All wheat accessions were evaluated for seedling resistance to races QFCSC, QTHJC, RCRSC, RKQQC, TPMKC, TTTTF and TTKSK in a greenhouse and for adult plant resistance to bulked U.S. races (QFCSC, QTHJC, RCRSC, RKQQC and TPMKC) in the field at the USDA Cereal Disease Laboratory in St. Paul, MN in 2008. Field disease ratings were based on the percentage infection of the stems using the modified Cobb scale [28] when susceptible controls reached 60–70% severity. Seedling IT was scored using the Stakman scale [24] . Details on plant culture, inoculation methods, and scoring methods for the greenhouse and field experiments were described [29] .
To meet the data format required for association analysis, original seedling IT data were converted to a 0–9 linear disease scale as we described in a preliminary report [30] . Simple infection types were converted as follows: 0, 1−, 1, 1+, 2−, 2, 2+, 3−, 3 and 3+ were coded as 0, 1, 2, 3, 4, 5, 6, 7, 8 and 9, respectively. For lines with heterogeneous reactions, only the most prevalent IT was used. The semicolon symbol for hypersensitive fleck “;” was converted to 0. IT 4 was converted to 9. Special annotation code “S” for susceptible was converted to 9 and “S LIF” for low infection frequency was converted to 8. Special annotation codes “C” for extra chlorosis and “N” for extra necrosis were ignored. Double minus and double plus annotations were converted to single minus and single plus, respectively. Complex ranges such as ;12+ were first collapsed to ;2+. Then the first and last ITs of the range were converted and averaged with the first IT being double-weighted because the most prevalent IT is always listed first. Mesothetic reaction types X−, X, and X+ were converted to linearized scores of 4, 5, and 6, respectively. Y and Z mesothetic infection types were treated similarly to X. The conversion algorithm is implemented with examples as an editable Excel spreadsheet inTable S3 . Each IT score was based on one replication comprising five to six seedlings per isolate, except for TTKSK, in which two replications were used for each accession and a mean value was used for association analysis.
To meet the data format required for association analysis, original seedling IT data were converted to a 0–9 linear disease scale as we described in a preliminary report [30] . Simple infection types were converted as follows: 0, 1−, 1, 1+, 2−, 2, 2+, 3−, 3 and 3+ were coded as 0, 1, 2, 3, 4, 5, 6, 7, 8 and 9, respectively. For lines with heterogeneous reactions, only the most prevalent IT was used. The semicolon symbol for hypersensitive fleck “;” was converted to 0. IT 4 was converted to 9. Special annotation code “S” for susceptible was converted to 9 and “S LIF” for low infection frequency was converted to 8. Special annotation codes “C” for extra chlorosis and “N” for extra necrosis were ignored. Double minus and double plus annotations were converted to single minus and single plus, respectively. Complex ranges such as ;12+ were first collapsed to ;2+. Then the first and last ITs of the range were converted and averaged with the first IT being double-weighted because the most prevalent IT is always listed first. Mesothetic reaction types X−, X, and X+ were converted to linearized scores of 4, 5, and 6, respectively. Y and Z mesothetic infection types were treated similarly to X. The conversion algorithm is implemented with examples as an editable Excel spreadsheet in
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