Comparative transcriptome analysis provides key insights into seedling development in switchgrass (Panicum virgatum L.)
Abstract Background Switchgrass (Panicum virgatum L.), a warm-season perennial C4 plant, can be used as a forage plant, a soil and water conservation plant, a windbreak plant, and as a good source of biofuels and alternative energy with low planting costs. However, switchgrass exhibits low rates of...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2019-08-01
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| Series: | Biotechnology for Biofuels |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13068-019-1534-4 |
| _version_ | 1811257492335755264 |
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| author | Shumeng Zhang Fengli Sun Weiwei Wang Guoyu Yang Chao Zhang Yongfeng Wang Shudong Liu Yajun Xi |
| author_facet | Shumeng Zhang Fengli Sun Weiwei Wang Guoyu Yang Chao Zhang Yongfeng Wang Shudong Liu Yajun Xi |
| author_sort | Shumeng Zhang |
| collection | DOAJ |
| description | Abstract Background Switchgrass (Panicum virgatum L.), a warm-season perennial C4 plant, can be used as a forage plant, a soil and water conservation plant, a windbreak plant, and as a good source of biofuels and alternative energy with low planting costs. However, switchgrass exhibits low rates of seedling development compared to other crops, which means it is typically out-competed by weeds. There is a large variation in seedling development rates among different plantlets in switchgrass, which limits its usefulness for large-scale cultivation. Little is currently known about the molecular reasons for slow seedling growth. Results Characterization of the seedling development process via growth indices indicated a relatively stagnant growth stage in switchgrass. A total of 678 differentially expressed genes (DEGs) were identified from the comparison of transcriptomes from slowly developed (sd) and rapidly developed (rd) switchgrass seedlings. Gene ontology and pathway enrichment analysis showed that DEGs were enriched in diterpenoid biosynthesis, thiamine metabolism, and circadian rhythm. Transcription factor enrichment and expression analyses showed MYB-related, bHLH and NAC family genes were essential for seedling growth. The transcriptome results were consistent with those of quantitative real-time polymerase chain reaction. Then, the expression profiles of maize and switchgrass were compared during seedling leaf development. A total of 128 DEGs that play key roles in seedling growth were aligned to maize genes. Transcriptional information and physiological indices suggested that several genes involved in the circadian rhythm, thiamine metabolism, energy metabolism, gibberellic acid biosynthesis, and signal transduction played important roles in seedling development. Conclusions The seedling development process of switchgrass was characterized, and the molecular differences between slowly developed and rapidly developed seedlings were discussed. This study provides new insights into the reasons for slow seedling development in switchgrass and will be useful for the genetic improvement of switchgrass and other crops. |
| first_indexed | 2024-04-12T17:58:18Z |
| format | Article |
| id | doaj.art-2efdd12cecd44d6a9bf9b2fc3083d45b |
| institution | Directory Open Access Journal |
| issn | 1754-6834 |
| language | English |
| last_indexed | 2024-04-12T17:58:18Z |
| publishDate | 2019-08-01 |
| publisher | BMC |
| record_format | Article |
| series | Biotechnology for Biofuels |
| spelling | doaj.art-2efdd12cecd44d6a9bf9b2fc3083d45b2022-12-22T03:22:16ZengBMCBiotechnology for Biofuels1754-68342019-08-0112111810.1186/s13068-019-1534-4Comparative transcriptome analysis provides key insights into seedling development in switchgrass (Panicum virgatum L.)Shumeng Zhang0Fengli Sun1Weiwei Wang2Guoyu Yang3Chao Zhang4Yongfeng Wang5Shudong Liu6Yajun Xi7State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityState Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityState Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityState Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityState Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityState Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityState Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityState Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityAbstract Background Switchgrass (Panicum virgatum L.), a warm-season perennial C4 plant, can be used as a forage plant, a soil and water conservation plant, a windbreak plant, and as a good source of biofuels and alternative energy with low planting costs. However, switchgrass exhibits low rates of seedling development compared to other crops, which means it is typically out-competed by weeds. There is a large variation in seedling development rates among different plantlets in switchgrass, which limits its usefulness for large-scale cultivation. Little is currently known about the molecular reasons for slow seedling growth. Results Characterization of the seedling development process via growth indices indicated a relatively stagnant growth stage in switchgrass. A total of 678 differentially expressed genes (DEGs) were identified from the comparison of transcriptomes from slowly developed (sd) and rapidly developed (rd) switchgrass seedlings. Gene ontology and pathway enrichment analysis showed that DEGs were enriched in diterpenoid biosynthesis, thiamine metabolism, and circadian rhythm. Transcription factor enrichment and expression analyses showed MYB-related, bHLH and NAC family genes were essential for seedling growth. The transcriptome results were consistent with those of quantitative real-time polymerase chain reaction. Then, the expression profiles of maize and switchgrass were compared during seedling leaf development. A total of 128 DEGs that play key roles in seedling growth were aligned to maize genes. Transcriptional information and physiological indices suggested that several genes involved in the circadian rhythm, thiamine metabolism, energy metabolism, gibberellic acid biosynthesis, and signal transduction played important roles in seedling development. Conclusions The seedling development process of switchgrass was characterized, and the molecular differences between slowly developed and rapidly developed seedlings were discussed. This study provides new insights into the reasons for slow seedling development in switchgrass and will be useful for the genetic improvement of switchgrass and other crops.http://link.springer.com/article/10.1186/s13068-019-1534-4SwitchgrassSeedling developmentTranscriptomeCircadian rhythmGibberellic acidThiamine metabolism |
| spellingShingle | Shumeng Zhang Fengli Sun Weiwei Wang Guoyu Yang Chao Zhang Yongfeng Wang Shudong Liu Yajun Xi Comparative transcriptome analysis provides key insights into seedling development in switchgrass (Panicum virgatum L.) Biotechnology for Biofuels Switchgrass Seedling development Transcriptome Circadian rhythm Gibberellic acid Thiamine metabolism |
| title | Comparative transcriptome analysis provides key insights into seedling development in switchgrass (Panicum virgatum L.) |
| title_full | Comparative transcriptome analysis provides key insights into seedling development in switchgrass (Panicum virgatum L.) |
| title_fullStr | Comparative transcriptome analysis provides key insights into seedling development in switchgrass (Panicum virgatum L.) |
| title_full_unstemmed | Comparative transcriptome analysis provides key insights into seedling development in switchgrass (Panicum virgatum L.) |
| title_short | Comparative transcriptome analysis provides key insights into seedling development in switchgrass (Panicum virgatum L.) |
| title_sort | comparative transcriptome analysis provides key insights into seedling development in switchgrass panicum virgatum l |
| topic | Switchgrass Seedling development Transcriptome Circadian rhythm Gibberellic acid Thiamine metabolism |
| url | http://link.springer.com/article/10.1186/s13068-019-1534-4 |
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