Results of linkage disequilibrium analysis.

Results of linkage disequilibrium analysis.</p

Summary report for Pod index in wild cacao and Summary report for Pod index in cultivated cacao.

http://dx.doi.org/10.13140/RG.2.2.24148.88966. (TIF)</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

Physical map of <i>T</i>. <i>cacao</i> L. showing annotated candidate genes, which were co-localised with SNP markers associated with yield-related and other traits.

Gene loci and proteins are shown on the right and genetic distances (Mb) are shown on the left. No candidate genes were identified on chromosomes 2 and 10.</p

Plot of log of K versus number of clusters based on STRUCTURE analysis.

Analysis of population structure of 421 cacao accessions using STRUCTURE—estimated 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

Plots modelling the decay in pairwise linkage disequilibrium coefficients (<i>r</i>²) 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

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 “11” 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 × 10−5 (–log10 (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 “11” 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 × 10−5 (–log10 (P) = 4.088) and the blue line corresponds to a significance level of 0.005. Fig 6 Quantile–quantile plots of estimated−log10 (P) from genome-wide association studies using TASSEL MLM. Quantile–quantile plots of estimated−log10 (P) for filament anthocyanin intensity; Quantile–quantile plots of estimated−log10 (P) for fruit surface (ridges) anthocyanin intensity; Quantile–quantile plots of estimated−log10 (P) for log fruit length; Quantile–quantile plots of estimated−log10 (P) for log seed length; Quantile–quantile plots of estimated−log10 (P) for log seed number; Quantile–quantile plots of estimated−log10 (P) for seed length to width ratio; Quantile–quantile plots of estimated−log10 (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

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