Transcriptomal dissection of soybean circadian rhythmicity in two geographically, phenotypically and genetically distinct cultivars
Abstract Background 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. Results We used two geographically, phenotypically and genetically distinct cul...
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| Format: | Article |
| Language: | English |
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BMC
2021-07-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-021-07869-8 |
| _version_ | 1819156671911428096 |
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| author | Yanlei Yue Ze Jiang Enoch Sapey Tingting Wu Shi Sun Mengxue Cao Tianfu Han Tao Li Hai Nian Bingjun Jiang |
| author_facet | Yanlei Yue Ze Jiang Enoch Sapey Tingting Wu Shi Sun Mengxue Cao Tianfu Han Tao Li Hai Nian Bingjun Jiang |
| author_sort | Yanlei Yue |
| collection | DOAJ |
| description | Abstract Background 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. Results 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. Conclusions 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. |
| first_indexed | 2024-12-22T15:56:35Z |
| format | Article |
| id | doaj.art-475f40eb51fe46c599f7fb1a529377d8 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-22T15:56:35Z |
| publishDate | 2021-07-01 |
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| series | BMC Genomics |
| spelling | doaj.art-475f40eb51fe46c599f7fb1a529377d82022-12-21T18:20:46ZengBMCBMC Genomics1471-21642021-07-0122111310.1186/s12864-021-07869-8Transcriptomal dissection of soybean circadian rhythmicity in two geographically, phenotypically and genetically distinct cultivarsYanlei Yue0Ze Jiang1Enoch Sapey2Tingting Wu3Shi Sun4Mengxue Cao5Tianfu Han6Tao Li7Hai Nian8Bingjun Jiang9College of Life Sciences, Henan Agricultural UniversityState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural UniversityMARA Key Lab of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural SciencesMARA Key Lab of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural SciencesMARA Key Lab of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural SciencesCollege of Life Sciences, Henan Agricultural UniversityMARA Key Lab of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural SciencesCollege of Life Sciences, Henan Agricultural UniversityState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural UniversityMARA Key Lab of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural SciencesAbstract Background 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. Results 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. Conclusions 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.https://doi.org/10.1186/s12864-021-07869-8SoybeanCircadian rhythmicityTime-series transcriptomeJ/GmELF3aGmFT family |
| spellingShingle | Yanlei Yue Ze Jiang Enoch Sapey Tingting Wu Shi Sun Mengxue Cao Tianfu Han Tao Li Hai Nian Bingjun Jiang Transcriptomal dissection of soybean circadian rhythmicity in two geographically, phenotypically and genetically distinct cultivars BMC Genomics Soybean Circadian rhythmicity Time-series transcriptome J/GmELF3a GmFT family |
| title | Transcriptomal dissection of soybean circadian rhythmicity in two geographically, phenotypically and genetically distinct cultivars |
| title_full | Transcriptomal dissection of soybean circadian rhythmicity in two geographically, phenotypically and genetically distinct cultivars |
| title_fullStr | Transcriptomal dissection of soybean circadian rhythmicity in two geographically, phenotypically and genetically distinct cultivars |
| title_full_unstemmed | Transcriptomal dissection of soybean circadian rhythmicity in two geographically, phenotypically and genetically distinct cultivars |
| title_short | Transcriptomal dissection of soybean circadian rhythmicity in two geographically, phenotypically and genetically distinct cultivars |
| title_sort | transcriptomal dissection of soybean circadian rhythmicity in two geographically phenotypically and genetically distinct cultivars |
| topic | Soybean Circadian rhythmicity Time-series transcriptome J/GmELF3a GmFT family |
| url | https://doi.org/10.1186/s12864-021-07869-8 |
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