Supplement 5

1. Supplement 5 Comparison of homoeologous Kanota x Ogle (KO) linkage groups 24_26_34 and 22_44_18 and the location of As-Vrn1 mapped as an RFLP in KO. Stacked horizontal lines show the locations of additional markers placed on the map framework. Solid lines are used to join markers found in common between homologous oat groups, while dotted lines join markers found in common between homoeologous oat groups or chromosomes from different species. A list of markers joined by lines is provided separately. Boxes show the approximate locations of QTL identified in previous studies, some of which are placed on the KO map using comparative mapping (Wight et al. 2006). The letters in each box indicate which reference should be consulted for further information concerning the particular QTL: H, Holland et al. 1997; h, Holland et al. 2002; S, Siripoonwiwat et al. 1996. The letters in bold text in grey boxes indicate QTLs for which the experiment-wide type I error rate was p <0.05 or the comparison-wide type I error rate was p <0.001. The remaining QTL had comparison-wide type I error rates of p <0.05. The framework marker on KO group 24_26_34 corresponding to the regions on the U86 and U71P maps containing QTLs for flowering time and vernalization response is highlighted and boxed, as is the location of the Vrn1 gene on group KO 22. Other groups and highlighted markers provide comparative mapping evidence for the location of Vrn1 in this region. The OT (Ogle x TAM O-301) hexaploid oat map is from Portyanko et al. (2001), the fragment of the barley SM (‘Steptoe’ x ‘Morex’) chromosome 5H map is from Kleinhofs et al. 1993, and the simplified diagram of the fine mapping of the Vrn1 region of wheat chromosome 5Am is based on the work of Yan et al. (2003). The location of the Vrn-H1 gene on the barley map presented has been determined using the Graingenes database CMap comparative mapping function (http://wheat.pw.usda.gov/cmap/) and the results of von Zitzewitz et al. (2005). (See figure on next page)

2. KO group 22_44_18 opt-9086_c [0] S cdo482b [2] Barley SM chromosome 5H mwg851b [0] mwg851c [3] umn5596_1 [26] abg314b [6] abg463 [11] [0] umn5245_3 cdo484 [14] S [6] opt-4800 abg390 [21] abg391 [24] abc482 [30] [20] opt-2130_c [22] opt-8386_c abc155 [37] umn5004 [62] abg495a [44] S H H H H isu1507 [67] mwg877 [47] [32] opt-7581 opt-9724 [73] OT group 1 H H h h h wg908 [51] [36] opt-18063 opt-13454 [74] h h h iest9 [53] wg644 cdo1081a [0] opt-7417_c [76] [41] opt-9567 H H cdo504 [58] opt-8196 [79] S h mwg514b [64] [52] opt-12104 opt-18069 [89] cdo484a [94] [57] cdo590a h [61] cdo795a [64] opt-13764 opt-1641_c [104] cisu128b [33] [68] opt-8018_c opt-17202 [107] [70] opt-13924_c opt-6646 [111] Vrn1 [74] opt-14251_c opt-5664 [112] H cdo87 [43] isu1961crv [114] isu1877b [44] [83] opt-5986 opt-0526 [114] rz912 [46] cdo708b [119] cisu92 [50] aco168a [128] [93] bcd961 cdo590a [57] cdo608drv [133] rz474a [59] cdo795a [65] opt-15453 [142] isu1093 [68] opt-8693 [143] psr153 [70] opt-5272 [144] psr144 [71] h opt-11625_c [146] adh2a [72] opt-9929_c [148] cisu59a [73] opt-14108 [151] opt-6715 [155] cdo1196 [158] H S bcd327 [167] m Wheat chromosome 5A csu25 [178] KO group 24_26_34 isu1961brv (Vrn-H1) e40m48-173.t [39] isu1961a cdo504 wg644 0.1 Vrn1 0.9 • See details of connecting • lines on following page cdo708

3. Details of map joins represented by connecting lines: