Additional file 1 of The origin and evolution of cultivated rice and genomic signatures of heterosis for yield traits in super-hybrid rice

Additional file 1: Table S1. Comparative characteristics of various hybrid rice varieties. Table S2. Information on the genomic datasets employed for phylogeny reconstruction, encompassing 34 genomes including 33 genomes from Oryzeae and Brachypodium distachyon as outgroup. Table S3. Distribution of gene duplication types in ancestral nodes of cultivated rice, focusing on tandem duplication, genomic collinearity, and other duplication forms, based on O. sativa Nipponbare (japonica) and O. sativa 93–11 (indica). Table S4. A chi-square test was conducted comparing transposable elements (TEs) annotated in the japonica representative Nipponbare and the indica representative 93–11 against duplicated genes. TE-associated genes were defined as those located within 2 kb upstream or downstream of TE regions. Table S5. GO enrichment analysis results (Q-value < 0.05) for 24,916 genes from 1,383 gene duplications originating from the MRCA of Oryza sativa in Fig. 1, based on 20 genomes using the OmicShare cloud platform ( https://www.omicshare.com/ ). Table S6. KEGG pathway enrichment analysis results (Q-value < 0.05) for 24,916 genes from 1,383 gene duplications originating from the MRCA of Oryza sativa, based on 20 genomes using the OmicShare cloud platform ( https://www.omicshare.com/ ). Table S7. Summary of divergence time estimation of 54 putative domesticated genes. These genes were identified in 30 regions of genomic low nucleotide diversity. The MRCA of O. sativa, japonica, indica, and aus in the table correspond to nodes of the species tree in Fig. 1, the time unit: million years ago (Mya). Table S8. Summary of Ks (synonymous substitution rate) values for 54 orthologous gene pairs of putatively domesticated genes, identified across 30 genomic regions exhibiting low nucleotide diversity. To approximate the onset of domestication process for various cultivated rice ancestors, we employed multiple representative genomes from different Oryza subgroups. This was done to calculate the Ks values for those 54 orthologous domesticated genes, thereby providing an estimation of the origin of domestication process. The domestication origin of MRCA of O. sativa was inferred from a comparison between O. rufipogon w1943 and O. rufipogon w1654. The domestication origin of MRCA of japonica is inferred from a comparison between O. rufipogon w1943 and O. sativa Nipponbare. The domestication origin of the MRCA of indica was inferred from a comparison between O. rufipogon w1654 and O. sativa 93–11. Lastly, the domestication origin of the MRCA of aus was inferred from a comparison between O. nivara and O. sativa aus N22. Table S9: Metadata of whole-genome sequencing datasets obtained from ENA used in TreeMix analysis. Table S10. Detailed quality assessment of newly sequenced whole-genome data preprocessing results for five super-hybrid rice varieties and their parental progenitors in this study. Table S11. Quantification of SNPs, InDels, and SVs detected in newly sequenced whole-genome data for five super-hybrid rice varieties with their parental progenitors and Oryza rufipogon in this study. Table S12. Quantification on the classification of genomic variants and their distribution in different rice varieties from newly sequenced whole genome sequencing data in this study. Table S13. Summary of heritability estimates for five super rice hybrids, their parental lines, and Nipponbare. This analysis is based on hybrid data derived from 90,113 SNP loci, where P1 and P2 denote the maternal and paternal parents, respectively, and Gamma represents the fraction of genetic contribution from P1 to the hybrid. Table S14. The information of RNA sequencing data for the three super-hybrid rice varieties (LYP9, Y900, and XLY900) with their parental progenitors. Table S15. Summary of gene expression profiles across three super-hybrid rice varieties and their progenitors. This table presents a comprehensive overview of gene expression data collected from three super-hybrid rice varieties: LYP9, Y900, and XLY900. It also includes data from their progenitors: GX24S, PA64 s, R900, 93–11, and Y58S. The data encompasses gene expression levels in different plant tissues, specifically leaves, stems, and panicles, offering insights into the gene expression dynamics across various stages of plant growth and development in both the hybrid varieties and their ancestral lines. Table S16. Differential gene expression clustering in super-hybrid rice varieties and their progenitors. This table delineates the results of gene expression clustering using the MFUZZ algorithm for three super-hybrid rice varieties, namely LYP9, Y900, and XLY900, along with their progenitor strains. Displayed within the table are clusters of differentially expressed genes. Each gene's expression data is associated with a specific tissue sample, using a naming convention that includes the gene identifier, variety code, and tissue type, separated by underscores. Table S17. Summary of the gene expression patterns in various tissue samples.'M_'indicates genes expressed from the paternal side,'F_'designates maternal gene expression, and'F1_*'highlights the gene expression in the hybrid progeny. The patterns of gene expression are coded as follows: POD for positive overdominance, NOD for negative overdominance, PD for positive dominance, ND for negative dominance, PPD for positive partial dominance, NPD for negative partial dominance, and A for additive expression. For comprehensive definitions of these terms, readers are directed to consult the Methods section of the document. Table S18. Summary of annotation information for genes related to yield traits from the China Rice Data Center database ( https://www.ricedata.cn/ ). Table S19. Summary of eQTL genes identified for three super-hybrid rice varieties and their progenitors. This table provides a compilation of eQTL genes that have been identified in three super-hybrid rice varieties, namely LYP9, Y900 and XLY900, employing a significance threshold of P-value < 1e-5, and for LYP9 with a relaxed threshold of P-value < 1e-4. Table S20. Trait ontology annotations for marker genes with significant eQTL signals. This table provides detailed trait ontology annotations for marker genes that exhibit strong eQTL signals, aiding in the elucidation of genetic influences on specific traits. The associated trait information for each gene was sourced from The Rice Annotation Project (RAP, http://rice.uga.edu/ ). Table S21. Gene Ontology (GO) enrichment analysis for eQTL genes specifically expressed in LYP9. Table S22. GO enrichment analysis for eQTL genes specifically expressed in Y900. Table S23. GO enrichment analysis for eQTL genes specifically expressed in XLY900. Table S24. KEGG pathway enrichment analysis of eQTL genes in three super-hybrid rice varieties (LYP9, Y900, and XLY900). Table S25. Summary of yield-related genes linked to de novo SNP loci in four super-hybrid rice varieties. This table compiles a list of yield-related genes that are associated with de novo single nucleotide polymorphism (SNP) loci identified in four super-hybrid rice varieties: Y1, Y2, Y900, and XLY900. Notably, these specific SNP loci have not been detected in the LYP9 variety. Table S26. Characterization of trait-associated genes with de novo SNP loci and expression profiles. This table outlines the traits of genes linked with de novo SNP (single nucleotide polymorphism) loci as indicated in Fig. 8a, detailing the gene IDs, gene names, chromosomal positions, gene start and end points, and trait descriptions. Genes that are highly expressed are highlighted in red. Additionally, the table includes information on where these genes are expressed across three super-hybrid rice varieties LYP9, Y900, and XLY900.