Development and implementation of high-throughput SNP genotyping in barley

Timothy J Close, Prasanna R Bhat, Stefano Lonardi, Yonghui Wu, Nils Rostoks, Luke Ramsay, Arnis Druka, Nils Stein, Jan T Svensson, Steve Wanamaker, Serdar Bozdag, Mikeal L Roose, Matthew J Moscou, Shiaoman Chao, Rajeev K Varshney, Péter Szűcs, Kazuhiro Sato, Patrick M Hayes, David E Matthews, Andris KleinhofsGary J Muehlbauer, Joseph DeYoung, David F Marshall, Kavitha Madishetty, Raymond D Fenton, Pascal Condamine, Andreas Graner, Robbie Waugh

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444 Citations (Scopus)

Abstract

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 in consensus maps and problematic when fine resolution is critical including comparative genome analyses and map-based cloning. Here we provide a new paradigm, a high-density consensus genetic map of barley based only on complete and error-free datasets and genic markers, represented accurately by graphs and approximately by a best-fit linear order, and supported by a readily available SNP genotyping resource.
Original languageEnglish
Article number582
JournalBMC Genomics
Volume10
DOIs
Publication statusPrint publication - 4 Dec 2009
Externally publishedYes

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    Close, T. J., Bhat, P. R., Lonardi, S., Wu, Y., Rostoks, N., Ramsay, L., Druka, A., Stein, N., Svensson, J. T., Wanamaker, S., Bozdag, S., Roose, M. L., Moscou, M. J., Chao, S., Varshney, R. K., Szűcs, P., Sato, K., Hayes, P. M., Matthews, D. E., ... Waugh, R. (2009). Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics, 10, [582]. https://doi.org/10.1186/1471-2164-10-582