Single Marker and Haplotype-Based Association Analysis of Semolina and Pasta Colour in Elite Durum Wheat Breeding Lines Using a High-Density Consensus Map

<div><p>Association mapping is usually performed by testing the correlation between a single marker and phenotypes. However, because patterns of variation within genomes are inherited as blocks, clustering markers into haplotypes for genome-wide scans could be a worthwhile approach to improve statistical power to detect associations. The availability of high-density molecular data allows the possibility to assess the potential of both approaches to identify marker-trait associations in durum wheat. In the present study, we used single marker- and haplotype-based approaches to identify loci associated with semolina and pasta colour in durum wheat, the main objective being to evaluate the potential benefits of haplotype-based analysis for identifying quantitative trait loci. One hundred sixty-nine durum lines were genotyped using the Illumina 90K Infinium iSelect assay, and 12,234 polymorphic single nucleotide polymorphism (SNP) markers were generated and used to assess the population structure and the linkage disequilibrium (LD) patterns. A total of 8,581 SNPs previously localized to a high-density consensus map were clustered into 406 haplotype blocks based on the average LD distance of 5.3 cM. Combining multiple SNPs into haplotype blocks increased the average polymorphism information content (PIC) from 0.27 per SNP to 0.50 per haplotype. The haplotype-based analysis identified 12 loci associated with grain pigment colour traits, including the five loci identified by the single marker-based analysis. Furthermore, the haplotype-based analysis resulted in an increase of the phenotypic variance explained (50.4% on average) and the allelic effect (33.7% on average) when compared to single marker analysis. The presence of multiple allelic combinations within each haplotype locus offers potential for screening the most favorable haplotype series and may facilitate marker-assisted selection of grain pigment colour in durum wheat. These results suggest a benefit of haplotype-based analysis over single marker analysis to detect loci associated with colour traits in durum wheat.</p></div

Boxplot of polymorphism information content (PIC) for individual SNP and haplotype.

<p>The average PIC was 0.27 for individual SNP and 0.5 for haplotypes.</p

Linkage disequilibrium (LD) scatterplot based on all pairwise comparisons between adjacent loci in the breeding panel.

<p>The green horizontal line shows the critical r² while the red curve displays the LD decay.</p

Correlation coefficients among colour traits for 169 durum lines.

<p>Correlation coefficients among colour traits for 169 durum lines.</p

Individual SNP and haplotype loci significantly associated with colour traits.

<p>Individual SNP and haplotype loci significantly associated with colour traits.</p

Population structure of the breeding panel as revealed by discriminant analysis of principal components.

<p>Each color represents a sub-population. The first 56 axes explained 80% of the total variance.</p

Average values (minimum, maximum) of color traits for the whole population (WP) and least squares means by sub-populations (SP).

<p>Average values (minimum, maximum) of color traits for the whole population (WP) and least squares means by sub-populations (SP).</p

High density mapping and haplotype analysis of the major stem-solidness locus <i>SSt1</i> in durum and common wheat

<div><p>Breeding for solid-stemmed durum <i>(Triticum turgidum</i> L. var <i>durum</i>) and common wheat (<i>Triticum aestivum</i> L.) cultivars is one strategy to minimize yield losses caused by the wheat stem sawfly (<i>Cephus cinctus</i> Norton). Major stem-solidness QTL have been localized to the long arm of chromosome 3B in both wheat species, but it is unclear if these QTL span a common genetic interval. In this study, we have improved the resolution of the QTL on chromosome 3B in a durum (Kofa/W9262-260D3) and common wheat (Lillian/Vesper) mapping population. Coincident QTL (LOD = 94–127, <i>R</i>^<i>2</i> = 78–92%) were localized near the telomere of chromosome 3BL in both mapping populations, which we designate <i>SSt1</i>. We further examined the <i>SSt1</i> interval by using available consensus maps for durum and common wheat and compared genetic to physical intervals by anchoring markers to the current version of the wild emmer wheat (WEW) reference sequence. These results suggest that the <i>SSt1</i> interval spans a physical distance of 1.6 Mb in WEW (positions 833.4–835.0 Mb). In addition, minor QTL were identified on chromosomes 2A, 2D, 4A, and 5A that were found to synergistically enhance expression of <i>SSt1</i> to increase stem-solidness. These results suggest that developing new wheat cultivars with improved stem-solidness is possible by combining <i>SSt1</i> with favorable alleles at minor loci within both wheat species.</p></div

Synergistic two-way interactions between <i>SSt1</i> and minor QTL identified in the Kofa/W9262-260D3 (durum) and Lillian/Vesper (common wheat) mapping populations.

<p>Synergistic two-way interactions between <i>SSt1</i> and minor QTL identified in the Kofa/W9262-260D3 (durum) and Lillian/Vesper (common wheat) mapping populations.</p

Haplotypes of 103 durum cultivars within the Kofa/W9262-260D3 <i>SSt1</i> QTL interval.

<p>Stem-solidness LS means for each line are shown in the bar chart along the top X-axis. The matrix consists of 90K genotypic data where cells shaded in blue denote expression of the W9262-260D3 (solid-stem) allele, whereas cells shaded in red denote expression of the Kofa (hollow-stem) allele. The name and position of each 90K probe, the anchored physical position on WEW chromosome 3B, and the corresponding position on the common wheat consensus map are shown. Two dimensional (row and column) hierarchical cluster analysis was performed to group lines into haplotypes as indicated by the colorized dendogram along the top X-axis, whereas similarly marker order is shown along the left Y-axis. *Lines showing identical haplotypes (n = 45) were collapsed into a single haplotype (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0175285#pone.0175285.s002" target="_blank">S2A Table</a>).</p