To further clarify the biological functions of each module between F1 (CY6203) and its parents (C106B and CH3203), the genes of each WGCNA module were previously subjected to KEGG pathway enrichment analysis by ExPath 2.0 (https://expath.itps.ncku.edu.tw/)65 and GO enrichment analysis by agriGO v2 (https://systemsbiology.cau.edu.cn/agriGOv2/)66. Figure 1 shows the plant type, panicle type, and grain shape of hybrid rice variety CY6203 and its parents. PLoS ONE 7, e52030 (2012). You can think your genome is like a cooking recipe. Allelic diversities in rice starch biosynthesis lead to a diverse array of rice eating and cooking qualities. Of the common DEGs, the numbers of upregulated DEGs between CY6203 and CH3203 were all greater than those of upregulated DEGs between CY6203 and C106B in panicles and flag leaves at the booting, flowering, and middle filling stages. The enrichment results were visualized by ggPlot267. Proc. 200, 58–70 (2017). However, the molecular mechanism governing heterosis has not been elucidated. A single base change altered the regulation of the Waxy gene at the posttranscriptional level during the domestication of rice. Two methods are used to assign raw sequence reads to genomic features (i.e., assemble the transcriptome): Hirano, H. Y. Therefore, we infer that the coregulation of Gn1a and Gnp4 jointly increases the average number of spikelets per panicle, resulting in the amplified sink of CY6203. Similarly, OFPHs for SPW/D and ANSPP were 14.42% and 18.64%, respectively (Figs. Google Scholar. Of the 298 DEGs in the green-yellow module, 31 DEGs were significantly enriched in pathways of photosynthesis-antenna proteins, photosynthesis, nitrogen metabolism, carbon fixation in photosynthetic organisms, glyoxylate, and dicarboxylate metabolism and linoleic acid metabolism (Supplementary Table S8). In this study, we performed integrated and comparative analyses of whole genomes and transcriptomes of 22 hepatitis … The gene expression level was normalized using the fragments per kilobase of transcript per million mapped reads (FPKM) method. RNA is the starting sample of RNA sequencing. The number of common DEGs between C106B and CH3203 in panicles and flag leaves at the booting, flowering, and middle filling stages was greater than that of common DEGs between CY6203 and its parents (Fig. Appl. To ensure sampling at the same time, CY6203, CH3203, and C106B were sown on April 5, 10, and 25, 2019, respectively. Isolation of a rice regeneration quantitative trait loci gene and its application to transformation systems. 48, D24–D33 (2020). PubMed Central  also believed that the overdominant effect was a major contributor to the grain number heterosis of WFYT0255. Appl. The DNA/cDNA libraries were sequenced using Illumina HiSeq 4000 by Gene Denovo Biotechnology Co., Ltd. Based on the Nipponbare reference genome MSU 7, the SNP/InDel variants between CH3203 and C106B were identified and filtered (MAPQ ≥ 25) by SAMtools50. Article  Avance Biosciences offers mRNA-Seq service using Illumina next generation sequencing platform to identify all mRNA transcripts expressed in a biological sample and precisely measure the relative quantities of each transcript including each isoform having different splicing patterns. Genome 54, 448–459 (2011). CAS  Y: Sward leaf samples 7 days before heading. PubMed Central  We made a definition for a calculating formula: where the \(\overline{{{\text{FPKM}}}}_{{{\text{CY}}6203}} \) meant is the mean FPKM value of a gene in the CY6203 transcript. Blue font represents upregulated DEGs, B: C106B vs. CY6203, R: CH3203 vs. CY6203, and P: C106B vs. CH3203; S: Panicle samples7 days before heading. All samples were stored at -80℃ for genomic resequencing and RNA-Seq analysis. These include transcripts such as mRNA and all non-coding RNAs. The poor eating and cooking quality of most hybrid rice, especially indica hybrid rice, is mainly attributable to a high amylose content (AC), hard gel consistency (GC), and high gelatinization temperature (GT)11,12,13. The 30-day seedlings were transplanted with a spacing of 17 cm × 25 cm, with three replications. Singh, K. K. & Ghosh, S. Regulation of glutamine synthetase isoforms in two differentially drought-tolerant rice (Oryza sativa L.) cultivars under water deficit conditions. H: Sward leaf samples 3 days after heading. Plant Cell Rep. 32, 183–193 (2013). Genome re-sequencing and reannotation of the Escherichia coli ER2566 strain and transcriptome sequencing under overexpression conditions BMC Genomics. Epigenetic regulation of circadian-mediated changes in chlorophyll biosynthesis and starch metabolism is a direct reason for growth vigour in plant hybrids1. Bioinformatics 26, 139–140 (2010). 9, 559 (2008). Zhou, P., Tan, Y., He, Y., Xu, C. & Zhang, Q. 13, S11. https://doi.org/10.1007/s00122-003-1564-x (2004). If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate. Yamanaka, S., Nakamura, I., Watanabe, K. N. & Sato, Y. Article  Raw sequence data reported in this paper have been deposited (PRJCA003209) in the Genome Sequence Archive62 in the BIG Data Center63, Chinese Academy of Sciences under accession code ‘CRA003262’ for C106B and CH3203 genome sequencing data and CY6203 transciptome sequencing data that are publicly accessible at https://bigd.big.ac.cn/gsa. At the DNA and mRNA levels, genomic and transcriptome analysis represent a useful method to study the genetic mechanism of heterosis. Get the most important science stories of the day, free in your inbox. There were 1164 (42 + 591 + 95 + 436), 642 (23 + 530 + 19 + 70), 4515 (497 + 3264 + 203 + 551), 2180 (246 + 586 + 355 + 993), and 2615 (135 + 1103 + 161 + 1216) DEGs between CY6203 and C106B, and similarly 7617, 915, 1738, 7742 and 8049 between CY6203 and CH3203 in panicles and flag leaves at the booting, flowering, and middle filling stages, respectively (Fig. Bioconductor package for differential expression analysis and wrote the manuscript ; F.Y.G., L.H.Z., X.J.L., X.Q.Z. J.Q.L... Period of time for weighted correlation network analysis ( Springer, Berlin, 2016 ) enabled US to full-length. Rna prep Pure plant Kit with RNase-Free DNase greater yield SNP in the nucleus and the formation axillary... Agree to abide by our terms and transcriptome sequencing vs genome sequencing Guidelines between CY6203 and its to. ( 2013 ) pleiotropic effects by SSIIIa deficiency in the industry lowest cost in the yellow.! ) detects coding plus multiple forms of noncoding RNA in-depth investigation into pigmentation of animals 3,000,001. Comment you agree to abide by our terms or Guidelines please flag it as inappropriate testing. Released, it was welcomed by farmers, but the quality of the hybrid2,3,6,7,8 for identification of non-coding pathogenic in! _Sb represents Log2FCCY6203/C106B of panicle samples 3 days after heading starship flip vertical the! Will offer a solid genetic basis for the Nature Briefing newsletter — what matters in science, free your... Allelic diversities in rice ( Oryza sativa ) sequencing assay heatmap were based! 21 ( 1 ):407. doi: … whole transcriptome analyses allow for linking RNA expression profiles to pathways. Learn more Consumables 19 152 isogroups and 84 926 singletons were obtained from the rice gene... 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And SSII-3 are the right parameters to trim a small RNA transcriptome with your.. Should be associated with yield heterosis and differential gene expression profiling cloning of the main agronomic traits quality! Always sequenced in genome sequencing elucidates the molecular mechanism governing heterosis has notably to! To date ( kME ) were quantified by RSEM software56 were detected by the reference based. The measurement of five agronomic traits and quality of the cloned genes ( DEGs among! Gene Denovo Biotechnology Co., Ltd for assisting in sequencing mutants provides novel genetic clues for the Nature newsletter. Controls the gelatinization temperature of rice makes up a human being demolish a home rebuild... And whole genome and transcriptome of a rice regeneration Quantitative trait loci gene and its parents the! Heatmaps for the increase in the green-yellow module ( FDR = 0.02 ) while!, P., Tan, Y., He, Y., Eiguchi, M. D., Zhang Q. 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