Genome-Wide Association Mapping for Kernel and Malting Quality Traits Using Historical European Barley Records

<div><p>Malting quality is an important trait in breeding barley (<i>Hordeum vulgare</i> L.). It requires elaborate, expensive phenotyping, which involves micro-malting experiments. Although there is abundant historical information available for different cultivars in different years and trials, that historical information is not often used in genetic analyses. This study aimed to exploit historical records to assist in identifying genomic regions that affect malting and kernel quality traits in barley. This genome-wide association study utilized information on grain yield and 18 quality traits accumulated over 25 years on 174 European spring and winter barley cultivars combined with diversity array technology markers. Marker-trait associations were tested with a mixed linear model. This model took into account the genetic relatedness between cultivars based on principal components scores obtained from marker information. We detected 140 marker-trait associations. Some of these associations confirmed previously known quantitative trait loci for malting quality (on chromosomes 1H, 2H, and 5H). Other associations were reported for the first time in this study. The genetic correlations between traits are discussed in relation to the chromosomal regions associated with the different traits. This approach is expected to be particularly useful when designing strategies for multiple trait improvements.</p></div

Manhattan plot for GWAS of grain yield (GY), considering eigenvalues (PCA scores) as fixed effects. The significance threshold is -log₁₀(P) >3.65.

<p>Manhattan plot for GWAS of grain yield (GY), considering eigenvalues (PCA scores) as fixed effects. The significance threshold is -log₁₀(P) >3.65.</p

Barley consensus map with DArT markers significantly associated with kernel and malting quality traits.

<p>Only markers with the highest effect on a given chromosomal position are depicted. All MTAs that reflect kernel and malting quality parameters are defined either with a strict significance threshold = -log₁₀(P)>3.65 (dark red) or a liberal significance threshold = -log₁₀(P) <3.35 (light red). DArT = Diversity Array Technology, MTA = marker-trait association, GY = grain yield, TGW = thousand grain weight, HLW = hectoliter weight, KF = kernel formation, GF = glume fineness, SF = sieve fraction, K_RP = raw kernel protein content, M_RP = raw malt protein content, solN = soluble nitrogen, solP = soluble protein, Visc = viscosity, Col = color, Fria = friability, VZ45 = saccharification number VZ45°C, Extr = malt extract, FiAt = final attenuation, MQI = malting quality index.</p

Scatter plot of the first two principal components show the distribution among the cultivars.

<p>Cultivars are classified by type: 2-row spring (blue), 2-row winter (red), and 6-row winter (green). The variance explained by each principal component is given in the axis heading.</p

Genome-wide marker-trait associations (MTAs) detected at a significance threshold of –log₁₀(P) >3.35 with the PCA scores fixed model are compared with known reference quantitative trait loci (QTLs) in the same chromosomal regions.

<p>Abbreviations: Chr = chromosome; Chr-Pos = position of MTA on the chromosome; DArT: diversity array technology; Ref QTL = reference QTL; GY = grain yield, TGW = thousand grain weight, HLW = hectoliter weight, KF = kernel formation, GF = glume fineness, SF = sieve fraction, K_RP = raw kernel protein content, M_RP = raw malt protein content, solN = soluble nitrogen, solP = soluble protein, Visc = viscosity, Col = color, Fria = friability, VZ45 = saccharification number VZ45°C, Extr = malt extract, FiAt = final attenuation, MQI = malting quality index.</p><p>Genome-wide marker-trait associations (MTAs) detected at a significance threshold of –log₁₀(P) >3.35 with the PCA scores fixed model are compared with known reference quantitative trait loci (QTLs) in the same chromosomal regions.</p

Intrachromosomal Linkage disequilibrium (LD)-decay between all pairs of DArT markers for chromosome 1H. LD between markers (<i>r</i>²) is a function of marker distances (cM).

<p>Intrachromosomal Linkage disequilibrium (LD)-decay between all pairs of DArT markers for chromosome 1H. LD between markers (<i>r</i>²) is a function of marker distances (cM).</p

Summary statistics of the 839 DArT markers used in this study.

<p>Summary statistics of the 839 DArT markers used in this study.</p

Correlation matrix of yield, kernel quality, and malting quality parameters based on BLUES for each cultivar.

<p>The Pearson coefficients of the two sided test are given only for the significant phenotypic trait correlations. BLUES = best linear unbiased estimators, GY = grain yield, MY = marketable yield, TGW = thousand grain weight, HLW = hectoliter weight, KF = kernel formation, GF = glume fineness, SF = sieve fraction, K_RP = raw kernel protein content, M_RP = raw malt protein content, solN = soluble nitrogen, solP = soluble protein, Visc = viscosity, Col = color, Fria = friability, VZ45 = saccharification number VZ45°C, Extr = malt extract, FiAt = final attenuation, MQI = malting quality index.</p