Additional file 2: of Allelic variants of OsSUB1A cause differential expression of transcription factor genes in response to submergence in rice

Table S1. List of genes represented in Rice TF Primer Platform (Caldana et al., 2007). Complete list of 2508 TF genes, their primer sequences and their corresponding PCR efficiencies. Genes were presented with version 2.0 and version 5.0 RGAP genome annotations. Table S2. Transcription factor genes with and without annotations in version 5.0 and 7.0 of RGAP Pseudomolecule. Table S3. Expression profile of transcription factor genes in IR64 control and stress-treated plants upon submergence. Recorded Ct, R2, Efficiency and ΔCt values for all reactions. The list of used reference genes and their distribution on the plates is also given. Table S4. Expression profile of transcription factor genes in IR64-Sub1 control and stress-treated plants upon submergence. Worksheets record Ct, R2, Efficiency and ΔCt values for all reactions. The list of used reference genes and their distribution on the plates is also given. Table S5. Promoter sequences of SUB1A-1 and SUB1A-2. Table S6. Moderated t-tests results from LIMMA package for identifying differentially expressed genes. P-values were recorded and FDR corrections were also performed. Table S7. Details about the list of differentially expressed genes and their putative functions. (DOCX 29 kb

Additional file 3; Figure S2. of Allelic variants of OsSUB1A cause differential expression of transcription factor genes in response to submergence in rice

Sequence alignment of the SUB1A-1 and SUB1A-2 upstream promoter regions. 2 kb upstream of the start site (promoter regions) were analysed for SUB1A-1 and SUB1A-2 alleles and putative cis-regulatory elements were identified. (XLSX 3.76 kb

Additional file 1: Figure S1. of Allelic variants of OsSUB1A cause differential expression of transcription factor genes in response to submergence in rice

The submergence tolerance locus Sub1 in rice. The Sub1 locus is located on rice chromosome 9 with a variable number of SUB1 genes. In different rice genotypes, SUB1A is either absent or present as different allele. (a). Introgression of the Sub1 locus into the rice variety IR64 (IR64-Sub1) enhanced survival after complete submergence. (b). The photo shows the IRRI demonstration field plot in the Philippines. Phenotyping for submergence tolerance can also be conducted by submerging plants grown in trays (inlay). The SUB1A-1 and SUB1A-2 alleles are both highly expressed in nodes of submerged plants but SUB1A-1 expression is higher in internodes. (c). Schematic illustration based on (Singh et al., 2010). (PPTX 3066 kb