Additional file 6 of Allele and transcriptome mining in Gossypium hirsutum reveals variation in candidate genes at genetic loci affecting cotton fiber quality and textile flammability

Supplementary Material 6: Supplemental Table S1. Newick tree and taxa list for Gossypium hirsutum historic germplasm and select breeding lines from the USDA germplasm that were sequenced for this present manuscript. NWK formatted string text can be further inspected with a Newick tree viewer (eg. https://icytree.org). Supplemental Table S2. Planting years for the MAGIC RILs that were grown for isolation of RNA from 8- and 16-DPA fiber cells. All plants were grown in the same field in New Orleans, LA, USA. Supplemental Table S3. ANOVA statistics that show that the year-to-year effect of RNA expression of the A07-1731 (Gohir.A07G191600) gene is negligible. Supplemental Table S4. ANOVA statistics that show that the year-to-year effect of RNA expression of the D13-1792 (Gohir.D13G17450) gene is negligible. Supplemental Table S5. Variant Call Format (vcf) file annotated by SnpEff software for selected variants observed in the present germplasm. Supplemental Table S6. Fasta sequence of the 277-bp insertion that is annotated as transposable element TE0077021 in the WHU G. hirsutum reference genome and is associated with increased fiber expression of A07-1731 and increased fiber strength. Supplemental Table S7. Thirteen genes that were identified as potentially involved in textile flammability (Table 1, Table S10 in [27]) were BLASTed against the JGIv3.1 cotton reference genome to find homeologs and gene family members that have >90% identity to the prior candidates. The homologs of these 278 genes in three other cotton reference genomes are shown, along with the JGI annotations. Supplemental Table S8. 10,418 genes that are presented in the Supplemental Table S5 vcf file. The annotation columns indicate the potential flammability genes; the standard deviation (>45%) of fiber RNA expression in 550 MAGIC RILs at 8- and 6-DPA; and if the SnpEff software predicts consequential DNA variation in the historic germplasm. Supplemental Table S9. 2,517 genes that show more than 45% standard deviation in the 550 MAGIC RILs developing fiber RNA at 8-days post anthesis (DPA). Annotation columns show gene length; percent sandard deviation (pcSD); the average RPKM expression of the top decile (p90) and lowest decile (p10); SnpEff software prediction (see also Supplemental Table S5); and presence in the FR-300 potential flammability genes. Supplemental Table S10. 2,729 genes that show more than 45% standard deviation in the 550 MAGIC RILs developing fiber RNA at 16-days post anthesis (DPA). Annotation columns show gene length; percent sandard deviation (pcSD); the average RPKM expression of the top decile (p90) and lowest decile (p10); SnpEff software prediction (see also Supplemental Table S5); and presence in the FR-300 potential flammability genes. Supplemental Table S11. PCR-based SNP markers are shown for select, representative haplotypes from the sequenced lines including the parental lines of the MAGIC RILs to identify haplotypes at the qA07-STR-60-99Mb cotton fiber strength locus. Supplemental Table S12. PCR-based SNP markers were run on 43 of the sequenced G. hirsutum lines to identify haplotypes at the qA07-STR-60-99Mb cotton fiber strength locus. Supplemental Table S13. SNAPER-type PCR based SNP assay primers and an SSR-type length polymorphism primers. Supplemental Table S14. The data of select genes plotted in Figures 2, 3, 4 for RNA expression of 8-DPA fiber cells. P10 is the average expression of the bottom decile (10%) of RPKM values, P90 is the average of the top decile, PCSD is the percent standard deviation. Supplemental Table S15. The data of select genes plotted in Figures 2, 3, 4 for RNA expression of 16-DPA fiber cells. P10 is the average expression of the bottom decile (10%) of RPKM values, P90 is the average of the top decile, PCSD is the percent standard deviation. Supplemental Table S16. The BLAST results (-task blastn-short) of the putative transposable element TE0076021 that is in the promoter of A07-1731 (Gohir.A07G191600), in 24 of the 132 sequenced cotton lines, against the gene-space of the JGI reference genome, including coding sequences (CDS) and introns and untranslated regions (UTRs). Supplemental Table S17. The BLAST results (-task blastn-short) of the putative transposable element TE0076021 that is in the promoter of A07-1731 (Gohir.A07G191600), in 24 of the 132 sequenced cotton lines, against the coding sequences (CDS) of the JGI reference genome. Supplemental Table S18. The BLAST results (-task blastn-short) of the putative transposable element TE0076021 that is in the promoter of A07-1731 (Gohir.A07G191600), in 24 of the 132 sequenced cotton lines, against the whole genome of the JGI reference sequence. Supplemental Table S19. The data plotted in Figure 5. RNA expression of 16-DPA fiber cells for the A07-1731 and D13-1792 genes, fiber strength (STR) as measured by HVI, and genotypes of each RIL at both loci. Supplemental Table S20. Additive epistasis ANOVA test of the influence of the A07-D13 genotypes on fiber strength (STR-125). Supplemental Table S21. Select SNPs from Supplemental Table S5-VCF including the putative nuclear export signal (NES) variant at A07:89,996,543 in the A07-1731 strength (STR) gene. Of the 132 lines of historic and breeding germplasm, 24 are homozygous for the alternative (ALT, 1/1:) allele and 30 are heterogenous