Figure 1.
Figure 1.

Genetic relationship among 148 Oregon barley coordinated agricultural project (CAP) accessions. The unweighted pair-group method using arithmetic average (UPGMA) tree is drawn to scale, with branch lengths representing the dissimilarities (1 – shared alleles) from the same kinship matrix estimated for the association mapping analysis with the EMMA package implementation for the R software environment. Roman numerals indicate the CAP germplasm set (I or II) and the numbers for each accession are the synonym identifications for The Hordeum Toolbox (THT) database (see materials and methods). Circles indicate vernalization insensitive accessions, while triangles indicate vernalization sensitive accessions. Accessions with a green label are low temperature susceptible and blue labeled accessions are low temperature tolerant. The inset panel displays the mean percent low temperature (LT) tolerance for the different FR-H2 and FR-H1 haplotypes with respective standard error bars. Within the panel is the likelihood-ratio-based R2 for the model without the markers (base [b]) and for the model with the markers (marker [m]). The FR-H2 and FR-H1 haplotype for each accession is color coded in accordance to the inset panel with the outside tree brackets. FR-H2 is represented by marker 12_31236; FR-H1 is represented by marker VRN-H1a (Supplemental Table S1).

 


Figure 2.
Figure 2.

Phenotypic frequency distribution for low temperature tolerance (LTT) evaluated in the Oregon Barley coordinated agricultural project (CAP) germplasm. Coordinated agricultural project I and II were evaluated for LTT at St. Paul, MN (SPMN). Three checks used were: Orca is low temperature susceptible and has a spring growth habit, Strider is low temperature tolerant and has a winter growth habit, and Dicktoo is low temperature tolerant and has a facultative growth habit.

 


Figure 3.
Figure 3.

Phenotypic frequency distributions for heading date (HD) and final leaf number (FLN) evaluated in the Oregon Barley coordinated agricultural project (CAP) germplasm. Coordinated agricultural project I and II were evaluated for HD spring planted (S) and HD fall planted (F) under field conditions at Corvallis, OR (COR). Heading date and FLN were measured with and without vernalization (V+ and V–) under greenhouse (GH) conditions. Maja (facultative growth habit) and Strider (winter growth habit) were used as checks for the HD experiments.

 


Figure 4.
Figure 4.

Low temperature tolerance (LTT) association scan for the Oregon Barley coordinated agricultural project (CAP) I and II germplasm evaluated at St. Paul, MN (SPMN). (A) Genome-wide association scan showing LTT quantitative trait loci (QTL) on 5H. The significance threshold was determined with a false discovery rate (FDR) α level of 0.05 (dashed line). (B) Close-up of the 5H chromosomal region (consensus map position from 108–140 cM) with r2 LD plot of the significant markers. 12_30854 is a single nucleotide polymorphism (SNP) in HvCBF9; 12_31236 is a SNP in barley heat shock transcription factor similar to Arabidopsis HSFB2b; 11_11456 is a SNP in barley gene similar to Arabidopsis Glu-tRNA amidotransferase subunit C; and VRN-H1a is a specific HvBM5A intron 1 amplicon (see Supplemental Table S1). LD, linkage disequilibrium.

 


Figure 5.
Figure 5.

Heading date (HD) and final leaf number (FLN) association scans for Oregon Barley coordinated agricultural project (CAP) I and II. Significance thresholds were determined with a false discovery rate (FDR) level of 0.05 (dashed line). Left panels show the vernalization sensitivity scans and right panels show the flowering time scans. Environments and treatments are coded as follows: COR, Corvallis, OR; GH, greenhouse; S, spring planted; (V–), not vernalized; F, fall planted; (V+), vernalized.

 


Figure 6.
Figure 6.

Biplot of vernalization sensitivity vs. low temperature tolerance (LTT) for seven haplotypes at the FR-H2, FR-H1, and VRN-H2 loci respectively in Oregon Barley coordinated agricultural project (CAP) I and II germplasm. HD COR (S), heading date, field spring planted, at Corvallis, OR; LTT SPMN (%), LTT percent survival at St. Paul, MN. Dashed lines indicate the median for each trait. FR-H2 represents marker 12_31236; FR-H1 represents marker VRN-H1a; and VRN-H2 represents marker VRN-H2b (Supplemental Tables S1 and S3).