The Construction of lncRNA/circRNA–miRNA–mRNA Networks Reveals Functional Genes Related to Growth Traits in <i>Schima superba</i>
<i>Schima superba</i> is a precious timber and fire-resistant tree species widely distributed in southern China. Currently, there is little knowledge related to its growth traits, especially with respect to molecular breeding. The lack of relevant information has delayed the development...
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MDPI AG
2024-02-01
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| Series: | International Journal of Molecular Sciences |
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| author | Qingsong Bai Lingling Shi Kejian Li Fang Xu Weihua Zhang |
| author_facet | Qingsong Bai Lingling Shi Kejian Li Fang Xu Weihua Zhang |
| author_sort | Qingsong Bai |
| collection | DOAJ |
| description | <i>Schima superba</i> is a precious timber and fire-resistant tree species widely distributed in southern China. Currently, there is little knowledge related to its growth traits, especially with respect to molecular breeding. The lack of relevant information has delayed the development of modern breeding. The purpose is to identify probable functional genes involved in <i>S. superba</i> growth through whole transcriptome sequencing. In this study, a total of 32,711 mRNAs, 525 miRNAs, 54,312 lncRNAs, and 1522 circRNAs were identified from 10 <i>S. superba</i> individuals containing different volumes of wood. Four possible regulators, comprising three lncRNAs, one circRNA, and eleven key miRNAs, were identified from the regulatory networks of lncRNA–miRNA–mRNA and circRNA–miRNA–mRNA to supply information on ncRNAs. Several candidate genes involved in phenylpropane and cellulose biosynthesis pathways, including <i>Ss4CL2</i>, <i>SsCSL1</i>, and <i>SsCSL2</i>, and transcription factors, including <i>SsDELLA2</i> (<i>SsSLR</i>), <i>SsDELLA3</i> (<i>SsSLN</i>), <i>SsDELLA5</i> (<i>SsGAI-like2</i>), and <i>SsNAM1</i>, were identified to reveal the molecular regulatory mechanisms regulating the growth traits of <i>S. superba</i>. The results not merely provide candidate functional genes related to <i>S. superba</i> growth trait and will be useful to carry out molecular breeding, but the strategy and method also provide scientists with an effective approach to revealing mechanisms behind important economic traits in other species. |
| first_indexed | 2024-03-07T22:28:15Z |
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| language | English |
| last_indexed | 2024-03-07T22:28:15Z |
| publishDate | 2024-02-01 |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-05dec99480434e208214a2255fdc13ec2024-02-23T15:20:03ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672024-02-01254217110.3390/ijms25042171The Construction of lncRNA/circRNA–miRNA–mRNA Networks Reveals Functional Genes Related to Growth Traits in <i>Schima superba</i>Qingsong Bai0Lingling Shi1Kejian Li2Fang Xu3Weihua Zhang4Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, ChinaGuangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, ChinaGuangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, ChinaGuangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, ChinaGuangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, China<i>Schima superba</i> is a precious timber and fire-resistant tree species widely distributed in southern China. Currently, there is little knowledge related to its growth traits, especially with respect to molecular breeding. The lack of relevant information has delayed the development of modern breeding. The purpose is to identify probable functional genes involved in <i>S. superba</i> growth through whole transcriptome sequencing. In this study, a total of 32,711 mRNAs, 525 miRNAs, 54,312 lncRNAs, and 1522 circRNAs were identified from 10 <i>S. superba</i> individuals containing different volumes of wood. Four possible regulators, comprising three lncRNAs, one circRNA, and eleven key miRNAs, were identified from the regulatory networks of lncRNA–miRNA–mRNA and circRNA–miRNA–mRNA to supply information on ncRNAs. Several candidate genes involved in phenylpropane and cellulose biosynthesis pathways, including <i>Ss4CL2</i>, <i>SsCSL1</i>, and <i>SsCSL2</i>, and transcription factors, including <i>SsDELLA2</i> (<i>SsSLR</i>), <i>SsDELLA3</i> (<i>SsSLN</i>), <i>SsDELLA5</i> (<i>SsGAI-like2</i>), and <i>SsNAM1</i>, were identified to reveal the molecular regulatory mechanisms regulating the growth traits of <i>S. superba</i>. The results not merely provide candidate functional genes related to <i>S. superba</i> growth trait and will be useful to carry out molecular breeding, but the strategy and method also provide scientists with an effective approach to revealing mechanisms behind important economic traits in other species.https://www.mdpi.com/1422-0067/25/4/2171<i>Schima superba</i>non-coding RNAregulatory networkgrowth traitcandidate gene |
| spellingShingle | Qingsong Bai Lingling Shi Kejian Li Fang Xu Weihua Zhang The Construction of lncRNA/circRNA–miRNA–mRNA Networks Reveals Functional Genes Related to Growth Traits in <i>Schima superba</i> International Journal of Molecular Sciences <i>Schima superba</i> non-coding RNA regulatory network growth trait candidate gene |
| title | The Construction of lncRNA/circRNA–miRNA–mRNA Networks Reveals Functional Genes Related to Growth Traits in <i>Schima superba</i> |
| title_full | The Construction of lncRNA/circRNA–miRNA–mRNA Networks Reveals Functional Genes Related to Growth Traits in <i>Schima superba</i> |
| title_fullStr | The Construction of lncRNA/circRNA–miRNA–mRNA Networks Reveals Functional Genes Related to Growth Traits in <i>Schima superba</i> |
| title_full_unstemmed | The Construction of lncRNA/circRNA–miRNA–mRNA Networks Reveals Functional Genes Related to Growth Traits in <i>Schima superba</i> |
| title_short | The Construction of lncRNA/circRNA–miRNA–mRNA Networks Reveals Functional Genes Related to Growth Traits in <i>Schima superba</i> |
| title_sort | construction of lncrna circrna mirna mrna networks reveals functional genes related to growth traits in i schima superba i |
| topic | <i>Schima superba</i> non-coding RNA regulatory network growth trait candidate gene |
| url | https://www.mdpi.com/1422-0067/25/4/2171 |
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