Figure S1. Mutant alleles of EMF2B.
EMF2B genes with 21 exons (dark boxes) and 20 introns (lines) with UTR shown as
white boxes. T-DNA insertions shown as gray triangles and the TILLING point mutation
at the vertical line labeled with the basepair 7475 mutation GT.
Figure S2. RT PCR of emf2b-1.
RT PCR was performed on leaf tissue from plants homozygous and heterozygous for the
emf2b-1 mutations and wild type Dongjin. EMF2B gene expression is not detectable in
the emf2b-1 homozyogous mutants suggesting this is a null allele. Top lanes Lanes 1-5:
Homozygous emf2b-1; Lanes 6 and 7 are heterozygous for the emf2b-1 mutation; Lanes 8
and 9 are wild type; lane 10 is no template control and M is Promega 1k ladder.
Figure S3. Enlarged emf2b-1 mutant carpel with multiple fused stigma. In three out of
twenty-four flowers examined a single enlarged carpel was observed with multiple fused
stigma as shown here.
Scale bar = 1 mm
Figure S4. Genes significantly differentially expressed in the emf2b-1 mutant versus wild
type.
The majority of significantly differentially expressed genes are up regulated in the emf2b
mutant compared to wild type. Each dot represents an individual gene. Genes
significantly differently expressed in mutant versus wild type are red while gene that do
not show a statistically significant difference are in black. Y-axis is the log of fold change
where positive values show higher expression in the emf2b mutant and negative values
are more strongly expressed in wild type. The x-axis is the mean of normalized counts
with highest number of counts to the right.
Figure S5. Molecular function Gene Ontology Analysis of genes differentially expressed
in emf2b panicles versus wild type. Darker colors of boxes (more red) correspond to more
significant adjusted p-value. Boxes include GO term, adjusted P-value, GO description,
item number mapping the GO in the query list and the background. Genes differentially
expressed in emf2b compared to wild type are enriched for the DNA binding and
transcription factor activity molecular functions.
Figure S6. Quantitative Real Time PCR validation of RNAseq for OsMADS1,
OsMADS6, and OsMADS34 expression. Both OsMADS1 and OsMADS6 show a drastic
reduction in expression in emf2b relative to wild type (log fold change 1). OsMADS6
could not be detected in the second emf2b sample. While OsMADS34 expression
appeared slightly up-regulated in emf2b compared to wild type this was not significant in
the qRT-PCR. This is most likely due to the less sensitive nature of qRT-PCR compared
to RNAseq. Samples are biological replicates collected from two different plants either
wild type or homozygous for emf2b-1.
Appendix S1. Genes differentially expressed in emf2b mutant
Differentially expressed genes at inflorescence stage 7 in emf2b mutant versus wild type.
Genes were identified as differentially expressed with the DESeq2 package in R at a false
discovery rate of 10%.
Appendix S2. Differentially expressed transcription factors in the emf2b mutant
Gene Ontology Analysis was performed on all differentially expressed genes. All 422
genes identified with a molecular function of transcription factor are listed here.