Table S1: Rosaceae conserved orthologous set (RosCOS) marker design notes for mapped markers. Each Fragaria vesca× F. bucharica (FVxFB) linkage group (LG) is discussed along with information on the bin (LG:bin) in which the RosCOS marker is located, its orthologous ‘Golden Delicious’ (GD) apple LG, and additional comments.

LG:bin / RosCOS / Apple LG / Comments / LG:bin / RosCOS / Apple LG / Comments
I:08 / 1 RosCOS available, none mapped / V:15 / No RosCOS available
I:21 / 2343 / 2 & 15 / Homeologous LG; mapped on LG2 only / V:21 / No RosCOS available
I:41 / 1 RosCOS available, none mapped / V:29 / No RosCOS available
I:45 / No RosCOS available / V:37 / 3749 / 13 / Single occurrence in GD genome database
I:47 / No RosCOS available / V:37 / 3055 / 13 / Single occurrence in GD genome database
I:90 / 1623(759) / 12 / Designed for GD LG3 / V:37 / 1435 / 4 & 13 / Non-homeologous LG; mapped on LG13 only
I:90 / 2105 / 15 / Single occurrence in GD genome database / V:37 / 1629 / 13 / Single occurrence in GD genome database
II:00 / No RosCOS available / V:37 / 2372(2143) / 4 & 13 / Non-homeologous LG; mapped on LG13 only
II:08 / 1222(596) / 5 / Designed for GD LG10 / V:37 / 1271 / 16 / Single occurrence in GD genome database
II:08 / 530 / 5 / Designed for GD LG7 / V:46 / 3695 / 16 / Single occurrence in GD genome database
II:08 / 2134 / 10 & 12 / Non-homeologous LG; mapped on LG10 only / V:48 / 2591 / 6 / Single occurrence in GD genome database
II:14 / 1338 / 5 / Single occurrence in GD genome database / V:73 / 1814 / 6 / Single occurrence in GD genome database
II:14 / 52 / 5 / Single occurrence in GD genome database / V:73 / 1410 / 6 / Single occurrence in GD genome database
II:14 / 1272 / 7 / Single occurrence in GD genome database / V:73 / 1167 / 6 / Single occurrence in GD genome database
II:29 / 1341 / 5 & 10 / Homeologous LG; mapped to LG5 only; designed for GD LG12 / V:73 / 3782 / 6 / Designed for GD LG15
II:29 / 3781 / 5 / Designed for GD LG8 / V:73 / 1261 / 6 / Single occurrence in GD genome database
II:29 / 2054 / 8 & 10 / Non-homeologous LG; mapped on LG10 only / V:73 / 2411 / 4 / Designed for GD LG16
II:29 / 2596 / 5 & 10 / Homeologous LG; mapped on LG10 only / V:73 / 1378 / 8 & 15 / Homeologous LG; mapped on LG8 only
II:29 / 2118 / 8 / Single occurrence in GD genome database / V:81 / 510 / 14 / Designed for GD LG13
II:47 / 1125 / 8 / Designed for GD LG11 / VI:07 / 1354 / 4 & 12 / Homeologous LG; mapped on both LG
II:56 / 1549(2673) / 15 / Designed for GD LG1 / VI:14 / 1659 / 4 & 12 / Homeologous LG; mapped on LG12 only
II:75 / No RosCOS available / VI:14 / 1617 / 12 / Single occurrence in GD genome database
III:13 / 1381 / 17 / Single occurrence in GD genome database / VI:31 / 1367 / 4 & 7 / Non-homeologous LG; mapped on LG7 only
III:13 / 645 / 9 & 17 / Homeologous LG; mapped to LG17 only / VI:43 / No RosCOS available
III:17 / No RosCOS available / VI:68 / 1360 / 14 / Single occurrence in GD genome database
III:44 / 2 RosCOS available, none mapped / VI:68 / 1412 / 17 / Designed for GD LG5
III:53 / 1248(1920) / 3 / Single occurrence in GD genome database / VI:70 / No RosCOS available
III:53 / 601 / 11 / Single occurrence in GD genome database / VI:72 / 1097 / 17 / Single occurrence in GD genome database
III:53 / 509 / 3 & 11 / Homeologous LG; mapped on both LG / VI:87 / No RosCOS available
III:53 / 1363(3268) / 3 / Single occurrence in GD genome database / VI:115 / 2970 / 12 & 14 / Homeologous LG; mapped on LG14 only
III:53 / 2409 / 3 / Single occurrence in GD genome database / VII:21 / 1281 / 2 / Designed for GD LG10
III:53 / 2603 / 11 / Single occurrence in GD genome database / VII:40 / 2 RosCOS available, none mapped
III:57 / 1259 / 3 & 11 / Homeologous LG; mapped on LG11 only / VII:45 / No RosCOS available
IV:20 / 4 RosCOS available, none mapped / VII:64 / 1291 / 2 / Single occurrence in GD genome database
IV:26 / 3524 / 4 / Designed for GD LG5 / VII:70 / No RosCOS available
IV:46 / No RosCOS available / VII:89 / No RosCOS available
IV:68 / 1217 / 14 / Single occurrence in GD genome database / VII:90 / No RosCOS available
IV:80 / 1 RosCOS available, none mapped