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

3. KO_24_26_34KO_22_44_18OT_1SM_5Hwheat_5Am opt-15408opt-15408_c umn6003bumn6003a umn6003bumn6003c cdo1469cdicdo1469adi cdo1523acdo1523b cdo241cdo241a cdo419bcdo419e cdo484bcdo484acdo484 cdo419bcdo419 cdo1437acdo1437b umn5207bumn5207a bcd1797dbcd1797a bcd1968bbcd1968c cdo1505acdo1505b bcd1734 isu1877isu1877b wg644 cdo504 Vrn1 isu1961brvisu1961crvisu1961a cdo708bcdo708 bcd1643abcd1643c aco168baco168a umn589aumn589b cdo590acdo590ccdo590a cdo795acdo795bcdo795a umn363aumn363b cdo419fcdo419e cdo419fcdo419 Details of map joins represented by connecting lines: