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Wei X, Wang X, Zhao Y, Chen W, Nath UK, Yang S, Su H, Wang Z, Zhang W, Tian B, Wei F, Yuan Y, Zhang X. Transcriptome analysis reveals the potential lncRNA-mRNA modules involved in genetic male sterility and fertility of Chinese cabbage (brassica rapa L. ssp. pekinensis). BMC PLANT BIOLOGY 2024; 24:289. [PMID: 38627624 PMCID: PMC11020818 DOI: 10.1186/s12870-024-05003-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 04/09/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) play a crucial role in regulating gene expression vital for the growth and development of plants. Despite this, the role of lncRNAs in Chinese cabbage (Brassica rapa L. ssp. pekinensis) pollen development and male fertility remains poorly understood. RESULTS In this study, we characterized a recessive genic male sterile mutant (366-2 S), where the delayed degradation of tapetum and the failure of tetrad separation primarily led to the inability to form single microspores, resulting in male sterility. To analyze the role of lncRNAs in pollen development, we conducted a comparative lncRNA sequencing using anthers from the male sterile mutant line (366-2 S) and the wild-type male fertile line (366-2 F). We identified 385 differentially expressed lncRNAs between the 366-2 F and 366-2 S lines, with 172 of them potentially associated with target genes. To further understand the alterations in mRNA expression and explore potential lncRNA-target genes (mRNAs), we performed comparative mRNA transcriptome analysis in the anthers of 366-2 S and 366-2 F at two stages. We identified 1,176 differentially expressed mRNAs. Remarkably, GO analysis revealed significant enrichment in five GO terms, most notably involving mRNAs annotated as pectinesterase and polygalacturonase, which play roles in cell wall degradation. The considerable downregulation of these genes might contribute to the delayed degradation of tapetum in 366-2 S. Furthermore, we identified 15 lncRNA-mRNA modules through Venn diagram analysis. Among them, MSTRG.9997-BraA04g004630.3 C (β-1,3-glucanase) is associated with callose degradation and tetrad separation. Additionally, MSTRG.5212-BraA02g040020.3 C (pectinesterase) and MSTRG.13,532-BraA05g030320.3 C (pectinesterase) are associated with cell wall degradation of the tapetum, indicating that these three candidate lncRNA-mRNA modules potentially regulate pollen development. CONCLUSION This study lays the foundation for understanding the roles of lncRNAs in pollen development and for elucidating their molecular mechanisms in regulating male sterility in Chinese cabbage.
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Affiliation(s)
- Xiaochun Wei
- Institute of Vegetables, Henan Academy of Agricultural Sciences, Graduate T & R Base of Zhengzhou University, Zhengzhou, 450002, Henan, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Xiaoqing Wang
- Institute of Vegetables, Henan Academy of Agricultural Sciences, Graduate T & R Base of Zhengzhou University, Zhengzhou, 450002, Henan, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Yanyan Zhao
- Institute of Vegetables, Henan Academy of Agricultural Sciences, Graduate T & R Base of Zhengzhou University, Zhengzhou, 450002, Henan, China
| | - Weiwei Chen
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Ujjal Kumar Nath
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Shuangjuan Yang
- Institute of Vegetables, Henan Academy of Agricultural Sciences, Graduate T & R Base of Zhengzhou University, Zhengzhou, 450002, Henan, China
| | - Henan Su
- Institute of Vegetables, Henan Academy of Agricultural Sciences, Graduate T & R Base of Zhengzhou University, Zhengzhou, 450002, Henan, China
| | - Zhiyong Wang
- Institute of Vegetables, Henan Academy of Agricultural Sciences, Graduate T & R Base of Zhengzhou University, Zhengzhou, 450002, Henan, China
| | - Wenjing Zhang
- Institute of Vegetables, Henan Academy of Agricultural Sciences, Graduate T & R Base of Zhengzhou University, Zhengzhou, 450002, Henan, China
| | - Baoming Tian
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Fang Wei
- Institute of Vegetables, Henan Academy of Agricultural Sciences, Graduate T & R Base of Zhengzhou University, Zhengzhou, 450002, Henan, China.
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
| | - Yuxiang Yuan
- Institute of Vegetables, Henan Academy of Agricultural Sciences, Graduate T & R Base of Zhengzhou University, Zhengzhou, 450002, Henan, China.
| | - Xiaowei Zhang
- Institute of Vegetables, Henan Academy of Agricultural Sciences, Graduate T & R Base of Zhengzhou University, Zhengzhou, 450002, Henan, China.
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Yuan C, He RR, Zhao WL, Chen YQ, Zhang YC. Insights into the roles of long noncoding RNAs in the communication between plants and the environment. THE PLANT GENOME 2023; 16:e20277. [PMID: 36345558 DOI: 10.1002/tpg2.20277] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
In addition to coding proteins, RNA molecules, especially long noncoding RNAs (lncRNAs), have well-established functions in regulating gene expression. The number of studies focused on the roles played by different types of lncRNAs in a variety of plant biological processes has markedly increased. These lncRNA roles involve plant vegetative and reproductive growth and responses to biotic and abiotic stresses. In this review, we examine the classification, mechanisms, and functions of lncRNAs and then emphasize the roles played by these lncRNAs in the communication between plants and the environment mainly with respect to the following environmental factors: temperature, light, water, salt stress, and nutrient deficiencies. We also discuss the consensus among researchers and the remaining challenges and underscore the exciting ways lncRNAs may affect the biology of plants.
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Affiliation(s)
- Chao Yuan
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen Univ., Guangzhou, 510275, P. R. China
| | - Rui-Rui He
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen Univ., Guangzhou, 510275, P. R. China
| | - Wen-Long Zhao
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen Univ., Guangzhou, 510275, P. R. China
| | - Yue-Qin Chen
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen Univ., Guangzhou, 510275, P. R. China
- MOE Key Laboratory of Gene Function and Regulation, Sun Yat-sen Univ., Guangzhou, 510275, China
| | - Yu-Chan Zhang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen Univ., Guangzhou, 510275, P. R. China
- MOE Key Laboratory of Gene Function and Regulation, Sun Yat-sen Univ., Guangzhou, 510275, China
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3
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Li C, Lai X, Yu X, Xiong Z, Chen J, Lang X, Feng H, Wan X, Liu K. Plant long noncoding RNAs: Recent progress in understanding their roles in growth, development, and stress responses. Biochem Biophys Res Commun 2023; 671:270-277. [PMID: 37311264 DOI: 10.1016/j.bbrc.2023.05.103] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 05/25/2023] [Indexed: 06/15/2023]
Abstract
Long noncoding RNA (lncRNA) transcripts are longer than 200 nt and are not translated into proteins. LncRNAs function in a wide variety of processes in plants and animals, but, perhaps because of their lower expression and conservation levels, plant lncRNAs had attracted less attention than protein-coding mRNAs. Now, recent studies have made remarkable progress in identifying lncRNAs and understanding their functions. In this review, we discuss a number of lncRNAs that have important functions in growth, development, reproduction, responses to abiotic stresses, and regulation of disease and insect resistance in plants. Additionally, we describe the known mechanisms of action of plant lncRNAs according to their origins within the genome. This review thus provides a guide for identifying and functionally characterizing new lncRNAs in plants.
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Affiliation(s)
- Chunmei Li
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China; Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China; College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Xiaofeng Lai
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China; College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Xuanyue Yu
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China; Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Zhiwen Xiong
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China; Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Jie Chen
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China; College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Xingxuan Lang
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China; College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Haotian Feng
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China; Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Xiaorong Wan
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China; Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China; College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China.
| | - Kai Liu
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China; Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China; College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China.
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4
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Mao J, Wei S, Chen Y, Yang Y, Yin T. The proposed role of MSL-lncRNAs in causing sex lability of female poplars. HORTICULTURE RESEARCH 2023; 10:uhad042. [PMID: 37188057 PMCID: PMC10177001 DOI: 10.1093/hr/uhad042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/02/2023] [Indexed: 05/17/2023]
Abstract
Labile sex expression is frequently observed in dioecious plants, but the underlying genetic mechanism remains largely unknown. Sex plasticity is also observed in many Populus species. Here we carried out a systematic study on a maleness-promoting gene, MSL, detected in the Populus deltoides genome. Our results showed that both strands of MSL contained multiple cis-activating elements, which generated long non-coding RNAs (lncRNAs) promoting maleness. Although female P. deltoides did not have the male-specific MSL gene, a large number of partial sequences with high sequence similarity to this gene were detected in the female poplar genome. Based on sequence alignment, the MSL sequence could be divided into three partial sequences, and heterologous expression of these partial sequences in Arabidopsis confirmed that they could promote maleness. Since activation of the MSL sequences can only result in female sex lability, we propose that MSL-lncRNAs might play a role in causing sex lability of female poplars.
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Affiliation(s)
| | | | - Yingnan Chen
- State Key Laboratory for Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of Tree Genetics and Breeding of Jiangsu Province, Nanjing Forestry University, Nanjing, 210037, China
| | - Yonghua Yang
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
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Wu M, Luo Z, Cao S. Promoter Variation of the Key Apple Fruit Texture Related Gene MdPG1 and the Upstream Regulation Analysis. PLANTS (BASEL, SWITZERLAND) 2023; 12:1452. [PMID: 37050079 PMCID: PMC10096972 DOI: 10.3390/plants12071452] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Abstract
MdPG1 encoding polygalacturonase in apple (Malus × domestica) is a key gene associated with fruit firmness and texture variations among apple cultivars. However, the causative variants of MdPG1 are still not known. In this study, we identified a SNPA/C variant within an ERF-binding element located in the promoter region of MdPG1. The promoter containing the ERF-binding element with SNPA, rather than the SNPC, could be strongly bound and activated by MdCBF2, a member of the AP2/ERF transcription factor family, as determined by yeast-one-hybrid and dual-luciferase reporter assays. We also demonstrated that the presence of a novel long non-coding RNA, lncRNAPG1, in the promoter of MdPG1 was a causative variant. lncRNAPG1 was specifically expressed in fruit tissues postharvest. lncRNAPG1 could reduce promoter activity when it was fused to the promoter of MdPG1 and a tobacco gene encoding Mg-chelatase H subunit (NtCHLH) in transgenic tobacco cells but could not reduce promoter activity when it was supplied in a separate gene construct, indicating a cis-regulatory effect. Our results provide new insights into genetic regulation of MdPG1 allele expression and are also useful for the development of elite apple cultivars.
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Affiliation(s)
- Mengmeng Wu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agriculture Sciences, Zhengzhou 450009, China
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhengrong Luo
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Shangyin Cao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agriculture Sciences, Zhengzhou 450009, China
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6
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Lohani N, Golicz AA, Allu AD, Bhalla PL, Singh MB. Genome-wide analysis reveals the crucial role of lncRNAs in regulating the expression of genes controlling pollen development. PLANT CELL REPORTS 2023; 42:337-354. [PMID: 36653661 DOI: 10.1007/s00299-022-02960-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
The genomic location and stage-specific expression pattern of many long non-coding RNAs reveal their critical role in regulating protein-coding genes crucial in pollen developmental progression and male germ line specification. Long non-coding RNAs (lncRNAs) are transcripts longer than 200 bp with no apparent protein-coding potential. Multiple investigations have revealed high expression of lncRNAs in plant reproductive organs in a cell and tissue-specific manner. However, their potential role as essential regulators of molecular processes involved in sexual reproduction remains largely unexplored. We have used developing field mustard (Brassica rapa) pollen as a model system for investigating the potential role of lncRNAs in reproductive development. Reference-based transcriptome assembly performed to update the existing genome annotation identified novel expressed protein-coding genes and long non-coding RNAs (lncRNAs), including 4347 long intergenic non-coding RNAs (lincRNAs, 1058 expressed) and 2,045 lncRNAs overlapping protein-coding genes on the opposite strand (lncNATs, 780 expressed). The analysis of expression profiles reveals that lncRNAs are significant and stage-specific contributors to the gene expression profile of developing pollen. Gene co-expression networks accompanied by genome location analysis identified 38 cis-acting lincRNA, 31 cis-acting lncNAT, 7 trans-acting lincRNA and 14 trans-acting lncNAT to be substantially co-expressed with target protein-coding genes involved in biological processes regulating pollen development and male lineage specification. These findings provide a foundation for future research aiming at developing strategies to employ lncRNAs as regulatory tools for gene expression control during reproductive development.
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Affiliation(s)
- Neeta Lohani
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia
- School of Science, Western Sydney University, Richmond, Australia
| | - Agnieszka A Golicz
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Gießen, Gießen, Germany
| | - Annapurna D Allu
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Prem L Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia
| | - Mohan B Singh
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia.
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7
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A survey of transcriptome complexity using full-length isoform sequencing in the tea plant Camellia sinensis. Mol Genet Genomics 2022; 297:1243-1255. [PMID: 35763065 DOI: 10.1007/s00438-022-01913-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 05/29/2022] [Indexed: 10/17/2022]
Abstract
Tea is one of the most popular beverages and its leaves are rich in catechins, contributing to the diverse flavor as well as beneficial for human health. However, the study of the post-transcriptional regulatory mechanism affecting the synthesis of catechins remains insufficient. Here, we sequenced the transcriptome using PacBio sequencing technology and obtained 63,111 full-length high-quality isoforms, including 1302 potential novel genes and 583 highly reliable fusion transcripts. We also identified 1204 lncRNAs with high quality, containing 188 known and 1016 novel lncRNAs. In addition, 311 mis-annotated genes were corrected based on the high-quality Isoseq reads. A large number of alternative splicing (AS) events (3784) and alternative polyadenylation (APA) genes (18,714) were analyzed, accounting for 8.84% and 43.7% of the total annotated genes, respectively. We also found that 2884 genes containing AS and APA features exhibited higher expression levels than other genes. These genes are mainly involved in amino acid biosynthesis, carbon fixation in photosynthetic organisms, phenylalanine, tyrosine, tryptophan biosynthesis, and pyruvate metabolism, suggesting that they play an essential role in the catechins content of tea polyphenols. Our results further improved the level of genome annotation and indicated that post-transcriptional regulation plays a crucial part in synthesizing catechins.
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8
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Wu L, Liu S, Qi H, Cai H, Xu M. Research Progress on Plant Long Non-Coding RNA. PLANTS 2020; 9:plants9040408. [PMID: 32218186 PMCID: PMC7237992 DOI: 10.3390/plants9040408] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/10/2020] [Accepted: 03/17/2020] [Indexed: 12/17/2022]
Abstract
Non-coding RNAs (ncRNAs) that were once considered “dark matter” or “transcriptional noise” in genomes are research hotspots in the field of epigenetics. The most well-known microRNAs (miRNAs) are a class of short non-coding, small molecular weight RNAs with lengths of 20–24 nucleotides that are highly conserved throughout evolution. Through complementary pairing with the bases of target sites, target gene transcripts are cleaved and degraded, or translation is inhibited, thus regulating the growth and development of organisms. Unlike miRNAs, which have been studied thoroughly, long non-coding RNAs (lncRNAs) are a group of poorly conserved RNA molecules with a sequence length of more than 200 nucleotides and no protein encoding capability; they interact with large molecules, such as DNA, RNA, and proteins, and regulate protein modification, chromatin remodeling, protein functional activity, and RNA metabolism in vivo through cis- or trans-activation at the transcriptional, post-transcriptional, and epigenetic levels. Research on plant lncRNAs is just beginning and has gradually emerged in the field of plant molecular biology. Currently, some studies have revealed that lncRNAs are extensively involved in plant growth and development and stress response processes by mediating the transmission and expression of genetic information. This paper systematically introduces lncRNA and its regulatory mechanisms, reviews the current status and progress of lncRNA research in plants, summarizes the main techniques and strategies of lncRNA research in recent years, and discusses existing problems and prospects, in order to provide ideas for further exploration and verification of the specific evolution of plant lncRNAs and their biological functions.
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Affiliation(s)
- Ling Wu
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China; (L.W.); (S.L.); (H.C.)
| | - Sian Liu
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China; (L.W.); (S.L.); (H.C.)
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Haoran Qi
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China; (L.W.); (S.L.); (H.C.)
| | - Heng Cai
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China; (L.W.); (S.L.); (H.C.)
| | - Meng Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China; (L.W.); (S.L.); (H.C.)
- Correspondence: ; Tel.: +86-15094307586
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10
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Abstract
Long non-coding RNAs (lncRNAs) exert a multitude of functions in regulating numerous biological processes. Recent studies have uncovered a growing number of lncRNAs within the plant genome. These molecules show striking tissue-specific expression patterns, suggesting that they exert regulatory functions in the growth and development processes of plants. Plant reproductive development is tightly regulated by both environmental and endogenous factors. As plant reproductive development is a crucial aspect of crop breeding, lncRNAs that modulate reproductive development are now particularly worth regarding. Here, we summarize findings that implicate lncRNAs in the control of plant reproductive development, especially in flowering control. Additionally, we elaborate on the regulation mechanisms of lncRNAs, tools for research on their function and mechanism, and potential directions of future research.
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Mishra A, Bohra A. Non-coding RNAs and plant male sterility: current knowledge and future prospects. PLANT CELL REPORTS 2018; 37:177-191. [PMID: 29332167 DOI: 10.1007/s00299-018-2248-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 01/02/2018] [Indexed: 06/07/2023]
Abstract
Latest outcomes assign functional role to non-coding (nc) RNA molecules in regulatory networks that confer male sterility to plants. Male sterility in plants offers great opportunity for improving crop performance through application of hybrid technology. In this respect, cytoplasmic male sterility (CMS) and sterility induced by photoperiod (PGMS)/temperature (TGMS) have greatly facilitated development of high-yielding hybrids in crops. Participation of non-coding (nc) RNA molecules in plant reproductive development is increasingly becoming evident. Recent breakthroughs in rice definitively associate ncRNAs with PGMS and TGMS. In case of CMS, the exact mechanism through which the mitochondrial ORFs exert influence on the development of male gametophyte remains obscure in several crops. High-throughput sequencing has enabled genome-wide discovery and validation of these regulatory molecules and their target genes, describing their potential roles performed in relation to CMS. Discovery of ncRNA localized in plant mtDNA with its possible implication in CMS induction is intriguing in this respect. Still, conclusive evidences linking ncRNA with CMS phenotypes are currently unavailable, demanding complementing genetic approaches like transgenics to substantiate the preliminary findings. Here, we review the recent literature on the contribution of ncRNAs in conferring male sterility to plants, with an emphasis on microRNAs. Also, we present a perspective on improved understanding about ncRNA-mediated regulatory pathways that control male sterility in plants. A refined understanding of plant male sterility would strengthen crop hybrid industry to deliver hybrids with improved performance.
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Affiliation(s)
- Ankita Mishra
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India
| | - Abhishek Bohra
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India.
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Hou X, Du Y, Liu X, Zhang H, Liu Y, Yan N, Zhang Z. Genome-Wide Analysis of Long Non-Coding RNAs in Potato and Their Potential Role in Tuber Sprouting Process. Int J Mol Sci 2017; 19:ijms19010101. [PMID: 29286332 PMCID: PMC5796051 DOI: 10.3390/ijms19010101] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 12/20/2017] [Accepted: 12/28/2017] [Indexed: 11/16/2022] Open
Abstract
Sprouting is a key factor affecting the quality of potato tubers. The present study aimed to compare the differential expression of long non-coding RNAs (lncRNAs) in the apical meristem during the dormancy release and sprouting stages by using lncRNA sequencing. Microscopic observations and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed the changes in the morphology and expression of lncRNAs in potato tubers during sprouting. Meristematic cells of potato tuber apical buds divided continuously and exhibited vegetative cone bulging and vascularisation. In all, 3175 lncRNAs were identified from the apical buds of potato tubers, among which 383 lncRNAs were up-regulated and 340 were down-regulated during sprouting. The GO enrichment analysis revealed that sprouting mainly influenced the expression of lncRNAs related to the cellular components of potato apical buds (e.g., cytoplasm and organelles) and cellular metabolic processes. The KEGG enrichment analysis also showed significant enrichment of specific metabolic pathways. In addition, 386 differentially expressed lncRNAs during sprouting were identified as putative targets of 235 potato miRNAs. Quantitative real-time polymerase chain reaction results agreed with the sequencing data. Our study provides the first systematic study of numerous lncRNAs involved in the potato tuber sprouting process and lays the foundation for further studies to elucidate their precise functions.
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Affiliation(s)
- Xiaodong Hou
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Yongmei Du
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Xinmin Liu
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Hongbo Zhang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Yanhua Liu
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Ning Yan
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Zhongfeng Zhang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
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Li ZF, Zhang YC, Chen YQ. miRNAs and lncRNAs in reproductive development. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 238:46-52. [PMID: 26259173 DOI: 10.1016/j.plantsci.2015.05.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/24/2015] [Accepted: 05/25/2015] [Indexed: 05/14/2023]
Abstract
Non-coding RNAs (ncRNAs) regulate gene expression at the transcriptional and post-transcriptional levels. Many ncRNAs have been identified in the past decade, including small ncRNAs, such as microRNAs (miRNAs), and long ncRNAs (lncRNAs). These novel molecules have important roles in a wide range of biological processes such as the regulation of reproduction and sex determination. Due to their ability to regulate specific genes or entire gene families, these molecules have the potential for uses in the development of breeding strategies as well as in the genetic modification of agronomic traits. In this review, we summarize recent progress on the understanding of plant miRNAs and lncRNAs in male and female development. We also discuss future challenges of using these molecules in agricultural applications, including transgenic plants in hybrid breeding, for novel genetic trait selection, for rapid character screening, and genetic modification for crop improvement.
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Affiliation(s)
- Zhe-Feng Li
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou 510275, China
| | - Yu-Chan Zhang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou 510275, China
| | - Yue-Qin Chen
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou 510275, China.
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14
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Song JH, Cao JS, Wang CG. BcMF11, a novel non-coding RNA gene from Brassica campestris, is required for pollen development and male fertility. PLANT CELL REPORTS 2013; 32:21-30. [PMID: 23064614 DOI: 10.1007/s00299-012-1337-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 08/09/2012] [Accepted: 08/17/2012] [Indexed: 05/23/2023]
Abstract
KEY MESSAGE : BcMF11 as a non-coding RNA gene has an essential role in pollen development, and might be useful for regulating the pollen fertility of crops by antisense RNA technology. We previously identified a 828-bp full-length cDNA of BcMF11, a novel pollen-specific non-coding mRNA-like gene from Chinese cabbage (Brassica campestris L. ssp. chinensis Makino). However, little information is known about the function of BcMF11 in pollen development. To investigate its exact biological roles in pollen development, the BcMF11 cDNA was antisense inhibited in transgenic Chinese cabbage under the control of a tapetum-specific promoter BcA9 and a constitutive promoter CaMV 35S. Antisense RNA transgenic plants displayed decreasing expression of BcMF11 and showed distinct morphological defects. Pollen germination test in vitro and in vivo of the transgenic plants suggested that inhibition of BcMF11 decreased pollen germination efficiency and delayed the pollen tubes' extension in the style. Under scanning electron microscopy, many shrunken and collapsed pollen grains were detected in the antisense BcMF11 transgenic Chinese cabbage. Further cytological observation revealed abnormal pollen development process in transgenic plants, including delayed degradation of tapetum, asynchronous separation of microspore, and aborted development of pollen grain. These results suggest that BcMF11, as a non-coding RNA, plays an essential role in pollen development and male fertility.
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Affiliation(s)
- Jiang-Hua Song
- College of Horticulture, Anhui Agricultural University, Hefei 230036, PR China
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15
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Grant-Downton R, Rodriguez-Enriquez J. Emerging Roles for Non-Coding RNAs in Male Reproductive Development in Flowering Plants. Biomolecules 2012; 2:608-21. [PMID: 24970151 PMCID: PMC4030863 DOI: 10.3390/biom2040608] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 11/19/2012] [Accepted: 11/23/2012] [Indexed: 01/07/2023] Open
Abstract
Knowledge of sexual reproduction systems in flowering plants is essential to humankind, with crop fertility vitally important for food security. Here, we review rapidly emerging new evidence for the key importance of non-coding RNAs in male reproductive development in flowering plants. From the commitment of somatic cells to initiating reproductive development through to meiosis and the development of pollen—containing the male gametes (sperm cells)—in the anther, there is now overwhelming data for a diversity of non-coding RNAs and emerging evidence for crucial roles for them in regulating cellular events at these developmental stages. A particularly exciting development has been the association of one example of cytoplasmic male sterility, which has become an unparalleled breeding tool for producing new crop hybrids, with a non-coding RNA locus.
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Affiliation(s)
- Robert Grant-Downton
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
| | - Josefina Rodriguez-Enriquez
- Instituto de Bioorgánica Antonio González (IUBO) University of La Laguna, Avenida Astrofísico Francisco Sánchez, 38206 La Laguna Tenerife, Spain.
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16
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BcMF20, a putative pollen-specific transcription factor from Brassica campestris ssp. chinensis. Mol Biol Rep 2011; 38:5321-5. [DOI: 10.1007/s11033-011-0682-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2010] [Accepted: 01/10/2011] [Indexed: 01/08/2023]
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