College of Life Sciences, Henan Agricultural University, 450002, Zhengzhou, China.
State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 510642, Guangzhou, China.
BMC Genomics. 2021 Jul 10;22(1):529. doi: 10.1186/s12864-021-07869-8.
In soybean, some circadian clock genes have been identified as loci for maturity traits. However, the effects of these genes on soybean circadian rhythmicity and their impacts on maturity are unclear.
We used two geographically, phenotypically and genetically distinct cultivars, conventional juvenile Zhonghuang 24 (with functional J/GmELF3a, a homolog of the circadian clock indispensable component EARLY FLOWERING 3) and long juvenile Huaxia 3 (with dysfunctional j/Gmelf3a) to dissect the soybean circadian clock with time-series transcriptomal RNA-Seq analysis of unifoliate leaves on a day scale. The results showed that several known circadian clock components, including RVE1, GI, LUX and TOC1, phase differently in soybean than in Arabidopsis, demonstrating that the soybean circadian clock is obviously different from the canonical model in Arabidopsis. In contrast to the observation that ELF3 dysfunction results in clock arrhythmia in Arabidopsis, the circadian clock is conserved in soybean regardless of the functional status of J/GmELF3a. Soybean exhibits a circadian rhythmicity in both gene expression and alternative splicing. Genes can be grouped into six clusters, C1-C6, with different expression profiles. Many more genes are grouped into the night clusters (C4-C6) than in the day cluster (C2), showing that night is essential for gene expression and regulation. Moreover, soybean chromosomes are activated with a circadian rhythmicity, indicating that high-order chromosome structure might impact circadian rhythmicity. Interestingly, night time points were clustered in one group, while day time points were separated into two groups, morning and afternoon, demonstrating that morning and afternoon are representative of different environments for soybean growth and development. However, no genes were consistently differentially expressed over different time-points, indicating that it is necessary to perform a circadian rhythmicity analysis to more thoroughly dissect the function of a gene. Moreover, the analysis of the circadian rhythmicity of the GmFT family showed that GmELF3a might phase- and amplitude-modulate the GmFT family to regulate the juvenility and maturity traits of soybean.
These results and the resultant RNA-seq data should be helpful in understanding the soybean circadian clock and elucidating the connection between the circadian clock and soybean maturity.
在大豆中，一些生物钟基因已被鉴定为成熟性状的基因座。然而，这些基因对大豆生物钟节律的影响及其对成熟的影响尚不清楚。
我们使用了两个在地理、表型和遗传上都不同的品种，传统的早熟品种中黄 24（具有功能性 J/GmELF3a，它是生物钟必不可少的组成部分 EARLY FLOWERING 3 的同源物）和长生育期品种华夏 3（具有功能缺失的 j/Gmelf3a），通过对单叶进行时间序列转录组 RNA-Seq 分析，在一天的时间尺度上对大豆生物钟进行了剖析。结果表明，几个已知的生物钟成分，包括 RVE1、GI、LUX 和 TOC1，在大豆中的相位与拟南芥不同，表明大豆生物钟明显不同于拟南芥的典型模型。与 ELF3 功能障碍导致拟南芥时钟节律紊乱的观察结果相反，无论 J/GmELF3a 的功能状态如何，大豆生物钟都是保守的。大豆的基因表达和可变剪接都表现出昼夜节律性。基因可以分为六个簇，C1-C6，具有不同的表达谱。与白天簇（C2）相比，更多的基因被分为夜间簇（C4-C6），这表明夜间对基因表达和调控至关重要。此外，大豆染色体具有昼夜节律性激活，表明高级染色体结构可能影响昼夜节律性。有趣的是，夜间时间点聚集在一组中，而日间时间点分为两组，即上午和下午，表明上午和下午代表大豆生长和发育的不同环境。然而，没有基因在不同时间点始终表现出差异表达，这表明有必要进行昼夜节律性分析以更彻底地剖析基因的功能。此外，对 GmFT 家族的昼夜节律性分析表明，GmELF3a 可能通过相位和振幅调节 GmFT 家族来调节大豆的幼年期和成熟期性状。
这些结果和由此产生的 RNA-seq 数据应该有助于理解大豆生物钟，并阐明生物钟与大豆成熟之间的联系。
