GMT Tutorial Exercise 20 - Workflow 2 - Step 5

Browse the worksheets where several genetic maps have been aligned to view the distribution of markers

1. In the polymorphism viewer, click on the worksheet "tab" where aligned genetic maps of interest to your work are found:
   • In the Barley Polymorphism Viewer macro, genetic maps for barley (listed below) are found on worksheets Aligned Maps, DArT Consensus Map, and SCRI SNP map.
   • In the Wheat Polymorphism Viewer macro, genetic maps for the different wheat chromosomes (listed below) are shown on separate worksheets for each linkage group, labelled 1A, 1B, 1D, 2A, etc.
2. On these worksheets, the following information is found:
   • The maps' names are written at the top, above several columns showing chromosome names, names of features / markers and their map location in centiMorgan (cM).
   • Markers available as MRT^TM markers are identified by listing their MRT number (hvnnnn or tannnn, respectively) next to their published name.
   • When markers exist on more than one map, a line has been drawn between corresponding markers.
3. You can browse the maps to identify multiplex-ready^TM markers in a chromosome region of interest for your work.
4. Markers in the selected "Whole Genome Scan" marker kit are highlighted in grey:

Maps in the Barley Polymorphism Viewer macro

Maps on the Aligned Maps worksheet

• Ramsay et al. map:
  Ramsay L, Macaulay M, Ivanissevich SD, MacLean K, Cardle L, Fuller J, Edwards KJ, Tuvesson S, Morgante M, Massari A, Maestri E, Marmiroli N, Sjakste T, Ganal M, Powell W, Waugh R (2000) A simple sequence repeat-based linkage map of barley. Genetics 156:1997-2005
• AB-QTL map:
  Hearnden P, Eckermann P, McMichael G, Hayden M, Eglinton J, Chalmers K (2007) A genetic map of 1,000 SSR and DArT markers in a wide barley cross. Theoretical and Applied Genetics 115:383-391
• Varshney et al. 2006:
  Varshney RK, Grosse I, Hahnel U, Siefken R, Prasad M, Stein N, Langridge P, Altschmied L, Graner A (2006) Genetic mapping and BAC assignment of EST-derived SSR markers shows non-uniform distribution of genes in the barley genome. Theoretical and Applied Genetics 113:239-250
• SCRI SNP Consensus Map (Truncated):
  A truncated version of the map presented in Rostoks N, Mudie S, Cardle L, Russell J, Ramsay L, Booth A, Svensson J, Wanamaker S, Walia H, Rodriguez E, Hedley P, Liu H, Morris J, Close T, Marshall D, Waugh R (2005) Genome-wide SNP discovery and linkage analysis in barley based on genes responsive to abiotic stress. Molecular Genetics and Genomics 274:515-527
• DArT Consensus Map:
  Wenzl P, Li H, Carling J, Zhou M, Raman H, Paul E, Hearnden P, Maier C, Xia L, Caig V, Ovesna J, Cakir M, Poulsen D, Wang J, Raman R, Smith K, Muehlbauer G, Chalmers K, Kleinhofs A, Huttner E, Kilian A (2006) A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits. BMC Genomics 7:206

Maps on the DArT Consensus Map worksheet

• This worksheet provides more detailed information for the DArT Consensus Map that is also shown on the Aligned Map worksheet.
  Beside the marker positions on the consensus map, it also shows on which of the contributing component maps a marker had been originally located.

Maps on the SCRI SNP map worksheet

• This worksheet shows the SCRI SNP Consensus Map, developed at the Scottish Crop Research Institute (SCRI), Invergowrie, Dundee, DD2 5DA, UK. This map set data can be downloaded from the SCRI CMap installation, where this map set is referred to as "Barley, Consensus SNP 2005".

Maps in the Wheat Polymorphism Viewer macro

• Map 1 "“ STM; Hayden et al. 2006:
  Hayden MJ, Stephenson P, Logojan AM, Khatkar D, Rogers C, Elsden J, Koebner RMD, Snape JW, Sharp PJ (2006) Development and genetic mapping of sequence-tagged microsatellites (STMs) in bread wheat (Triticum aestivum L.). Theoretical and Applied Genetics 113:1271-1281
• Map 2 - SSR Consensus ; Somers et al. 2004:
  Somers D, Isaac P, Edwards K (2004) A high-density microsatellite consensus map for bread wheat (Triticum aestivum L.). Theoretical and Applied Genetics 109:1105-1114
• Map 3 - SSR Composite; Sourdille et al. 2005:
  Supplementary online information for Sourdille P, Singh S, Cadalen T, Brown-Guedira G, Gay G, Qi L, Gill B, Dufour P, Murigneux A, Bernard M (2004) Microsatellite-based deletion bin system for the establishment of genetic-physical map relationships in wheat (Triticum aestivum L.). Functional & Integrative Genomics 4:12-25. See column heading "ITMI RFLP + µsats" in the Excel files for groups 1 to 7, available at http://wheat.pw.usda.gov/ggpages/SSRclub/GeneticPhysical/.
• Map 4 - BARC SSR; Qi et al. 2004:
  Song Q, Shi J, Singh S, Fickus E, Costa J, Lewis J, Gill B, Ward R, Cregan P (2005) Development and mapping of microsatellite (SSR) markers in wheat. Theoretical and Applied Genetics 110:550-560
• Map 5 - CFA & CFD SSR; Sourdille et al. 2004:
  Supplementary online information for Sourdille P, Singh S, Cadalen T, Brown-Guedira G, Gay G, Qi L, Gill B, Dufour P, Murigneux A, Bernard M (2004) Microsatellite-based deletion bin system for the establishment of genetic-physical map relationships in wheat (Triticum aestivum L.). Functional & Integrative Genomics 4:12-25. See column heading "CtCS map" in the Excel files for groups 1 to 7, available at http://wheat.pw.usda.gov/ggpages/SSRclub/GeneticPhysical/.
• Map 6 - SSR Composite; Rudi et al. 2004:
  Rudi Appels' 2004 composite wheat map, available from GrainGenes:
  http://wheat.pw.usda.gov/cgi-bin/graingenes/report.cgi?class=mapdata;name=Wheat,+Composite,+2004 (general info)
  http://rye.pw.usda.gov/cgi-bin/cmap/map_set_info?map_set_aid=Wheat_Composite_2004;data_source=GrainGenes (CMAP link)