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Title: Linking the potato genome to the Conserved Ortholog Set (COS) markers

Author
item LINDQVIST-KREUZE, HANNELE - International Potato Center
item CHO, K - International Potato Center
item PORTAL, LETICIA - International Potato Center
item RODRIGUEZ, FLOR - Inia Carillanca
item SIMON, REINHARD - International Potato Center
item MUELLER, LUKAS - Boyce Thompson Institute
item Spooner, David
item BONIERBALE, MEREDITH - International Potato Center

Submitted to: BioMed Central (BMC) Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/5/2013
Publication Date: 6/8/2013
Publication URL: http://handle.nal.usda.gov/10113/56793
Citation: Lindqvist-Kreuze, H., Cho, K., Portal, L., Rodriguez, F., Simon, R., Mueller, L., Spooner, D.M., Bonierbale, M. 2013. Linking the potato genome to the Conserved Ortholog Set (COS) markers. BioMed Central (BMC) Genetics. Available: http://www.biomedcentral.com/1471-2156/14/51/abstract.

Interpretive Summary: The use of DNA markers has greatly aided all phases of plant research from helping to investigate relationships of plants (taxonomy) to helping to determine the relative location of genes on chromosomes (genetic maps). One class of markers, technically termed conserved ortholog set (COS) markers refer to DNA fragments that are present in only one copy in the plant across a wide range of related plant species. A comprehensive list of these markers is available at Sol Genomics Network website (http://www.sgn.cornell.edu). Many of these COS markers have been placed in the genetic maps of species in the tomato and potato family. Because of their value in biological studies, there has been much research into the discovery of COS markers across wide groups of related plants. This paper investigates 300 of these COS markers in the tomato and potato family to see if they are truly single-copy DNA fragments in six wild and cultivated potato species. We found that most of these COS markers are present as a single copy as expected, and occur in their expected position on chromosomes as determined by prior research. However, we did find some COS markers that are present in multiple copies and found these occur in unexpected chromosome locations. This research is helpful in the identification of those COS markers that may not be useful for the taxonomy and genetic map investigations, thereby saving time and money and increasing accuracy in investigations.

Technical Abstract: 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://www.sgn.cornell.edu) and many of these have been placed in the genetic maps of solanaceous species. We amplified over 300 COS markers from eight potato species or hybrids involving Solanum phureja, S. goniocalyx, S. paucissectum, S. chomatophilum, S. tuberosum and S. berthaultii. By BLASTn 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 present as a 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. 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.