Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, People's Republic of China.
Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.
Sci Rep. 2020 Nov 17;10(1):19935. doi: 10.1038/s41598-020-76762-3.
The yield heterosis of rice is sought by farmers and strong contributes to food safety, but the quality of hybrid rice may be reduced. Therefore, developing new varieties with both high yield and good quality is a heavily researched topic in hybrid rice breeding. However, the molecular mechanism governing yield heterosis and high rice quality has not been elucidated to date. In this study, a comparative transcriptomics and genomic analysis was performed on a hybrid rice variety, Chuanyou6203 (CY6203), and its parents to investigate the molecular mechanism and gene regulation network governing the formation of yield and quality stages. A total of 66,319 SNPs and InDels between CH3203 and C106B were detected in the 5'-UTR, exon, intronic, and 3'-UTR regions according to the reference genome annotation, which involved 7473 genes. A total of 436, 70, 551, 993, and 1216 common DEGs between CY6203 and both of its parents were identified at the same stage in panicles and flag leaves. 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. Approximately 40.61% of mRNA editing ratios were between 0.4 and 0.6, and 1.68% of mRNA editing events (editing ratio ≥ 0.8) in CY6203 favored one of its parents at three stages or a particular stage, suggesting that the hypothetical heterosis mechanism of CY6203 might involve dominance or epistasis. Also 15,934 DEGs were classified into 19 distinct modules that were classified into three groups by the weighted gene coexpression network analysis. Through transcriptome analysis of panicles and flag leaves in the yield and quality stages, the DEGs in the green-yellow module primarily contributed to the increase in the source of CY6203 due to an in increase in photosynthetic efficiency and nitrogen utilization efficiency, and a small number of DEGs related to the grain number added spikelet number per panicle amplified its sink. The balanced expression of the major high-quality alleles of C106B and CH3203 in CY6203 contributed to the outstanding quality of CY6203. Our transcriptome and genome analyses offer a new data set that may help to elucidate the molecular mechanism governing the yield heterosis and high quality of a hybrid rice variety.
水稻的杂种优势是农民所追求的，这对食品安全有很大的贡献，但杂交水稻的品质可能会降低。因此，培育既高产又优质的新品种是杂交水稻育种的一个重要研究课题。然而，到目前为止，还没有阐明控制产量杂种优势和水稻高质量的分子机制。在这项研究中，对杂交水稻品种川优 6203（CY6203）及其亲本进行了比较转录组学和基因组分析，以研究控制产量和品质形成的分子机制和基因调控网络。根据参考基因组注释，在 5'-UTR、外显子、内含子和 3'-UTR 区域共检测到 CH3203 和 C106B 之间的 66319 个 SNPs 和 InDels，涉及 7473 个基因。在抽穗期和旗叶期，在同一阶段共鉴定出 CY6203 与其两个亲本之间的 436、70、551、993 和 1216 个共同差异表达基因。在抽穗期和旗叶期的孕穗期、开花期和中期灌浆期，CY6203 与 CH3203 之间上调差异表达基因的数量均大于 CY6203 与 C106B 之间上调差异表达基因的数量。大约 40.61%的 mRNA 编辑比率在 0.4 到 0.6 之间，在三个阶段或一个特定阶段，CY6203 中 1.68%的 mRNA 编辑事件（编辑比率≥0.8）有利于其一个亲本，表明 CY6203 的假设杂种优势机制可能涉及显性或上位性。在产量和品质阶段的穗和叶片的转录组分析中，绿色-黄色模块中的差异表达基因主要通过提高光合效率和氮素利用效率来增加 CY6203 的源，而少量与增加每穗小穗数有关的差异表达基因则增加了其库。CY6203 中 C106B 和 CH3203 的主要优质等位基因的平衡表达有助于其优异的品质。我们的转录组和基因组分析提供了一个新的数据集，可能有助于阐明控制杂交水稻品种产量杂种优势和高质量的分子机制。
