An Improved Consensus Linkage Map of Barley Based on Flow-Sorted Chromosomes and Single Nucleotide Polymorphism Markers

María Muñoz-Amatriaín, Matthew J. Moscou, Prasanna R. Bhat, Jan T. Svensson, Jan Bartoš, Pavla Suchánková, Hana Šimková, Takashi R. Endo, Raymond D. Fenton, Stefano Lonardi, Ana M. Castillo, Shiaoman Chao, Luis Cistué, Alfonso Cuesta-Marcos, Kerrie L. Forrest, Matthew J. Hayden, Patrick M. Hayes, Richard D. Horsley, Kihara Makoto, David MoodyKazuhiro Sato, María P. Vallés, Brande B.H. Wulff, Gary J. Muehlbauer, Jaroslav Doležel, Timothy J. Close*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

114 Scopus citations


Recent advances in high-throughput genotyping have made it easier to combine information from different mapping populations into consensus genetic maps, which provide increased marker density and genome coverage compared to individual maps. Previously, a single nucleotide polymorphism (SNP)-based genotyping platform was developed and used to genotype 373 individuals in four barley (Hordeum vulgare L.) mapping populations. This led to a 2943 SNP consensus genetic map with 975 unique positions. In this work, we add data from six additional populations and more individuals from one of the original populations to develop an improved consensus map from 1133 individuals. A stringent and systematic analysis of each of the 10 populations was performed to achieve uniformity. This involved reexamination of the four populations included in the previous map. As a consequence, we present a robust consensus genetic map that contains 2994 SNP loci mapped to 1163 unique positions. The map spans 1137.3 cM with an average density of one marker bin per 0.99 cM. A novel application of the genotyping platform for gene detection allowed the assignment of 2930 genes to flow-sorted chromosomes or arms, confirmed the position of 2545 SNP-mapped loci, added chromosome or arm allocations to an additional 370 SNP loci, and delineated pericentromeric regions for chromosomes 2H to 7H. Marker order has been improved and map resolution has been increased by almost 20%. These increased precision outcomes enable more optimized SNP selection for marker-assisted breeding and support association genetic analysis and map-based cloning. It will also improve the anchoring of DNA sequence scaffolds and the barley physical map to the genetic map.

Original languageEnglish (US)
Article numberPLANTGENOME2011080023
JournalPlant Genome
Issue number3
StatePublished - Nov 2011

Bibliographical note

Funding Information:
This work was supported by the USA National Science Foundation (DBI‐0321756 to TJC and SL), the Human Frontier Science Program (LT000218/2011‐L to MJM) and Gatsby Charitable Foundation (MJM and BBHW), the Czech Ministry of Education Youth and Sports and the European Regional Development Fund (LC06004 and CZ.1.05/2.1.00/01.0007 to JD, JB, HŠ and PS), the Ministry of Science and Innovation of Spain (AGL2007‐62930/AGR and GEN2006‐28560), and the Agriculture and Food Research Initiative Plant Genome, Genetics and Breeding Program of USDA's Cooperative State Research and Extension Service (2009‐65300‐05645 to TJC, SL and GJM). Authors thank Dr. Adam J. Lukaszewski for seeds of wheat‐barley addition lines.

Publisher Copyright:
© 2011 The Authors.

ASJC Scopus subject areas

  • Genetics
  • Agronomy and Crop Science
  • Plant Science


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