Open Access Research article

A gene-based SNP resource and linkage map for the copepod Tigriopus californicus

Brad R Foley1, Colin G Rose12, Daniel E Rundle13, Wai Leong1, Gary W Moy4, Ronald S Burton4 and Suzanne Edmands1*

Author Affiliations

1 Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-0371, USA

2 Windward School, Los Angeles, CA 90066-2104, USA

3 Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 01730, USA

4 Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92037, USA

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BMC Genomics 2011, 12:568  doi:10.1186/1471-2164-12-568

Published: 21 November 2011

Abstract

Background

As yet, few genomic resources have been developed in crustaceans. This lack is particularly evident in Copepoda, given the extraordinary numerical abundance, and taxonomic and ecological diversity of this group. Tigriopus californicus is ideally suited to serve as a genetic model copepod and has been the subject of extensive work in environmental stress and reproductive isolation. Accordingly, we set out to develop a broadly-useful panel of genetic markers and to construct a linkage map dense enough for quantitative trait locus detection in an interval mapping framework for T. californicus--a first for copepods.

Results

One hundred and ninety Single Nucleotide Polymorphisms (SNPs) were used to genotype our mapping population of 250 F2 larvae. We were able to construct a linkage map with an average intermarker distance of 1.8 cM, and a maximum intermarker distance of 10.3 cM. All markers were assembled into linkage groups, and the 12 linkage groups corresponded to the 12 known chromosomes of T. californicus. We estimate a total genome size of 401.0 cM, and a total coverage of 73.7%. Seventy five percent of the mapped markers were detected in 9 additional populations of T. californicus. Of available model arthropod genomes, we were able to show more colocalized pairs of homologues between T. californicus and the honeybee Apis mellifera, than expected by chance, suggesting preserved macrosynteny between Hymenoptera and Copepoda.

Conclusions

Our study provides an abundance of linked markers spanning all chromosomes. Many of these markers are also found in multiple populations of T. californicus, and in two other species in the genus. The genomic resource we have developed will enable mapping throughout the geographical range of this species and in closely related species. This linkage map will facilitate genome sequencing, mapping and assembly in an ecologically and taxonomically interesting group for which genomic resources are currently under development.