Supplemental Material for Best et al., 2021
Figure S1 shows a gel image of ali1-1 genotyping marker. Figure S2 and S3 shows allele frequency plots of all ten chromosomes for replicate one and two, respectively, of wild-type pools of F2 plants of ali1-1/ali1-1 crossed with Mo17. Figure S4 and S5 shows allele frequency plots of all ten chromosomes for replicate one and two, respectively, of ali1-1/ali1-1 pools of F2 plants of ali1-1/ali1-1 crossed with Mo17. Figure S6 shows the mapping results of ali1 for chromosome 10 of the two respective samples combined together. Figure S7 shows the ali1 gene structure and phylogenetic analysis across 32 plant taxa. Figure S8 shows the ali1 gene structure from the RNA sequencing results. Figure S9 shows a multiple sequence alignment of ALI1 protein sequences from different taxa.
Table S1 has the primers used in this study. Table S2 shows sequencing information and statistics. Table S3 has the segregation ratios for ali1-1 and Rp1-D21 to show linkage disequilibrium between loci. BLASTn results of ali1 sequence against the NCBI EST dataset is provided in Table S4. Table S5 contains stomatal indices and densities for ali1-1 as compared to wild-type siblings when grown in the greenhouse. Table S6 shows stomatal indices and densities for ali1-1as compared to wild-type siblings when grown in the field. Table S7 shows transcriptomic results for NPC genes in ali1-1compared to wild-type siblings for the tassel node just before emergence from the lead whorl. Table S8 shows transcriptomic data from tassel tissue for known interactors of the AAAS protein from Homo sapiens. Table S9 shows transcriptomic results for NPC genes in ali1-1 compared to wild-type siblings from SAM and surrounding tissue of 15 DAP plants. Table S10 shows transcriptomic data from seedling tissue for known interactors of AAAS protein from Homo sapiens.
File S1 has coding sequence single nucleotide polymorphisms (SNP) between maize inbred B73 and maize inbred Mo17. Column 1 is chromosome number and columns 2 and 3 are SNP positions. File S2 and S3 are DESeq2 results of mRNA differential expression of ali1-1 tassels before emergence from leaf whorl and 15 DAP SAM and surrounding tissue, respectively, as compared to wild type. Column 1 is maize identification number, column 2 is the baseMean for all samples, column 3 is the log2 fold change (negative indicates lower expression in ali1-1 mutant and positive indicates higher expression in ali1-1 mutant as compared to wild type), column 4 is log2 fold change SE, column 5 is Wald statistic, column 6 is Wald test P-value, and column 7 is Benjamini-Hochberg multiple testing adjusted P-value. File S4 and S5 are filtered lists of single nucleotide polymorphisms (SNP) in replicate one and two of ali1-1 RNA-sequencing mutant pools. Files S6 and S7 are filtered lists of single nucleotide polymorphisms (SNP) in replicate one and two of wild-type sibling RNA-sequencing pools. File S8 shows a filtered list of single nucleotide polymorphisms (SNP) in 9 individual ali1-1; BC1 F2 plants of DNA-sequencing. For Files S4-S8, column 1 is chromosome number, column 2 is SNP position, column 3 is reference nucleotide, column 4 is non-reference nucleotide, column 5 is forward strand reference read count, column 6 is reverse strand reference read count, column 7 is forward strand non-reference read count, column 8 is reverse strand non-reference read count, column 9 is snpEff annotation of the SNP, column 10 is highest Arabidopsis BLASTP hit, column 11 is e-value score for BLAST, and column 12 is Arabidopsis annotation. File S9 and S10 are selected gene lists of DESeq2 results of mRNA differential expression of ali1-1 tassels before emergence from leaf whorl and 15 DAP SAM and surrounding tissue, respectively, as compared to wild type.
