SupplementaryTable 1. Breeding programs of the Barley Coordinated Agricultural Project contributing germplasm to the association mapping panel for spot blotch resistance
Breeding program / Location / Breeder / Growth habit / Row typea / Primary use
University of Minnesota (MN) / St. Paul, MN / Kevin Smith / Spring / Six (384) / Malting
North Dakota State University (N6) / Fargo, ND / Richard Horsley / Spring / Six (384) / Malting
USDA-ARS Aberdeen (AB) / Aberdeen, ID / Don Obert / Spring / Six (145)/Two (239) / Malting/feed
Utah State University (UT) / Logan, UT / David Hole / Spring / Six (354)/Two (30) / Feed
Busch Agricultural Resources Inc. (BA) / Ft. Collins, CO / Blake Cooper / Spring / Six (150)/Two (234) / Malting
North Dakota State University (N2) / Fargo, ND / Richard Horsley / Spring / Two (384) / Malting
Washington State University (WA) / Pullman, WA / Steve Ullrich / Spring / Six (32)/Two (352) / Malting/feed/food
Montana State University (MT) / Bozeman, MT / Tom Blake / Spring / Two (384) / Malting/feed/food
Oregon State University (OR) / Corvallis, OR / Patrick Hayes / Winter/facultative / Six (306)/Two (78) / Malting/feed/food
Virginia Polytechnic Inst. & State Univ. (VT) / Blacksburg, VA / Carl Griffey / Winter / Six (384) / Feed

aThe number in the parentheses is the number of lines of each row type from the respective breeding programs.

Supplementary Table 2. Number and percentage of significant pair-wise marker associations across ranges of genetic distance (cM) in the individual panels of CAPI, CAPII, CAPIII, and CAPIV of US barley breeding germplasma
Genetic distance
range (cM) / CAPI / CAPII / CAPIII / CAPIV
0-5 / 7,634b (58.0%c) / 7,578 (61.1%) / 8,327 (57.5%) / 7,849 (54.6%)
5-10 / 2,446 (18.6%) / 2,359 (19.0%) / 2,954 (20.4%) / 2,770 (19.3%)
10-15 / 1,189 (9.0%) / 1,002 (8.1%) / 1,407 (9.7%) / 1,391 (9.7%)
15-20 / 773 (5.9%) / 619 (5.0%) / 788 (5.4%) / 940 (6.5%)
20-25 / 538 (4.1%) / 348 (2.8%) / 436 (3.0%) / 691 (4.8%)
25-50 / 552 (4.2%) / 481 (3.9%) / 560 (3.9%) / 703 (4.9%)
50-200 / 31 (0.2%) / 19 (0.1%) / 3 (0.1%) / 33 (0.2%)

aCAPI, CAPII, CAPIII, and CAPIV are four individual panels from 2006 to 2009 comprising both spring and winter/facultative breeding lines. Bonferroni multiple testing correction p=0.05.

bNumber of significant pair-wise marker associations in each genetic distance range.

cPercentage of significant pair-wise marker associations in each genetic distance range.

Supplementary Table 3. SNP markers found significantly associated with spot blotch seedling and/or adult plant resistance in a two-rowed spring panel (CAP-S2) of US barley breeding germplasm
SNP / Chromosome / Positiona / Seedling / Adult
Marker / q-valueb / R2c / q-value / R2
11_10764 / 1H / 41.0 / 1×10-9 / 0.03 / 1×10-5 / 0.02
12_30336 / 1H / 41.8 / 3×10-7 / 0.02 / 4×10-2 / 0.01
11_10275 / 1H / 42.5 / 4×10-2 / 0.01 / - / -
11_10565 / 3H / 19.2 / 1×10-2 / 0.01 / 5×10-6 / 0.02
11_20162 / 7H / 31.8 / 1×10-27 / 0.08 / 9×10-15 / 0.05
11_10920 / 7H / 31.8 / 2×10-2 / 0.01 / - / -
12_30893 / 7H / 37.6 / 3×10-3 / 0.01 / - / -

aGenetic position (in cM) of marker on chromosome.

bq-value (multiple testing corrected p-value).

cVariation explained by the individual SNP marker.

Supplementary Table 4. Summary of allele effects for different combinations of spot blotch resistance QTL in US barley breeding germplasm

Germplasma / Rcs-qtl-1H-11_10764 / Rcs-qtl-3H-11_10565 / Rcs-qtl-7H-11_20162 / None
No.b / IRc / Severityd / No. / IR / Severity / No. / IR / Severity / No. / IR / Severity
MN / 0 / - / - / 0 / - / - / 0 / - / - / 0 / - / -
N6 / 0 / - / - / 0 / - / - / 0 / - / - / 0 / - / -
AB / 16 / 6.3 / 27.0 / 0 / - / - / 15 / 5.6 / 30.7 / 5 / 6.8 / 44.5
UT / 1 / 4.5 / 12.0 / 3 / 6.9 / 34.6 / 57 / 5.0 / 24.3 / 16 / 6.4 / 28.2
BA / 21 / 5.2 / 39.7 / 13 / 7.2 / 38.9 / 11 / 6.0 / 32.8 / 4 / 7.1 / 45.2
N2 / 0 / - / - / 0 / 5 / 4.9 / 25.9 / 0 / - / -
WA / 13 / 5.4 / 39.2 / 14 / 6.3 / 39.6 / 106 / 5.6 / 35.6 / 19 / 6.7 / 44.7
MT / 11 / 5.2 / 46.0 / 6 / 7.0 / 23.0 / 7 / 4.8 / 33.0 / 12 / 6.7 / 51.0
OR / 24 / 6.1 / - / 5 / 6.5 / - / 30 / 4.8 / - / 26 / 5.7 / -
VT / 48 / 5.6 / - / 2 / 5.9 / - / 94 / 4.2 / - / 172 / 5.3 / -
All programs / 134 / 5.5 (14%) / 32.8 (23%) / 43 / 6.7 (0%) / 34 (20%) / 325 / 5.1 (20%) / 30.4 (29%) / 254 / 6.4 / 42.7
Continued on next page.
Germplasm / Rcs-qtl-3H-11_10565
Rcs-qtl-7H-11_20162 / Rcs-qtl-1H-11_10764
Rcs-qtl-7H-11_20162 / Rcs-qtl-1H-11_10764
Rcs-qtl-3H-11_10565 / All Three QTL
No. / IR / Severity / No. / IR / Severity / No. / IR / Severity / No. / IR / Severity
MN / 12 / 3.6 / 3.1 / 0 / - / - / 8 / 4.6 / 4.3 / 362 / 3.2 / 3.0
N6 / 57 / 3.6 / 7.8 / 4 / 3.4 / 2.6 / 5 / 5.4 / 9.9 / 310 / 3.0 / 2.5
AB / 18 / 5.1 / 22.7 / 75 / 4.2 / 22.5 / 43 / 5.1 / 25.7 / 197 / 2.9 / 6.3
UT / 50 / 4.3 / 23.0 / 38 / 4.3 / 13.9 / 34 / 5.1 / 17.8 / 129 / 3.2 / 6.0
BA / 27 / 5.6 / 31.1 / 103 / 4.7 / 16.6 / 39 / 4.7 / 19.5 / 169 / 2.7 / 1.8
N2 / 2 / 3.9 / 33.8 / 15 / 4.5 / 23.9 / 21 / 5.7 / 19.2 / 333 / 3.8 / 8.1
WA / 46 / 4.8 / 33.4 / 64 / 4.3 / 21.9 / 28 / 5.1 / 28.4 / 77 / 3.3 / 16.7
MT / 2 / 4.7 / 10.8 / 88 / 4.8 / 29.7 / 81 / 6.0 / 25.5 / 159 / 4.5 / 12.8
OR / 4 / 4.5 / - / 220 / 4.9 / - / 10 / 6.0 / - / 47 / 3.8 / -
VT / 0 / - / - / 33 / 5.0 / - / 0 / - / - / 1 / 3.7 / -
All programs / 218 / 4.5 (30%) / 20.7 (52%) / 640 / 4.4 (31%) / 18.7 (56%) / 269 / 5.3 (5%) / 18.8 (56%) / 1784 / 3.4 (47%) / 7.1 (83%)

aUS barley breeding germplasm: University of Minnesota (MN), North Dakota State University (N6), USDA-ARS Aberdeen (AB), Utah State University (UT), Busch Agricultural Resources Inc. (BA), North Dakota State University (N2), Washington State University (WA), Montana State University (MT), Oregon State University (OR), and Virginia Polytechnic Institution and State University (VT). See Supplementary Table 1 for more details on the individual breeding programs.

bNumber of lines carrying the resistance allele(s) for the respective QTL.

cMean infection response (IR) at seedling stage. Percentage in parentheses is the disease reduction as assessed by IR at seedling stage compared to barley lines lacking any resistance QTL.

dMean disease severity (%) at adult plant stage. Percentage in parentheses is the disease reduction as assessed by severity at adult stage compared to barley lines lacking any resistance QTL.

Supplementary Table 5. Genotypes of Steptoe, Morex, Dicktoo, Harrington and TR306 at the three spot blotch resistance QTL identified in this study
Mapping population / Rcs-qtl-1H-11_10764 a / Rcs-qtl-3H-11_10565 / Rcs-qtl-7H-11_20162
Steptoe/Morex / A/Ab / B/B / A/B
Dicktoo/Morex / A/A / A/B / A/B
Harrington/Morex / A/A / B/B / A/B
Harrington/TR306 / A/A / B/B / A/B

aResistance alleles at the three QTL are homozygous “A” at Rcs-qtl-1H-11_10764, homozygous“B” at Rcs-qtl-3H-11_10565, and homozygous “B” at Rcs-qtl-7H-11_20162.

bLoci previously identified by Bilgic et al. (2005) are listed in bold.