BMC Genomics Research article BioMed Central Open Access Development and implementation of high-throughput SNP genotyping in barley Timothy J Close*1, Prasanna R Bhat1,12, Stefano Lonardi2, Yonghui Wu2,13, Nils Rostoks3,14, Luke Ramsay3, Arnis Druka3, Nils Stein4, Jan T Svensson1,15, Steve Wanamaker1, Serdar Bozdag2,16, Mikeal L Roose1, Matthew J Moscou1,17, Shiaoman Chao5, Rajeev K Varshney4,18, Péter Szűcs6, Kazuhiro Sato7, Patrick M Hayes6, David E Matthews8, Andris Kleinhofs9, Gary J Muehlbauer10, Joseph DeYoung11, David F Marshall3, Kavitha Madishetty1, Raymond D Fenton1, Pascal Condamine1,19, Andreas Graner4 and Robbie Waugh3 Address: 1Department of Botany & Plant Sciences, University of California (UCR), Riverside, CA, 92521, USA, 2Department of Computer Sciences, University of California (UCR), Riverside, CA, 92521, USA, 3Scottish Crop Research Institute (SCRI), Invergowrie, Dundee, DD2 5DA, UK, 4Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, D-06466, Gatersleben, Germany, 5USDA-ARS Biosciences Research Lab, Fargo, ND, 58105-5674, USA, 6Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA, 7Research Institute for Bioresources, Okayama University, Kurashiki, 710-0046, Japan, 8USDA-ARS, Cornell University, Ithaca, NY, 14853, USA, 9Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA, 10Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA, 11Southern California Genotyping Consortium, University of California, Los Angeles, CA, 90095, USA, 12Monsanto Research Centre, Bangalore, 560092, India, 13Google, Mountain View, CA, 94043, USA, 14Faculty of Biology, University of Latvia, 4 Kronvalda Boulevard, Riga, LV-1586, Latvia, 15University of Copenhagen, Frederiksberg C, DK-1871, Denmark, 16NIH National Cancer Institute, Neuro-Oncology Branch, Bethesda, MD, 20892, USA, 17Department of Plant Pathology, Iowa State University, Ames, Iowa, 50011, USA, 18International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru - 502 324, Andhra Pradesh, India and 19NetSocial Marketing, Le Puech, 15600 Montmurat, France Email: Timothy J Close* - timothy.close@ucr.edu; Prasanna R Bhat - prasannarb@gmail.com; Stefano Lonardi - stelo@cs.ucr.edu; Yonghui Wu - yonghui@cs.ucr.edu; Nils Rostoks - nrostoks@latnet.lv; Luke Ramsay - Luke.Ramsay@scri.ac.uk; Arnis Druka - arnisdruka@aol.com; Nils Stein - stein@ipk-gatersleben.de; Jan T Svensson - jsv@life.ku.dk; Steve Wanamaker - steve.wanamaker@ucr.edu; Serdar Bozdag - sbozdag@cs.ucr.edu; Mikeal L Roose - mikeal.roose@ucr.edu; Matthew J Moscou - moscou@iastate.edu; Shiaoman Chao - Shiaoman.Chao@ars.usda.gov; Rajeev K Varshney - r.k.varshney@cgiar.org; Péter Szűcs - Peter.Szucs@oregonstate.edu; Kazuhiro Sato - kazsato@rib.okayama-U.ac.jp; Patrick M Hayes - hayesp@css.orst.edu; David E Matthews - Matthews@greengenes.cit.cornell.edu; Andris Kleinhofs - andyk@wsu.edu; Gary J Muehlbauer - Gary.J.Muehlbauer- 1@tc.umn.edu; Joseph DeYoung - Jdeyoung@mednet.ucla.edu; David F Marshall - D.F.Marshall@scri.sari.ac.uk; Kavitha Madishetty - kavithavcs@yahoo.com; Raymond D Fenton - raymond.fenton@ucr.edu; Pascal Condamine - pascalcondamine@yahoo.fr; Andreas Graner - a_graner@IPK-Gatersleben.de; Robbie Waugh - rwaugh@scri.sari.ac.uk * Corresponding author Published: 4 December 2009 BMC Genomics 2009, 10:582 doi:10.1186/1471-2164-10-582 This article is available from: http://www.biomedcentral.com/1471-2164/10/582 Received: 31 July 2009 Accepted: 4 December 2009 © 2009 Close et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: High density genetic maps of plants have, nearly without exception, made use of marker datasets containing missing or questionable genotype calls derived from a variety of genic and non-genic or anonymous markers, and been presented as a single linear order of genetic loci for each linkage group. The consequences of missing or erroneous data include falsely separated markers, expansion of cM distances and incorrect marker order. These imperfections are amplified Page 1 of 13 (page number not for citation purposes)