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.

附加文件1：表S1. 不同杂交水稻品种的比较特征。表S2. 用于系统发育重建的基因组数据集信息，包含34个基因组，其中33个来自稻族（Oryzeae），二穗短柄草（Brachypodium distachyon）作为外类群。表S3. 基于日本晴（O. sativa Nipponbare，粳稻）和93-11（O. sativa 93-11，籼稻）的栽培稻祖先节点基因复制类型分布，重点关注串联复制、基因组共线性及其他复制形式。表S4. 对粳稻代表品种日本晴和籼稻代表品种93-11中注释的转座元件（transposable elements, TEs）与复制基因进行卡方检验的结果。TE关联基因定义为位于TE区域上游或下游2kb范围内的基因。表S5. 基于20个基因组，利用OmicShare云平台（https://www.omicshare.com/）对水稻（Oryza sativa）最近共同祖先（most recent common ancestor, MRCA）起源的1383个基因复制事件中的24916个基因进行的基因本体（Gene Ontology, GO）富集分析结果（Q值<0.05）。表S6. 基于20个基因组，利用OmicShare云平台（https://www.omicshare.com/）对水稻最近共同祖先起源的1383个基因复制事件中的24916个基因进行的京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes, KEGG）通路富集分析结果（Q值<0.05）。表S7. 54个推定驯化基因的分化时间估算总结。这些基因在30个核苷酸多样性较低的基因组区域中被鉴定。表中水稻、粳稻、籼稻和aus稻的最近共同祖先对应图1中的物种树节点，时间单位为百万年前（million years ago, Mya）。表S8. 30个核苷酸多样性较低的基因组区域中鉴定的54个推定驯化基因同源基因对的同义替换率（synonymous substitution rate, Ks）值总结。为了估算不同栽培稻祖先的驯化过程起始时间，我们使用了稻属不同亚群的多个代表性基因组，计算这54个同源驯化基因的Ks值，从而提供驯化过程起源的估算。水稻最近共同祖先的驯化起源通过比较普通野生稻（O. rufipogon）w1943和普通野生稻w1654推断；粳稻最近共同祖先的驯化起源通过比较普通野生稻w1943和日本晴（O. sativa Nipponbare）推断；籼稻最近共同祖先的驯化起源通过比较普通野生稻w1654和93-11（O. sativa 93-11）推断；最后，aus稻最近共同祖先的驯化起源通过比较尼瓦拉野生稻（O. nivara）和aus稻N22（O. sativa aus N22）推断。表S9：用于TreeMix分析的、来自欧洲核苷酸档案库（European Nucleotide Archive, ENA）的全基因组测序数据集元数据。表S10. 本研究中5个超级杂交水稻品种及其亲本祖先新测序全基因组数据预处理结果的详细质量评估。表S11. 本研究中5个超级杂交水稻品种及其亲本祖先和普通野生稻新测序全基因组数据中检测到的单核苷酸多态性（single nucleotide polymorphism, SNPs）、插入缺失（insertions and deletions, InDels）和结构变异（structural variations, SVs）的量化。表S12. 本研究新测序全基因组数据中不同水稻品种的基因组变异分类及其分布的量化。表S13. 5个超级杂交水稻、其亲本系及日本晴的遗传力估算总结。该分析基于90113个SNP位点的杂交数据，其中P1和P2分别表示母本和父本，Gamma表示P1对杂交种的遗传贡献比例。表S14. 3个超级杂交水稻品种（LYP9、Y900和XLY900）及其亲本祖先的RNA测序数据信息。表S15. 3个超级杂交水稻品种及其亲本的基因表达谱总结。该表全面概述了从3个超级杂交水稻品种（LYP9、Y900和XLY900）及其亲本（GX24S、PA64s、R900、93-11和Y58S）收集的基因表达数据。数据涵盖不同植物组织（叶片、茎和穗）中的基因表达水平，为杂交品种及其祖先系植物生长发育各阶段的基因表达动态提供见解。表S16. 超级杂交水稻品种及其亲本的差异基因表达聚类。该表描述了利用MFUZZ算法对3个超级杂交水稻品种（LYP9、Y900和XLY900）及其亲本株系进行基因表达聚类的结果，展示了差异表达基因的聚类。每个基因的表达数据与特定组织样本相关联，命名规则包含基因标识符、品种代码和组织类型，用下划线分隔。表S17. 不同组织样本中基因表达模式的总结。'M_'表示父本表达的基因，'F_'表示母本表达的基因，'F1_*'表示杂交后代的基因表达。表达模式编码如下：POD为正超显性，NOD为负超显性，PD为正显性，ND为负显性，PPD为正部分显性，NPD为负部分显性，A为加性表达。这些术语的详细定义请参考本文的方法部分。表S18. 来自中国水稻数据中心数据库（https://www.ricedata.cn/）的产量性状相关基因注释信息总结。表S19. 3个超级杂交水稻品种（LYP9、Y900和XLY900）中鉴定的表达数量性状位点（expression quantitative trait locus, eQTL）基因总结。该表汇编了在3个超级杂交水稻品种中鉴定的eQTL基因，采用的显著性阈值为P值<1e-5（LYP9采用宽松阈值P值<1e-4）。表S20. 具有显著eQTL信号的标记基因的性状本体注释。该表提供了具有强eQTL信号的标记基因的详细性状本体注释，有助于阐明遗传因素对特定性状的影响。每个基因的相关性状信息来源于水稻注释项目（The Rice Annotation Project, RAP，http://rice.uga.edu/）。表S21. 仅在LYP9中表达的eQTL基因的GO富集分析。表S22. 仅在Y900中表达的eQTL基因的GO富集分析。表S23. 仅在XLY900中表达的eQTL基因的GO富集分析。表S24. 3个超级杂交水稻品种（LYP9、Y900和XLY900）中eQTL基因的KEGG通路富集分析。表S25. 与4个超级杂交水稻品种（Y1、Y2、Y900和XLY900）中从头单核苷酸多态性（SNP）位点相关的产量相关基因总结。值得注意的是，这些特定SNP位点未在LYP9品种中检测到。表S26. 具有从头SNP位点和表达谱的性状关联基因的特征描述。该表概述了图8a中所示的与从头SNP位点相关的基因性状，详细列出了基因ID、基因名称、染色体位置、基因起始和终止位点以及性状描述。高表达基因以红色突出显示。此外，该表还包含这些基因在3个超级杂交水稻品种（LYP9、Y900和XLY900）中的表达位置信息。