Additional file 2 of Production Assessment and Genome Comparison Revealed High Yield Potential and Novel Specific Alleles Associated with Fertility and Yield in Neo-Tetraploid Rice

Additional file 2 Table S1a. Field performance of neo-tetraploid rice lines in 2017 late season (2017-LS) and 2018 early season (2018-ES). Table S1b. Average field performance of autotetraploid rice lines in 2017 late season and 2018 early season. Table S1c. Heterosis performance between neo-tetraploid and autotetraploid rice lines. Table S1d. List of the autotetraploid and neo-tetraploid rice materials used in this study. Table S2. Quality evaluation of genome sequencing data. Table S3. Mapping quality of sequencing reads to MSU7 reference genome. Table S4. Number of genomic variations against MSU7 reference genome. Table S5. Variation validation using previously sequenced individuals. Table S6. Validation of variations using Sanger sequencing. Table S7. Non-parental chromosome blocks that shared by 13 neo-tetraploid rice lines. Table S8. GO enrichment analysis of 222 non-parental genes in neo-tetraploid rice. Table S9. Reported QTLs that co-localized with non-parental variations in neo-tetraploid rice. Table S10. Non-parental genes that expressed in reproductive tissues using RiceXPro database. Table S11. Non-parental genes that expressed in reproductive tissues using RNA-Seq data of neo-tetraploid rice Huaduo1. Table S12. Non-parental genes that expressed in reproductive tissues in both RiceXPro and RNA-Seq data. Table S13. Gene annotation and primer sequences for CRISPR/Cas9 vector construction. Table S14. Genotype of CRISPR/Cas9 knockout lines of nine non-parental genes. Table S15. Pollen fertility and main agronomic traits of CRISPR/Cas9 knockout mutants. Table S16. Version, function and parameters of main software that used for genome re-sequencing and RNA-Seq data analysis.