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Abstract

 

doi:10.3835/plantgenome2011.08.0023

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

  1. María Muñoz-Amatriaín,
  2. Matthew J. Moscou,
  3. Prasanna R. Bhat,
  4. Jan T. Svensson,
  5. Jan Bartoš,
  6. Pavla Suchánková,
  7. Hana Šimková,
  8. Takashi R. Endo,
  9. Raymond D. Fenton,
  10. Stefano Lonardi,
  11. Ana M. Castillo,
  12. Shiaoman Chao,
  13. Luis Cistué,
  14. Alfonso Cuesta-Marcos,
  15. Kerrie L. Forrest,
  16. Matthew J. Hayden,
  17. Patrick M. Hayes,
  18. Richard D. Horsley,
  19. Kihara Makoto,
  20. David Moody,
  21. Kazuhiro Sato,
  22. María P. Vallés,
  23. Brande B.H. Wulff,
  24. Gary J. Muehlbauer,
  25. Jaroslav Doležel and
  26. Timothy J. Close*
  1. M. Muñoz-Amatriaín and G.J. Muehlbauer, Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, St. Paul, MN 55108; M.J. Moscou and B.B.H. Wulff, The Sainsbury Lab., Norwich Research Park, Norwich, NR4 7UH, UK; P.R. Bhat, J.T. Svensson, R.D. Fenton, and T.J. Close, Dep. of Botany and Plant Sciences, Univ. of California, Riverside, CA 92521; J.T. Svensson, Dep. of Plant Biology, Univ. of Copenhagen, DK-1871 Frederiksberg C, Denmark; J. Bartos, P. Suchánková, H. Šimková, and J. Doležel, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovská 6, CZ-77200 Olomouc, Czech Republic; T.R. Endo, Lab. of Plant Genetics, Graduate School of Agriculture, Kyoto Univ., Kyoto, Japan; S. Lonardi, Dep. of Computer Science and Engineering, Univ. of California, Riverside, CA 92521; A.M. Castillo, L. Cistué, and M.P. Vallés, Departamento de Genética y Producción Vegetal, Estación Experimental Aula Dei, CSIC, 50059, Zaragoza, Spain; S. Chao, USDA-ARS, Biosciences Research Lab., Fargo, ND, 58105-5674; A. Cuesta-Marcos, P.M. Hayes, and L. Cistué, Dep. of Crop and Soil Science, Oregon State Univ., Corvallis, OR 97331; K. L. Forrest and M.J. Hayden, Dep. of Primary Industries Victoria, Victorian AgriBiosciences Centre, La Trobe R&D Park, Bundoora, VIC 3083, Australia; R.D. Horsley, Dep. of Plant Sciences, North Dakota State Univ., Fargo, ND 58108; K. Makoto, Bioresources Research and Development Dep., Sapporo Breweries Ltd., 37-1, Nittakizaki, Ota, Gunma 370-0393, Japan; D. Moody, InterGrain Pty Ltd, Kensington, WA 6100, Australia; K. Sato, Institute of Plant Science and Resources, Okayama Univ., Kurashiki, 710-0046, Japan. M. Muñoz-Amatriaín and M.J. Moscou contributed equally to this work

Abstract

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.

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