Genetic mapping of quantitative trait loci for end-use quality and grain minerals in hard red winter wheat

To meet the demands of different wheat-based food products, traits related to end-use quality become indispensable components in wheat improvement. Thus, markers associated with these traits are valuable for the timely evaluation of protein content, kernel physical characteristics, and rheological properties. Hereunder, we report the mapping results of quantitative trait loci (QTLs) linked to end-use quality traits. We used a dense genetic map with 5199 SNPs from a 90K array based on a recombinant inbred line (RIL) population derived from ‘CO960293-2’/‘TAM 111’. The population was evaluated for flour protein concentration, kernel characteristics, dough rheological properties, and grain mineral concentrations. An inclusive composite interval mapping model for individual and across-environment QTL analyses revealed 22 consistent QTLs identified in two or more environments. Chromosomes 1A, 1B, and 1D had clustered QTLs associated with rheological parameters. Glu-D1 loci from CO960293-2 and either low-molecular-weight glutenin subunits or gliadin loci on 1A, 1B, and 1D influenced dough mixing properties substantially, with up to 34.2% of the total phenotypic variation explained (PVE). A total of five QTLs associated with grain Cd, Co, and Mo concentrations were identified on 3B, 5A, and 7B, explaining up to 11.6% of PVE. The results provide important genetic resources towards understanding the genetic bases of end-use quality traits. Information about the novel and consistent QTLs provided solid foundations for further characterization and marker designing to assist selections for end-use quality improvements.Horticulture and Landscape Architectur

Mapping of quantitative trait loci for grain yield and its components in a US popular winter wheat TAM 111 using 90K SNPs.

Stable quantitative trait loci (QTL) are important for deployment in marker assisted selection in wheat (Triticum aestivum L.) and other crops. We reported QTL discovery in wheat using a population of 217 recombinant inbred lines and multiple statistical approach including multi-environment, multi-trait and epistatic interactions analysis. We detected nine consistent QTL linked to different traits on chromosomes 1A, 2A, 2B, 5A, 5B, 6A, 6B and 7A. Grain yield QTL were detected on chromosomes 2B.1 and 5B across three or four models of GenStat, MapQTL, and QTLNetwork while the QTL on chromosomes 5A.1, 6A.2, and 7A.1 were only significant with yield from one or two models. The phenotypic variation explained (PVE) by the QTL on 2B.1 ranged from 3.3-25.1% based on single and multi-environment models in GenStat and was pleiotropic or co-located with maturity (days to heading) and yield related traits (test weight, thousand kernel weight, harvest index). The QTL on 5B at 211 cM had PVE range of 1.8-9.3% and had no significant pleiotropic effects. Other consistent QTL detected in this study were linked to yield related traits and agronomic traits. The QTL on 1A was consistent for the number of spikes m-2 across environments and all the four analysis models with a PVE range of 5.8-8.6%. QTL for kernels spike-1 were found in chromosomes 1A, 2A.1, 2B.1, 6A.2, and 7A.1 with PVE ranged from 5.6-12.8% while QTL for thousand kernel weight were located on chromosomes 1A, 2B.1, 5A.1, 6A.2, 6B.1 and 7A.1 with PVEranged from 2.7-19.5%. Among the consistent QTL, five QTL had significant epistatic interactions (additive × additive) at least for one trait and none revealed significant additive × additive × environment interactions. Comparative analysis revealed that the region within the confidence interval of the QTL on 5B from 211.4-244.2 cM is also linked to genes for aspartate-semialdehyde dehydrogenase, splicing regulatory glutamine/lysine-rich protein 1 isoform X1, and UDP-glucose 6-dehydrogenase 1-like isoform X1. The stable QTL could be important for further validation, high throughput SNP development, and marker-assisted selection (MAS) in wheat

Genomewide scan for multi-trait QTL for grain yield and agronomic traits.

<p>The upper graph is the QTL profile plot with the y-axis representing the log of likelihood, -log (P), for declaring significance of QTL. The red horizontal line represents the threshold corrected for the number of independent tests using Li and Ji [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0189669#pone.0189669.ref038" target="_blank">38</a>]. The lower profile is the genomewide heat map of significant QTL across environments. The <i>y</i>-axis is the traits and the <i>x</i>-axis represents the chromosomes. The light blue to blue color indicates the high value allele originates from CO9602932 and the yellow-red color indicates the high value allele originates from TAM 111.</p

Summary of consistent QTL for yield, yield components and agronomic traits.

<p>Summary of consistent QTL for yield, yield components and agronomic traits.</p

Significant marker-to-trait influences based on a subset of markers in combined analysis of pleiotropy and epitasis.

<p>Significant marker-to-trait influences based on a subset of markers in combined analysis of pleiotropy and epitasis.</p

Interactions and pleiotropic patterns based on markers linked to significant QTL from multi-environment and multi-trait QTL analysis.

<p>(<b>A)</b> Eigentraits (ET) generated through singular value decomposition of phenotypic data. The first three ET explained approximately 90% of the phenotypic variation and were used for combined analysis of pleiotropy and epistasis (CAPE). The legend indicates the direction of variance among traits. For instance, for ET1, kernel spike^-1 (KPS) and thousand kernel weight (TKW) vary in opposite direction compared to grain yield (GY) and spike m^-2 (SPM). (<b>B)</b> Interaction patterns from CAPE with main effects (brown and blue) depicted on the concentric rings and interactions depicted by color-coded arrow lines within the plot. Brown arrow line represents enhancing effect whereas blue arrow line indicates repressing effect.</p

Multitrait QTL detected using data pooled across environments.

<p>Multitrait QTL detected using data pooled across environments.</p