Scopus | Web of Science® | Altmetric |
---|---|---|
?
|
?
|
Type: | Journal article |
Title: | Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism |
Author: | Baxter, S. Davey, J. Johnston, J. Shelton, A. Heckel, D. Jiggins, C. Blaxter, M. |
Citation: | PLoS One, 2011; 6(4):1-12 |
Publisher: | Public Library of Science |
Issue Date: | 2011 |
ISSN: | 1932-6203 1932-6203 |
Editor: | Ingvarsson, P.K. |
Statement of Responsibility: | Simon W. Baxter, John W. Davey, J. Spencer Johnston, Anthony M. Shelton, David G. Heckel, Chris D. Jiggins and Mark L. Blaxter |
Abstract: | Restriction-site associated DNA (RAD) sequencing is a powerful new method for targeted sequencing across the genomes of many individuals. This approach has broad potential for genetic analysis of non-model organisms including genotype-phenotype association mapping, phylogeography, population genetics and scaffolding genome assemblies through linkage mapping. We constructed a RAD library using genomic DNA from a Plutella xylostella (diamondback moth) backcross that segregated for resistance to the insecticide spinosad. Sequencing of 24 individuals was performed on a single Illumina GAIIx lane (51 base paired-end reads). Taking advantage of the lack of crossing over in homologous chromosomes in female Lepidoptera, 3,177 maternally inherited RAD alleles were assigned to the 31 chromosomes, enabling identification of the spinosad resistance and W/Z sex chromosomes. Paired-end reads for each RAD allele were assembled into contigs and compared to the genome of Bombyx mori (n = 28) using BLAST, revealing 28 homologous matches plus 3 expected fusion/breakage events which account for the difference in chromosome number. A genome-wide linkage map (1292 cM) was inferred with 2,878 segregating RAD alleles inherited from the backcross father, producing chromosome and location specific sequenced RAD markers. Here we have used RAD sequencing to construct a genetic linkage map de novo for an organism that has no previous genome data. Comparative analysis of P. xyloxtella linkage groups with B. mori chromosomes shows for the first time, genetic synteny appears common beyond the Macrolepidoptera. RAD sequencing is a powerful system capable of rapidly generating chromosome specific data for non-model organisms. |
Keywords: | Sex Chromosomes Animals Moths Bombyx Macrolides DNA Genetic Markers Drug Combinations Chromosome Mapping Contig Mapping Restriction Mapping Sequence Analysis, DNA Genomics Chromosome Segregation Base Sequence Synteny Insecticide Resistance Genotype Alleles Open Reading Frames Models, Biological Female Male Genome, Insect Genetic Linkage Chromosomes, Insect |
Rights: | Copyright: © 2011 Baxter et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
DOI: | 10.1371/journal.pone.0019315 |
Published version: | http://dx.doi.org/10.1371/journal.pone.0019315 |
Appears in Collections: | Aurora harvest Environment Institute publications Molecular and Biomedical Science publications |
Files in This Item:
File | Description | Size | Format | |
---|---|---|---|---|
hdl_76121.pdf | Published version | 462.77 kB | Adobe PDF | View/Open |
Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.