Identification of long noncoding RNAs involved in plumule-vernalization of Chinese cabbage
Vernalization is a phenomenon in which plants must undergo a period of continuous low temperatures to change from the vegetative growth stage to the reproductive growth stage. Chinese cabbage is a heading vegetable, and flowering time is an essential developmental trait. Premature vernalization lead...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-03-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2023.1147494/full |
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| author | Yun Dai Yun Dai Guoliang Li Guoliang Li Xinyu Gao Xinyu Gao Shaoxing Wang Shaoxing Wang Ze Li Ze Li Chao Song Chao Song Shifan Zhang Shifan Zhang Fei Li Fei Li Zhiyuan Fang Zhiyuan Fang Rifei Sun Rifei Sun Hui Zhang Hui Zhang Shujiang Zhang Shujiang Zhang |
| author_facet | Yun Dai Yun Dai Guoliang Li Guoliang Li Xinyu Gao Xinyu Gao Shaoxing Wang Shaoxing Wang Ze Li Ze Li Chao Song Chao Song Shifan Zhang Shifan Zhang Fei Li Fei Li Zhiyuan Fang Zhiyuan Fang Rifei Sun Rifei Sun Hui Zhang Hui Zhang Shujiang Zhang Shujiang Zhang |
| author_sort | Yun Dai |
| collection | DOAJ |
| description | Vernalization is a phenomenon in which plants must undergo a period of continuous low temperatures to change from the vegetative growth stage to the reproductive growth stage. Chinese cabbage is a heading vegetable, and flowering time is an essential developmental trait. Premature vernalization leads to premature bolting, which causes a loss of product value and yield. While research into vernalization has provided a wealth of information, a complete understanding of the molecular mechanism for controlling vernalization requirements has not yet been elucidated. In this study, using high-throughput RNA sequencing, we analyzed the plumule-vernalization response of mRNA and long noncoding RNA in the bolting-resistant Chinese cabbage double haploid (DH) line ‘Ju Hongxin’ (JHX). A total of 3382 lncRNAs were identified, of which 1553 differentially expressed (DE) lncRNAs were characterized as plumule-vernalization responses. The ceRNA network revealed that 280 ceRNA pairs participated in the plumule-vernalization reaction of Chinese cabbage. Through identifying DE lncRNAs in Chinese cabbage and analyzing anti-, cis-, and trans-functional analysis, some candidate lncRNAs related to vernalization promoting flowering of Chinese cabbage and their regulated mRNA genes were found. Moreover, the expression of several critical lncRNAs and their targets was verified using qRT-PCR. Furthermore, we identified the candidate plumule-vernalization-related long noncoding RNAs that regulate BrFLCs in Chinese cabbage, which was interesting and different from previous studies and was a new discovery. Our findings expand the knowledge of lncRNAs in the vernalization of Chinese cabbage, and the identified lncRNAs provide rich resources for future comparative and functional studies. |
| first_indexed | 2024-04-10T00:41:48Z |
| format | Article |
| id | doaj.art-69e0dad4cecd43ee952b9954292d96df |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-10T00:41:48Z |
| publishDate | 2023-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-69e0dad4cecd43ee952b9954292d96df2023-03-14T05:34:35ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2023-03-011410.3389/fpls.2023.11474941147494Identification of long noncoding RNAs involved in plumule-vernalization of Chinese cabbageYun Dai0Yun Dai1Guoliang Li2Guoliang Li3Xinyu Gao4Xinyu Gao5Shaoxing Wang6Shaoxing Wang7Ze Li8Ze Li9Chao Song10Chao Song11Shifan Zhang12Shifan Zhang13Fei Li14Fei Li15Zhiyuan Fang16Zhiyuan Fang17Rifei Sun18Rifei Sun19Hui Zhang20Hui Zhang21Shujiang Zhang22Shujiang Zhang23Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, ChinaState Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, ChinaInstitute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, ChinaState Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, ChinaInstitute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, ChinaState Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, ChinaInstitute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, ChinaState Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, ChinaInstitute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, ChinaState Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, ChinaInstitute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, ChinaState Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, ChinaInstitute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, ChinaState Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, ChinaInstitute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, ChinaState Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, ChinaInstitute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, ChinaState Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, ChinaInstitute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, ChinaState Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, ChinaInstitute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, ChinaState Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, ChinaInstitute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, ChinaState Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, ChinaVernalization is a phenomenon in which plants must undergo a period of continuous low temperatures to change from the vegetative growth stage to the reproductive growth stage. Chinese cabbage is a heading vegetable, and flowering time is an essential developmental trait. Premature vernalization leads to premature bolting, which causes a loss of product value and yield. While research into vernalization has provided a wealth of information, a complete understanding of the molecular mechanism for controlling vernalization requirements has not yet been elucidated. In this study, using high-throughput RNA sequencing, we analyzed the plumule-vernalization response of mRNA and long noncoding RNA in the bolting-resistant Chinese cabbage double haploid (DH) line ‘Ju Hongxin’ (JHX). A total of 3382 lncRNAs were identified, of which 1553 differentially expressed (DE) lncRNAs were characterized as plumule-vernalization responses. The ceRNA network revealed that 280 ceRNA pairs participated in the plumule-vernalization reaction of Chinese cabbage. Through identifying DE lncRNAs in Chinese cabbage and analyzing anti-, cis-, and trans-functional analysis, some candidate lncRNAs related to vernalization promoting flowering of Chinese cabbage and their regulated mRNA genes were found. Moreover, the expression of several critical lncRNAs and their targets was verified using qRT-PCR. Furthermore, we identified the candidate plumule-vernalization-related long noncoding RNAs that regulate BrFLCs in Chinese cabbage, which was interesting and different from previous studies and was a new discovery. Our findings expand the knowledge of lncRNAs in the vernalization of Chinese cabbage, and the identified lncRNAs provide rich resources for future comparative and functional studies.https://www.frontiersin.org/articles/10.3389/fpls.2023.1147494/fullplumule-vernalizationlncRNAsmRNAsceRNAsshoot apical meristemFLCs |
| spellingShingle | Yun Dai Yun Dai Guoliang Li Guoliang Li Xinyu Gao Xinyu Gao Shaoxing Wang Shaoxing Wang Ze Li Ze Li Chao Song Chao Song Shifan Zhang Shifan Zhang Fei Li Fei Li Zhiyuan Fang Zhiyuan Fang Rifei Sun Rifei Sun Hui Zhang Hui Zhang Shujiang Zhang Shujiang Zhang Identification of long noncoding RNAs involved in plumule-vernalization of Chinese cabbage Frontiers in Plant Science plumule-vernalization lncRNAs mRNAs ceRNAs shoot apical meristem FLCs |
| title | Identification of long noncoding RNAs involved in plumule-vernalization of Chinese cabbage |
| title_full | Identification of long noncoding RNAs involved in plumule-vernalization of Chinese cabbage |
| title_fullStr | Identification of long noncoding RNAs involved in plumule-vernalization of Chinese cabbage |
| title_full_unstemmed | Identification of long noncoding RNAs involved in plumule-vernalization of Chinese cabbage |
| title_short | Identification of long noncoding RNAs involved in plumule-vernalization of Chinese cabbage |
| title_sort | identification of long noncoding rnas involved in plumule vernalization of chinese cabbage |
| topic | plumule-vernalization lncRNAs mRNAs ceRNAs shoot apical meristem FLCs |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2023.1147494/full |
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