31 research outputs found
SAT, a flexible and optimized Web application for SSR marker development-1
<p><b>Copyright information:</b></p><p>Taken from "SAT, a flexible and optimized Web application for SSR marker development"</p><p>http://www.biomedcentral.com/1471-2105/8/465</p><p>BMC Bioinformatics 2007;8():465-465.</p><p>Published online 29 Nov 2007</p><p>PMCID:PMC2216045.</p><p></p>c. restriction digestion, d. SSR detection, e. Clustering, f. Assembly, g. Primer design, h. Virtual PCR. Results of each analysis step are stored in a MySQL database
Results of linkage disequilibrium analysis.
Results of linkage disequilibrium analysis.</p
Plot of log of K versus number of clusters based on STRUCTURE analysis.
Analysis of population structure of 421 cacao accessions using STRUCTUREâestimated LnP(K) of possible clusters (K) from 2 to 15. When K is approaching a true value, L(K) plateaus (or continues increasing slightly).</p
Most significant, yield-related and other marker-trait associations and variation explained.
Most significant, yield-related and other marker-trait associations and variation explained.</p
Correlograms showing Pearson correlations for quantitative traits and Spearman correlations for anthocyanin intensity in various plant organs.
Positive correlations are displayed as blue circles and negative correlations as orange circles. The sizes of the circles are proportional to the correlation coefficients. The plant organs for which anthocyanin intensity was measured were the flower ligule, filament and pedicel, and mature fruit ridges and seed cotyledons).</p
Coefficients of membership for clusters of accessions based on STRUCTURE analysis.
http://dx.doi.org/10.13140/RG.2.2.27504.33282. (DOCX)</p
Summary of significantly positive marker-trait associations (<i>TASSEL</i> MLM and GAPIT FarmCPU).
http://dx.doi.org/10.13140/RG.2.2.34215.21927. (XLSX)</p
Descriptors and sample sizes used for phenotypic characterisation.
Descriptors and sample sizes used for phenotypic characterisation.</p
Manhattan plots from genome-wide association analysis.
Genome-wide association plots across 8 cacao chromosomes for seven phenotypic traits that had statistically significant MTAs: filament anthocyanin intensity, fruit surface (ridges) anthocyanin intensity, log fruit length, log seed length, log seed number, seed length to width ratio, seed number.
Based on TASSEL version 5.2.50 MLM results for 421 cacao accessions (612 SNPs).Chromosome â11â was designated for unmapped SNP markers (some of which have recently been mapped).X- and Y-axes represent the SNP markers along each chromosome and the -log10(P-value), respectively.The red horizontal line corresponds to the Bonferonni significance threshold of P-values †8.17 Ă 10â5 (âlog10 (P) = 4.088) and the blue line corresponds to a significance level of 0.005. Based on TASSEL version 5.2.50 MLM results for 421 cacao accessions (612 SNPs). Chromosome â11â was designated for unmapped SNP markers (some of which have recently been mapped). X- and Y-axes represent the SNP markers along each chromosome and the -log10(P-value), respectively. The red horizontal line corresponds to the Bonferonni significance threshold of P-values †8.17 Ă 10â5 (âlog10 (P) = 4.088) and the blue line corresponds to a significance level of 0.005. Fig 6 Quantileâquantile plots of estimatedâlog10 (P) from genome-wide association studies using TASSEL MLM. Quantileâquantile plots of estimatedâlog10 (P) for filament anthocyanin intensity; Quantileâquantile plots of estimatedâlog10 (P) for fruit surface (ridges) anthocyanin intensity; Quantileâquantile plots of estimatedâlog10 (P) for log fruit length; Quantileâquantile plots of estimatedâlog10 (P) for log seed length; Quantileâquantile plots of estimatedâlog10 (P) for log seed number; Quantileâquantile plots of estimatedâlog10 (P) for seed length to width ratio; Quantileâquantile plots of estimatedâlog10 (P) for seed number. The plots provide no evidence of bias in the GWAS, such as due to genotyping artifacts, and display the extent to which the observed distribution of the test statistic followed the expected (null) distribution. The red line represents expected P-values with no associations.</p
Plots modelling the decay in pairwise linkage disequilibrium coefficients (<i>r</i><sup>2</sup>) as a function of the distance between markers in megabases (Mb).
Plot of pairwise linkage disequilibrium coefficients (r2) on chromosome 1; Plot of pairwise linkage disequilibrium coefficients (r2) on chromosome 4; Plot of pairwise linkage disequilibrium coefficients (r2) on chromosome 5; Plot of pairwise linkage disequilibrium coefficients (r2) on chromosome 7; Plot of pairwise linkage disequilibrium coefficients (r2) on chromosome 9. Heatmap of linkage disequilibrium (r2) across the chromosomes 4 and 5 based on data for 421 cacao accessions genotyped using 612 filtered SNPs. Markers were ordered on the x and y axes in the Heatmap according to location along the chromosomes and each cell of the heatmap represents a single marker pair. The upper triangle, above the black diagonal on the heatmap, is colour-coded based on the r2 value between SNPs while colours depicted in the lower triangle are based on P-values for the corresponding r2 values.</p