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Li J, Zhang W, Lu Q, Sun J, Cheng C, Huang S, Li S, Li Q, Zhang W, Zhou C, Liu B, Xiang F. GmDFB1, an ARM-repeat superfamily protein, regulates floral organ identity through repressing siRNA- and miRNA-mediated gene silencing in soybean. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024. [PMID: 38860597 DOI: 10.1111/jipb.13709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 05/04/2024] [Indexed: 06/12/2024]
Abstract
The development of flowers in soybean (Glycine max) is essential for determining the yield potential of the plant. Gene silencing pathways are involved in modulating flower development, but their full elucidation is still incomplete. Here, we conducted a forward genetic screen and identified an abnormal flower mutant, deformed floral bud1-1 (Gmdfb1-1), in soybean. We mapped and identified the causal gene, which encodes a member of the armadillo (ARM)-repeat superfamily. Using small RNA sequencing (sRNA-seq), we found an abnormal accumulation of small interfering RNAs (siRNAs) and microRNA (miRNAs) in the Gmdfb1 mutants. We further demonstrated that GmDFB1 interacts with the RNA exosome cofactor SUPER KILLER7 (GmSKI7). Additionally, GmDFB1 interacts with the PIWI domain of ARGONAUTE 1 (GmAGO1) to inhibit the cleavage efficiency on the target genes of sRNAs. The enhanced gene silencing mediated by siRNA and miRNA in the Gmdfb1 mutants leads to the downregulation of their target genes associated with flower development. This study revealed the crucial role of GmDFB1 in regulating floral organ identity in soybean probably by participating in two distinct gene silencing pathways.
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Affiliation(s)
- Jie Li
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Wenxiao Zhang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Qing Lu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Jiaqi Sun
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Chuang Cheng
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Shiyu Huang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Shuo Li
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Qiang Li
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Wei Zhang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Chuanen Zhou
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Bin Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Fengning Xiang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
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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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3
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Ding X, Guo J, Lv M, Wang H, Sheng Y, Liu Y, Gai J, Yang S. The miR156b-GmSPL2b module mediates male fertility regulation of cytoplasmic male sterility-based restorer line under high-temperature stress in soybean. PLANT BIOTECHNOLOGY JOURNAL 2023. [PMID: 37057908 PMCID: PMC10363761 DOI: 10.1111/pbi.14056] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 02/17/2023] [Accepted: 04/01/2023] [Indexed: 06/19/2023]
Abstract
High-temperature (HT) stress at flowering stage causes significant damage to soybean, including pollen abortion and fertilization failure, but few genes involved in male fertility regulation under HT stress in soybean have been characterized. Here, we demonstrated that miR156b-GmSPL2b module involved in male fertility regulation of soybean cytoplasmic male sterility (CMS)-based restorer line under HT stress. Overexpression of miR156b decreased male fertility in soybean CMS-based restorer line and its hybrid F1 with CMS line under HT stress. RNA-seq analysis found that miR156b mediated male fertility regulation in soybean under HT stress by regulating the expression of pollen development and HT response related genes. Metabolomic analysis of miR156bOE revealed reduction in flavonoid content under HT stress. Integrated transcriptomic and metabolomic analysis showed that the overexpression of miR156b caused flavonoid metabolism disorder in soybean flower bud under HT stress. Knockout of GmSPL2b also decreased the thermotolerance of soybean CMS-based restorer line during flowering. Moreover, GmSPL2b turned out to be directly bounded to the promoter of GmHSFA6b. Further verification indicated that GmHSFA6b overexpression enhanced HT tolerance in Arabidopsis during flowering. Substance content and gene expression analysis revealed that miR156b-GmSPL2b may mediate reactive oxygen species clearance by regulating flavonoid metabolism, thus participating in the regulation of male fertility in soybean under HT stress. This study not only provided important progress for understanding the molecular mechanism of miR156b-GmSPL2b regulating the male fertility of soybean CMS-based restorer line under HT stress, but also provided genetic resources and theoretical basis for creating HT-tolerant strong restorer lines.
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Affiliation(s)
- Xianlong Ding
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture and Rural Affairs of the People's Republic of China), MOE National Innovation Platform for Soybean Bio-breeding Industry and Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Jinfeng Guo
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture and Rural Affairs of the People's Republic of China), MOE National Innovation Platform for Soybean Bio-breeding Industry and Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Menglin Lv
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture and Rural Affairs of the People's Republic of China), MOE National Innovation Platform for Soybean Bio-breeding Industry and Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Hongjie Wang
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture and Rural Affairs of the People's Republic of China), MOE National Innovation Platform for Soybean Bio-breeding Industry and Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Ying Sheng
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture and Rural Affairs of the People's Republic of China), MOE National Innovation Platform for Soybean Bio-breeding Industry and Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Ying Liu
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture and Rural Affairs of the People's Republic of China), MOE National Innovation Platform for Soybean Bio-breeding Industry and Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Junyi Gai
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture and Rural Affairs of the People's Republic of China), MOE National Innovation Platform for Soybean Bio-breeding Industry and Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Shouping Yang
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture and Rural Affairs of the People's Republic of China), MOE National Innovation Platform for Soybean Bio-breeding Industry and Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, China
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4
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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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5
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Li C, Nong W, Zhao S, Lin X, Xie Y, Cheung MY, Xiao Z, Wong AYP, Chan TF, Hui JHL, Lam HM. Differential microRNA expression, microRNA arm switching, and microRNA:long noncoding RNA interaction in response to salinity stress in soybean. BMC Genomics 2022; 23:65. [PMID: 35057741 PMCID: PMC8780314 DOI: 10.1186/s12864-022-08308-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 01/10/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Soybean is a major legume crop with high nutritional and environmental values suitable for sustainable agriculture. Noncoding RNAs (ncRNAs), including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), are important regulators of gene functions in eukaryotes. However, the interactions between these two types of ncRNAs in the context of plant physiology, especially in response to salinity stress, are poorly understood. RESULTS Here, we challenged a cultivated soybean accession (C08) and a wild one (W05) with salt treatment and obtained their small RNA transcriptomes at six time points from both root and leaf tissues. In addition to thoroughly analyzing the differentially expressed miRNAs, we also documented the first case of miRNA arm-switching (miR166m), the swapping of dominant miRNA arm expression, in soybean in different tissues. Two arms of miR166m target different genes related to salinity stress (chloroplastic beta-amylase 1 targeted by miR166m-5p and calcium-dependent protein kinase 1 targeted by miR166m-3p), suggesting arm-switching of miR166m play roles in soybean in response to salinity stress. Furthermore, two pairs of miRNA:lncRNA interacting partners (miR166i-5p and lncRNA Gmax_MSTRG.35921.1; and miR394a-3p and lncRNA Gmax_MSTRG.18616.1) were also discovered in reaction to salinity stress. CONCLUSIONS This study demonstrates how ncRNA involves in salinity stress responses in soybean by miRNA arm switching and miRNA:lncRNA interactions. The behaviors of ncRNAs revealed in this study will shed new light on molecular regulatory mechanisms of stress responses in plants, and hence provide potential new strategies for crop improvement.
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Affiliation(s)
- Chade Li
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
| | - Wenyan Nong
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
| | - Shancen Zhao
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, P.R. China
| | - Xiao Lin
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
| | - Yichun Xie
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
| | - Ming-Yan Cheung
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
| | - Zhixia Xiao
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
| | - Annette Y P Wong
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
| | - Ting Fung Chan
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China.
| | - Jerome H L Hui
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China.
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China.
| | - Hon-Ming Lam
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, P.R. China.
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6
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Zhang C, Fu F, Lin C, Ding X, Zhang J, Yan H, Wang P, Zhang W, Peng B, Zhao L. MicroRNAs Involved in Regulatory Cytoplasmic Male Sterility by Analysis RNA-seq and Small RNA-seq in Soybean. Front Genet 2021; 12:654146. [PMID: 34054917 PMCID: PMC8153375 DOI: 10.3389/fgene.2021.654146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
Cytoplasmic male sterility (CMS) is an important plant characteristic for exploiting heterosis to enhance crop traits during breeding. However, the CMS regulatory network remains unclear in plants, even though researchers have attempted to isolate genes associated with CMS. In this study, we performed high-throughput sequencing and degradome analyses to identify microRNAs (miRNAs) and their targets in a soybean CMS line (JLCMS9A) and its maintainer line (JLCMS9B). Additionally, the differentially expressed genes during reproductive development were identified using RNA-seq data. A total of 280 miRNAs matched soybean miRNA sequences in miRBase, including mature miRNAs and pre-miRNAs. Of the 280 miRNAs, 30, 23, and 21 belonged to the miR166, miR156, and miR171 families, respectively. Moreover, 410 novel low-abundant miRNAs were identified in the JLCMS9A and JLCMS9B flower buds. Furthermore, 303 and 462 target genes unique to JLCMS9A and JLCMS9B, respectively, as well as 782 common targets were predicted based on the degradome analysis. Target genes differentially expressed between the CMS line and the maintainer line were revealed by an RNA-seq analysis. Moreover, all target genes were annotated with diverse functions related to biological processes, cellular components, and molecular functions, including transcriptional regulation, the nucleus, meristem maintenance, meristem initiation, cell differentiation, auxin-activated signaling, plant ovule development, and anther development. Finally, a network was built based on the interactions. Analyses of the miRNA, degradome, and transcriptome datasets generated in this study provided a comprehensive overview of the reproductive development of a CMS soybean line. The data presented herein represent useful information for soybean hybrid breeding. Furthermore, the study results indicate that miRNAs might contribute to the soybean CMS regulatory network by modulating the expression of CMS-related genes. These findings lay the foundation for future studies on the molecular mechanisms underlying soybean CMS.
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Affiliation(s)
- Chunbao Zhang
- Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Fuyou Fu
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada
| | - Chunjing Lin
- Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Xiaoyang Ding
- Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Jingyong Zhang
- Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Hao Yan
- Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Pengnian Wang
- Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Wei Zhang
- Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Bao Peng
- Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Limei Zhao
- Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
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7
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Ding X, Guo J, Zhang Q, Yu L, Zhao T, Yang S. Heat-Responsive miRNAs Participate in the Regulation of Male Fertility Stability in Soybean CMS-Based F 1 under High Temperature Stress. Int J Mol Sci 2021; 22:2446. [PMID: 33671046 PMCID: PMC7957588 DOI: 10.3390/ijms22052446] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/10/2021] [Accepted: 02/24/2021] [Indexed: 11/18/2022] Open
Abstract
MicroRNAs (miRNAs), a class of noncoding small RNAs (sRNAs), are widely involved in the response to high temperature (HT) stress at both the seedling and flowering stages. To dissect the roles of miRNAs in regulating male fertility in soybean cytoplasmic male sterility (CMS)-based F1 under HT, sRNA sequencing was performed using flower buds from HT-tolerant and HT-sensitive CMS-based F1 combinations (NF1 and YF1, respectively). A total of 554 known miRNAs, 59 new members of known miRNAs, 712 novel miRNAs, and 1145 target genes of 580 differentially expressed miRNAs (DEMs) were identified under normal temperature and HT conditions. Further integrated analysis of sRNA and transcriptome sequencing found that 21 DEMs and 15 differentially expressed target genes, such as gma-miR397a/Laccase 2, gma-miR399a/Inorganic phosphate transporter 1-4, and gma-miR4413a/PPR proteins, mitochondrial-like, were negatively regulated under HT stress. Furthermore, all members of the gma-miR156 family were suppressed by HT stress in both NF1 and YF1, but were highly expressed in YF1 under HT condition. The negative correlation between gma-miR156b and its target gene squamosa promoter-binding protein-like 2b was confirmed by expression analysis, and overexpression of gma-miR156b in Arabidopsis led to male sterility under HT stress. With these results, we proposed that miRNAs play an important role in the regulation of male fertility stability in soybean CMS-based F1 under HT stress.
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Affiliation(s)
| | | | | | | | - Tuanjie Zhao
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (X.D.); (J.G.); (Q.Z.); (L.Y.)
| | - Shouping Yang
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (X.D.); (J.G.); (Q.Z.); (L.Y.)
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8
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Huang J, Wang C, Li X, Fang X, Huang N, Wang Y, Ma H, Wang Y, Copenhaver GP. Conservation and Divergence in the Meiocyte sRNAomes of Arabidopsis, Soybean, and Cucumber. PLANT PHYSIOLOGY 2020; 182:301-317. [PMID: 31719152 PMCID: PMC6945826 DOI: 10.1104/pp.19.00807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 10/22/2019] [Indexed: 05/15/2023]
Abstract
Meiosis is a critical process for sexual reproduction. During meiosis, genetic information on homologous chromosomes is shuffled through meiotic recombination to produce gametes with novel allelic combinations. Meiosis and recombination are orchestrated by several mechanisms including regulation by small RNAs (sRNAs). Our previous work in Arabidopsis (Arabidopsis thaliana) meiocytes showed that meiocyte-specific sRNAs (ms-sRNAs) have distinct characteristics, including positive association with the coding region of genes that are transcriptionally upregulated during meiosis. Here, we characterized the ms-sRNAs in two important crops, soybean (Glycine max) and cucumber (Cucumis sativus). Ms-sRNAs in soybean have the same features as those in Arabidopsis, suggesting that they may play a conserved role in eudicots. We also investigated the profiles of microRNAs (miRNAs) and phased secondary small interfering RNAs in the meiocytes of all three species. Two conserved miRNAs, miR390 and miR167, are highly abundant in the meiocytes of all three species. In addition, we identified three novel cucumber miRNAs. Intriguingly, our data show that the previously identified phased secondary small interfering RNA pathway involving soybean-specific miR4392 is more abundant in meiocytes. These results showcase the conservation and divergence of ms-sRNAs in flowering plants, and broaden our understanding of sRNA function in crop species.
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Affiliation(s)
- Jiyue Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
- University of North Carolina at Chapel Hill Department of Biology and the Integrative Program for Biological and Genome Sciences, Genome Science Building, Chapel Hill, North Carolina 27599-3280
| | - Cong Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Xiang Li
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Xiaolong Fang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Ning Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Ying Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Hong Ma
- Department of Biology, the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, Pennsylvania 16802
| | - Yingxiang Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Gregory P Copenhaver
- University of North Carolina at Chapel Hill Department of Biology and the Integrative Program for Biological and Genome Sciences, Genome Science Building, Chapel Hill, North Carolina 27599-3280
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599
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9
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Liang Y, Zhang Y, Xu L, Zhou D, Jin Z, Zhou H, Lin S, Cao J, Huang L. CircRNA Expression Pattern and ceRNA and miRNA-mRNA Networks Involved in Anther Development in the CMS Line of Brassica campestris. Int J Mol Sci 2019; 20:ijms20194808. [PMID: 31569708 PMCID: PMC6801457 DOI: 10.3390/ijms20194808] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 09/20/2019] [Accepted: 09/24/2019] [Indexed: 12/16/2022] Open
Abstract
Male-sterile plants provide an important breeding tool for the heterosis of hybrid crops, such as Brassicaceae. In the last decade, circular RNAs (circRNAs), as a novel class of covalently closed and single-stranded endogenous non-coding RNAs (ncRNAs), have received much attention because of their functions as “microRNA (miRNA) sponges” and “competing endogenous RNAs” (ceRNAs). However, the information about circRNAs in the regulation of male-sterility and anther development is limited. In this study, we established the Polima cytoplasm male sterility (CMS) line “Bcpol97-05A”, and the fertile line, “Bcajh97-01B”, in Brassicacampestris L. ssp. chinensis Makino, syn. B. rapa ssp. chinensis, and performed RNA expression profiling comparisons between the flower buds of the sterile line and fertile line by whole-transcriptome sequencing. A total of 31 differentially expressed (DE) circRNAs, 47 DE miRNAs, and 4779 DE mRNAs were identified. By using Cytoscape, the miRNA-mediated regulatory network and ceRNA network were constructed, and the circRNA A02:23507399|23531438 was hypothesized to be an important circRNA regulating anther development at the post-transcriptional level. The gene ontology (GO) analysis demonstrated that miRNAs and circRNAs could regulate the orderly secretion and deposition of cellulose, sporopollenin, pectin, and tryphine; the timely degradation of lipids; and the programmed cell death (PCD) of tapetum cells, which play key roles in anther development. Our study revealed a new circRNA–miRNA–mRNA network, which is involved in the anther development of B. campestris, which enriched the understanding of CMS in flowering plants, and laid a foundation for further study on the functions of circRNAs and miRNAs during anther development.
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Affiliation(s)
- Yuwei Liang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China.
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China.
| | - Yuzhi Zhang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China.
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China.
| | - Liai Xu
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China.
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China.
| | - Dong Zhou
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China.
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China.
| | - Zongmin Jin
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China.
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China.
| | - Huiyan Zhou
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China.
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China.
| | - Sue Lin
- Institute of Life Sciences, Wenzhou University, Wenzhou 325000, China.
| | - Jiashu Cao
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China.
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China.
| | - Li Huang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China.
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China.
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10
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Ramesh SV, Govindasamy V, Rajesh MK, Sabana AA, Praveen S. Stress-responsive miRNAome of Glycine max (L.) Merrill: molecular insights and way forward. PLANTA 2019; 249:1267-1284. [PMID: 30798358 DOI: 10.1007/s00425-019-03114-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 02/18/2019] [Indexed: 06/09/2023]
Abstract
MAIN CONCLUSION Analysis of stress-associated miRNAs of Glycine max (L.) Merrill reveals wider ramifications of small RNA-mediated (conserved and legume-specific miRNAs) gene regulatory foot prints in molecular adaptive responses. MicroRNAs (miRNAs) are indispensable components of gene regulatory mechanism of plants. Soybean is a crop of immense commercial potential grown worldwide for its edible oil and soy meal. Intensive research efforts, using the next generation sequencing and bioinformatics techniques, have led to the identification and characterization of numerous small RNAs, especially microRNAs (miRNAs), in soybean. Furthermore, studies have unequivocally demonstrated the significance of miRNAs during the developmental processes and various stresses in soybean. In this review, we summarize the current state of understanding of miRNA-based abiotic and biotic stress responses in soybean. In addition, the molecular insights gained from the stress-related soybean miRNAs have been compared to the miRNAs of other crops, especially legumes, and the core commonalities have been highlighted, though differences among them were not ignored. Nature of response of soybean-derived conserved miRNAs during various stresses was also analyzed to gain deeper insights regarding sRNAome-based defense responses. This review further provides way forward in legume small RNA transcriptomics based on the adaptive responses of soybean and other legume-derived miRNAs.
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Affiliation(s)
- S V Ramesh
- ICAR-Indian Institute of Soybean Research (ICAR-IISR), Indore, Madhya Pradesh, 452001, India.
- ICAR-Central Plantation Crops Research Institute (ICAR-CPCRI), Kasaragod, Kerala, 671124, India.
| | - V Govindasamy
- ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, 110012, India
| | - M K Rajesh
- ICAR-Central Plantation Crops Research Institute (ICAR-CPCRI), Kasaragod, Kerala, 671124, India
| | - A A Sabana
- ICAR-Central Plantation Crops Research Institute (ICAR-CPCRI), Kasaragod, Kerala, 671124, India
| | - Shelly Praveen
- ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, 110012, India
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