View Full Table | Close Full ViewTable 1.

Criteria for defining spring, facultative, and winter germplasm groups in Oregon Barley coordinated agricultural project (CAP) I and II based on phenotype.

 
LTT SPMN (% survival) HD COR (S) (days to flower)
Spring Facultative Winter Spring Facultative Winter
Maximum 40 85 80 195 199 250
Minimum 0 45 25 169 172 200
Mean 14.8 67.8 64.6 179.3 181.1 241.8
Standard deviation 13.3 9.2 11.9 6.4 7 16.5
Number of lines 31 67 50 31 67 50
LTT SPMN, low temperature tolerance at St. Paul, MN.
HD COR (S), heading date at Corvallis, OR, spring planted.
§The spring check is Orca with LTT SPMN = 0% and HD COR (S) = 174 d.
The facultative checks are Dicktoo with LTT SPMN = 80% and HD COR (S) = 178 d and Maja with LTT SPMN = 75% and HD COR (S) = 180 d.
#The winter check is Strider with LTT SPMN = 72.5% and HD COR (S) = 250 d.
††A value of 250 d was assigned to those lines that never flowered in the experiment.



View Full Table | Close Full ViewTable 2.

Summary of phenotyping experiments conducted using Oregon Barley coordinated agricultural project (CAP) I, CAP II, and CAP I and II germplasm.

 
Germplasm set Environment and trait measured
Field LT tolerance Controlled LTT Field VRN sensitivity (S) Greenhouse VRN sensitivity (V–) Field flowering time (F) Greenhouse lowering time (V+)
%SURV %SURV %SURV %SURV HD HD FLN HD HD FLN
CAP I POR 2006 FCCO 2006 MRI 2006 COR 2008 COR 2008 COR 2006 COR 2008 COR 2008
CAP II COR 2009 COR 2009 COR 2007 COR 2009 COR 2009
CAP I and II SPMN 2009 COR 2009
Lines submitted to the Barley Coordinated Agricultural Project in 2006 (CAP I) and 2007 (CAP II).
Field, evaluated in the field; Controlled, evaluated in growth chamber with temperature and day length control; V+, vernalized; V–, not vernalized; F, fall planted; S, spring planted; LTT, low temperature tolerance; VRN, vernalization.
§%SURV, percent survival; HD, heading date; FLN, final leaf number.
Location code and year of the trial: POR, Pendleton, OR; FCCO, Fort Collins, CO; MRI, Agricultural Research Institute of the Hungarian Academy of Sciences, Martonvásár, Hungary; SPMN, St. Paul, MN; COR, Corvallis, OR.



View Full Table | Close Full ViewTable 3.

Pearson correlation coefficients among traits measured in the Oregon Barley coordinated agricultural project (CAP) I and II germplasm.

 
Trait and environment HD COR (S) HD GH (V–) FLN GH (V–) HD COR (F) HD GH (V+) FLN GH (V+)
LTT SPMN 0.31 0.28 0.31 0.49 0.15 0.09
HD COR (S) 0.86 0.81 0.42 0.42 0.40
HD GH (V–) 0.93 0.33 0.48 0.49
FLN GH (V–) 0.31 0.46 0.53
HD COR (F) 0.17 0.16
HD GH (V+) 0.85
*Significant at the 0.05 probability level.
***Significant at the 0.001 probability level.
LTT, low temperature tolerance; HD, heading date; FLN, final leaf number; GH, greenhouse; SPMN, St. Paul, MN; COR, Corvallis, OR; (S), spring planted; (F), fall planted; (V-), without vernalization; (V+), vernalized.



View Full Table | Close Full ViewTable 4.

Linear mixed model explaining the proportion of variation for low temperature tolerance in Oregon Barley coordinated agricultural project (CAP) I and II. are calculated for each individual significant marker and interaction between markers. Marker 12_3123 is approximately 2 cM from the C-repeat binding factor (CBF) gene cluster at FR-H2 and is a single nucleotide polymorphism (SNP) within a heat-shock transcription factor similar to Arabidopsis HSFB2b. Marker VRN-H1a is at FR-H1 and is a specific HvBM5A amplicon (see Supplemental Table S1). The effect of the interaction without the base model between FR-H1 and FR-H2 is = 0.25.

 
Model Model Model form –2 log likelihood LRT p value
1 Intercept y = μ + e 1351.6
2 Q y = μ + Qυ + e 1309.0 42.6 <0.001 0.25
3 K y = μ + Zu + e 1276.6 75.0 <0.001 0.40
4 Q + K y = μ + Qυ + Zu + e 1273.2 3.5 0.327 0.41
5 12_31236 + K y = μ + m1 + Zu + e 1253.2 23.5 <0.001 0.49
6 VRN-H1a + K y = μ + m2 + Zu + e 1234.9 41.8 <0.001 0.55
7 12_31236 + VRN-H1a + K y = μ + m1 + m2 + Zu + e 1205.9 29.0 <0.001 0.63
8 12_31236 × VRN-H1a + K y = μ + m1 + m2 + m1 × m2 + Zu + e 1195.3 10.6 0.014 0.65
Models used for likelihood ratio tests (LRTs): alternative hypothesis 2 and 3 against null hypothesis 1; alternative hypothesis 4 against null hypothesis 3; alternative hypothesis 5 and 6 against null hypothesis 3; alternative hypothesis 7 against null hypothesis 6; and alternative hypothesis 8 against null hypothesis 7.
Proportion of the variation explained by the base model.
§Proportion of the variation explained by the full model.



View Full Table | Close Full ViewTable 5.

Linear mixed model explaining the proportion of variation for flowering time for the Oregon Barley coordinated agricultural project (CAP) I and II spring planted at Corvallis, OR. are calculated for each individual significant marker and interaction between markers. Marker VRN-H2b is a specific amplicon of ZCCT-Hb (see Supplemental Table S1). The effect of this marker is = 0.29.

 
Model Model Model form –2 log likelihood LRT p value
1 Intercept y = μ + e 1436.7
2 Q y = μ + Qυ + e 1392.2 44.5 <0.001 0.26
3 K y = μ + Zu + e 1364.9 71.8 <0.001 0.38
4 Q + K y = μ + Qυ + Zu + e 1364.4 0.5 0.327 0.39
5 VRN-H2b + K y = μ + m1 + Zu + e 1272.2 92.7 <0.001 0.67
Models used for the likelihood ratio tests (LRTs): alternative hypothesis 2 and 3 against null hypothesis 1; alternative hypothesis 4 against null hypothesis 3; and alternative hypothesis 5 against null hypothesis 3.
Proportion of the variation explained by the base model.
§Proportion of the variation explained by the full model.