Circadian clock regulation in soybean senescence: a transcriptome analysis of early and late senescence types
Abstract Background Plant senescence is the process of physiological maturation of plants and is important for crop yield and quality. Senescence is controlled by several factors, such as temperature and photoperiod. However, the molecular basis by which these genes promote senescence in soybeans is...
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BMC
2025-01-01
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| Online Access: | https://doi.org/10.1186/s12864-024-11095-3 |
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| author | Prakash Basnet Sevin Lee Ka Hee Moon Nam-Il Park Gang-Seob Lee Seongkon Lee Taeyoung Um Ik-Young Choi |
| author_facet | Prakash Basnet Sevin Lee Ka Hee Moon Nam-Il Park Gang-Seob Lee Seongkon Lee Taeyoung Um Ik-Young Choi |
| author_sort | Prakash Basnet |
| collection | DOAJ |
| description | Abstract Background Plant senescence is the process of physiological maturation of plants and is important for crop yield and quality. Senescence is controlled by several factors, such as temperature and photoperiod. However, the molecular basis by which these genes promote senescence in soybeans is not well understood. We identified senescence-related genes via transcriptome analysis of early-senescence (ES)- and late-senescence (LS)-type plants to elucidate the molecular mechanisms of senescence in soybeans. Results We obtained early-senescence (ES)- and late-senescence (LS)-type F7 plants from a cross between a hybrid (Glycine max × Glycine soja) and the Glycine max cultivar. The ES-type plants presented the reproductive (R2) growth stage at 50 days after sowing (DAS) and the R7 growth stage at 95 DAS, whereas the LS-type plants presented the beginning of the R1 and R6 growth stages at 50 and 95 DAS, respectively. To understand the molecular mechanisms underlying this senescence, we performed transcriptome analysis of leaves from 50 to 95 DAS of ES- and LS-type plants. A total of 2,414 and 2,471 genes at 50 and 95 DAS, respectively, were differentially expressed between ES-type and LS-type plants. Twenty-three candidate genes associated with the circadian clock, chlorophyll biosynthesis, phytohormones, and senescence-associated protein kinases were identified, and their expression levels were analyzed. In addition, to understand interaction between circadian clock and senescence, we analyzed expression patterns of seven circadian clock-related genes during the time period (light and dark condition): CIRCADIAN CLOCK ASSOCIATED 1 (CCA1), LATE ELONGATED HYPOCOTYL (LHY), CONSTANS-LIKE 9 (COL9), LUX ARRHYTHMO (LUX) EARLY FLOWERING 3 (ELF3), PSEUDO-RESPONSE REGULATOR5 (PRR5) and GIGANTEA (GI). The expression patterns of circadian clock-related genes were similar in the ES- and LS-type plants. However, the transcription levels of these genes were compared between ES- and LS-type plants, and the expression of these genes was greater than that in LS-type plants during the period when expression increased. Therefore, each set of candidate genes regulated senescence in each plant by regulating their expression level. Conclusions These findings provide novel insights into the regulation of senescence in soybean plants, which could lead to the development of new strategies to improve agriculture. |
| format | Article |
| id | doaj-art-2f73a4333e494ce097a777215be26a85 |
| institution | Kabale University |
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| language | English |
| publishDate | 2025-01-01 |
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| series | BMC Genomics |
| spelling | doaj-art-2f73a4333e494ce097a777215be26a852025-01-26T12:16:37ZengBMCBMC Genomics1471-21642025-01-0126111310.1186/s12864-024-11095-3Circadian clock regulation in soybean senescence: a transcriptome analysis of early and late senescence typesPrakash Basnet0Sevin Lee1Ka Hee Moon2Nam-Il Park3Gang-Seob Lee4Seongkon Lee5Taeyoung Um6Ik-Young Choi7Department of Agricultural and Life Industry, Kangwon National UniversityDepartment of Agricultural and Life Industry, Kangwon National UniversityDepartment of Agricultural and Life Industry, Kangwon National UniversityDepartment of Plant Science, Gangneung-Wonju National UniversityDepartment of Coastal Agricultural Research Institute, Kyungpook National UniversityDepartment of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development AdministrationAgriculture and Life Sciences Research Institute, Kangwon National UniversityDepartment of Agricultural and Life Industry, Kangwon National UniversityAbstract Background Plant senescence is the process of physiological maturation of plants and is important for crop yield and quality. Senescence is controlled by several factors, such as temperature and photoperiod. However, the molecular basis by which these genes promote senescence in soybeans is not well understood. We identified senescence-related genes via transcriptome analysis of early-senescence (ES)- and late-senescence (LS)-type plants to elucidate the molecular mechanisms of senescence in soybeans. Results We obtained early-senescence (ES)- and late-senescence (LS)-type F7 plants from a cross between a hybrid (Glycine max × Glycine soja) and the Glycine max cultivar. The ES-type plants presented the reproductive (R2) growth stage at 50 days after sowing (DAS) and the R7 growth stage at 95 DAS, whereas the LS-type plants presented the beginning of the R1 and R6 growth stages at 50 and 95 DAS, respectively. To understand the molecular mechanisms underlying this senescence, we performed transcriptome analysis of leaves from 50 to 95 DAS of ES- and LS-type plants. A total of 2,414 and 2,471 genes at 50 and 95 DAS, respectively, were differentially expressed between ES-type and LS-type plants. Twenty-three candidate genes associated with the circadian clock, chlorophyll biosynthesis, phytohormones, and senescence-associated protein kinases were identified, and their expression levels were analyzed. In addition, to understand interaction between circadian clock and senescence, we analyzed expression patterns of seven circadian clock-related genes during the time period (light and dark condition): CIRCADIAN CLOCK ASSOCIATED 1 (CCA1), LATE ELONGATED HYPOCOTYL (LHY), CONSTANS-LIKE 9 (COL9), LUX ARRHYTHMO (LUX) EARLY FLOWERING 3 (ELF3), PSEUDO-RESPONSE REGULATOR5 (PRR5) and GIGANTEA (GI). The expression patterns of circadian clock-related genes were similar in the ES- and LS-type plants. However, the transcription levels of these genes were compared between ES- and LS-type plants, and the expression of these genes was greater than that in LS-type plants during the period when expression increased. Therefore, each set of candidate genes regulated senescence in each plant by regulating their expression level. Conclusions These findings provide novel insights into the regulation of senescence in soybean plants, which could lead to the development of new strategies to improve agriculture.https://doi.org/10.1186/s12864-024-11095-3SoybeanInbred linesSenescenceCircadian clockTranscriptome analysis |
| spellingShingle | Prakash Basnet Sevin Lee Ka Hee Moon Nam-Il Park Gang-Seob Lee Seongkon Lee Taeyoung Um Ik-Young Choi Circadian clock regulation in soybean senescence: a transcriptome analysis of early and late senescence types BMC Genomics Soybean Inbred lines Senescence Circadian clock Transcriptome analysis |
| title | Circadian clock regulation in soybean senescence: a transcriptome analysis of early and late senescence types |
| title_full | Circadian clock regulation in soybean senescence: a transcriptome analysis of early and late senescence types |
| title_fullStr | Circadian clock regulation in soybean senescence: a transcriptome analysis of early and late senescence types |
| title_full_unstemmed | Circadian clock regulation in soybean senescence: a transcriptome analysis of early and late senescence types |
| title_short | Circadian clock regulation in soybean senescence: a transcriptome analysis of early and late senescence types |
| title_sort | circadian clock regulation in soybean senescence a transcriptome analysis of early and late senescence types |
| topic | Soybean Inbred lines Senescence Circadian clock Transcriptome analysis |
| url | https://doi.org/10.1186/s12864-024-11095-3 |
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