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Open Access Research article

A second-generation anchored genetic linkage map of the tammar wallaby (Macropus eugenii)

Chenwei Wang12*, Lee Webley12, Ke-jun Wei23, Matthew J Wakefield24, Hardip R Patel23, Janine E Deakin23, Amber Alsop23, Jennifer A Marshall Graves23, Desmond W Cooper25, Frank W Nicholas1 and Kyall R Zenger126

Author Affiliations

1 Reprogen, Faculty of Veterinary Science, The University of Sydney, Sydney, NSW 2006, Australia

2 Australian Research Council Centre of Excellence for Kangaroo Genomics

3 Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia

4 Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia

5 School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW 2052, Australia

6 School of Marine & Tropical Biology, James Cook University, Townsville, QLD 4811, Australia

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BMC Genetics 2011, 12:72  doi:10.1186/1471-2156-12-72

Published: 19 August 2011

Abstract

Background

The tammar wallaby, Macropus eugenii, a small kangaroo used for decades for studies of reproduction and metabolism, is the model Australian marsupial for genome sequencing and genetic investigations. The production of a more comprehensive cytogenetically-anchored genetic linkage map will significantly contribute to the deciphering of the tammar wallaby genome. It has great value as a resource to identify novel genes and for comparative studies, and is vital for the ongoing genome sequence assembly and gene ordering in this species.

Results

A second-generation anchored tammar wallaby genetic linkage map has been constructed based on a total of 148 loci. The linkage map contains the original 64 loci included in the first-generation map, plus an additional 84 microsatellite loci that were chosen specifically to increase coverage and assist with the anchoring and orientation of linkage groups to chromosomes. These additional loci were derived from (a) sequenced BAC clones that had been previously mapped to tammar wallaby chromosomes by fluorescence in situ hybridization (FISH), (b) End sequence from BACs subsequently FISH-mapped to tammar wallaby chromosomes, and (c) tammar wallaby genes orthologous to opossum genes predicted to fill gaps in the tammar wallaby linkage map as well as three X-linked markers from a published study. Based on these 148 loci, eight linkage groups were formed. These linkage groups were assigned (via FISH-mapped markers) to all seven autosomes and the X chromosome. The sex-pooled map size is 1402.4 cM, which is estimated to provide 82.6% total coverage of the genome, with an average interval distance of 10.9 cM between adjacent markers. The overall ratio of female/male map length is 0.84, which is comparable to the ratio of 0.78 obtained for the first-generation map.

Conclusions

Construction of this second-generation genetic linkage map is a significant step towards complete coverage of the tammar wallaby genome and considerably extends that of the first-generation map. It will be a valuable resource for ongoing tammar wallaby genetic research and assembling the genome sequence. The sex-pooled map is available online at http://compldb.angis.org.au/ webcite.