Supplemental Data

Files in this Data Supplement:

• Supplemental Table 1 - Supplemental Table 1. Hybridization intensities and expression ratios of flavanone 3-hydroxylase cDNAs detected in microarray experiment comparing flower bud RNAs of isogenic lines of the Wp locus in soybean.
• Supplemental Figure 4 - Supplemental Figure 4. The scatter plot of the log values of the microarray Replicate 2 intensities listed in Supplemental Table 3. The scatter plot of the log values of hybridization intensities from a cDNA microarray replicate of the one described and which results are shown in (A) but with the dyes swapped. The Cy5 probe were RNAs from seed coats of the wpwp mutant line while the Cy3 probe were RNAs from seed coats of the WpWp isogenic line. The two outermost diagonal lines indicate expression either 2.8 higher or 0.3 lower than equivalent levels. The sixteen points enclosed in the oval line represent repeats of the two flavanone 3-hydroxylase cDNAs on the array that are over-expressed in the WpWp purple flower line (Gm-c1019-683 and Gm-c1012-2646).
• Supplemental Figure 5 - Supplemental Figure 5. Likely base paring and folding of the Tgm-Express inverted repeats flanked by the target site duplication (TGA). The differing bases in the repeats form the loops of the two hairpins. Except for this structure, the rest of the insertion in the wpmutant gene, does not have any similarity to other previously characterized soybean Tgm elements.
• Supplemental Figure 6 - Supplemental Figure 6. Variant flavanone 3-hydroxylase cDNAs from LN89-5320-8-53 (wpm) and LN89-5322-2 (wp) mutant isolines. (A) Ethidium bromide-stained gels showing the expected ~1.4-kb cDNA amplified via RT-PCR with RNA from the LN89-5320-6 (Wp) line. In contrast a 2.3 kb or larger cDNAs were amplified from RNAs of the mutant isolines (wpm and wp). The (+) and (–) at top indicate reactions with and without Superscript RTII. The primers used for the PCR amplification of reverse transcribed cDNAs were the 7F and 1428R and the tissue source of the RNAs was the seed coats. (B) Same as (A) except for the conditions of the PCR reactions which were those that favored amplification of longer DNA fragments. The broad bands obtained from mutant lines RNA samples in (A) were resolved into a group of discreet bands around that same size, 2.3 kb and larger.
• Supplemental Table 2 - Supplemental Table 2. Hybridization intensities and expression ratios of flavanone 3-hydroxylase cDNAs detected in a second microarray experiment comparing younger flower bud RNAs of isogenic lines of the Wp locus in soybean.
• Supplemental Table 3 - Supplemental Table 3. Hybridization intensities and expression ratios of flavanone 3-hydroxylase cDNAs detected in microarray experiment comparing seed coat RNAs of isogenic lines of the Wp locus in soybean.
• Supplemental Table 4 - Supplemental Table 4. Comparison of Glycine max F3H amino acid sequence to other known F3H sequences.
• Supplemental Table 5 - Supplemental Table 5. F3H1 and F3H2 genomic sequences alignment.
• Supplemental Table 6 - Supplemental Table 6. Mutant allele wp (top sequence) and Wp F3H1 (bottom sequence) genomic sequences alignment. The two sequences differ only by a large 5.7 kb insertion.
• Supplemental Figure 1 - Supplemental Figure 1. The scatter plot of the log values of the microarray Replicate 1 intensities listed in Supplemental Table 1. The scatter plot of the log values of hybridization intensities from a cDNA microarray slide probed with Cy5 labeled RNA from purple flower buds with the WpWp genotype and Cy3 labeled RNA from pink flower buds of the isogenic wpwp mutant line. The two outermost diagonal lines indicate expression either 2.8 higher or 0.3 lower than equivalent levels. Fifteen of the points enclosed in the oval line represent repeats of two flavanone 3-hydroxylase cDNAs on the array that are over-expressed in the WpWp purple flower line (Gm-c1019-683 and Gm-c1012-2646).
• Supplemental Figure 2 - Supplemental Figure 2. Graphic visualization of the microarray hybridization intensities listed in Supplemental Table 1. A bar graph representing intensity values for the two F3H cDNAs (Gm-c1019-683 and Gm-c1012-2646) hybridizing differentially to RNAs from the two isolines (WpWp and wpwp) in the two microarray experiments with the dyes Cy5 and Cy3 swapped. Solid black and gray bars represent intensities for each one of two cDNAs in the first microarray hybridization experiment and the checkered black and gray bars are intensity values for those two cDNAs in the experiment with the dyes swapped. In both experiments the cDNAs hybridized more strongly to RNAs from the WpWp isoline. Standard deviation of the eight intensity values represented in each bar is indicated by a vertical line at top of each bar.
• Supplemental Figure 3 - Supplemental Figure 3. The scatter plot of the log values of the microarray Replicate 1 intensities listed in Supplemental Table 3. The scatter plot of the log values of hybridization intensities from a cDNA microarray slide probed with Cy5 labeled RNA from seed coats (10-25 mg seeds) with the WpWp genotype and Cy3 labeled RNA from seed coats (10-25 mg seeds) of the isogenic wpwp mutant line. The two outermost diagonal lines indicate expression either 2.8 higher or 0.3 lower than equivalent levels. The fifteen points enclosed in the oval line represent repeats of two flavanone 3-hydroxylase cDNAs on the array that are over-expressed in the WpWp purple flower line (Gm-c1019-683 and Gm-c1012-2646).