Additional file 1 of Genomic introgressions from African rice (Oryza glaberrima) in Asian rice (O. sativa) lead to the identification of key QTLs for panicle architecture

Additional file 1: Table S1. CSSL information showing Og_MG12 introgression(s) for each line and their localization(s) (chromosome and left-right SSR markers). Target fragments were those selected so as to constitute the whole Og_MG12 genome with the 60 CSSLs. Table S2. Quantification of panicle traits in the CSSLs and parents Os_Caiapó and O.g_MG12. Abbreviations: RL, Rachis Length; PBN, Primary Branch Number; PBL, Primary Branch Length; SBN, Secondary Branch Number; SpN, Spikelet Number; SBN/PBN, ratio of SBN and PBN. Table S3. Variance analysis done on panicle traits for the 60 CSSLs and their parents phenotyped the year 1. Table S4. Significant line*trait associations observed in the population studied based on a Dunnett's test. Table S5. QTL and GWAS sites colocalized with the QTLs detected in this study. Table S6. Metrics of genome quality obtained for Os_Caiapó and Og_MG12 genome ONT sequencing assemblies. Table S7. Summary of the positions (in bp) of structural variations observed in the QTLs detected. Table S8. Genes described in the FunRiceGenes database located within each QTL detected in this study. Table S9. Gene synteny and description of loci annotated between the RM10 and RM420 markers in Os_Caiapó (RAP_db and MSU annotations) and Og_MG12 (RAP_db, MSU and OglaRS2). Genes highlighted in yellow are absent in the q_7 region of Og_MG12, genes highlighted in green are annotated in the Og_MG12 q_7 region but are absent in the Os_Caiapó genome, genes highlighted in light green are duplicated in the Og_MG12 q_7 region and genes highlighted in pink are annotated in the Og_MG12 q_7 region, are absent in the Os_ Caiapó q_7 region but are present in other chromosomes in the Os_Caiapó genome. Table S10. Amino acid modifications in proteins encoded by candidate genes in q_7. Table S11. TFBS variations in the promoters of candidate genes present in q_7. Abbreviations: EIN3, ETHYLENE-INSENSITIVE-LIKE3; C2H2, C2H2-Type Zinc finger; AP2, AP2-ERF; bHLH, basic helix-loop-helix; TCP, TEOSINTE-BRANCHED1; SBN, SQUAMOSA BINDING PROTEIN; NY-YB, nuclear factor Y; HB, HOMEODOMAIN; MADS, MADS-BOX; bZIP, basic leucine zipper; TBP, TATA-box-binding.