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

Published: 8 June 2013

Additional files

Additional file 1: Table S1:

Summary of all COS markers utilized in this study showing the marker locations in the DM genome, in the consensus potato genetic maps, and in TomEXPEN genetic map. The markers that were selected based on co-localization with the QTL for late blight resistance, maturity, ascorbic acid synthesis and carotenoid synthesis are shown in their corresponding columns, together with the literature reference. Also the PCR primer sequences for each marker are shown.

Format: XLSX Size: 64KB Download file

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Additional file 2: Table S3:

Genetic linkage maps of the populations BCT, PCC1 and PD. For BCT all 12 linkage groups are shown, while for the other populations only the linkage groups where COS markers were mapped are shown. The denotation on the top of each linkage group indicates the name of the population. The markers are on the left of the groups and the cumulative distance in cM on the right.

Format: XLSX Size: 25KB Download file

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Additional file 3: Table S2:

Single copy COS markers and the corresponding DM gene hits with putative functions and co-localization with the QTL for late blight resistance, maturity, ascorbic acid synthesis and carotenoid synthesis.

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Additional file 4: Figure S1:

Graph of GO terms in the biological process category that are significantly enriched between the COSII-DM list and the TAIR9 gene model list. The Singular Enrichment Analysis (SEA) tool on the AgriGO website creates colors for nine significance levels. White corresponds to no difference (lowest level); yellow to the first level, light orange to the second level. The graph highlights that overall terms are slightly differently enriched and group into two broad categories: a) cellular metabolic processes and b) response to stimulus.

Format: PPTX Size: 298KB Download file

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