Figure 1.
Figure 1.

Population structure and relationship among lines in three association mapping populations (CAP I, CAP II, and CAP III). S: posterior probability of group belonging from STRUCTURE software (Pritchard et al., 2000). C1: light-color, Oregon intermated lines, lines derived by several cycles of intermating progeny derived from crosses among relatively few parents (Kold, Strider, 88Ab536, Excel, Legacy, and Orca); dark-color, non-Oregon intermated lines, lines that are genetically distant to Oregon lines: Hundred, Eight-Twelve, UTWB940119, UTWB94061, UTWB971412, Dicktoo, and Luca. C2: dark-colors (dark-blue and blue) are Oregon CAP I related lines, sister lines with a sib in CAP I; blue are sister lines with a sib in CAP I; dark-blue are Oregon lines derived from crosses with a non-CAP I donor (Bu27); light-colors (white and light-blue) are unrelated germplasm; light-blue are Idaho lines not used as parents of CAP I, Nebraska lines not used as parents of CAP I, and Oregon hooded lines that share one parent (Kold) with CAP I while the other parent (Hoody) is not a parent of CAP I lines; white are other unrelated lines. C3: light-color (Doyce), lines derived from crosses with Doyce; dark-color, Oregon intermated lines.

 


Figure 2.Figure 2.Figure 2.Figure 2.Figure 2.
Figure 2.

Histograms for malt extract (A), wort β glucan (B), α-amylase activity (C), diastatic power(D), and grain protein content (E) based on malt analyses of grain produced from three association mapping arrays (CAP I, CAP II, and CAP III) grown at Corvallis and Pendleton, OR. ME, malt extract; BG, wort β glucan; AA, α-amylase; DP, diastatic power; GPC, grain protein content.

 


Figure 3.
Figure 3.

(previous page) Cumulative distribution function (cdf) of p values in genome-wide scans for the CAP I barley array for all traits and environments. A close-up of the critical region is shown for each plot. The different curves correspond to different models compared: Naïve, marker regression without correction for population structure; Q, posterior probabilities matrix inferred from software STRUCTURE (Pritchard et al., 2000); P, fixed-effects matrix from principal component analysis; M, fixed-effects matrix from nonmetric multidimensional scaling; K, mixed models using kinship matrix as implemented by efficient mixed model association (EMMA [Kang et al., 2008]); QK, mixed models with Q matrix as fixed effects and kinship matrix as random effects; PK.E, mixed models with P matrix as fixed effects and K matrix as random effects; and MK, mixed models with M matrix as fixed effects and K matrix as random effects. ME, malt extract; CO, Corvalis location; BG, wort β glucan; AA, α-amylase; DP, diastatic power; GPC, grain protein content; PE, Pendleton location.

 


Figure 4.
Figure 4.

Profile of significance levels for malt extract (ME) with all the markers in the structured association mixed model in all populations for all the environments. QTL, quantitative trait loci.

 


Figure 5.
Figure 5.

Profile of significance levels for wort β glucan (BG) content with all the markers in the structured association mixed model in all populations for all the environments. QTL, quantitative trait loci.

 


Figure 6.
Figure 6.

Profile of significance levels for α-amylase (AA) content with all the markers in the structured association mixed model in all populations for all the environments. QTL, quantitative trait loci.

 


Figure 7.
Figure 7.

Profile of significance levels for diastatic power (DP) content with all the markers in the structured association mixed model in all populations for all the environments. QTL, quantitative trait loci.