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Open Access Research article

Linking the potato genome to the conserved ortholog set (COS) markers

Hannele Lindqvist-Kreuze1*, Kwangsoo Cho14, Leticia Portal1, Flor Rodríguez12, Reinhard Simon1, Lukas A Mueller3, David M Spooner2 and Merideth Bonierbale1

Author affiliations

1 International Potato Center, Lima, Peru

2 USDA-Agricultural Research Service, Vegetable Crops Research Unit, University of Wisconsin, Madison, WI, USA

3 Boyce Thompson Institute for Plant Research, Ithaca, NY, USA

4 Current address: Highland Agriculture Research Center, Rural Development Administration, Pyeongchang, South Korea

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Citation and License

BMC Genetics 2013, 14:51  doi:10.1186/1471-2156-14-51

Published: 8 June 2013

Abstract

Background

Conserved ortholog set (COS) markers are an important functional genomics resource that has greatly improved orthology detection in Asterid species. A comprehensive list of these markers is available at Sol Genomics Network (http://solgenomics.net/ webcite) and many of these have been placed on the genetic maps of a number of solanaceous species.

Results

We amplified over 300 COS markers from eight potato accessions involving two diploid landraces of Solanum tuberosum Andigenum group (formerly classified as S. goniocalyx, S. phureja), and a dihaploid clone derived from a modern tetraploid cultivar of S. tuberosum and the wild species S. berthaultii, S. chomatophilum, and S. paucissectum. By BLASTn (Basic Local Alignment Search Tool of the NCBI, National Center for Biotechnology Information) algorithm we mapped the DNA sequences of these markers into the potato genome sequence. Additionally, we mapped a subset of these markers genetically in potato and present a comparison between the physical and genetic locations of these markers in potato and in comparison with the genetic location in tomato. We found that most of the COS markers are single-copy in the reference genome of potato and that the genetic location in tomato and physical location in potato sequence are mostly in agreement. However, we did find some COS markers that are present in multiple copies and those that map in unexpected locations. Sequence comparisons between species show that some of these markers may be paralogs.

Conclusions

The sequence-based physical map becomes helpful in identification of markers for traits of interest thereby reducing the number of markers to be tested for applications like marker assisted selection, diversity, and phylogenetic studies.

Keywords:
Conserved ortholog set (COS); Genetic mapping; Potato genome; Solanum