Abstract
BackgroundIn 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.ResultsWe 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.ConclusionsThese 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.
Highlights
In soybean, some circadian clock genes have been identified as loci for maturity traits
Soybean exhibits a different circadian clock from the known canonical Arabidopsis model Transcriptomes of the unifoliate leaves sampled on the third continuous light day after entraining seedlings of both cultivars for seven short days (12 h light and 12 h night) (Fig. 1 A), were sequenced from a minimum of 53,600,114 reads to a maximum of 95,131,850, with an average of 72,751,819 reads (Table S1)
We found that the EARLY FLOWERING 3 (ELF3) homologs J/GmELF3a, GmELF3b, GmELF3c and GmELF4a all showed a robust and very similar circadian clock rhythmicity in both cultivars with a peak in the evening and a trough at dawn, the functional J/GmELF3a was expressed at a higher level in Zhonghuang 24 (ZH24) than was the nonfunctional j/Gmelf3a in Huaxia 3 (HX3) (Fig. 1 C)
Summary
Some circadian clock genes have been identified as loci for maturity traits. In the model plant Arabidopsis thaliana, more than 20 clock related components have been identified, such as CIRCADIAN CLOCK ASSOCIATED 1 (CCA1), LATE ELONGATED HYPOCOTYL (LHY), PSEUDO RESPONSE REGULATOR 5 (PRR5), PRR7, PRR9, GIGA NTEA (GI), TIMING OF CAB EXPRESSION 1 (TOC1/ PRR1), LUX ARRHYTHMO (LUX), EARLY FLOWERING 3 (ELF3) and ELF4 [6, 7]. These components modulate each other at different time points to form morning-, afternoon-, and evening-phased interlocking transcriptional-translational feedback loops to make up a complex circadian clock network [6]. The EC is essential in maintaining regular circadian rhythms, and its dysfunction results in clock arrhythmia [8,9,10,11]
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