Selection of suitable reference lncRNAs for gene expression analysis in Osmanthus fragrans under abiotic stresses, hormone treatments, and metal ion treatments
IntoductionOsmanthus fragrans, a well-regarded traditional flower in China, holds extensive applications in gardening, food, cosmetics, and traditional Chinese medicine. Despite its importance, research on long non-coding RNAs (lncRNAs) in O. fragrans has been constrained by the absence of reliable...
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Frontiers Media S.A.
2025-01-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2024.1492854/full |
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| author | Yingting Zhang Yingting Zhang Qingyu Yan Hui Xia Xiangling Zeng Xiangling Zeng Xiangling Zeng Jie Yang Jie Yang Jie Yang Xuan Cai Xuan Cai Xuan Cai Zeqing Li Zeqing Li Hongguo Chen Hongguo Chen Hongguo Chen Jingjing Zou Jingjing Zou Jingjing Zou |
| author_facet | Yingting Zhang Yingting Zhang Qingyu Yan Hui Xia Xiangling Zeng Xiangling Zeng Xiangling Zeng Jie Yang Jie Yang Jie Yang Xuan Cai Xuan Cai Xuan Cai Zeqing Li Zeqing Li Hongguo Chen Hongguo Chen Hongguo Chen Jingjing Zou Jingjing Zou Jingjing Zou |
| author_sort | Yingting Zhang |
| collection | DOAJ |
| description | IntoductionOsmanthus fragrans, a well-regarded traditional flower in China, holds extensive applications in gardening, food, cosmetics, and traditional Chinese medicine. Despite its importance, research on long non-coding RNAs (lncRNAs) in O. fragrans has been constrained by the absence of reliable reference genes (RGs).MethodsWe employed five distinct algorithms, i.e., delta-Ct, NormFinder, geNorm, BestKeeper, and RefFinder, to evaluate the expression stability of 17 candidate RGs across various experimental conditions.Results and discussionThe results indicated the most stable RG combinations under different conditions as follows: cold stress: lnc00249739 and lnc00042194; drought stress: lnc00042194 and lnc00174850; salt stress: lnc00239991 and lnc00042194; abiotic stress: lnc00239991, lnc00042194, lnc00067193, and lnc00265419; ABA treatment: lnc00239991 and 18S; MeJA treatment: lnc00265419 and lnc00249739; ethephon treatment: lnc00229717 and lnc00044331; hormone treatments: lnc00265419 and lnc00239991; Al3+ treatment: lnc00087780 and lnc00265419; Cu2+ treatment: lnc00067193 and 18S; Fe2+ treatment: lnc00229717 and ACT7; metal ion treatment: lnc00239991 and lnc00067193; flowering stage: lnc00229717 and RAN1; different tissues: lnc00239991, lnc00042194, lnc00067193, TUA5, UBQ4, and RAN1; and across all samples: lnc00239991, lnc00042194, lnc00265419 and UBQ4. The reliability of these selected RGs was further validated by analyzing the expression patterns of lnc00003036, lnc00126603, and lnc00250780. This study represents the first comprehensive evaluation of lncRNA RG stability in O. fragrans, significantly enhancing the accuracy and depth of lncRNA expression analyses in this species, contributing to advancements in plant stress resistance breeding and improving environmental adaptability. |
| format | Article |
| id | doaj-art-5d6202da94d24beab5f15b27392bbd6b |
| institution | Kabale University |
| issn | 1664-462X |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Plant Science |
| spelling | doaj-art-5d6202da94d24beab5f15b27392bbd6b2025-01-21T08:37:03ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2025-01-011510.3389/fpls.2024.14928541492854Selection of suitable reference lncRNAs for gene expression analysis in Osmanthus fragrans under abiotic stresses, hormone treatments, and metal ion treatmentsYingting Zhang0Yingting Zhang1Qingyu Yan2Hui Xia3Xiangling Zeng4Xiangling Zeng5Xiangling Zeng6Jie Yang7Jie Yang8Jie Yang9Xuan Cai10Xuan Cai11Xuan Cai12Zeqing Li13Zeqing Li14Hongguo Chen15Hongguo Chen16Hongguo Chen17Jingjing Zou18Jingjing Zou19Jingjing Zou20National Forestry and Grassland Administration Engineering Research Center for Osmanthus fragrans, Hubei University of Science and Technology, Xianning, ChinaOsmanthus Innovation Center of National Engineering Research Center for Floriculture, Hubei University of Science and Technology, Xianning, ChinaNational Forestry and Grassland Administration Engineering Research Center for Osmanthus fragrans, Hubei University of Science and Technology, Xianning, ChinaCollege of Forestry, Central South University of Forestry and Technology, Changsha, ChinaNational Forestry and Grassland Administration Engineering Research Center for Osmanthus fragrans, Hubei University of Science and Technology, Xianning, ChinaOsmanthus Innovation Center of National Engineering Research Center for Floriculture, Hubei University of Science and Technology, Xianning, ChinaResearch Center for Osmanthus fragrans, Xianning Research Academy of Industrial Technology of Osmanthus fragrans, Xianning, ChinaNational Forestry and Grassland Administration Engineering Research Center for Osmanthus fragrans, Hubei University of Science and Technology, Xianning, ChinaOsmanthus Innovation Center of National Engineering Research Center for Floriculture, Hubei University of Science and Technology, Xianning, ChinaResearch Center for Osmanthus fragrans, Xianning Research Academy of Industrial Technology of Osmanthus fragrans, Xianning, ChinaNational Forestry and Grassland Administration Engineering Research Center for Osmanthus fragrans, Hubei University of Science and Technology, Xianning, ChinaOsmanthus Innovation Center of National Engineering Research Center for Floriculture, Hubei University of Science and Technology, Xianning, ChinaResearch Center for Osmanthus fragrans, Xianning Research Academy of Industrial Technology of Osmanthus fragrans, Xianning, ChinaNational Forestry and Grassland Administration Engineering Research Center for Osmanthus fragrans, Hubei University of Science and Technology, Xianning, ChinaOsmanthus Innovation Center of National Engineering Research Center for Floriculture, Hubei University of Science and Technology, Xianning, ChinaNational Forestry and Grassland Administration Engineering Research Center for Osmanthus fragrans, Hubei University of Science and Technology, Xianning, ChinaOsmanthus Innovation Center of National Engineering Research Center for Floriculture, Hubei University of Science and Technology, Xianning, ChinaResearch Center for Osmanthus fragrans, Xianning Research Academy of Industrial Technology of Osmanthus fragrans, Xianning, ChinaNational Forestry and Grassland Administration Engineering Research Center for Osmanthus fragrans, Hubei University of Science and Technology, Xianning, ChinaOsmanthus Innovation Center of National Engineering Research Center for Floriculture, Hubei University of Science and Technology, Xianning, ChinaResearch Center for Osmanthus fragrans, Xianning Research Academy of Industrial Technology of Osmanthus fragrans, Xianning, ChinaIntoductionOsmanthus fragrans, a well-regarded traditional flower in China, holds extensive applications in gardening, food, cosmetics, and traditional Chinese medicine. Despite its importance, research on long non-coding RNAs (lncRNAs) in O. fragrans has been constrained by the absence of reliable reference genes (RGs).MethodsWe employed five distinct algorithms, i.e., delta-Ct, NormFinder, geNorm, BestKeeper, and RefFinder, to evaluate the expression stability of 17 candidate RGs across various experimental conditions.Results and discussionThe results indicated the most stable RG combinations under different conditions as follows: cold stress: lnc00249739 and lnc00042194; drought stress: lnc00042194 and lnc00174850; salt stress: lnc00239991 and lnc00042194; abiotic stress: lnc00239991, lnc00042194, lnc00067193, and lnc00265419; ABA treatment: lnc00239991 and 18S; MeJA treatment: lnc00265419 and lnc00249739; ethephon treatment: lnc00229717 and lnc00044331; hormone treatments: lnc00265419 and lnc00239991; Al3+ treatment: lnc00087780 and lnc00265419; Cu2+ treatment: lnc00067193 and 18S; Fe2+ treatment: lnc00229717 and ACT7; metal ion treatment: lnc00239991 and lnc00067193; flowering stage: lnc00229717 and RAN1; different tissues: lnc00239991, lnc00042194, lnc00067193, TUA5, UBQ4, and RAN1; and across all samples: lnc00239991, lnc00042194, lnc00265419 and UBQ4. The reliability of these selected RGs was further validated by analyzing the expression patterns of lnc00003036, lnc00126603, and lnc00250780. This study represents the first comprehensive evaluation of lncRNA RG stability in O. fragrans, significantly enhancing the accuracy and depth of lncRNA expression analyses in this species, contributing to advancements in plant stress resistance breeding and improving environmental adaptability.https://www.frontiersin.org/articles/10.3389/fpls.2024.1492854/fullOsmanthus fragransreference lncRNAsflowering stageabiotic stresshormone treatmentmetal ion treatment |
| spellingShingle | Yingting Zhang Yingting Zhang Qingyu Yan Hui Xia Xiangling Zeng Xiangling Zeng Xiangling Zeng Jie Yang Jie Yang Jie Yang Xuan Cai Xuan Cai Xuan Cai Zeqing Li Zeqing Li Hongguo Chen Hongguo Chen Hongguo Chen Jingjing Zou Jingjing Zou Jingjing Zou Selection of suitable reference lncRNAs for gene expression analysis in Osmanthus fragrans under abiotic stresses, hormone treatments, and metal ion treatments Frontiers in Plant Science Osmanthus fragrans reference lncRNAs flowering stage abiotic stress hormone treatment metal ion treatment |
| title | Selection of suitable reference lncRNAs for gene expression analysis in Osmanthus fragrans under abiotic stresses, hormone treatments, and metal ion treatments |
| title_full | Selection of suitable reference lncRNAs for gene expression analysis in Osmanthus fragrans under abiotic stresses, hormone treatments, and metal ion treatments |
| title_fullStr | Selection of suitable reference lncRNAs for gene expression analysis in Osmanthus fragrans under abiotic stresses, hormone treatments, and metal ion treatments |
| title_full_unstemmed | Selection of suitable reference lncRNAs for gene expression analysis in Osmanthus fragrans under abiotic stresses, hormone treatments, and metal ion treatments |
| title_short | Selection of suitable reference lncRNAs for gene expression analysis in Osmanthus fragrans under abiotic stresses, hormone treatments, and metal ion treatments |
| title_sort | selection of suitable reference lncrnas for gene expression analysis in osmanthus fragrans under abiotic stresses hormone treatments and metal ion treatments |
| topic | Osmanthus fragrans reference lncRNAs flowering stage abiotic stress hormone treatment metal ion treatment |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2024.1492854/full |
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