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Zhou L, Mao Y, Yang Y, Wang J, Zhong X, Han Y, Zhang Y, Shi Q, Huang X, Meyers BC, Zhu J, Yang Z. Temperature and light reverse the fertility of rice P/TGMS line ostms19 via reactive oxygen species homeostasis. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:2020-2032. [PMID: 38421616 PMCID: PMC11182586 DOI: 10.1111/pbi.14322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/30/2024] [Accepted: 02/17/2024] [Indexed: 03/02/2024]
Abstract
P/TGMS (Photo/thermo-sensitive genic male sterile) lines are crucial resources for two-line hybrid rice breeding. Previous studies revealed that slow development is a general mechanism for sterility-fertility conversion of P/TGMS in Arabidopsis. However, the difference in P/TGMS genes between rice and Arabidopsis suggests the presence of a distinct P/TGMS mechanism in rice. In this study, we isolated a novel P/TGMS line, ostms19, which shows sterility under high-temperature conditions and fertility under low-temperature conditions. OsTMS19 encodes a novel pentatricopeptide repeat (PPR) protein essential for pollen formation, in which a point mutation GTA(Val) to GCA(Ala) leads to ostms19 P/TGMS phenotype. It is highly expressed in the tapetum and localized to mitochondria. Under high temperature or long-day photoperiod conditions, excessive ROS accumulation in ostms19 anthers during pollen mitosis disrupts gene expression and intine formation, causing male sterility. Conversely, under low temperature or short-day photoperiod conditions, ROS can be effectively scavenged in anthers, resulting in fertility restoration. This indicates that ROS homeostasis is critical for fertility conversion. This relationship between ROS homeostasis and fertility conversion has also been observed in other tested rice P/TGMS lines. Therefore, we propose that ROS homeostasis is a general mechanism for the sterility-fertility conversion of rice P/TGMS lines.
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Affiliation(s)
- Lei Zhou
- Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life SciencesShanghai Normal UniversityShanghaiChina
| | - Yi‐Chen Mao
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life SciencesShanghai Normal UniversityShanghaiChina
| | - Yan‐Ming Yang
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life SciencesShanghai Normal UniversityShanghaiChina
| | - Jun‐Jie Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life SciencesShanghai Normal UniversityShanghaiChina
| | - Xiang Zhong
- Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life SciencesShanghai Normal UniversityShanghaiChina
| | - Yu Han
- Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life SciencesShanghai Normal UniversityShanghaiChina
| | - Yan‐Fei Zhang
- Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life SciencesShanghai Normal UniversityShanghaiChina
| | - Qiang‐Sheng Shi
- Jiangxi Yangtze River Economic Zone Research InstituteJiujiang UniversityJiujiangJiangxiChina
| | - Xue‐hui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life SciencesShanghai Normal UniversityShanghaiChina
| | | | - Jun Zhu
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life SciencesShanghai Normal UniversityShanghaiChina
| | - Zhong‐Nan Yang
- Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life SciencesShanghai Normal UniversityShanghaiChina
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2
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Numan M, Sun Y, Li G. Exploring the emerging role of long non-coding RNAs (lncRNAs) in plant biology: Functions, mechanisms of action, and future directions. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 212:108797. [PMID: 38850732 DOI: 10.1016/j.plaphy.2024.108797] [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: 11/14/2023] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/10/2024]
Abstract
Long non-coding RNAs (lncRNAs) are a class of RNA transcripts that surpass 200 nucleotides in length and lack discernible coding potential. LncRNAs that have been functionally characterized have pivotal functions in several plant processes, including the regulation of flowering, and development of lateral roots. It also plays a crucial role in the plant's response to abiotic stressors and exhibits vital activities in environmental adaptation. The progress in NGS (next-generation sequencing) and functional genomics technology has facilitated the discovery of lncRNA in plant species. This review is a brief explanation of lncRNA genomics, its molecular role, and the mechanism of action in plants. The review also addresses the challenges encountered in this field and highlights promising molecular and computational methodologies that can aid in the comparative and functional analysis of lncRNAs.
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Affiliation(s)
- Mian Numan
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China.
| | - Yuge Sun
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China.
| | - Guanglin Li
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China.
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Zhan J, Bélanger S, Lewis S, Teng C, McGregor M, Beric A, Schon MA, Nodine MD, Meyers BC. Premeiotic 24-nt phasiRNAs are present in the Zea genus and unique in biogenesis mechanism and molecular function. Proc Natl Acad Sci U S A 2024; 121:e2402285121. [PMID: 38739785 PMCID: PMC11127045 DOI: 10.1073/pnas.2402285121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 04/12/2024] [Indexed: 05/16/2024] Open
Abstract
Reproductive phasiRNAs (phased, small interfering RNAs) are broadly present in angiosperms and play crucial roles in sustaining male fertility. While the premeiotic 21-nt (nucleotides) phasiRNAs and meiotic 24-nt phasiRNA pathways have been extensively studied in maize (Zea mays) and rice (Oryza sativa), a third putative category of reproductive phasiRNAs-named premeiotic 24-nt phasiRNAs-have recently been reported in barley (Hordeum vulgare) and wheat (Triticum aestivum). To determine whether premeiotic 24-nt phasiRNAs are also present in maize and related species and begin to characterize their biogenesis and function, we performed a comparative transcriptome and degradome analysis of premeiotic and meiotic anthers from five maize inbred lines and three teosinte species/subspecies. Our data indicate that a substantial subset of the 24-nt phasiRNA loci in maize and teosinte are already highly expressed at the premeiotic phase. The premeiotic 24-nt phasiRNAs are similar to meiotic 24-nt phasiRNAs in genomic origin and dependence on DCL5 (Dicer-like 5) for biogenesis, however, premeiotic 24-nt phasiRNAs are unique in that they are likely i) not triggered by microRNAs, ii) not loaded by AGO18 proteins, and iii) not capable of mediating PHAS precursor cleavage. In addition, we also observed a group of premeiotic 24-nt phasiRNAs in rice using previously published data. Together, our results indicate that the premeiotic 24-nt phasiRNAs constitute a unique class of reproductive phasiRNAs and are present more broadly in the grass family (Poaceae) than previously known.
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Affiliation(s)
- Junpeng Zhan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan430070, China
- Hubei Hongshan Laboratory, Wuhan430070, China
- Donald Danforth Plant Science Center, St. Louis, MO63132
| | - Sébastien Bélanger
- Donald Danforth Plant Science Center, St. Louis, MO63132
- The James Hutton Institute, Dundee, ScotlandDD2 5DA, United Kingdom
| | - Scott Lewis
- Donald Danforth Plant Science Center, St. Louis, MO63132
- Division of Biology and Biomedical Sciences, Washington University, St. Louis, MO63130
| | - Chong Teng
- Donald Danforth Plant Science Center, St. Louis, MO63132
- Genome Center, University of California, Davis, CA95616
- Department of Plant Sciences, University of California, Davis, CA95616
| | | | - Aleksandra Beric
- Donald Danforth Plant Science Center, St. Louis, MO63132
- Division of Plant Science and Technology, University of Missouri, Columbia, MO65211
| | - Michael A. Schon
- Laboratory of Molecular Biology, Wageningen University, Wageningen6708 PB, the Netherlands
| | - Michael D. Nodine
- Laboratory of Molecular Biology, Wageningen University, Wageningen6708 PB, the Netherlands
| | - Blake C. Meyers
- Donald Danforth Plant Science Center, St. Louis, MO63132
- Genome Center, University of California, Davis, CA95616
- Department of Plant Sciences, University of California, Davis, CA95616
- Division of Plant Science and Technology, University of Missouri, Columbia, MO65211
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Min Q, Zheng K, Liu T, Wang Z, Xue X, Li W, Liu Y, Zhang Y, Qiao F, Chen J, Su X, Han S. Transcriptomic Profiles of Long Noncoding RNAs and Their Target Protein-Coding Genes Reveals Speciation Adaptation on the Qinghai-Xizang (Tibet) Plateau in Orinus. BIOLOGY 2024; 13:349. [PMID: 38785831 PMCID: PMC11118044 DOI: 10.3390/biology13050349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/07/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024]
Abstract
Long noncoding RNAs (lncRNAs) are RNA molecules longer than 200 nt, which lack the ability to encode proteins and are involved in multifarious growth, development, and regulatory processes in plants and mammals. However, the environmental-regulated expression profiles of lncRNAs in Orinus that may associated with their adaptation on the Qinghai-Xizang (Tibet) Plateau (QTP) have never been characterized. Here, we utilized transcriptomic sequencing data of two Orinus species (O. thoroldii and O. kokonoricus) to identify 1624 lncRNAs, including 1119 intergenic lncRNAs, 200 antisense lncRNAs, five intronic lncRNAs, and 300 sense lncRNAs. In addition, the evolutionary relationships of Orinus lncRNAs showed limited sequence conservation among 39 species, which implied that Orinus-specific lncRNAs contribute to speciation adaptation evolution. Furthermore, considering the cis-regulation mechanism, from 286 differentially expressed lncRNAs (DElncRNAs) and their nearby protein coding genes (PCGs) between O. thoroldii and O. kokonoricus, 128 lncRNA-PCG pairs were obtained in O. thoroldii, whereas 92 lncRNA-PCG pairs were obtained in O. kokonoricus. In addition, a total of 19 lncRNA-PCG pairs in O. thoroldii and 14 lncRNA-PCG pairs in O. kokonoricus were found to participate in different biological processes, indicating that the different expression profiles of DElncRNAs between O. thoroldii and O. kokonoricus were associated with their adaptation at different elevations on the QTP. We also found several pairs of DElncRNA nearby transcription factors (TFs), indicating that these DElncRNAs regulate the expression of TFs to aid O. thoroldii in adapting to the environment. Therefore, this work systematically identified a series of lncRNAs in Orinus, laying the groundwork for further exploration into the biological function of Orinus in environmental adaptation.
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Affiliation(s)
- Qinyue Min
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, School of Life Sciences, Qinghai Normal University, Xining 810008, China; (Q.M.); (Z.W.); (Y.L.); (Y.Z.); (F.Q.); (J.C.)
| | - Kaifeng Zheng
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (K.Z.); (X.X.); (W.L.)
| | - Tao Liu
- School of Ecology and Environmental Science, Qinghai University of Science and Technology, Xining 810016, China;
| | - Zitao Wang
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, School of Life Sciences, Qinghai Normal University, Xining 810008, China; (Q.M.); (Z.W.); (Y.L.); (Y.Z.); (F.Q.); (J.C.)
| | - Xiuhua Xue
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (K.Z.); (X.X.); (W.L.)
| | - Wanjie Li
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (K.Z.); (X.X.); (W.L.)
| | - Yuping Liu
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, School of Life Sciences, Qinghai Normal University, Xining 810008, China; (Q.M.); (Z.W.); (Y.L.); (Y.Z.); (F.Q.); (J.C.)
| | - Yanfen Zhang
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, School of Life Sciences, Qinghai Normal University, Xining 810008, China; (Q.M.); (Z.W.); (Y.L.); (Y.Z.); (F.Q.); (J.C.)
| | - Feng Qiao
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, School of Life Sciences, Qinghai Normal University, Xining 810008, China; (Q.M.); (Z.W.); (Y.L.); (Y.Z.); (F.Q.); (J.C.)
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining 810008, China
| | - Jinyuan Chen
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, School of Life Sciences, Qinghai Normal University, Xining 810008, China; (Q.M.); (Z.W.); (Y.L.); (Y.Z.); (F.Q.); (J.C.)
| | - Xu Su
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, School of Life Sciences, Qinghai Normal University, Xining 810008, China; (Q.M.); (Z.W.); (Y.L.); (Y.Z.); (F.Q.); (J.C.)
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining 810008, China
| | - Shengcheng Han
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (K.Z.); (X.X.); (W.L.)
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining 810008, China
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5
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Wang M, Peng X, Wang C, Tang X. Identification of two plastid transit peptides for construction of pollen-inactivation system in rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:33. [PMID: 38694254 PMCID: PMC11058180 DOI: 10.1007/s11032-024-01471-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/22/2024] [Indexed: 05/04/2024]
Abstract
Hybrid seed production technology (SPT) is achieved through the utilization of a recessive nuclear male-sterile mutant transformed with a transgenic cassette comprising three essential components: the wild-type gene to restore the fertility of the male-sterile mutant, an α-amylase gene to disrupt transgenic pollen grains, and red fluorescence protein gene DsRed to distinguish the transgenic seeds from the nontransgenic male sterile seeds. In rice, we establish the pollen disruption system by introducing an amyloplast targeting signal peptide (ASP) at the N-terminus of maize α-amylase protein ZM-AA1ΔSP (ZM-AA1 with the N-terminal signal peptide removed). The ASP facilitates the transport of ZM-AA1ΔSP protein into amyloplast where it degrades starch, resulting in disruption of the pollen fertility. To obtain such signal peptides for rice, we searched the rice proteins homologous to the defined wheat amyloplast proteins followed by protein-protein interaction network predictions and targeting signal peptides prediction. These analyses enabled the identification of four candidate ASPs in rice, which were designated as ASP1, ASP2, ASP3, and ASP4, respectively. ASP1 and ASP2, when linked with ZM-AA1ΔSP, exhibited the capability to disrupt transgenic pollen grains, whereas ASP3 and ASP4 did not produce this effect. Interestingly, the localization experiments showed that ASP3 and ASP4 were able to target the proteins into chloroplast. The ASP1 and ASP2 sequences provide valuable tools for genetic engineering of the rice male-sterile system, which will contribute to the hybrid rice breeding and production. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01471-y.
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Affiliation(s)
- Menglong Wang
- School of Life Sciences, Huizhou University, Huizhou, 516007 China
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631 China
| | - Xiaoqun Peng
- School of Life Sciences, Huizhou University, Huizhou, 516007 China
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631 China
| | - Changjian Wang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631 China
| | - Xiaoyan Tang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631 China
- Shenzhen Institute of Molecular Crop Design, Shenzhen, 518107 China
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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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Zhan J, Bélanger S, Lewis S, Teng C, McGregor M, Beric A, Schon MA, Nodine MD, Meyers BC. Premeiotic 24-nt phasiRNAs are present in the Zea genus and unique in biogenesis mechanism and molecular function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.29.587306. [PMID: 38617318 PMCID: PMC11014486 DOI: 10.1101/2024.03.29.587306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Reproductive phasiRNAs are broadly present in angiosperms and play crucial roles in sustaining male fertility. While the premeiotic 21-nt phasiRNAs and meiotic 24-nt phasiRNA pathways have been extensively studied in maize (Zea mays) and rice (Oryza sativa), a third putative category of reproductive phasiRNAs-named premeiotic 24-nt phasiRNAs-have recently been reported in barley (Hordeum vulgare) and wheat (Triticum aestivum). To determine whether premeiotic 24-nt phasiRNAs are also present in maize and related species and begin to characterize their biogenesis and function, we performed a comparative transcriptome and degradome analysis of premeiotic and meiotic anthers from five maize inbred lines and three teosinte species/subspecies. Our data indicate that a substantial subset of the 24-nt phasiRNA loci in maize and teosinte are already highly expressed at premeiotic phase. The premeiotic 24-nt phasiRNAs are similar to meiotic 24-nt phasiRNAs in genomic origin and dependence on DCL5 for biogenesis, however, premeiotic 24-nt phasiRNAs are unique in that they are likely (i) not triggered by microRNAs, (ii) not loaded by AGO18 proteins, and (iii) not capable of mediating cis-cleavage. In addition, we also observed a group of premeiotic 24-nt phasiRNAs in rice using previously published data. Together, our results indicate that the premeiotic 24-nt phasiRNAs constitute a unique class of reproductive phasiRNAs and are present more broadly in the grass family (Poaceae) than previously known.
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Affiliation(s)
- Junpeng Zhan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Sébastien Bélanger
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
- The James Hutton Institute, Dundee, Scotland DD2 5DA, UK
| | - Scott Lewis
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
- Division of Biology and Biomedical Sciences, Washington University, St. Louis, MO 63130, USA
| | - Chong Teng
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | | | - Aleksandra Beric
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
| | - Michael A. Schon
- Laboratory of Molecular Biology, Wageningen University, Wageningen 6708 PB, the Netherlands
| | - Michael D. Nodine
- Laboratory of Molecular Biology, Wageningen University, Wageningen 6708 PB, the Netherlands
| | - Blake C. Meyers
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
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Shi D, Huang H, Zhang Y, Qian Z, Du J, Huang L, Yan X, Lin S. The roles of non-coding RNAs in male reproductive development and abiotic stress responses during this unique process in flowering plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 341:111995. [PMID: 38266717 DOI: 10.1016/j.plantsci.2024.111995] [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: 09/10/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 01/26/2024]
Abstract
Successful male reproductive development is the guarantee for sexual reproduction of flowering plants. Male reproductive development is a complicated and multi-stage process that integrates physiological processes and adaptation and tolerance to a myriad of environmental stresses. This well-coordinated process is governed by genetic and epigenetic machineries. Non-coding RNAs (ncRNAs) play pleiotropic roles in the plant growth and development. The identification, characterization and functional analysis of ncRNAs and their target genes have opened a new avenue for comprehensively revealing the regulatory network of male reproductive development and its response to environmental stresses in plants. This review briefly addresses the types, origin, biogenesis and mechanisms of ncRNAs in plants, highlights important updates on the roles of ncRNAs in regulating male reproductive development and emphasizes the contribution of ncRNAs, especially miRNAs and lncRNAs, in responses to abiotic stresses during this unique process in flowering plants.
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Affiliation(s)
- Dexi Shi
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Huiting Huang
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Yuting Zhang
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Zhihao Qian
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Jiao Du
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Li Huang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Xiufeng Yan
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou 325035, China.
| | - Sue Lin
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou 325035, China.
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9
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Shi C, Zou W, Zhu Y, Zhang J, Teng C, Wei H, He H, He W, Liu X, Zhang B, Zhang H, Leng Y, Guo M, Wang X, Chen W, Zhang Z, Qian H, Cui Y, Jiang H, Chen Y, Fei Q, Meyers BC, Liang W, Qian Q, Shang L. mRNA cleavage by 21-nucleotide phasiRNAs determines temperature-sensitive male sterility in rice. PLANT PHYSIOLOGY 2024; 194:2354-2371. [PMID: 38060676 DOI: 10.1093/plphys/kiad654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 11/15/2023] [Indexed: 04/02/2024]
Abstract
Temperature-sensitive male sterility is one of the core components for hybrid rice (Oryza sativa) breeding based on the 2-line system. We previously found that knockout of ARGONAUTE 1d (AGO1d) causes temperature-sensitive male sterility in rice by influencing phased small interfering RNA (phasiRNA) biogenesis and function. However, the specific phasiRNAs and their targets underlying the temperature-sensitive male sterility in the ago1d mutant remain unknown. Here, we demonstrate that the ago1d mutant displays normal female fertility but complete male sterility at low temperature. Through a multiomics analysis of small RNA (sRNA), degradome, and transcriptome, we found that 21-nt phasiRNAs account for the greatest proportion of the 21-nt sRNA species in rice anthers and are sensitive to low temperature and markedly downregulated in the ago1d mutant. Moreover, we found that 21-nt phasiRNAs are essential for the mRNA cleavage of a set of fertility- and cold tolerance-associated genes, such as Earlier Degraded Tapetum 1 (EDT1), Tapetum Degeneration Retardation (TDR), OsPCF5, and OsTCP21, directly or indirectly determined by AGO1d-mediated gene silencing. The loss of function of 21-nt phasiRNAs can result in upregulation of their targets and causes varying degrees of defects in male fertility and grain setting. Our results highlight the essential functions of 21-nt phasiRNAs in temperature-sensitive male sterility in rice and suggest their promising application in 2-line hybrid rice breeding in the future.
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Affiliation(s)
- Chuanlin Shi
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Wenli Zou
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yiwang Zhu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Jie Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chong Teng
- Donald Danforth Plant Science Center, Saint Louis, MI 63132, USA
| | - Hua Wei
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Huiying He
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Wenchuang He
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xiangpei Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Bin Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Hong Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yue Leng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Mingliang Guo
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xianmeng Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Wu Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Zhipeng Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Hongge Qian
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yan Cui
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Hongshuang Jiang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Ying Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Qili Fei
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Blake C Meyers
- Donald Danforth Plant Science Center, Saint Louis, MI 63132, USA
- Division of Plant Sciences and Technology, University of Missouri-Columbia, Columbia, MI 65211, USA
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qian Qian
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, Zhejiang, China
- Yazhouwan National Laboratory, No. 8 Huanjin Road, Yazhou District, Sanya City, Hainan Province 572024, China
| | - Lianguang Shang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Yazhouwan National Laboratory, No. 8 Huanjin Road, Yazhou District, Sanya City, Hainan Province 572024, China
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10
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Zheng X, Wei F, Cheng C, Qian Q. A historical review of hybrid rice breeding. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:532-545. [PMID: 38103034 DOI: 10.1111/jipb.13598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/13/2023] [Accepted: 12/13/2023] [Indexed: 12/17/2023]
Abstract
The development of germplasm resources and advances in breeding methods have led to steady increases in yield and quality of rice (Oryza sativa L.). Three milestones in the recent history of rice breeding have contributed to these increases: dwarf rice breeding, hybrid rice breeding, and super rice breeding. On the 50th anniversary of the success of three-line hybrid rice, we highlight important scientific discoveries in rice breeding that were made by Chinese scientists and summarize the broader history of the field. We discuss the strategies that could be used in the future to optimize rice breeding further in the hope that China will continue to play a leading role in international rice breeding.
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Affiliation(s)
- Xiaoming Zheng
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Fei Wei
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Cheng Cheng
- Yazhouwan National Laboratory, Sanya City, 572024, China
| | - Qian Qian
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Yazhouwan National Laboratory, Sanya City, 572024, China
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11
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Wang H, Jia Y, Bai X, Gong W, Liu G, Wang H, Xin J, Wu Y, Zheng H, Liu H, Wang J, Zou D, Zhao H. Whole-Transcriptome Profiling and Functional Prediction of Long Non-Coding RNAs Associated with Cold Tolerance in Japonica Rice Varieties. Int J Mol Sci 2024; 25:2310. [PMID: 38396991 PMCID: PMC10889138 DOI: 10.3390/ijms25042310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/07/2024] [Accepted: 02/10/2024] [Indexed: 02/25/2024] Open
Abstract
Low-temperature chilling is a major abiotic stress leading to reduced rice yield and is a significant environmental threat to food security. Low-temperature chilling studies have focused on physiological changes or coding genes. However, the competitive endogenous RNA mechanism in rice at low temperatures has not been reported. Therefore, in this study, antioxidant physiological indices were combined with whole-transcriptome data through weighted correlation network analysis, which found that the gene modules had the highest correlation with the key antioxidant enzymes superoxide dismutase and peroxidase. The hub genes of the superoxide dismutase-related module included the UDP-glucosyltransferase family protein, sesquiterpene synthase and indole-3-glycerophosphatase gene. The hub genes of the peroxidase-related module included the WRKY transcription factor, abscisic acid signal transduction pathway-related gene plasma membrane hydrogen-ATPase and receptor-like kinase. Therefore, we selected the modular hub genes and significantly enriched the metabolic pathway genes to construct the key competitive endogenous RNA networks, resulting in three competitive endogenous RNA networks of seven long non-coding RNAs regulating three co-expressed messenger RNAs via four microRNAs. Finally, the negative regulatory function of the WRKY transcription factor OsWRKY61 was determined via subcellular localization and validation of the physiological indices in the mutant.
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Affiliation(s)
| | - Yan Jia
- Correspondence: (Y.J.); (H.Z.)
| | | | | | | | | | | | | | | | | | | | | | - Hongwei Zhao
- Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of Education/College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (H.W.); (X.B.); (W.G.); (G.L.); (H.W.); (J.X.); (Y.W.); (H.Z.); (H.L.); (J.W.); (D.Z.)
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12
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Babaei S, Bhalla PL, Singh MB. Identifying long non-coding RNAs involved in heat stress response during wheat pollen development. FRONTIERS IN PLANT SCIENCE 2024; 15:1344928. [PMID: 38379952 PMCID: PMC10876783 DOI: 10.3389/fpls.2024.1344928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 01/17/2024] [Indexed: 02/22/2024]
Abstract
Introduction Wheat is a staple food crop for over one-third of the global population. However, the stability of wheat productivity is threatened by heat waves associated with climate change. Heat stress at the reproductive stage can result in pollen sterility and failure of grain development. Methods This study used transcriptome data analysis to explore the specific expression of long non-coding RNAs (lncRNAs) in response to heat stress during pollen development in four wheat cultivars. Results and discussion We identified 11,054 lncRNA-producing loci, of which 5,482 lncRNAs showed differential expression in response to heat stress. Heat-responsive lncRNAs could target protein-coding genes in cis and trans and in lncRNA-miRNA-mRNA regulatory networks. Gene ontology analysis predicted that target protein-coding genes of lncRNAs regulate various biological processes such as hormonal responses, protein modification and folding, response to stress, and biosynthetic and metabolic processes. We also noted some paired lncRNA/protein-coding gene modules and some lncRNA-miRNA-mRNA regulatory modules shared in two or more wheat cultivars. These modules were related to regulating plant responses to heat stress, such as heat-shock proteins and transcription factors, and protein domains, such as MADS-box, Myc-type, and Alpha crystallin/Hsp20 domain. Conclusion Our results provide the basic knowledge and molecular resources for future functional studies investigating wheat reproductive development under heat stress.
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Affiliation(s)
| | | | - Mohan B. Singh
- Plant Molecular Biology and Biotechnology Laboratory, School of Agriculture, Food and Ecosystem Sciences, The University of Melbourne, Melbourne, VIC, Australia
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13
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Cai J, Zhang Y, He R, Jiang L, Qu Z, Gu J, Yang J, Legascue MF, Wang ZY, Ariel F, Adelson DL, Zhu Y, Wang D. LncRNA DANA1 promotes drought tolerance and histone deacetylation of drought responsive genes in Arabidopsis. EMBO Rep 2024; 25:796-812. [PMID: 38177920 PMCID: PMC10897447 DOI: 10.1038/s44319-023-00030-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 11/29/2023] [Accepted: 12/04/2023] [Indexed: 01/06/2024] Open
Abstract
Although many long noncoding RNAs have been discovered in plants, little is known about their biological function and mode of action. Here we show that the drought-induced long intergenic noncoding RNA DANA1 interacts with the L1p/L10e family member protein DANA1-INTERACTING PROTEIN 1 (DIP1) in the cell nucleus of Arabidopsis, and both DANA1 and DIP1 promote plant drought resistance. DANA1 and DIP1 increase histone deacetylase HDA9 binding to the CYP707A1 and CYP707A2 loci. DIP1 further interacts with PWWP3, a member of the PEAT complex that associates with HDA9 and has histone deacetylase activity. Mutation of DANA1 enhances CYP707A1 and CYP707A2 acetylation and expression resulting in impaired drought tolerance, in agreement with dip1 and pwwp3 mutant phenotypes. Our results demonstrate that DANA1 is a positive regulator of drought response and that DANA1 works jointly with the novel chromatin-related factor DIP1 on epigenetic reprogramming of the plant transcriptome during the response to drought.
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Affiliation(s)
- Jingjing Cai
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, 330031, Jiangxi, China
| | - Yongdi Zhang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, 330031, Jiangxi, China
| | - Reqing He
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, 330031, Jiangxi, China
| | - Liyun Jiang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, 330031, Jiangxi, China
| | - Zhipeng Qu
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, 5005, SA, Australia
| | - Jinbao Gu
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, 510316, Guangdong, China
| | - Jun Yang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, 330031, Jiangxi, China
| | - María Florencia Legascue
- Instituto de Agrobiotecnología del Litoral, CONICET, FBCB, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, Santa Fe, 3000, Argentina
| | - Zhen-Yu Wang
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, 510316, Guangdong, China
| | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral, CONICET, FBCB, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, Santa Fe, 3000, Argentina
| | - David L Adelson
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, 5005, SA, Australia
| | - Youlin Zhu
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, 330031, Jiangxi, China
| | - Dong Wang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, 330031, Jiangxi, China.
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14
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Weng M, Zhang D, Wang H, Yang C, Lin H, Pan Y, Lin Y. Long non-coding RNAs and their potential function in response to postharvest senescence of Sparassis latifolia during cold storage. Sci Rep 2024; 14:747. [PMID: 38185662 PMCID: PMC10772075 DOI: 10.1038/s41598-023-46744-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 11/04/2023] [Indexed: 01/09/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) have been shown to play crucial roles in response to aging processes. However, how lncRNAs regulate postharvest senescence of Sparassis latifolia (S. latifolia) with oriented polypropylene (OPP) film packing during cold storage remains unclear. In this study, we performed RNA-seq using the fruiting bodies of S. latifolia stored at 4 ℃ for 0, 8, 16 and 24 days after harvest, and profiled the lncRNA and mRNA transcriptome, respectively. In total, 1003 putative lncRNAs were identified, and there were 495, 483 and 162 differentially expressed (DE) lncRNAs, and 3680, 3941 and 1870 differentially expressed mRNAs after 8, 16 and 24 days of storage, respectively, compared to 0 day of storage. Target genes of differentially expressed lncRNAs were found to significantly associate with carbon and energy metabolism, response to abiotic stimulus, amino acid biosynthesis and metabolism, and protein synthesis and transcription. In addition, DE-lncRNA-mRNA co-expression networks in response to aging stress were also constructed. Taken together, these results confirm the regulatory role of lncRNAs in postharvest senescence of S. latifolia and will facilitate for improving preservation method.
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Affiliation(s)
- Mengting Weng
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
- National and Local Joint Engineering Research Center for Breeding & Cultivation of Featured Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
| | - Di Zhang
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
- National and Local Joint Engineering Research Center for Breeding & Cultivation of Featured Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
| | - Hongyu Wang
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
- National and Local Joint Engineering Research Center for Breeding & Cultivation of Featured Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
| | - Chi Yang
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
- National and Local Joint Engineering Research Center for Breeding & Cultivation of Featured Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
| | - Hongyi Lin
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
- National and Local Joint Engineering Research Center for Breeding & Cultivation of Featured Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
| | - Yanfang Pan
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Yanquan Lin
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China.
- National and Local Joint Engineering Research Center for Breeding & Cultivation of Featured Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China.
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15
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Lu Z, Wang X, Lin X, Mostafa S, Bao H, Ren S, Cui J, Jin B. Genome-Wide Identification and Characterization of Long Non-Coding RNAs Associated with Floral Scent Formation in Jasmine ( Jasminum sambac). Biomolecules 2023; 14:45. [PMID: 38254645 PMCID: PMC10812929 DOI: 10.3390/biom14010045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/19/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as curial regulators of diverse biological processes in plants. Jasmine (Jasminum sambac) is a world-renowned ornamental plant for its attractive and exceptional flower fragrance. However, to date, no systematic screening of lncRNAs and their regulatory roles in the production of the floral fragrance of jasmine flowers has been reported. In this study, we identified a total of 31,079 novel lncRNAs based on an analysis of strand-specific RNA-Seq data from J. sambac flowers at different stages. The lncRNAs identified in jasmine flowers exhibited distinct characteristics compared with protein-coding genes (PCGs), including lower expression levels, shorter transcript lengths, and fewer exons. Certain jasmine lncRNAs possess detectable sequence conservation with other species. Expression analysis identified 2752 differentially expressed lncRNAs (DE_lncRNAs) and 8002 DE_PCGs in flowers at the full-blooming stage. DE_lncRNAs could potentially cis- and trans-regulate PCGs, among which DE_lincRNAs and their targets showed significant opposite expression patterns. The flowers at the full-blooming stage are specifically enriched with abundant phenylpropanoids and terpenoids potentially contributed by DE_lncRNA cis-regulated PCGs. Notably, we found that many cis-regulated DE_lncRNAs may be involved in terpenoid and phenylpropanoid/benzenoid biosynthesis pathways, which potentially contribute to the production of jasmine floral scents. Our study reports numerous jasmine lncRNAs and identifies floral-scent-biosynthesis-related lncRNAs, which highlights their potential functions in regulating the floral scent formation of jasmine and lays the foundations for future molecular breeding.
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Affiliation(s)
- Zhaogeng Lu
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (Z.L.)
| | - Xinwen Wang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (Z.L.)
| | - Xinyi Lin
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (Z.L.)
| | - Salma Mostafa
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (Z.L.)
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Hongyan Bao
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (Z.L.)
| | - Shixiong Ren
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (Z.L.)
| | - Jiawen Cui
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (Z.L.)
| | - Biao Jin
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (Z.L.)
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16
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Luo L, Molthoff J, Li Q, Liu Y, Luo S, Li N, Xuan S, Wang Y, Shen S, Bovy AG, Zhao J, Chen X. Identification of candidate genes associated with less-photosensitive anthocyanin phenotype using an EMS mutant ( pind) in eggplant ( Solanum melongena L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1282661. [PMID: 38169942 PMCID: PMC10758619 DOI: 10.3389/fpls.2023.1282661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/24/2023] [Indexed: 01/05/2024]
Abstract
Eggplant (Solanum melongena L.) is a highly nutritious and economically important vegetable crop. However, the fruit peel of eggplant often shows poor coloration owing to low-light intensity during cultivation, especially in the winter. The less-photosensitive varieties produce anthocyanin in low light or even dark conditions, making them valuable breeding materials. Nevertheless, genes responsible for anthocyanin biosynthesis in less-photosensitive eggplant varieties are not characterized. In this study, an EMS mutant, named purple in the dark (pind), was used to identify the key genes responsible for less-photosensitive coloration. Under natural conditions, the peel color and anthocyanin content in pind fruits were similar to that of wildtype '14-345'. The bagged pind fruits were light purple, whereas those of '14-345' were white; and the anthocyanin content in the pind fruit peel was significantly higher than that in '14-345'. Genetic analysis revealed that the less-photosensitive trait was controlled by a single dominant gene. The candidate gene was mapped on chromosome 10 in the region 7.72 Mb to 11.71 Mb. Thirty-five differentially expressed genes, including 12 structural genes, such as CHS, CHI, F3H, DFR, ANS, and UFGT, and three transcription factors MYB113, GL3, and TTG2, were identified in pind using RNA-seq. Four candidate genes EGP21875 (myb domain protein 113), EGP21950 (unknown protein), EGP21953 (CAAX amino-terminal protease family protein), and EGP21961 (CAAX amino-terminal protease family protein) were identified as putative genes associated with less-photosensitive anthocyanin biosynthesis in pind. These findings may clarify the molecular mechanisms underlying less-photosensitive anthocyanin biosynthesis in eggplant.
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Affiliation(s)
- Lei Luo
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, International Joint R & D Center of Hebei Province in Modern Agricultural Biotechnology, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Jos Molthoff
- Plant Breeding, Wageningen University and Research, Wageningen, Netherlands
| | - Qiang Li
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, International Joint R & D Center of Hebei Province in Modern Agricultural Biotechnology, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Ying Liu
- Horticulture and Product Physiology, Wageningen University and Research, Wageningen, Netherlands
| | - Shuangxia Luo
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, International Joint R & D Center of Hebei Province in Modern Agricultural Biotechnology, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Na Li
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, International Joint R & D Center of Hebei Province in Modern Agricultural Biotechnology, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Shuxin Xuan
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, International Joint R & D Center of Hebei Province in Modern Agricultural Biotechnology, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Yanhua Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, International Joint R & D Center of Hebei Province in Modern Agricultural Biotechnology, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Shuxing Shen
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, International Joint R & D Center of Hebei Province in Modern Agricultural Biotechnology, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Arnaud G. Bovy
- Plant Breeding, Wageningen University and Research, Wageningen, Netherlands
| | - Jianjun Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, International Joint R & D Center of Hebei Province in Modern Agricultural Biotechnology, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Xueping Chen
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, International Joint R & D Center of Hebei Province in Modern Agricultural Biotechnology, College of Horticulture, Hebei Agricultural University, Baoding, China
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17
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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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18
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Yang Y, Zhang C, Li H, Yang Z, Xu Z, Tai D, Ni D, Wei P, Yi C, Yang J, Ding Y. An epi-allele of SMS causes Sanming dominant genic male sterility in rice. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2701-2710. [PMID: 37930474 DOI: 10.1007/s11427-023-2457-7] [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: 08/27/2023] [Accepted: 09/22/2023] [Indexed: 11/07/2023]
Abstract
Male sterility is an important trait in rice for hybrid rice (Oryza sativa) breeding. However, the factors involved in dominant male sterility are largely unknown. Here, we identified a gene from Sanming dominant genic male sterile rice, named Sanming dominant male sterility (SMS), and reported that an epi-allele of this locus contributes to male sterility. Segregation analysis attributed dominant male sterility to a single locus, SMS, which we characterized using a male-sterile near isogenic line (NIL) of rice cultivar 93-11. The SMS locus was heterozygous in the male-sterile 93-11 NIL, containing an epi-allele identical to that in 93-11, and an epi-allele identical to that in rice cultivar Nipponbare, which we refer to as SMS9 and SMSN, respectively. SMS9 is silent and hyper-methylated, whereas SMSN is expressed and hypo-methylated in the 93-11 NIL. Overexpressing SMSN led to male sterility. Mutations in SMS rescued the male sterility of the 93-11 NIL. Interestingly, we observed the duplication of SMSN in Nipponbare, but did not observe the duplication of SMS9 in 93-11. Together, these findings suggest that the reduced methylation and enhanced expression of the SMSN epi-allele in the 93-11 NIL is responsible for its role in conferring dominant male sterility.
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Affiliation(s)
- Yachun Yang
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230036, China
- Institute of Health and Medicine, Hefei Comprehesive National Science Center, Hefei, 230031, China
| | - Cheng Zhang
- Institute of Health and Medicine, Hefei Comprehesive National Science Center, Hefei, 230031, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics; School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Hao Li
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230036, China
- Institute of Health and Medicine, Hefei Comprehesive National Science Center, Hefei, 230031, China
| | - Zeyuan Yang
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics; School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Zuntao Xu
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230036, China
- Institute of Health and Medicine, Hefei Comprehesive National Science Center, Hefei, 230031, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics; School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Dewei Tai
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230036, China
- Institute of Health and Medicine, Hefei Comprehesive National Science Center, Hefei, 230031, China
| | - Dahu Ni
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230036, China
| | - Pengcheng Wei
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230036, China
| | - Chengxin Yi
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230036, China
| | - Jianbo Yang
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230036, China.
| | - Yong Ding
- Institute of Health and Medicine, Hefei Comprehesive National Science Center, Hefei, 230031, China.
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics; School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China.
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19
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Domínguez-Rosas E, Hernández-Oñate MÁ, Fernandez-Valverde SL, Tiznado-Hernández ME. Plant long non-coding RNAs: identification and analysis to unveil their physiological functions. FRONTIERS IN PLANT SCIENCE 2023; 14:1275399. [PMID: 38023843 PMCID: PMC10644886 DOI: 10.3389/fpls.2023.1275399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 10/09/2023] [Indexed: 12/01/2023]
Abstract
Eukaryotic genomes encode thousands of RNA molecules; however, only a minimal fraction is translated into proteins. Among the non-coding elements, long non-coding RNAs (lncRNAs) play important roles in diverse biological processes. LncRNAs are associated mainly with the regulation of the expression of the genome; nonetheless, their study has just scratched the surface. This is somewhat due to the lack of widespread conservation at the sequence level, in addition to their relatively low and highly tissue-specific expression patterns, which makes their exploration challenging, especially in plant genomes where only a few of these molecules have been described completely. Recently published high-quality genomes of crop plants, along with new computational tools, are considered promising resources for studying these molecules in plants. This review briefly summarizes the characteristics of plant lncRNAs, their presence and conservation, the different protocols to find these elements, and the limitations of these protocols. Likewise, it describes their roles in different plant physiological phenomena. We believe that the study of lncRNAs can help to design strategies to reduce the negative effect of biotic and abiotic stresses on the yield of crop plants and, in the future, help create fruits and vegetables with improved nutritional content, higher amounts of compounds with positive effects on human health, better organoleptic characteristics, and fruits with a longer postharvest shelf life.
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Affiliation(s)
- Edmundo Domínguez-Rosas
- Coordinación de Tecnología de Alimentos de Origen Vegeta, Centro de Investigación en Alimentación y Desarrollo, Hermosillo, Sonora, Mexico
| | | | | | - Martín Ernesto Tiznado-Hernández
- Coordinación de Tecnología de Alimentos de Origen Vegeta, Centro de Investigación en Alimentación y Desarrollo, Hermosillo, Sonora, Mexico
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20
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Li M, Li W, Zhao M, Li Z, Wang GL, Liu W, Liang C. Transcriptome analysis reveals a lncRNA-miRNA-mRNA regulatory network in OsRpp30-mediated disease resistance in rice. BMC Genomics 2023; 24:643. [PMID: 37884868 PMCID: PMC10604448 DOI: 10.1186/s12864-023-09748-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/17/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) play critical roles in various biological processes in plants. Extensive studies utilizing high-throughput RNA sequencing have revealed that many lncRNAs are involved in plant disease resistance. Oryza sativa RNase P protein 30 (OsRpp30) has been identified as a positive regulator of rice immunity against fungal and bacterial pathogens. Nevertheless, the specific functions of lncRNAs in relation to OsRpp30-mediated disease resistance in rice remain elusive. RESULTS We conducted a comprehensive analysis of lncRNAs, miRNAs, and mRNAs expression patterns in wild type (WT), OsRpp30 overexpression (OsRpp30-OE), and OsRpp30 knockout (OsRpp30-KO) rice plants. In total, we identified 91 differentially expressed lncRNAs (DElncRNAs), 1671 differentially expressed mRNAs (DEmRNAs), and 41 differentially expressed miRNAs (DEmiRNAs) across the different rice lines. To gain further insights, we investigated the interaction between DElncRNAs and DEmRNAs, leading to the discovery of 10 trans- and 27 cis-targeting pairs specific to the OsRpp30-OE and OsRpp30-KO samples. In addition, we constructed a competing endogenous RNA (ceRNA) network comprising differentially expressed lncRNAs, miRNAs, and mRNAs to elucidate their intricate interplay in rice disease resistance. The ceRNA network analysis uncovered a set of gene targets regulated by lncRNAs and miRNAs, which were found to be involved in pathogen recognition, hormone pathways, transcription factor activation, and other biological processes related to plant immunity. CONCLUSIONS Our study provides a comprehensive expression profiling of lncRNAs, miRNAs, and mRNAs in a collection of defense mutants in rice. To decipher the putative functional significance of lncRNAs, we constructed trans- and cis-targeting networks involving differentially expressed lncRNAs and mRNAs, as well as a ceRNA network incorporating differentially expressed lncRNAs, miRNAs, and mRNAs. Together, the findings from this study provide compelling evidence supporting the pivotal roles of lncRNAs in OsRpp30-mediated disease resistance in rice.
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Affiliation(s)
- Minghua Li
- Department of Biology, Miami University, Oxford, OH, 45056, USA
| | - Wei Li
- Department of Plant Pathology, Ohio State University, Columbus, OH, 43210, USA
| | - Meixia Zhao
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
| | - Zhiqiang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Guo-Liang Wang
- Department of Plant Pathology, Ohio State University, Columbus, OH, 43210, USA.
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Chun Liang
- Department of Biology, Miami University, Oxford, OH, 45056, USA.
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21
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Chen YH, Lu J, Yang X, Huang LC, Zhang CQ, Liu QQ, Li QF. Gene editing of non-coding regulatory DNA and its application in crop improvement. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6158-6175. [PMID: 37549968 DOI: 10.1093/jxb/erad313] [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: 02/23/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023]
Abstract
The development of the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas) system has provided precise and efficient strategies to edit target genes and generate transgene-free crops. Significant progress has been made in the editing of protein-coding genes; however, studies on the editing of non-coding DNA with regulatory roles lags far behind. Non-coding regulatory DNAs, including those which can be transcribed into long non-coding RNAs (lncRNAs), and miRNAs, together with cis-regulatory elements (CREs), play crucial roles in regulating plant growth and development. Therefore, the combination of CRISPR/Cas technology and non-coding regulatory DNA has great potential to generate novel alleles that affect various agronomic traits of crops, thus providing valuable genetic resources for crop breeding. Herein, we review recent advances in the roles of non-coding regulatory DNA, attempts to edit non-coding regulatory DNA for crop improvement, and potential application of novel editing tools in modulating non-coding regulatory DNA. Finally, the existing problems, possible solutions, and future applications of gene editing of non-coding regulatory DNA in modern crop breeding practice are also discussed.
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Affiliation(s)
- Yu-Hao Chen
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Jun Lu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Xia Yang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Li-Chun Huang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Chang-Quan Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Qiao-Quan Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Qian-Feng Li
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou 225009, Jiangsu, China
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22
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Vashisht I, Dhaka N, Jain R, Sood A, Sharma N, Sharma MK, Sharma R. Non-coding RNAs-mediated environmental surveillance determines male fertility in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108030. [PMID: 37708711 DOI: 10.1016/j.plaphy.2023.108030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/16/2023]
Abstract
Plants are continuously exposed to environmental stresses leading to significant yield losses. With the changing climatic conditions, the intensity and duration of these stresses are expected to increase, posing a severe threat to crop productivity worldwide. Male gametogenesis is one of the most sensitive developmental stages. Exposure to environmental stresses during this stage leads to male sterility and yield loss. Elucidating the underlying molecular mechanism of environment-affected male sterility is essential to address this challenge. High-throughput RNA sequencing studies, loss-of-function phenotypes of sRNA biogenesis genes and functional genomics studies with non-coding RNAs have started to unveil the roles of small RNAs, long non-coding RNAs and the complex regulatory interactions between them in regulating male fertility under different growth regimes. Here, we discuss the current understanding of the non-coding RNA-mediated environmental stress surveillance and regulation of male fertility in plants. The candidate ncRNAs emerging from these studies can be leveraged to generate environment-sensitive male sterile lines for hybrid breeding or mitigate the impact of climate change on male fertility, as the situation demands.
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Affiliation(s)
- Ira Vashisht
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Namrata Dhaka
- Department of Biotechnology, Central University of Haryana, Mahendergarh, Haryana, 123031, India
| | - Rubi Jain
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India; Department of Biological Sciences, Birla Institute of Technology and Science (BITS) Pilani, Pilani Campus, Rajasthan, 333031, India
| | - Akanksha Sood
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS) Pilani, Pilani Campus, Rajasthan, 333031, India
| | - Niharika Sharma
- NSW Department of Primary Industries, Orange Agricultural Institute, Orange, NSW, 2800, Australia
| | - Manoj K Sharma
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Rita Sharma
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS) Pilani, Pilani Campus, Rajasthan, 333031, India.
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23
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Shi M, Wang C, Wang P, Yun F, Liu Z, Ye F, Wei L, Liao W. Role of methylation in vernalization and photoperiod pathway: a potential flowering regulator? HORTICULTURE RESEARCH 2023; 10:uhad174. [PMID: 37841501 PMCID: PMC10569243 DOI: 10.1093/hr/uhad174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 08/23/2023] [Indexed: 10/17/2023]
Abstract
Recognized as a pivotal developmental transition, flowering marks the continuation of a plant's life cycle. Vernalization and photoperiod are two major flowering pathways orchestrating numerous florigenic signals. Methylation, including histone, DNA and RNA methylation, is one of the recent foci in plant development. Considerable studies reveal that methylation seems to show an increasing potential regulatory role in plant flowering via altering relevant gene expression without altering the genetic basis. However, little has been reviewed about whether and how methylation acts on vernalization- and photoperiod-induced flowering before and after FLOWERING LOCUS C (FLC) reactivation, what role RNA methylation plays in vernalization- and photoperiod-induced flowering, how methylation participates simultaneously in both vernalization- and photoperiod-induced flowering, the heritability of methylation memory under the vernalization/photoperiod pathway, and whether and how methylation replaces vernalization/photoinduction to regulate flowering. Our review provides insight about the crosstalk among the genetic control of the flowering gene network, methylation (methyltransferases/demethylases) and external signals (cold, light, sRNA and phytohormones) in vernalization and photoperiod pathways. The existing evidence that RNA methylation may play a potential regulatory role in vernalization- and photoperiod-induced flowering has been gathered and represented for the first time. This review speculates about and discusses the possibility of substituting methylation for vernalization and photoinduction to promote flowering. Current evidence is utilized to discuss the possibility of future methylation reagents becoming flowering regulators at the molecular level.
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Affiliation(s)
- Meimei Shi
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Chunlei Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Peng Wang
- Vegetable and Flower Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Fahong Yun
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Zhiya Liu
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Fujin Ye
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Lijuan Wei
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Weibiao Liao
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
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Hazra S, Moulick D, Mukherjee A, Sahib S, Chowardhara B, Majumdar A, Upadhyay MK, Yadav P, Roy P, Santra SC, Mandal S, Nandy S, Dey A. Evaluation of efficacy of non-coding RNA in abiotic stress management of field crops: Current status and future prospective. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:107940. [PMID: 37738864 DOI: 10.1016/j.plaphy.2023.107940] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 07/23/2023] [Accepted: 08/04/2023] [Indexed: 09/24/2023]
Abstract
Abiotic stresses are responsible for the major losses in crop yield all over the world. Stresses generate harmful ROS which can impair cellular processes in plants. Therefore, plants have evolved antioxidant systems in defence against the stress-induced damages. The frequency of occurrence of abiotic stressors has increased several-fold due to the climate change experienced in recent times and projected for the future. This had particularly aggravated the risk of yield losses and threatened global food security. Non-coding RNAs are the part of eukaryotic genome that does not code for any proteins. However, they have been recently found to have a crucial role in the responses of plants to both abiotic and biotic stresses. There are different types of ncRNAs, for example, miRNAs and lncRNAs, which have the potential to regulate the expression of stress-related genes at the levels of transcription, post-transcription, and translation of proteins. The lncRNAs are also able to impart their epigenetic effects on the target genes through the alteration of the status of histone modification and organization of the chromatins. The current review attempts to deliver a comprehensive account of the role of ncRNAs in the regulation of plants' abiotic stress responses through ROS homeostasis. The potential applications ncRNAs in amelioration of abiotic stresses in field crops also have been evaluated.
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Affiliation(s)
- Swati Hazra
- Sharda School of Agricultural Sciences, Sharda University, Greater Noida, Uttar Pradesh 201310, India.
| | - Debojyoti Moulick
- Department of Environmental Science, University of Kalyani, Nadia, West Bengal 741235, India.
| | | | - Synudeen Sahib
- S. S. Cottage, Njarackal, P.O.: Perinad, Kollam, 691601, Kerala, India.
| | - Bhaben Chowardhara
- Department of Botany, Faculty of Science and Technology, Arunachal University of Studies, Arunachal Pradesh 792103, India.
| | - Arnab Majumdar
- Department of Earth Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, West Bengal 741246, India.
| | - Munish Kumar Upadhyay
- Department of Civil Engineering, Indian Institute of Technology Kanpur, Uttar Pradesh 208016, India.
| | - Poonam Yadav
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India.
| | - Priyabrata Roy
- Department of Molecular Biology and Biotechnology, University of Kalyani, West Bengal 741235, India.
| | - Subhas Chandra Santra
- Department of Environmental Science, University of Kalyani, Nadia, West Bengal 741235, India.
| | - Sayanti Mandal
- Department of Biotechnology, Dr. D. Y. Patil Arts, Commerce & Science College (affiliated to Savitribai Phule Pune University), Sant Tukaram Nagar, Pimpri, Pune, Maharashtra-411018, India.
| | - Samapika Nandy
- School of Pharmacy, Graphic Era Hill University, Bell Road, Clement Town, Dehradun, 248002, Uttarakhand, India; Department of Botany, Vedanta College, 33A Shiv Krishna Daw Lane, Kolkata-700054, India.
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, Kolkata, West Bengal 700073, India.
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25
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Tseng KC, Wu NY, Chow CN, Zheng HQ, Chou CY, Yang CW, Wang MJ, Chang SB, Chang WC. JustRNA: a database of plant long noncoding RNA expression profiles and functional network. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4949-4958. [PMID: 37523674 DOI: 10.1093/jxb/erad186] [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: 12/09/2022] [Accepted: 06/01/2023] [Indexed: 08/02/2023]
Abstract
Long noncoding RNAs (lncRNAs) are regulatory RNAs involved in numerous biological processes. Many plant lncRNAs have been identified, but their regulatory mechanisms remain largely unknown. A resource that enables the investigation of lncRNA activity under various conditions is required because the co-expression between lncRNAs and protein-coding genes may reveal the effects of lncRNAs. This study developed JustRNA, an expression profiling resource for plant lncRNAs. The platform currently contains 1 088 565 lncRNA annotations for 80 plant species. In addition, it includes 3692 RNA-seq samples derived from 825 conditions in six model plants. Functional network reconstruction provides insight into the regulatory roles of lncRNAs. Genomic association analysis and microRNA target prediction can be employed to depict potential interactions with nearby genes and microRNAs, respectively. Subsequent co-expression analysis can be employed to strengthen confidence in the interactions among genes. Chromatin immunoprecipitation sequencing data of transcription factors and histone modifications were integrated into the JustRNA platform to identify the transcriptional regulation of lncRNAs in several plant species. The JustRNA platform provides researchers with valuable insight into the regulatory mechanisms of plant lncRNAs. JustRNA is a free platform that can be accessed at http://JustRNA.itps.ncku.edu.tw.
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Affiliation(s)
- Kuan-Chieh Tseng
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Nai-Yun Wu
- Institute of Tropical Plant Sciences and Microbiology, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan
| | - Chi-Nga Chow
- Institute of Tropical Plant Sciences and Microbiology, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan
| | - Han-Qin Zheng
- Yourgene Health, No. 376-5 Fuxing Rd, Shulin Dist., New Taipei City 238, Taiwan
| | - Chin-Yuan Chou
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Chien-Wen Yang
- Institute of Tropical Plant Sciences and Microbiology, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan
| | - Ming-Jun Wang
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Song-Bin Chang
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Wen-Chi Chang
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
- Institute of Tropical Plant Sciences and Microbiology, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan
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26
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Yadav VK, Jalmi SK, Tiwari S, Kerkar S. Deciphering shared attributes of plant long non-coding RNAs through a comparative computational approach. Sci Rep 2023; 13:15101. [PMID: 37699996 PMCID: PMC10497521 DOI: 10.1038/s41598-023-42420-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 09/10/2023] [Indexed: 09/14/2023] Open
Abstract
Over the past decade, long non-coding RNA (lncRNA), which lacks protein-coding potential, has emerged as an essential regulator of the genome. The present study examined 13,599 lncRNAs in Arabidopsis thaliana, 11,565 in Oryza sativa, and 32,397 in Zea mays for their characteristic features and explored the associated genomic and epigenomic features. We found lncRNAs were distributed throughout the chromosomes and the Helitron family of transposable elements (TEs) enriched, while the terminal inverted repeat depleted in lncRNA transcribing regions. Our analyses determined that lncRNA transcribing regions show rare or weak signals for most epigenetic marks except for H3K9me2 and cytosine methylation in all three plant species. LncRNAs showed preferential localization in the nucleus and cytoplasm; however, the distribution ratio in the cytoplasm and nucleus varies among the studied plant species. We identified several conserved endogenous target mimic sites in the lncRNAs among the studied plants. We found 233, 301, and 273 unique miRNAs, potentially targeting the lncRNAs of A. thaliana, O. sativa, and Z. mays, respectively. Our study has revealed that miRNAs, which interact with lncRNAs, target genes that are involved in a diverse array of biological and molecular processes. The miRNA-targeted lncRNAs displayed a strong affinity for several transcription factors, including ERF and BBR-BPC, mutually present in all three plants, advocating their conserved functions. Overall, the present study showed that plant lncRNAs exhibit conserved genomic and epigenomic characteristics and potentially govern the growth and development of plants.
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Affiliation(s)
- Vikash Kumar Yadav
- School of Biological Sciences and Biotechnology, Goa University, Taleigao Plateau, Goa, 403206, India.
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Siddhi Kashinath Jalmi
- School of Biological Sciences and Biotechnology, Goa University, Taleigao Plateau, Goa, 403206, India
| | - Shalini Tiwari
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, 74078, OK, USA
| | - Savita Kerkar
- School of Biological Sciences and Biotechnology, Goa University, Taleigao Plateau, Goa, 403206, India
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Xu C, Xu Y, Wang Z, Zhang X, Wu Y, Lu X, Sun H, Wang L, Zhang Q, Zhang Q, Li X, Xiao J, Li X, Zhao M, Ouyang Y, Huang X, Zhang Q. Spontaneous movement of a retrotransposon generated genic dominant male sterility providing a useful tool for rice breeding. Natl Sci Rev 2023; 10:nwad210. [PMID: 37621414 PMCID: PMC10446136 DOI: 10.1093/nsr/nwad210] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/17/2023] [Accepted: 07/23/2023] [Indexed: 08/26/2023] Open
Abstract
Male sterility in plants provides valuable breeding tools in germplasm innovation and hybrid crop production. However, genetic resources for dominant genic male sterility, which hold great promise to facilitate breeding processes, are extremely rare in natural germplasm. Here we characterized the Sanming Dominant Genic Male Sterility in rice and identified the gene SDGMS using a map-based cloning approach. We found that spontaneous movement of a 1978-bp long terminal repeat (LTR) retrotransposon into the promoter region of the SDGMS gene activates its expression in anther tapetum, which causes abnormal programmed cell death of tapetal cells resulting in dominant male sterility. SDGMS encodes a ribosome inactivating protein showing N-glycosidase activity. The activation of SDGMS triggers transcription reprogramming of genes responsive to biotic stress leading to a hypersensitive response which causes sterility. The results demonstrate that an ectopic gene activation by transposon movement can give birth to a novel trait which enriches phenotypic diversity with practical utility.
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Affiliation(s)
- Conghao Xu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yifeng Xu
- Ningde Inspection and Testing Centre for Agricultural Product Quality and Safety, Ningde 352100, China
| | - Zhengji Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaoyu Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuying Wu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Xinyan Lu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Hongwei Sun
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Lei Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Qinglu Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Xu Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Mingfu Zhao
- Fujian Academy of Agricultural Sciences, Fuzhou 350018, China
| | - Yidan Ouyang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Xianbo Huang
- Sanming Institute of Agricultural Sciences, Shaxian 365509, China
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
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28
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Zhang YC, Yuan C, Chen YQ. Noncoding RNAs and their roles in regulating the agronomic traits of crops. FUNDAMENTAL RESEARCH 2023; 3:718-726. [PMID: 38933294 PMCID: PMC11197796 DOI: 10.1016/j.fmre.2023.02.020] [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: 10/07/2022] [Revised: 02/09/2023] [Accepted: 02/28/2023] [Indexed: 03/18/2023] Open
Abstract
Molecular breeding is one of the most effective methods for improving the performance of crops. Understanding the genome features of crops, especially the physiological functions of individual genes, is of great importance to molecular breeding. Evidence has shown that genomes of both animals and plants transcribe numerous non-coding RNAs, which are involved in almost every aspect of development. In crops, an increasing number of studies have proven that non-coding RNAs are new genetic resources for regulating crop traits. In this review, we summarize the current knowledge of non-coding RNAs, which are potential crop trait regulators, and focus on the functions of long non-coding RNAs (lncRNAs) in determining crop grain yield, phased small-interfering RNAs (phasiRNAs) in regulating fertility, small interfering RNAs (siRNAs) and microRNAs (miRNAs) in facilitating plant immune response and disease resistance, and miRNAs mediating nutrient and metal stress. Finally, we also discuss the next-generation method for ncRNA application in crop domestication and breeding.
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Affiliation(s)
- Yu-Chan Zhang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou 510275, China
| | - Chao Yuan
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yue-Qin Chen
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou 510275, China
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Panchal A, Maurya J, Seni S, Singh RK, Prasad M. An insight into the roles of regulatory ncRNAs in plants: An abiotic stress and developmental perspective. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107823. [PMID: 37327647 DOI: 10.1016/j.plaphy.2023.107823] [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: 03/01/2023] [Revised: 04/29/2023] [Accepted: 06/04/2023] [Indexed: 06/18/2023]
Abstract
Different environmental cues lead to changes in physiology, biochemistry and molecular status of plant's growth. Till date, various genes have been accounted for their role in regulating plant development and response to abiotic stress. Excluding genes that code for a functional protein in a cell, a large chunk of the eukaryotic transcriptome consists of non-coding RNAs (ncRNAs) which lack protein coding capacity but are still functional. Recent advancements in Next Generation Sequencing (NGS) technology have led to the unearthing of different types of small and large non-coding RNAs in plants. Non-coding RNAs are broadly categorised into housekeeping ncRNAs and regulatory ncRNAs which work at transcriptional, post-transcriptional and epigenetic levels. Diverse ncRNAs play different regulatory roles in nearly all biological processes including growth, development and response to changing environments. This response can be perceived and counteracted by plants using diverse evolutionarily conserved ncRNAs like miRNAs, siRNAs and lncRNAs to participate in complex molecular regimes by activating gene-ncRNA-mRNA regulatory modules to perform the downstream function. Here, we review the current understanding with a focus on recent advancements in the functional studies of the regulatory ncRNAs at the nexus of abiotic stresses and development. Also, the potential roles of ncRNAs in imparting abiotic stress tolerance and yield improvement in crop plants are also discussed with their future prospects.
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Affiliation(s)
- Anurag Panchal
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Jyoti Maurya
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Sushmita Seni
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Roshan Kumar Singh
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Manoj Prasad
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India; Department of Plant Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India.
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Li W, Zhao P, Sun J, Yu X, Zou L, Li S, Di R, Ruan M, Peng M. Biological function research of Fusarium oxysporum f. sp. cubense inducible banana long noncoding RNA Malnc2310 in Arabidopsis. PLANT MOLECULAR BIOLOGY 2023:10.1007/s11103-023-01360-6. [PMID: 37507516 DOI: 10.1007/s11103-023-01360-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 05/20/2023] [Indexed: 07/30/2023]
Abstract
Long noncoding RNAs (lncRNAs) participate in plant biological processes under biotic and abiotic stresses. However, little is known about the function and regulation mechanism of lncRNAs related to the pathogen at a molecular level. A banana lncRNA, Malnc2310, is a Fusarium oxysporum f. sp. cubense inducible lncRNA in roots. In this study, we demonstrate the nuclear localization of Malnc2310 by fluorescence in situ hybridization and it can bind to several proteins that are related to flavonoid pathway, pathogen response and programmed cell death. Overexpression of Malnc2310 increases susceptibility to Fusarium crude extract (Fu), salinity, and cold in transgenic Arabidopsis. In addition, Malnc2310 transgenic Arabidopsis accumulated more anthocyanins under Fusarium crude extract and cold treatments that are related to upregulation of these genes involved in anthocyanin biosynthesis. Based on our findings, we propose that Malnc2310 may participate in flavonoid metabolism in plants under stress. Furthermore, phenylalanine ammonia lyase (PAL) protein expression was enhanced in Malnc2310 overexpressed transgenic Arabidopsis, and Malnc2310 may participate in PAL regulation by binding to it. This study provides new insights into the role of Malnc2310 in mediating plant stress adaptation.
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Affiliation(s)
- Wenbin Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, P.R.China / Hainan Key Laboratory of Tropical Microbe Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory of Conservation and Utilization of Tropical Agricultural Biological Resources, Hainan Institute for Tropical Agricultural Resources, Haikou, China
| | - Pingjuan Zhao
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, P.R.China / Hainan Key Laboratory of Tropical Microbe Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jianbo Sun
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, P.R.China / Hainan Key Laboratory of Tropical Microbe Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xiaoling Yu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, P.R.China / Hainan Key Laboratory of Tropical Microbe Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Liangping Zou
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, P.R.China / Hainan Key Laboratory of Tropical Microbe Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Shuxia Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, P.R.China / Hainan Key Laboratory of Tropical Microbe Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory of Conservation and Utilization of Tropical Agricultural Biological Resources, Hainan Institute for Tropical Agricultural Resources, Haikou, China
| | - Rong Di
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, USA
| | - Mengbin Ruan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, P.R.China / Hainan Key Laboratory of Tropical Microbe Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
- Hainan Key Laboratory of Conservation and Utilization of Tropical Agricultural Biological Resources, Hainan Institute for Tropical Agricultural Resources, Haikou, China.
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, China.
| | - Ming Peng
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, P.R.China / Hainan Key Laboratory of Tropical Microbe Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, China.
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Li H, Wang W, Liu R, Tong B, Dai X, Lu Y, Yu Y, Dai S, Ruan L. Long non-coding RNA-mediated competing endogenous RNA regulatory network during flower development and color formation in Melastoma candidum. FRONTIERS IN PLANT SCIENCE 2023; 14:1215044. [PMID: 37575929 PMCID: PMC10415103 DOI: 10.3389/fpls.2023.1215044] [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: 05/01/2023] [Accepted: 07/06/2023] [Indexed: 08/15/2023]
Abstract
M. candidum, an evergreen shrubby flower known for its superior adaptation ability in South China, has gained increased attention in garden applications. However, scant attention has been paid to its flower development and color formation process at the non-coding RNA level. To fill this gap, we conducted a comprehensive analysis based on long non-coding RNA sequencing (lncRNA-seq), RNA-seq, small RNA sequencing (sRNA-seq), and widely targeted metabolome detection of three different flower developmental stages of M. candidum. After differentially expressed lncRNAs (DElncRNAs), differentially expressed mRNAs (DEmRNAs), differentially expressed microRNAs (DEmiRNAs), and differentially synthesized metabolites (DSmets) analyses between the different flower developmental stages, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were conducted to identify some key genes and metabolites in flavonoid, flavone, anthocyanin, carotenoid, and alkaloid-related GO terms and biosynthetic pathways. Three direct-acting models, including antisense-acting, cis-acting, and trans-acting between lncRNAs and mRNAs, were detected to illustrate the direct function of lncRNAs on target genes during flower development and color formation. Based on the competitive endogenous RNA (ceRNA) regulatory theory, we constructed a lncRNA-mediated regulatory network composed of DElncRNAs, DEmiRNAs, DEmRNAs, and DSmets to elucidate the indirect role of lncRNAs in the flower development and color formation of M. candidum. By utilizing correlation analyses between DERNAs and DSmets within the ceRNA regulatory network, alongside verification trials of the ceRNA regulatory mechanism, the study successfully illustrated the significance of lncRNAs in flower development and color formation process. This research provides a foundation for improving and regulating flower color at the lncRNA level in M. candidum, and sheds light on the potential applications of non-coding RNA in studies of flower development.
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Affiliation(s)
- Hui Li
- Department of Botany, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Wei Wang
- Department of Botany, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou, China
| | - Rui Liu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Botong Tong
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Xinren Dai
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Yan Lu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Nanjing, Jiangsu, China
| | - Yixun Yu
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Seping Dai
- Department of Botany, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou, China
| | - Lin Ruan
- Department of Botany, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou, China
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Liu K, Ma X, Zhao L, Lai X, Chen J, Lang X, Han Q, Wan X, Li C. Comprehensive transcriptomic analysis of three varieties with different brown planthopper-resistance identifies leaf sheath lncRNAs in rice. BMC PLANT BIOLOGY 2023; 23:367. [PMID: 37480003 PMCID: PMC10362764 DOI: 10.1186/s12870-023-04374-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 07/12/2023] [Indexed: 07/23/2023]
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) have been brought great attention for their crucial roles in diverse biological processes. However, systematic identification of lncRNAs associated with specialized rice pest, brown planthopper (BPH), defense in rice remains unexplored. RESULTS In this study, a genome-wide high throughput sequencing analysis was performed using leaf sheaths of susceptible rice Taichung Native 1 (TN1) and resistant rice IR36 and R476 with and without BPH feeding. A total of 2283 lncRNAs were identified, of which 649 lncRNAs were differentially expressed. During BPH infestation, 84 (120 in total), 52 (70 in total) and 63 (94 in total) of differentially expressed lncRNAs were found only in TN1, IR36 and R476, respectively. Through analyzing their cis-, trans-, and target mimic-activities, not only the lncRNAs targeting resistance genes (NBS-LRR and RLKs) and transcription factors, but also the lncRNAs acting as the targets of the well-studied stress-related miRNAs (miR2118, miR528, and miR1320) in each variety were identified. Before the BPH feeding, 238 and 312 lncRNAs were found to be differentially expressed in TN1 vs. IR36 and TN1 vs. R476, respectively. Among their putative targets, the plant-pathogen interaction pathway was significantly enriched. It is speculated that the resistant rice was in a priming state by the regulation of lncRNAs. Furthermore, the lncRNAs extensively involved in response to BPH feeding were identified by Weighted Gene Co-expression Network Analysis (WGCNA), and the possible regulation networks of the key lncRNAs were constructed. These lncRNAs regulate different pathways that contribute to the basal defense and specific resistance of rice to the BPH. CONCLUSION In summary, we identified the specific lncRNAs targeting the well-studied stress-related miRNAs, resistance genes, and transcription factors in each variety during BPH infestation. Additionally, the possible regulating network of the lncRNAs extensively responding to BPH feeding revealed by WGCNA were constructed. These findings will provide further understanding of the regulatory roles of lncRNAs in BPH defense, and lay a foundation for functional research on the candidate lncRNAs.
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Affiliation(s)
- Kai Liu
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests & 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
| | - Xiaozhi Ma
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510642, China
| | - Luyao Zhao
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests & 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
| | - Xiaofeng Lai
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests & 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
| | - Jie Chen
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests & 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
| | - Xingxuan Lang
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests & 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
| | - Qunxin Han
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests & 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
| | - Xiaorong Wan
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests & 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.
| | - Chunmei Li
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests & 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.
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Farinati S, Draga S, Betto A, Palumbo F, Vannozzi A, Lucchin M, Barcaccia G. Current insights and advances into plant male sterility: new precision breeding technology based on genome editing applications. FRONTIERS IN PLANT SCIENCE 2023; 14:1223861. [PMID: 37521915 PMCID: PMC10382145 DOI: 10.3389/fpls.2023.1223861] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/20/2023] [Indexed: 08/01/2023]
Abstract
Plant male sterility (MS) represents the inability of the plant to generate functional anthers, pollen, or male gametes. Developing MS lines represents one of the most important challenges in plant breeding programs, since the establishment of MS lines is a major goal in F1 hybrid production. For these reasons, MS lines have been developed in several species of economic interest, particularly in horticultural crops and ornamental plants. Over the years, MS has been accomplished through many different techniques ranging from approaches based on cross-mediated conventional breeding methods, to advanced devices based on knowledge of genetics and genomics to the most advanced molecular technologies based on genome editing (GE). GE methods, in particular gene knockout mediated by CRISPR/Cas-related tools, have resulted in flexible and successful strategic ideas used to alter the function of key genes, regulating numerous biological processes including MS. These precision breeding technologies are less time-consuming and can accelerate the creation of new genetic variability with the accumulation of favorable alleles, able to dramatically change the biological process and resulting in a potential efficiency of cultivar development bypassing sexual crosses. The main goal of this manuscript is to provide a general overview of insights and advances into plant male sterility, focusing the attention on the recent new breeding GE-based applications capable of inducing MS by targeting specific nuclear genic loci. A summary of the mechanisms underlying the recent CRISPR technology and relative success applications are described for the main crop and ornamental species. The future challenges and new potential applications of CRISPR/Cas systems in MS mutant production and other potential opportunities will be discussed, as generating CRISPR-edited DNA-free by transient transformation system and transgenerational gene editing for introducing desirable alleles and for precision breeding strategies.
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Xu Y, Yu D, Chen J, Duan M. A review of rice male sterility types and their sterility mechanisms. Heliyon 2023; 9:e18204. [PMID: 37519640 PMCID: PMC10372310 DOI: 10.1016/j.heliyon.2023.e18204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 07/07/2023] [Accepted: 07/11/2023] [Indexed: 08/01/2023] Open
Abstract
Male sterility plays an important role in the utilization of heterosis in rice. The establishment of male sterile lines in rice is one of the key technologies in hybrid rice production systems. The currently widely used male sterile line breeding systems mainly include: three-line hybrid rice based on cytoplasmic male sterility, two-line hybrid rice based on environmental sensitive gene male sterility, and third-generation hybrid rice based on nuclear gene male sterility Seed production system. This study reviewed the types and mechanisms of male sterility in rice, and looked forward to the development direction of hybrid rice.
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Affiliation(s)
- Yusheng Xu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Dong Yu
- Hunan Hybrid Rice Research Center, Changsha 410125, China
| | - Jin Chen
- Hunan Hybrid Rice Research Center, Changsha 410125, China
| | - Meijuan Duan
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
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35
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Kitazaki K, Oda K, Akazawa A, Iwahori R. Molecular genetics of cytoplasmic male sterility and restorer-of-fertility for the fine tuning of pollen production in crops. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:156. [PMID: 37330934 DOI: 10.1007/s00122-023-04398-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 06/01/2023] [Indexed: 06/20/2023]
Abstract
Cytoplasmic male sterility (CMS) is an increasingly important issue within the context of hybrid seed production. Its genetic framework is simple: S-cytoplasm for male sterility induction and dominant allele of the restorer-of-fertility gene (Rf) for suppression of S. However, breeders sometimes encounter a phenotype of CMS plants too complex to be explained via this simple model. The molecular basis of CMS provides clue to the mechanisms that underlie the expression of CMS. Mitochondria have been associated with S, and several unique ORFs to S-mitochondria are thought to be responsible for the induction of male sterility in various crops. Their functions are still the subject of debate, but they have been hypothesized to emit elements that trigger sterility. Rf suppresses the action of S by various mechanisms. Some Rfs, including those that encode the pentatricopeptide repeat (PPR) protein and other proteins, are now considered members of unique gene families that are specific to certain lineages. Additionally, they are thought to be complex loci in which several genes in a haplotype simultaneously counteract an S-cytoplasm and differences in the suite of genes in a haplotype can lead to multiple allelism including strong and weak Rf at phenotypic level. The stability of CMS is influenced by factors such as the environment, cytoplasm, and genetic background; the interaction of these factors is also important. In contrast, unstable CMS becomes inducible CMS if its expression can be controlled. CMS becomes environmentally sensitive in a genotype-dependent manner, suggesting the feasibility of controlling the expression of CMS.
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Affiliation(s)
- Kazuyoshi Kitazaki
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan.
| | - Kotoko Oda
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Akiho Akazawa
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Ryoma Iwahori
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
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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: 0] [Impact Index Per Article: 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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Han Y, Jiang SZ, Zhong X, Chen X, Ma CK, Yang YM, Mao YC, Zhou SD, Zhou L, Zhang YF, Huang XH, Zhang H, Li LG, Zhu J, Yang ZN. Low temperature compensates for defective tapetum initiation to restore the fertility of the novel TGMS line ostms15. PLANT BIOTECHNOLOGY JOURNAL 2023. [PMID: 37205779 PMCID: PMC10363753 DOI: 10.1111/pbi.14066] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/29/2023] [Accepted: 04/24/2023] [Indexed: 05/21/2023]
Abstract
In rice breeding, thermosensitive genic male sterility (TGMS) lines based on the tms5 locus have been extensively employed. Here, we reported a novel rice TGMS line ostms15 (Oryza sativa ssp. japonica ZH11) which show male sterility under high temperature and fertility under low temperature. Field evaluation from 2018 to 2021 revealed that its sterility under high temperature is more stable than that of tms5 (ZH11), even with occasional low temperature periods, indicating its considerable value for rice breeding. OsTMS15 encodes an LRR-RLK protein MULTIPLE SPOROCYTE1 (MSP1) which was reported to interact with its ligand to initiate tapetum development for pollen formation. In ostms15, a point mutation from GTA (Val) to GAA (Glu) in its TIR motif of the LRR region led to the TGMS phenotype. Cellular observation and gene expression analysis showed that the tapetum is still present in ostms15, while its function was substantially impaired under high temperature. However, its tapetum function was restored under low temperature. The interaction between mOsTMS15 and its ligand was reduced while this interaction was partially restored under low temperature. Slow development was reported to be a general mechanism of P/TGMS fertility restoration. We propose that the recovered protein interaction together with slow development under low temperature compensates for the defective tapetum initiation, which further restores ostms15 fertility. We used base editing to create a number of TGMS lines with different base substitutions based on the OsTMS15 locus. This work may also facilitate the mechanistic investigation and breeding of other crops.
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Affiliation(s)
- Yu Han
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Sheng-Zhe Jiang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Xiang Zhong
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Xing Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chang-Kai Ma
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yan-Ming Yang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yi-Chen Mao
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Si-Da Zhou
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Lei Zhou
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yan-Fei Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Xue-Hui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Hui Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Lai-Geng Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jun Zhu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Zhong-Nan Yang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
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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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Abstract
Robust plant immune systems are fine-tuned by both protein-coding genes and non-coding RNAs. Long non-coding RNAs (lncRNAs) refer to RNAs with a length of more than 200 nt and usually do not have protein-coding function and do not belong to any other well-known non-coding RNA types. The non-protein-coding, low expression, and non-conservative characteristics of lncRNAs restrict their recognition. Although studies of lncRNAs in plants are in the early stage, emerging studies have shown that plants employ lncRNAs to regulate plant immunity. Moreover, in response to stresses, numerous lncRNAs are differentially expressed, which manifests the actions of low-expressed lncRNAs and makes plant-microbe/insect interactions a convenient system to study the functions of lncRNAs. Here, we summarize the current advances in plant lncRNAs, discuss their regulatory effects in different stages of plant immunity, and highlight their roles in diverse plant-microbe/insect interactions. These insights will not only strengthen our understanding of the roles and actions of lncRNAs in plant-microbe/insect interactions but also provide novel insight into plant immune responses and a basis for further research in this field.
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Affiliation(s)
- Juan Huang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Wenling Zhou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoming Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
- HainanYazhou Bay Seed Lab, Sanya, China
| | - Yi Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
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Saxena S, Das A, Kaila T, Ramakrishna G, Sharma S, Gaikwad K. Genomic survey of high-throughput RNA-Seq data implicates involvement of long intergenic non-coding RNAs (lincRNAs) in cytoplasmic male-sterility and fertility restoration in pigeon pea. Genes Genomics 2023; 45:783-811. [PMID: 37115379 DOI: 10.1007/s13258-023-01383-9] [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: 07/29/2022] [Accepted: 10/21/2022] [Indexed: 04/29/2023]
Abstract
BACKGROUND Long-intergenic non-coding RNAs (lincRNAs) originate from intergenic regions and have no coding potential. LincRNAs have emerged as key players in the regulation of various biological processes in plant development. Cytoplasmic male-sterility (CMS) in association with restorer-of-fertility (Rf) systems makes it a highly reliable tool for exploring heterosis for producing commercial hybrid seeds. To date, there have been no reports of lincRNAs during pollen development in CMS and fertility restorer lines in pigeon pea. OBJECTIVE Identification of lincRNAs in the floral buds of cytoplasmic male-sterile (AKCMS11) and fertility restorer (AKPR303) pigeon pea lines. METHODS We employed a computational approach to identify lincRNAs in the floral buds of cytoplasmic male-sterile (AKCMS11) and fertility restorer (AKPR303) pigeon pea lines using RNA-Seq data. RESULTS We predicted a total of 2145 potential lincRNAs of which 966 were observed to be differentially expressed between the sterile and fertile pollen. We identified, 927 cis-regulated and 383 trans-regulated target genes of the lincRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the target genes revealed that these genes were specifically enriched in pathways like pollen and pollen tube development, oxidative phosphorylation, etc. We detected 23 lincRNAs that were co-expressed with 17 pollen-related genes with known functions. Fifty-nine lincRNAs were predicted to be endogenous target mimics (eTMs) for 25 miRNAs, and found to be associated with pollen development. The, lincRNA regulatory networks revealed that different lincRNA-miRNA-mRNA networks might be associated with CMS and fertility restoration. CONCLUSION Thus, this study provides valuable information by highlighting the functions of lincRNAs as regulators during pollen development in pigeon pea and utilization in hybrid seed production.
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Affiliation(s)
- Swati Saxena
- ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - Antara Das
- ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - Tanvi Kaila
- ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - G Ramakrishna
- ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - Sandhya Sharma
- ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India.
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Jin Y, Ivanov M, Dittrich AN, Nelson AD, Marquardt S. LncRNA FLAIL affects alternative splicing and represses flowering in Arabidopsis. EMBO J 2023:e110921. [PMID: 37051749 DOI: 10.15252/embj.2022110921] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 04/14/2023] Open
Abstract
How the noncoding genome affects cellular functions is a key biological question. A particular challenge is to distinguish the effects of noncoding DNA elements from long noncoding RNAs (lncRNAs) that coincide at the same loci. Here, we identified the flowering-associated intergenic lncRNA (FLAIL) in Arabidopsis through early flowering flail mutants. Expression of FLAIL RNA from a different chromosomal location in combination with strand-specific RNA knockdown characterized FLAIL as a trans-acting RNA molecule. FLAIL directly binds to differentially expressed target genes that control flowering via RNA-DNA interactions through conserved sequence motifs. FLAIL interacts with protein and RNA components of the spliceosome to affect target mRNA expression through co-transcriptional alternative splicing (AS) and linked chromatin regulation. In the absence of FLAIL, splicing defects at the direct FLAIL target flowering gene LACCASE 8 (LAC8) correlated with reduced mRNA expression. Double mutant analyses support a model where FLAIL-mediated splicing of LAC8 promotes its mRNA expression and represses flowering. Our study suggests lncRNAs as accessory components of the spliceosome that regulate AS and gene expression to impact organismal development.
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Affiliation(s)
- Yu Jin
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
| | - Maxim Ivanov
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
| | | | | | - Sebastian Marquardt
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
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Gullotta G, Korte A, Marquardt S. Functional variation in the non-coding genome: molecular implications for food security. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2338-2351. [PMID: 36316269 DOI: 10.1093/jxb/erac395] [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: 07/22/2022] [Accepted: 10/06/2022] [Indexed: 06/06/2023]
Abstract
The growing world population, in combination with the anticipated effects of climate change, is pressuring food security. Plants display an impressive arsenal of cellular mechanisms conferring resilience to adverse environmental conditions, and humans rely on these mechanisms for stable food production. The elucidation of the molecular basis of the mechanisms used by plants to achieve resilience promises knowledge-based approaches to enhance food security. DNA sequence polymorphisms can reveal genomic regions that are linked to beneficial traits of plants. However, our ability to interpret how a given DNA sequence polymorphism confers a fitness advantage at the molecular level often remains poor. A key factor is that these polymorphisms largely localize to the enigmatic non-coding genome. Here, we review the functional impact of sequence variations in the non-coding genome on plant biology in the context of crop breeding and agricultural traits. We focus on examples of non-coding with particularly convincing functional support. Our survey combines findings that are consistent with the view that the non-coding genome contributes to cellular mechanisms assisting many plant traits. Understanding how DNA sequence polymorphisms in the non-coding genome shape plant traits at the molecular level offers a largely unexplored reservoir of solutions to address future challenges in plant growth and resilience.
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Affiliation(s)
- Giorgio Gullotta
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Bülowsvej 21A, 1871 Frederiksberg, Denmark
| | - Arthur Korte
- Center for Computational and Theoretical Biology, University of Würzburg, Hubland Nord 32, 97074 Würzburg, Germany
| | - Sebastian Marquardt
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Bülowsvej 21A, 1871 Frederiksberg, Denmark
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Cui J, Qiu T, Li L, Cui S. De novo full-length transcriptome analysis of two ecotypes of Phragmites australis (swamp reed and dune reed) provides new insights into the transcriptomic complexity of dune reed and its long-term adaptation to desert environments. BMC Genomics 2023; 24:180. [PMID: 37020272 PMCID: PMC10077656 DOI: 10.1186/s12864-023-09271-y] [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: 10/29/2022] [Accepted: 03/23/2023] [Indexed: 04/07/2023] Open
Abstract
BACKGROUND The extremely harsh environment of the desert is changing dramatically every moment, and the rapid adaptive stress response in the short term requires enormous energy expenditure to mobilize widespread regulatory networks, which is all the more detrimental to the survival of the desert plants themselves. The dune reed, which has adapted to desert environments with complex and variable ecological factors, is an ideal type of plant for studying the molecular mechanisms by which Gramineae plants respond to combinatorial stress of the desert in their natural state. But so far, the data on the genetic resources of reeds is still scarce, therefore most of their research has focused on ecological and physiological studies. RESULTS In this study, we obtained the first De novo non-redundant Full-Length Non-Chimeric (FLNC) transcriptome databases for swamp reeds (SR), dune reeds (DR) and the All of Phragmites australis (merged of iso-seq data from SR and DR), using PacBio Iso-Seq technology and combining tools such as Iso-Seq3 and Cogent. We then identified and described long non-coding RNAs (LncRNA), transcription factor (TF) and alternative splicing (AS) events in reeds based on a transcriptome database. Meanwhile, we have identified and developed for the first time a large number of candidates expressed sequence tag-SSR (EST-SSRs) markers in reeds based on UniTransModels. In addition, through differential gene expression analysis of wild-type and homogenous cultures, we found a large number of transcription factors that may be associated with desert stress tolerance in the dune reed, and revealed that members of the Lhc family have an important role in the long-term adaptation of dune reeds to desert environments. CONCLUSIONS Our results provide a positive and usable genetic resource for Phragmites australis with a widespread adaptability and resistance, and provide a genetic database for subsequent reeds genome annotation and functional genomic studies.
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Affiliation(s)
- Jipeng Cui
- College of Life Sciences, Capital Normal University, Haidian District, Beijing, 100048, China
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Haidian District, Beijing, 100048, China
| | - Tianhang Qiu
- College of Life Sciences, Capital Normal University, Haidian District, Beijing, 100048, China
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Haidian District, Beijing, 100048, China
| | - Li Li
- College of Life Sciences, Capital Normal University, Haidian District, Beijing, 100048, China
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Haidian District, Beijing, 100048, China
| | - Suxia Cui
- College of Life Sciences, Capital Normal University, Haidian District, Beijing, 100048, China.
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Haidian District, Beijing, 100048, 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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Tao X, Li S, Chen G, Wang J, Xu S. Approaches for Modes of Action Study of Long Non-Coding RNAs: From Single Verification to Genome-Wide Determination. Int J Mol Sci 2023; 24:ijms24065562. [PMID: 36982636 PMCID: PMC10054671 DOI: 10.3390/ijms24065562] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/08/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nucleotides (nt) that are not translated into known functional proteins. This broad definition covers a large collection of transcripts with diverse genomic origins, biogenesis, and modes of action. Thus, it is very important to choose appropriate research methodologies when investigating lncRNAs with biological significance. Multiple reviews to date have summarized the mechanisms of lncRNA biogenesis, their localization, their functions in gene regulation at multiple levels, and also their potential applications. However, little has been reviewed on the leading strategies for lncRNA research. Here, we generalize a basic and systemic mind map for lncRNA research and discuss the mechanisms and the application scenarios of ‘up-to-date’ techniques as applied to molecular function studies of lncRNAs. Taking advantage of documented lncRNA research paradigms as examples, we aim to provide an overview of the developing techniques for elucidating lncRNA interactions with genomic DNA, proteins, and other RNAs. In the end, we propose the future direction and potential technological challenges of lncRNA studies, focusing on techniques and applications.
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Affiliation(s)
- Xiaoyuan Tao
- Xianghu Laboratory, Hangzhou 311231, China
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Sujuan Li
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Guang Chen
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jian Wang
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Shengchun Xu
- Xianghu Laboratory, Hangzhou 311231, China
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Correspondence:
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46
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Yue Z, Pan X, Li J, Si F, Yin L, Hou Y, Chen X, Li X, Zhang Y, Ma J, Yang J, Li H, Luan F, Huang W, Zhang X, Yuan L, Zhang R, Wei C. Whole-transcriptome analyses identify key differentially expressed mRNAs, lncRNAs, and miRNAs associated with male sterility in watermelon. FRONTIERS IN PLANT SCIENCE 2023; 14:1138415. [PMID: 36938061 PMCID: PMC10019506 DOI: 10.3389/fpls.2023.1138415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
Male sterility is a valuable trait for watermelon breeding, as watermelon hybrids exhibit obvious heterosis. However, the underlying regulatory mechanism is still largely unknown, especially regarding the related non-coding genes. In the present study, approximately 1035 differentially expressed genes (DEGs), as well as 80 DE-lncRNAs and 10 DE-miRNAs, were identified, with the overwhelming majority down-regulated in male-sterile floral buds. Enrichment analyses revealed that the general phenylpropanoid pathway as well as its related metabolisms was predicted to be altered in a mutant compared to its fertile progenitor. Meanwhile, the conserved genetic pathway DYT1-TDF1-AMS-MS188-MS1, as well as the causal gene ClAMT1 for the male-sterile mutant Se18, was substantially disrupted during male reproductive development. In addition, some targets of the key regulators AMS and MS188 in tapetum development were also down-regulated at a transcriptional level, such as ABCG26 (Cla004479), ACOS5 (Cla022956), CYP703A2 (Cla021151), PKSA (Cla021099), and TKPR1 (Cla002563). Considering lncRNAs may act as functional endogenous target mimics of miRNAs, competitive endogenous RNA networks were subsequently constructed, with the most complex one containing three DE-miRNAs, two DE-lncRNAs, and 21 DEGs. Collectively, these findings not only contribute to a better understanding of genetic regulatory networks underlying male sterility in watermelon, but also provide valuable candidates for future research.
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Affiliation(s)
- Zhen Yue
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaona Pan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Jiayue Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Fengfei Si
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Lijuan Yin
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Yinjie Hou
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaoyao Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Xin Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Yong Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Jianxiang Ma
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Jianqiang Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Hao Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Feishi Luan
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Wenfeng Huang
- Vegetable Research Institute of Hainan Academy of Agricultural Sciences, Haikou, Hainan, China
| | - Xian Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
- State Key Laboratory of Vegetable Germplasm Innovation, Tianjin, China
| | - Li Yuan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Ruimin Zhang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, China
| | - Chunhua Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
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Xue Y, Muhammad S, Yang J, Wang X, Zhao N, Qin B, Qiu Y, Du Z, Ulhassan Z, Zhou W, Liu F, Li R. Comparative transcriptome-wide identification and differential expression of genes and lncRNAs in rice near-isogenic line (KW- Bph36-NIL) in response to BPH feeding. FRONTIERS IN PLANT SCIENCE 2023; 13:1095602. [PMID: 36874914 PMCID: PMC9981640 DOI: 10.3389/fpls.2022.1095602] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/30/2022] [Indexed: 06/18/2023]
Abstract
Brown planthopper (BPH) is the most devastating pest of rice in Asia, causing substantial yield losses and has become a challenging task to be controlled under field conditions. Although extensive measures have been taken over the past decades, which resulted in the evolution of new resistant BPH strains. Therefore, besides other possible approaches, equipping host plants with resistant genes is the most effective and environment-friendly technique for BPH control. Here, we systematically analyzed transcriptome changes in the susceptible rice variety Kangwenqingzhan (KW) and the resistant near-isogenic line (NIL) KW-Bph36-NIL, through RNA-seq, depicting the differential expression profiles of mRNAs and long non-coding RNAs (lncRNAs) in rice before and after BPH feeding. We observed a proportion of genes (1.48%) and (2.74%) were altered in KW and NIL, respectively, indicating different responses of rice strains against BPH feeding. Nevertheless, we characterized 384 differentially expressed long non-coding RNAs (DELs) that can be impacted by the two strains by alternatively changing the expression patterns of the respective coding genes, suggesting their certain involvement in response to BPH feeding. In BPH invasion, KW and NIL responded differently by modifying the synthesis, storage, and transformation of intracellular substances, adjusting the nutrient accumulation and utilization inside and outside the cells. In addition, NIL expressed stronger resistance by acutely up-regulating genes and other transcription factors related to stress resistance and plant immunity. Altogether, our study elaborates valuable insights into the genome-wide DEGs and DELs expression profiles of rice under BPH invasion by high throughput sequencing and further suggests that NILs can be utilized in BPH resistance breeding programs in developing high-resistance rice lines.
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Affiliation(s)
- Yanxia Xue
- School of Electrical and Control Engineering, North University of China, Taiyuan, China
| | - Sajid Muhammad
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Jinlian Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Xuan Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Neng Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Baoxiang Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Yongfu Qiu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Zhimin Du
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zaid Ulhassan
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Weijun Zhou
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Fang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Rongbai Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
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Nie H, Cheng C, Kong J, Li H, Hua J. Plant non-coding RNAs function in pollen development and male sterility. FRONTIERS IN PLANT SCIENCE 2023; 14:1109941. [PMID: 36875603 PMCID: PMC9975556 DOI: 10.3389/fpls.2023.1109941] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Male sterility is classified as either cytoplasmic male sterility (CMS) or genic male sterility (GMS). Generally, CMS involves mitochondrial genomes interacting with the nuclear genome, while GMS is caused by nuclear genes alone. Male sterility is regulated by multilevel mechanisms in which non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and phased small interfering RNAs (phasiRNAs), which have been proven to be critical elements. The development of high-throughput sequencing technology offers new opportunities to evaluate the genetic mechanism of ncRNAs in plant male sterility. In this review, we summarize the critical ncRNAs that regulate gene expression in ways dependent on or independent of hormones, which involve the differentiation of the stamen primordia, degradation of the tapetum, formation of microspores, and the release of pollen. In addition, the key mechanisms of the miRNA-lncRNA-mRNA interaction networks mediating male sterility in plants are elaborated. We present a different perspective on exploring the ncRNA-mediated regulatory pathways that control CMS in plants and create male-sterile lines through hormones or genome editing. A refined understanding of the ncRNA regulatory mechanisms in plant male sterility for the development of new sterile lines would be conducive to improve hybridization breeding.
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Affiliation(s)
- Hushuai Nie
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, China
- Laboratory of Cotton Genetics, Genomics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Cheng Cheng
- Laboratory of Cotton Genetics, Genomics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Jie Kong
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, China
| | - Huijing Li
- Laboratory of Cotton Genetics, Genomics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Jinping Hua
- Laboratory of Cotton Genetics, Genomics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
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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: 0] [Impact Index Per Article: 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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50
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Xing M, Peng Z, Guan C, Guan M. Comparative study on abortion characteristics of Nsa CMS and Pol CMS and analysis of long non-coding RNAs related to pollen abortion in Brassica napus. PLoS One 2023; 18:e0284287. [PMID: 37053132 PMCID: PMC10101420 DOI: 10.1371/journal.pone.0284287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 03/28/2023] [Indexed: 04/14/2023] Open
Abstract
Cytoplasmic male sterile system (CMS) is one of the important methods for the utilization of heterosisin Brassica napus. The involvement of long non-coding RNAs (lncRNAs) in anther and pollen development in B.napus has been recognized, but there is little data on the involvement of lncRNAs in pollen abortion in different types of rapeseed CMS. The present study compared the cytological, physiological and biochemical characteristics of Nsa CMS (1258A) and Pol CMS (P5A) during pollen abortion, and high-throughput sequencing of flower buds of different sizes before and after pollen abortion. The results showed that insufficient energy supply was an important physiological basis for 1258A and P5A pollen abortion, and 1258A had excessive ROS (reactive oxygen species) accumulation in the stage of pollen abortion. Functional analysis showed that Starch and sucrose metabolism and Sulfur metabolism were significantly enriched before and after pollen abortion in 1258A and P5A, and a large number of genes were down-regulated. In 1258A, 227 lncRNAs had cis-targeting regulation, and 240 cis-target genes of the lncRNAs were identified. In P5A, 116 lncRNAs had cis-targeting regulation, and 101 cis-target genes of the lncRNAs were identified. There were five lncRNAs cis-target genes in 1258A and P5A during pollen abortion, and LOC106445716 encodes β-D-glucopyranosyl abscisate β-glucosidase and could regulate pollen abortion. Taken together, this study, provides a new perspective for lncRNAs to participate in the regulation of Nsa CMS and Pol CMS pollen abortion.
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Affiliation(s)
- Man Xing
- Hunan Branch of National Oilseed Crops Improvement Center, Changsha, China
- College of Agriculture, Hunan Agricultural University, Changsha, China
| | - Zechuan Peng
- Hunan Branch of National Oilseed Crops Improvement Center, Changsha, China
- College of Agriculture, Hunan Agricultural University, Changsha, China
| | - Chunyun Guan
- Hunan Branch of National Oilseed Crops Improvement Center, Changsha, China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha, China
| | - Mei Guan
- Hunan Branch of National Oilseed Crops Improvement Center, Changsha, China
- College of Agriculture, Hunan Agricultural University, Changsha, China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha, China
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