Search

Additional file 1: Table S1. Estimation results for the full sample.

Figure S3. Graphical representation of allelic patterns in the two fucosyltransferase. Substitution type indicates amino acids of WAB56–104-allele to CG14-allele. (a) LOC_Os06g10910 and (b) LOC_Os06g10920. Varietal names are abbreviated as follows: Nipponbare, Ni; WAB56–104, WAB; NERICA 1, NU1; NERICA 2, NU2; NERICA 3, NU3; NERICA 4, NU4; NERICA 5, NU5; NERICA 7, NU7; NERICA 8, NU8; NERICA 9, NU9. CDS posi. and A.A. posi. Represent positions in coding sequences and positions in deduced amino acid sequences, respectively. Alleles of CG14 are colored in gray. (PPTX 205 kb)

Figure S1. k-mer analysis (k-merlength = 17). The X-axis shows k-mer depth, and the Y-axis shows proportion that represents the frequency at that k-mer depth divided by to total frequency of all k-mer depth. (a) WAB56–104, (b) CG14, (c) NERICA 3, (d) NERICA 4, (e) NERICA 5, (f) NERICA 7. Arrow indicates a peak of heterogeneous sequences.Peak between 0 to 8 of k-mer depth would be due to sequencing error or contaminants. (PPTX 109 kb)

Figure S4. Graphical genotype of GBSSI and OsSWEET14 at gene level. Polymorphic position is indicated by vertical line. WAB56â 104 segment is presented by while rectangle, and CG14 allele is presented in gray rectangle. Arrow represent the position of gene. (a) GBSSI, (b) OsSWEET14. Representative polymorphic sites were used. (PPTX 76Â kb)

Figure S1. k-mer analysis (k-merlength = 17). The X-axis shows k-mer depth, and the Y-axis shows proportion that represents the frequency at that k-mer depth divided by to total frequency of all k-mer depth. (a) WAB56–104, (b) CG14, (c) NERICA 3, (d) NERICA 4, (e) NERICA 5, (f) NERICA 7. Arrow indicates a peak of heterogeneous sequences.Peak between 0 to 8 of k-mer depth would be due to sequencing error or contaminants. (PPTX 109 kb)

Figure S2. Phylogeny of genes for fucogalactoxyloglucan biosynthesis. Predicted proteins sequences were aligned by ‘CLUSTAL Ω’ and a phylogenetic dendrogram was constructed by ‘Simple Phylogeny’ using the neighbor-joining method with the option of ‘exclude gaps’. Twelve fucosyltransferase genes in Arabidopsis (AtFUT1 to AtFUT12), four candidate genes for galactosyltransferase in rice, four candidate genes for acetyltransferase genes in rice were analyzed together with the five fucosyltransferase genes with CG14-alleles. The five fucosyltransferase genes of interest were marked with a circle. (PPTX 85 kb)

Figure S2. Phylogeny of genes for fucogalactoxyloglucan biosynthesis. Predicted proteins sequences were aligned by ‘CLUSTAL Ω’ and a phylogenetic dendrogram was constructed by ‘Simple Phylogeny’ using the neighbor-joining method with the option of ‘exclude gaps’. Twelve fucosyltransferase genes in Arabidopsis (AtFUT1 to AtFUT12), four candidate genes for galactosyltransferase in rice, four candidate genes for acetyltransferase genes in rice were analyzed together with the five fucosyltransferase genes with CG14-alleles. The five fucosyltransferase genes of interest were marked with a circle. (PPTX 85 kb)