Transcriptome analysis and mining of genes related to shade tolerance in foxtail millet (Setaria italica (L.) P. Beauv.)
A stereo interplanting system with foxtail millet beneath chestnut trees is an effective planting method to raise the utilization of land in chestnut orchards, increase yields and improve quality of chestnut nuts. Consequently, exploration of genes involved in shade tolerance response in foxtail mil...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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The Royal Society
2022-10-01
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| Series: | Royal Society Open Science |
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| Online Access: | https://royalsocietypublishing.org/doi/10.1098/rsos.220953 |
| _version_ | 1827965679053045760 |
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| author | Dan Liu Yanjiao Cui Zilong Zhao Jing Zhang Suying Li Zhengli Liu |
| author_facet | Dan Liu Yanjiao Cui Zilong Zhao Jing Zhang Suying Li Zhengli Liu |
| author_sort | Dan Liu |
| collection | DOAJ |
| description | A stereo interplanting system with foxtail millet beneath chestnut trees is an effective planting method to raise the utilization of land in chestnut orchards, increase yields and improve quality of chestnut nuts. Consequently, exploration of genes involved in shade tolerance response in foxtail millet and breeding shade-tolerant varieties have become urgent issues. In this study, RNA-seq of leaf samples from two shade-tolerant varieties and three shade-intolerant varieties of foxtail millet at the booting stage was performed. Comparisons between the varieties revealed that 70 genes were commonly differentially expressed. Moreover, the ratio of net photosynthetic rate under shaded environment to that under light environment could be used as an indicator of shade tolerance. Subsequently, weighted gene co-expression network analysis was employed to construct a co-expression network and modules were correlated with this ratio. A total of 375 genes were identified as potentially relevant to shade tolerance, among which nine genes were also present in the 70 differentially expressed genes, which implied that they were good candidates for genes involved in shade tolerance. Our results provide valuable resources for elucidation of the molecular mechanisms underlying shade tolerance and will contribute to breeding of shade-tolerant foxtail millet that are adapted to the shaded environment under chestnut trees. |
| first_indexed | 2024-04-09T17:37:07Z |
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| id | doaj.art-35e50ab4afe64db29f56c39fce1141c6 |
| institution | Directory Open Access Journal |
| issn | 2054-5703 |
| language | English |
| last_indexed | 2024-04-09T17:37:07Z |
| publishDate | 2022-10-01 |
| publisher | The Royal Society |
| record_format | Article |
| series | Royal Society Open Science |
| spelling | doaj.art-35e50ab4afe64db29f56c39fce1141c62023-04-17T11:00:59ZengThe Royal SocietyRoyal Society Open Science2054-57032022-10-0191010.1098/rsos.220953Transcriptome analysis and mining of genes related to shade tolerance in foxtail millet (Setaria italica (L.) P. Beauv.)Dan Liu0Yanjiao Cui1Zilong Zhao2Jing Zhang3Suying Li4Zhengli Liu5Tianjin Key Laboratory of Crop Genetics and Breeding, Institute of Crop Sciences, Tianjin Academy of Agricultural Sciences, Tianjin, People's Republic of ChinaDepartment of Life Sciences, Tangshan Normal University, Tangshan, People's Republic of ChinaDepartment of Life Sciences, Tangshan Normal University, Tangshan, People's Republic of ChinaDepartment of Life Sciences, Tangshan Normal University, Tangshan, People's Republic of ChinaDepartment of Life Sciences, Tangshan Normal University, Tangshan, People's Republic of ChinaDepartment of Life Sciences, Tangshan Normal University, Tangshan, People's Republic of ChinaA stereo interplanting system with foxtail millet beneath chestnut trees is an effective planting method to raise the utilization of land in chestnut orchards, increase yields and improve quality of chestnut nuts. Consequently, exploration of genes involved in shade tolerance response in foxtail millet and breeding shade-tolerant varieties have become urgent issues. In this study, RNA-seq of leaf samples from two shade-tolerant varieties and three shade-intolerant varieties of foxtail millet at the booting stage was performed. Comparisons between the varieties revealed that 70 genes were commonly differentially expressed. Moreover, the ratio of net photosynthetic rate under shaded environment to that under light environment could be used as an indicator of shade tolerance. Subsequently, weighted gene co-expression network analysis was employed to construct a co-expression network and modules were correlated with this ratio. A total of 375 genes were identified as potentially relevant to shade tolerance, among which nine genes were also present in the 70 differentially expressed genes, which implied that they were good candidates for genes involved in shade tolerance. Our results provide valuable resources for elucidation of the molecular mechanisms underlying shade tolerance and will contribute to breeding of shade-tolerant foxtail millet that are adapted to the shaded environment under chestnut trees.https://royalsocietypublishing.org/doi/10.1098/rsos.220953Chinese chestnutdifferentially expressed genesfoxtail milletnet photosynthetic rateshade toleranceweighted gene co-expression network analysis |
| spellingShingle | Dan Liu Yanjiao Cui Zilong Zhao Jing Zhang Suying Li Zhengli Liu Transcriptome analysis and mining of genes related to shade tolerance in foxtail millet (Setaria italica (L.) P. Beauv.) Royal Society Open Science Chinese chestnut differentially expressed genes foxtail millet net photosynthetic rate shade tolerance weighted gene co-expression network analysis |
| title | Transcriptome analysis and mining of genes related to shade tolerance in foxtail millet (Setaria italica (L.) P. Beauv.) |
| title_full | Transcriptome analysis and mining of genes related to shade tolerance in foxtail millet (Setaria italica (L.) P. Beauv.) |
| title_fullStr | Transcriptome analysis and mining of genes related to shade tolerance in foxtail millet (Setaria italica (L.) P. Beauv.) |
| title_full_unstemmed | Transcriptome analysis and mining of genes related to shade tolerance in foxtail millet (Setaria italica (L.) P. Beauv.) |
| title_short | Transcriptome analysis and mining of genes related to shade tolerance in foxtail millet (Setaria italica (L.) P. Beauv.) |
| title_sort | transcriptome analysis and mining of genes related to shade tolerance in foxtail millet setaria italica l p beauv |
| topic | Chinese chestnut differentially expressed genes foxtail millet net photosynthetic rate shade tolerance weighted gene co-expression network analysis |
| url | https://royalsocietypublishing.org/doi/10.1098/rsos.220953 |
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