View Full Table | Close Full ViewTable 1.

The 16 models compared in the Barley CAP I germplasm array.

 
Structure covariate
Kinship matrix None Q-STRUCTURE PCA nMDS
None naïve Q P M
TASSEL K.T QK.T PK.T MK.T
EMMA K.E QK.E PK.E MK.E
SPAGeDi K.S QK.S PK.S MK.S
Models with either no-kinship matrix or kinship matrices as the ones proposed by Bradbury et al., 2007 (TASSEL), Kang et al., 2008 [efficient mixed model association (EMMA)], or the one using Ritland's (1996) coefficients implemented in SPAGeDi (Hardy and Vekemans, 2002).
No structure covariates used: naïve, a simple test of association (Kruskal–Wallis) with no correction for population structure, or a mixed model without inferred population structure as cofactor and using one of the three kinship matrices described. K.T, kinship matrix estimated using TASSEL (Bradbury et al., 2007); K.E, kinship matrix estimated using efficient mixed models approach (Kang et al., 2008); K.S, kinship matrix estimated using SPAGeDi (Hardy and Vekemans, 2002).
§Q-STRUCTURE, models including population structure estimated from STRUCTURE (Pritchard et al., 2000) either in a fixed-effects model (posterior probabilities matrix inferred from software STRUCTURE [Q], without kinship matrix) or in a mixed model following Yu et al. (2006) with one of the three matrices described.
PCA, principal component analysis. Models including population structure estimated from a principal component analysis implemented in R (R Development Core Team, 2005) following Price et al. (2006) without a kinship matrix (fixed-effects matrix from principal component analysis [P]) or using one of the three kinship matrices described.
#nMDS, nonmetric multidimensional scaling. Models including population structure estimated from a nonmetric multidimensional scaling analysis implemented in R (R Development Core Team, 2005) following Zhu and Yu (2009) without a kinship matrix (fixed-effects matrix from nonmetric multidimensional scaling [M]) or using one of the three kinship matrices described.



View Full Table | Close Full ViewTable 2.

Number and chromosome locations of single nucleotide polymorphisms (SNPs) showing significant [false discovery rate (FDR); p < 0.05] associations with four malting quality traits measured in three germplasm sets (CAP I, CAP II, and CAP III), each phenotyped in two environments. The significant associations are classified as follows: SNP, number of significant marker-trait association; Reported gene, the SNP is within genes previously reported to be associated with malting and/or brewing quality or within a 10 cM window of such a gene; Reported quantitative trait loci (QTL), the SNP is within a 10 cM window of a previously reported QTL associated with malting and brewing quality. The complete data from which this table is derived is presented in Supplemental Table S2. Summary tables for each germplasm set and environment combination are presented in Supplemental Table S3.

 
ME BG AA DP Total
Chromosome SNP Reported gene Reported QTL SNP Reported gene Reported QTL SNP Reported gene Reported QTL SNP Reported gene Reported QTL SNP Reported gene Reported QTL
1H 3 0 3 1 1 0 1 0 1 2 1 1 7 2 5
2H 1 0 0 3 3 2 0 0 0 0 0 0 4 3 2
3H 7 4 6 1 0 0 0 0 0 0 0 0 8 4 6
4H 1 0 1 1 1 1 0 0 0 1 1 1 3 2 3
5H 4 0 3 6 0 6 1 0 0 0 0 0 11 0 9
6H 0 0 0 1 1 1 0 0 0 1 0 0 2 1 1
7H 5 4 4 4 1 3 2 2 2 2 1 2 13 8 11
Total 21 8 17 17 7 13 4 2 3 6 3 4 48 20 37
ME, malt extract.
BG, wort β glucan.
§AA, α-amylase.
DP, diastatic power.



View Full Table | Close Full ViewTable 3

Evolution of allelic frequencies from CAP I to CAP III of markers with a significant marker-trait association in the CAP I array of barley germplasm; frequency of α-amylase alleles in CAP I and CAP III population with their standard error are provided, as well as the difference in frequency between them (Delta), p value for the test of delta not different from zero, the effect of the change and whether a marker close to that position was significant in CAP III or not.

 
Chromosome Position Marker Trait CAP I SE CAP III SE Delta p value Effect Other markers
1H 101.4 12_20187 ME 0.429 0.055 0.123 0.044 0.305 0.0001 +
1H 131.9 11_10782 ME 0.691 0.051 0.951 0.029 −0.26 0.0003 +
2H 125.5 11_10446 ME 0.547 0.056 0.474 0.069 0.073 0.0577 NS
3H 131.6 11_10842 ME 0.2 0.045 0.372 0.065 −0.172 0.0048 + 131.6 (11_10842)
4H 1.6 11_20145 ME 0.357 0.054 0.367 0.064 −0.01 0.2831 NS
5H 26.3 12_30167 ME 0.158 0.041 0.075 0.035 0.083 0.0414
5H 151.4 12_30062 ME 0.14 0.038 0 0 0.14 0.0096 161.6 (12_30642)
7H 133.8 11_10861 ME 0.593 0.056 0.481 0.068 0.112 0.0227 136.6 (11_10182)
2H 150.7 11_10791 BG 0.842 0.041 0.825 0.05 0.017 0.2233 NS
5H 102.1 11_20850 BG 0.298 0.051 0.16 0.049 0.138 0.0104 + 113.1 (12_30056)
6H 75.2 11_20889 BG 0.556 0.056 0.641 0.065 −0.085 0.0421
ME, malt extract; BG, wort β glucan.
Effect: whether the change was in the direction of increasing malt quality (+), decreasing it (–), or nonsignificant (NS).
§Other markers: position and marker name if there was a significant marker in CAP III within 10 cM of the one identified in CAP I.