Quantitative Trait Loci Associated with the Tocochromanol (Vitamin E) Pathway in Barley

The Genome-Wide Association Studies approach was used to detect Quantitative Trait Loci associated with tocochromanol concentrations using a panel of 1,466 barley accessions. All major tocochromanol types- α-, β-, δ-, γ-tocopherol and tocotrienol- were assayed. We found 13 single nucleotide polymorphisms associated with the concentration of one or more of these tocochromanol forms in barley, seven of which were within 2 cM of sequences homologous to cloned genes associated with tocochromanol production in barley and/or other plants. These associations confirmed a prior report based on bi-parental QTL mapping. This knowledge will aid future efforts to better understand the role of tocochromanols in barley, with specific reference to abiotic stress resistance. It will also be useful in developing barley varieties with higher tocochromanol concentrations, although at current recommended daily consumption amounts, barley would not be an effective sole source of vitamin E. However, it could be an important contributor in the context of whole grains in a balanced diet

Population Genomics Related to Adaptation in Elite Oat Germplasm

Six hundred thirty five oat ( L.) lines and 4561 single-nucleotide polymorphism (SNP) loci were used to evaluate population structure, linkage disequilibrium (LD), and genotype–phenotype association with heading date. The first five principal components (PCs) accounted for 25.3% of genetic variation. Neither the eigenvalues of the first 25 PCs nor the cross-validation errors from = 1 to 20 model-based analyses suggested a structured population. However, the PC and = 2 model-based analyses supported clustering of lines on spring oat vs. southern United States origin, accounting for 16% of genetic variation ( < 0.0001). Single-locus -statistic () in the highest 1% of the distribution suggested linkage groups that may be differentiated between the two population subgroups. Population structure and kinship-corrected LD of = 0.10 was observed at an average pairwise distance of 0.44 cM (0.71 and 2.64 cM within spring and southern oat, respectively). On most linkage groups LD decay was slower within southern lines than within the spring lines. A notable exception was found on linkage group Mrg28, where LD decay was substantially slower in the spring subpopulation. It is speculated that this may be caused by a heterogeneous translocation event on this chromosome. Association with heading date was most consistent across location-years on linkage groups Mrg02, Mrg12, Mrg13, and Mrg24

Quantitative Trait Loci Associated with the Tocochromanol (Vitamin E) Pathway in Barley

<div><p>The Genome-Wide Association Studies approach was used to detect Quantitative Trait Loci associated with tocochromanol concentrations using a panel of 1,466 barley accessions. All major tocochromanol types- α-, β-, δ-, γ-tocopherol and tocotrienol- were assayed. We found 13 single nucleotide polymorphisms associated with the concentration of one or more of these tocochromanol forms in barley, seven of which were within 2 cM of sequences homologous to cloned genes associated with tocochromanol production in barley and/or other plants. These associations confirmed a prior report based on bi-parental QTL mapping. This knowledge will aid future efforts to better understand the role of tocochromanols in barley, with specific reference to abiotic stress resistance. It will also be useful in developing barley varieties with higher tocochromanol concentrations, although at current recommended daily consumption amounts, barley would not be an effective sole source of vitamin E. However, it could be an important contributor in the context of whole grains in a balanced diet.</p></div

Significant SNPs associated with tocochromanols, and annotated sequences known or predicted to be associated with the tocochromanol biosynthesis pathway that occurred within 2 cM of a significant marker.

<p>*Regions, as defined in text, refer to chromosome regions with different QTLs/candidate genes. **Linkage map positions (Muñoz-Amatriaín et al. 2011).</p><p>***Genome sequence positions, (International Barley Genome Sequencing Consortium 2012).</p><p>Significant SNPs associated with tocochromanols, and annotated sequences known or predicted to be associated with the tocochromanol biosynthesis pathway that occurred within 2 cM of a significant marker.</p

Manhattan plots showing results of GWAS for concentrations of γT, γT3, TT3, TTP, and TTC.

<p>In analyses where one or more markers met the significance threshold determined by a false-discovery rate adjustment, a dotted line shows the significance threshold. Points in pink, adjacent to chromosome 7H, represent unmapped markers.</p

Means and standard errors for concentrations (mg/kg) of all tocochromanol forms and Total Tocochromanol (TTC) for accessions from each of the eight breeding programs, separated by year.

<p>Means and standard errors for concentrations (mg/kg) of all tocochromanol forms and Total Tocochromanol (TTC) for accessions from each of the eight breeding programs, separated by year.</p

Distributions of concentrations of all tocochromanol forms and Total Tocochromanol (TTC).

<p>Reliable data for βT3 and γT are not available for 2006. Red represents 2006 and blue represents 2007.</p