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Ebrahimi Naghani S, Šmeringai J, Pleskačová B, Dobisová T, Panzarová K, Pernisová M, Robert HS. Integrative phenotyping analyses reveal the relevance of the phyB-PIF4 pathway in Arabidopsis thaliana reproductive organs at high ambient temperature. BMC PLANT BIOLOGY 2024; 24:721. [PMID: 39075366 PMCID: PMC11285529 DOI: 10.1186/s12870-024-05394-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: 04/05/2024] [Accepted: 07/08/2024] [Indexed: 07/31/2024]
Abstract
BACKGROUND The increasing ambient temperature significantly impacts plant growth, development, and reproduction. Uncovering the temperature-regulating mechanisms in plants is of high importance, for increasing our fundamental understanding of plant thermomorphogenesis, for its potential in applied science, and for aiding plant breeders in improving plant thermoresilience. Thermomorphogenesis, the developmental response to warm temperatures, has been primarily studied in seedlings and in the regulation of flowering time. PHYTOCHROME B and PHYTOCHROME-INTERACTING FACTORs (PIFs), particularly PIF4, are key components of this response. However, the thermoresponse of other adult vegetative tissues and reproductive structures has not been systematically evaluated, especially concerning the involvement of phyB and PIFs. RESULTS We screened the temperature responses of the wild type and several phyB-PIF4 pathway Arabidopsis mutant lines in combined and integrative phenotyping platforms for root growth in soil, shoot, inflorescence, and seed. Our findings demonstrate that phyB-PIF4 is generally involved in the relay of temperature signals throughout plant development, including the reproductive stage. Furthermore, we identified correlative responses to high ambient temperature between shoot and root tissues. This integrative and automated phenotyping was complemented by monitoring the changes in transcript levels in reproductive organs. Transcriptomic profiling of the pistils from plants grown under high ambient temperature identified key elements that may provide insight into the molecular mechanisms behind temperature-induced reduced fertilization rate. These include a downregulation of auxin metabolism, upregulation of genes involved auxin signalling, miRNA156 and miRNA160 pathways, and pollen tube attractants. CONCLUSIONS Our findings demonstrate that phyB-PIF4 involvement in the interpretation of temperature signals is pervasive throughout plant development, including processes directly linked to reproduction.
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Affiliation(s)
- Shekoufeh Ebrahimi Naghani
- Hormonal Crosstalk in Plant Development, Mendel Center for Plant Genomics and Proteomics, CEITEC MU-Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 625 00, Czech Republic
| | - Ján Šmeringai
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 625 00, Czech Republic
- Mendel Center for Plant Genomics and Proteomics, CEITEC MU-Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic
| | | | | | - Klára Panzarová
- PSI - Photon Systems Instruments, Drasov, 66424, Czech Republic
| | - Markéta Pernisová
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 625 00, Czech Republic
- Mendel Center for Plant Genomics and Proteomics, CEITEC MU-Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic
| | - Hélène S Robert
- Hormonal Crosstalk in Plant Development, Mendel Center for Plant Genomics and Proteomics, CEITEC MU-Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic.
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Wang R, Zhang M, Wang H, Chen L, Zhang X, Guo L, Qi T, Tang H, Shahzad K, Wang H, Qiao X, Wu J, Xing C. Identification and characterization of circular RNAs involved in the fertility stability of cotton CMS-D2 restorer line under heat stress. BMC PLANT BIOLOGY 2024; 24:32. [PMID: 38183049 PMCID: PMC10768462 DOI: 10.1186/s12870-023-04706-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: 07/19/2023] [Accepted: 12/25/2023] [Indexed: 01/07/2024]
Abstract
BACKGROUND As a vital type of noncoding RNAs, circular RNAs (circRNAs) play important roles in plant growth and development and stress response. However, little is known about the biological roles of circRNAs in regulating the stability of male fertility restoration for cytoplasmic male sterility (CMS) conditioned by Gossypium harknessii cytoplasm (CMS-D2) cotton under high-temperature (HT) stress. RESULTS In this study, RNA-sequencing and bioinformatics analysis were performed on pollen grains of isonuclear alloplasmic near-isogenic restorer lines NH [N(Rf1rf1)] and SH [S(Rf1rf1)] with obvious differences in fertility stability under HT stress at two environments. A total of 967 circRNAs were identified, with 250 differentially expressed under HT stress. We confirmed the back-splicing sites of eight selected circRNAs using divergent primers and Sanger sequencing. Tissue-specific expression patterns of five differentially expressed circRNAs (DECs) were also verified by RT-PCR and qRT-PCR. Functional enrichment and metabolic pathway analysis revealed that the parental genes of DECs were significantly enriched in fertility-related biological processes such as pollen tube guidance and cell wall organization, as well as the Pentose and glucuronate interconversions, Steroid biosynthesis, and N-Glycan biosynthesis pathways. Moreover, we also constructed a putative circRNA-mediated competing endogenous RNA (ceRNA) network consisting of 21 DECs, eight predicted circRNA-binding miRNAs, and their corresponding 22 mRNA targets, especially the two ceRNA modules circRNA346-miR159a-MYB33 and circRNA484-miR319e-MYB33, which might play important biological roles in regulating pollen fertility stability of cotton CMS-D2 restorer line under HT stress. CONCLUSIONS Through systematic analysis of the abundance, characteristics and expression patterns of circRNAs, as well as the potential functions of their parent genes, our findings suggested that circRNAs and their mediated ceRNA networks acted vital biological roles in cotton pollen development, and might be also essential regulators for fertility stability of CMS-D2 restorer line under heat stress. This study will open a new door for further unlocking complex regulatory mechanisms underpinning the fertility restoration stability for CMS-D2 in cotton.
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Affiliation(s)
- Ruijie Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Meng Zhang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, 38 Huanghe Dadao, Anyang, 455000, Henan, China.
| | - Hui Wang
- Xiangyang Vocational and Technical College, Xiangyang, 441050, Hubei, China
| | - Liangliang Chen
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Xuexian Zhang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Liping Guo
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Tingxiang Qi
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Huini Tang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Kashif Shahzad
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Hailin Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Xiuqin Qiao
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Jianyong Wu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, 38 Huanghe Dadao, Anyang, 455000, Henan, China.
| | - Chaozhu Xing
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, 38 Huanghe Dadao, Anyang, 455000, Henan, China.
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