Genetic and physical map comparison for chromosome 5.

<p>Scatter plots of marker positions on the genetic map against the positions of the genome reference of both (A) ‘9930’ and (B) ‘Gy14’. These maps were drawn to their relative axis in a dot plot (C) of the two genomes for comparison.</p

Summary of marker properties on the array and in the 'good training set' subset.

<p>Summary of marker properties on the array and in the 'good training set' subset.</p

Application of cucumber genotyping array to four cucumber accessions.

<p>Genomic DNA of four cucumber accessions—H19, TL, G421, and WI 2757—was hybridized on the cucumber array. The genotype calls of the array were plotted as heatmap per chromosome where A is the ‘9930’ allele and B is the ‘Gy14’ allele. The mixed color blocks illustrate the polymorphic property of the SNPs on the array.</p

Illustration of genotype call refinement.

<p>Genotype call refinement was performed to improve the genotype call for stretches or blocks. Inconsistencies within a block were corrected to either the genotype block (AA—red; BB—green; AB—blue) or to no call (light gray). (A) An example of specific locus refinement by flanking loci according to the following criteria. First, six or more flanking loci from both sides of the locus were called other than the locus call, but consecutively. This locus was modified to the call of the flanking loci. Otherwise, if the flanking loci did not contain uniformly consecutive calls, the locus call was set to ‘no call’. (B) If a region was stretched out over 12 or more different consecutive calls, the whole region was set to ‘no call’. (C) A heatmap plot of the genotype calls, before and after refinement. To illuminate the improvement, a zoom into a subset of SNPs and RILs of 20 x 20 (left bottom corner) was plotted.</p

Example of three types of training sets.

<p>Hybridization signals of ‘GY14’ (green X), ‘9930’ (red circles), and their F₁ (blue triangles) were plotted as scatter plots of allele X signals against allele Y signals. (A) Three distinct clusters were generated. This was considered a probe set for a SNP with a good training set. (B) Three distinct clusters were generated, one of which was clustered incorrectly. This was also considered a good training set. (C) No distinct cluster was generated. These SNP probe sets were not included in the genotype call analysis.</p

Regional recombination rate.

<p>For each chromosome, a sliding window was run over 5 SNP markers on the genetic map. Within that window, the slope of the genetic distance (cM) vs. physical genomic distance (Mb) was calculated and plotted on a log scale. Markers whose order on the genetic map was inconsistent with their order on the genome were removed. The recombination rate was calculated for the 'Gy14' genome.</p

L'Écho : grand quotidien d'information du Centre Ouest

28 avril 19391939/04/28 (A68).Appartient à l’ensemble documentaire : PoitouCh

Additional file 5: Table S4. of A bulk segregant transcriptome analysis reveals metabolic and cellular processes associated with Orange allelic variation and fruit β-carotene accumulation in melon fruit

List of 79, 805, 37 and 122 genes that were differentially expressed at 10, 20, 30 DAA, and the mature stage, respectively. (XLSX 162 kb

Additional file 6: Table S5. of A bulk segregant transcriptome analysis reveals metabolic and cellular processes associated with Orange allelic variation and fruit β-carotene accumulation in melon fruit

List of genes exhibited significant up or down regulation in two fruit developmental stages. (XLSX 10 kb