Arbetsplatser i Kortedala och Gårdsten : branschstruktur och lokaliseringsmönster i två bostadsområden i Göteborg /

<p><b>Shoot (A-C) and root (D-F) ion content for <i>HKT1;1</i> native overexpression lines.</b> Statistical significance was determined using Tukey’s HSD test between each line within treatments. Bars with the same letters indicate no significant difference (<i>p</i> < 0.05). Error bars represent standard error of the mean where n = 12–18 plants.</p

Linkage disequilibrium between QTL and its highest LD marker for single SNPs and each of the different blocking methods.

<p>Each cell shows the number of times the method in the row produced a marker with marker-QTL LD (i.e., χ²′ or <i>r²</i>) at least 0.1 units higher than the marker-QTL LD produced by the method in the column. Mean and standard deviation of LD are given in the last two columns.</p

Power of detecting single causal SNPs left in the marker dataset or QTL pairs chosen on the basis of the different block methods (rows) for each analysis method (columns).

a<p>Powers not significantly different than highest power within row at 0.01 probability level.</p><p>Numerically greatest values within a row are underlined.</p

Properties of SNPs scored for the Barley Coordinated Agricultural Project with minor allele frequency ≥0.028.

<p>Properties of SNPs scored for the Barley Coordinated Agricultural Project with minor allele frequency ≥0.028.</p

Illustration of tree topology example described in text.

<p>Illustration of tree topology example described in text.</p

Power plotted against false discovery rate for the single SNP analysis and each level of QTL size (<i>p</i>).

<p>Triangles represent <i>p</i> = 0.12, squares represent <i>p</i> = 0.06, and circles represent <i>p</i> = 0.03. For all QTL sizes <i>h²</i> = 0.75.</p

Parsimony tree of alleles present at 4gamete block 325 (chromosome 3, position 126.3).

<p>Values in boxes represent, from top to bottom, SNP scores each allele, best linear unbiased estimate of allelic effect, and number of lines carrying that allele. The edge separating alleles 010 (III) and 011 (I) was associated with heading date in the TreeScan analysis. Alleles VI and V were recombinant alleles not included in the parsimony tree and therefore the dotted edges were not included in the TreeScan analysis.</p

Comparison of single SNPs and haplotype blocks inferred by the three blocking methods.

a<p>SNPs scored using two Barley oligonucleotide pool assays (Close et al. 2009).</p>b<p>Includes unblocked SNPs.</p>c<p>MAF, minor allele frequency.</p>d<p><i>H_e</i>, expected heterozygosity.</p

Power of detecting single QTL removed from marker dataset for different heritability and QTL size levels and empirical false-discovery rates.

a<p>Powers not significantly different than highest power within row at 0.01 probability level.</p><p>Numerically greatest values within a row are underlined.</p

Supplemental Material for Belamkar et al., 2018

File S1 contains supplementary Tables S1-S2 and Figures S1-S7. <div><br></div><div>File S2 has details of the preliminary yield trials (F_3:6) and advanced yield trials (F_3:7) grown in 2012-2015 and 2013-2016. The experimental design, number of locations, number of replicates per location, heritability for yield within and across locations is provided. </div><div><br></div><div>File S3 contains the R script developed for analyzing preliminary yield trials (F_3:6) grown in an augmented design. Mixed models incorporated both experimental design and spatial variation. </div><div><br></div><div>File S4 provides an example phenotypic dataset for utilizing the R script provided in File S3. </div><div><br></div><div>File S5 shows the SNP calling accuracy of 20 lines genotyped by genotyping-by-sequencing at least twice (biological replicates) over the years. The accuracy is presented as sequential pairwise comparisons of 20 unique samples. </div><div><br></div><div>File S6 contains the yield data (best linear unbiased predictors) of the preliminary yield trials (F_3:6) grown in 2012-2015 used for genomic selection. </div><div><br></div><div>File S7 contains the SNP marker data of 26,925 SNPs on the 1,110 F_3:6 lines grown in 2012-2015. The homozygous major, homozygous minor, and heterozygous genotypes are coded as 1, 0, and 0.5 in the genotype matrix. </div><div><br></div><div>File S8 shows the Akaike Information Criterion (AIC) values and the residual plots for each of the mixed models tested for the yield data collected on the preliminary yield trial (F_3:6) grown in McCook, NE in 2014.</div