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Li Z, Luo D, Tang M, Cao S, Pan J, Zhang W, Hu Y, Yue J, Huang Z, Li R, Chen P. Integrated Methylome and Transcriptome Analysis Provides Insights into the DNA Methylation Underlying the Mechanism of Cytoplasmic Male Sterility in Kenaf ( Hibiscus cannabinus L.). Int J Mol Sci 2022; 23:ijms23126864. [PMID: 35743303 PMCID: PMC9224340 DOI: 10.3390/ijms23126864] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/14/2022] [Accepted: 06/18/2022] [Indexed: 11/16/2022] Open
Abstract
Cytoplasmic male sterility (CMS) is widely exploited in hybrid seed production. Kenaf is an important fiber crop with high heterosis. The molecular mechanism of kenaf CMS remains unclear, particularly in terms of DNA methylation. Here, using the anthers of a kenaf CMS line (P3A) and its maintainer line (P3B), comparative physiological, DNA methylation, and transcriptome analyses were performed. The results showed that P3A had considerably lower levels of IAA, ABA, photosynthetic products and ATP contents than P3B. DNA methylome analysis revealed 650 differentially methylated genes (DMGs) with 313 up- and 337 down methylated, and transcriptome analysis revealed 1788 differentially expressed genes (DEGs) with 558 up- and 1230 downregulated genes in P3A compared with P3B. Moreover, 45 genes were characterized as both DEGs and DMGs, including AUX,CYP, BGL3B, SUS6, AGL30 and MYB21. Many DEGs may be regulated by related DMGs based on methylome and transcriptome studies. These DEGs were involved in carbon metabolism, plant hormone signal transduction, the TCA cycle and the MAPK signaling pathway and were shown to be important for CMS in kenaf. These results provide new insights into the epigenetic mechanism of CMS in kenaf and other crops.
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Affiliation(s)
- Zengqiang Li
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530004, China; (Z.L.); (D.L.); (M.T.); (S.C.); (J.P.); (W.Z.); (Y.H.); (J.Y.); (Z.H.)
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Dengjie Luo
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530004, China; (Z.L.); (D.L.); (M.T.); (S.C.); (J.P.); (W.Z.); (Y.H.); (J.Y.); (Z.H.)
| | - Meiqiong Tang
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530004, China; (Z.L.); (D.L.); (M.T.); (S.C.); (J.P.); (W.Z.); (Y.H.); (J.Y.); (Z.H.)
| | - Shan Cao
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530004, China; (Z.L.); (D.L.); (M.T.); (S.C.); (J.P.); (W.Z.); (Y.H.); (J.Y.); (Z.H.)
| | - Jiao Pan
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530004, China; (Z.L.); (D.L.); (M.T.); (S.C.); (J.P.); (W.Z.); (Y.H.); (J.Y.); (Z.H.)
| | - Wenxian Zhang
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530004, China; (Z.L.); (D.L.); (M.T.); (S.C.); (J.P.); (W.Z.); (Y.H.); (J.Y.); (Z.H.)
| | - Yali Hu
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530004, China; (Z.L.); (D.L.); (M.T.); (S.C.); (J.P.); (W.Z.); (Y.H.); (J.Y.); (Z.H.)
| | - Jiao Yue
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530004, China; (Z.L.); (D.L.); (M.T.); (S.C.); (J.P.); (W.Z.); (Y.H.); (J.Y.); (Z.H.)
| | - Zhen Huang
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530004, China; (Z.L.); (D.L.); (M.T.); (S.C.); (J.P.); (W.Z.); (Y.H.); (J.Y.); (Z.H.)
| | - Ru Li
- College of Life Science & Technology, Guangxi University, Nanning 530004, China;
| | - Peng Chen
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530004, China; (Z.L.); (D.L.); (M.T.); (S.C.); (J.P.); (W.Z.); (Y.H.); (J.Y.); (Z.H.)
- Correspondence: ; Tel.: +86-155-7894-7886
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Hamid R, Tomar RS, Marashi H, Shafaroudi SM, Golakiya BA, Mohsenpour M. Transcriptome profiling and cataloging differential gene expression in floral buds of fertile and sterile lines of cotton (Gossypium hirsutum L.). Gene 2018; 660:80-91. [PMID: 29577977 DOI: 10.1016/j.gene.2018.03.070] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 03/14/2018] [Accepted: 03/21/2018] [Indexed: 01/02/2023]
Abstract
Cytoplasmic Male Sterility is maternally inherited trait in plants, characterized by failure to produce functional pollen during anther development. Anther development is modulated through the interaction of nuclear and mitochondrial genes. In the present study, differential gene expression of floral buds at the sporogenous stage (SS) and microsporocyte stage (MS) between CGMS and its fertile maintainer line of cotton plants was studied. A total of 320 significantly differentially expressed genes, including 20 down-regulated and 37 up-regulated in CGMS comparing with its maintainer line at the SS stage, as well as and 89 down-regulated and 4 up-regulated in CGMS compared to the fertile line at MS stage. Comparing the two stages in the same line, there were 6 down-regulated differentially expressed genes only induced in CGMS and 9 up-regulated differentially expressed gene only induced in its maintainer. GO analysis revealed essential genes responsible for pollen development, and cytoskeleton category show differential expression between the fertile and CGMS lines. Validation studies by qRT-PCR shows concordance with RNA-seq result. A set of novel SSRs identified in this study can be used in evaluating genetic relationships among cultivars, QTL mapping, and marker-assisted breeding. We reported aberrant expression of genes related to pollen exine formation, and synthesis of pectin lyase, myosine heavy chain, tubulin, actin-beta, heat shock protein and myeloblastosis (MYB) protein as targets for CMS in cotton. The results of this study contribute to basic information for future screening of genes and identification of molecular portraits responsible for CMS as well as to elucidate molecular mechanisms that lead to CMS in cotton.
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Affiliation(s)
- Rasmieh Hamid
- Department of Biotechnology and Plant Breeding, Ferdowsi University of Mashhad, Iran
| | - Rukam S Tomar
- Department of Biotechnology and Biochemistry, Junagadh Agricultural University, Junagadh, Gujarat, India
| | - Hassan Marashi
- Department of Biotechnology and Plant Breeding, Ferdowsi University of Mashhad, Iran.
| | | | - Balaji A Golakiya
- Department of Biotechnology and Biochemistry, Junagadh Agricultural University, Junagadh, Gujarat, India
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Omidvar V, Mohorianu I, Dalmay T, Zheng Y, Fei Z, Pucci A, Mazzucato A, Večeřová V, Sedlářova M, Fellner M. Transcriptional regulation of male-sterility in 7B-1 male-sterile tomato mutant. PLoS One 2017; 12:e0170715. [PMID: 28178307 PMCID: PMC5298235 DOI: 10.1371/journal.pone.0170715] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/09/2017] [Indexed: 11/18/2022] Open
Abstract
The 7B-1 tomato (Solanum lycopersicum L. cv Rutgers) is a male-sterile mutant with enhanced tolerance to abiotic stress, which makes it a potential candidate for hybrid seed breeding and stress engineering. To underline the molecular mechanism regulating the male-sterility in 7B-1, transcriptomic profiles of the 7B-1 male-sterile and wild type (WT) anthers were studied using mRNA sequencing (RNA-Seq). In total, 768 differentially expressed genes (DEGs) were identified, including 132 up-regulated and 636 down-regulated transcripts. Gene ontology (GO) enrichment analysis of DEGs suggested a general impact of the 7B-1 mutation on metabolic processes, such as proteolysis and carbohydrate catabolic process. Sixteen candidates with key roles in regulation of anther development were subjected to further analysis using qRT-PCR and in situ hybridization. Cytological studies showed several defects associated with anther development in the 7B-1 mutant, including unsynchronized anther maturation, dysfunctional meiosis, arrested microspores, defect in callose degradation and abnormal tapetum development. TUNEL assay showed a defect in programmed cell death (PCD) of tapetal cells in 7B-1 anthers. The present study provides insights into the transcriptome of the 7B-1 mutant. We identified several genes with altered expression level in 7B-1 (including beta-1,3 glucanase, GA2oxs, cystatin, cysteine protease, pectinesterase, TA29, and actin) that could potentially regulate anther developmental processes, such as meiosis, tapetum development, and cell-wall formation/degradation.
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Affiliation(s)
- Vahid Omidvar
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University and Institute of Experimental Botany AS CR, Šlechtitelů 27, Olomouc-Holice, Czech Republic
| | - Irina Mohorianu
- School of Computing Sciences, University of East Anglia, Norwich, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Yi Zheng
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States of America
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States of America
| | - Anna Pucci
- Department of Agricultural and Forestry Sciences, University of Tuscia, Viterbo, Italy
| | - Andrea Mazzucato
- Department of Agricultural and Forestry Sciences, University of Tuscia, Viterbo, Italy
| | - Vendula Večeřová
- Department of Botany, Faculty of Science, Palacký University in Olomouc, Šlechtitelů 27, Olomouc-Holice, Czech Republic
| | - Michaela Sedlářova
- Department of Botany, Faculty of Science, Palacký University in Olomouc, Šlechtitelů 27, Olomouc-Holice, Czech Republic
| | - Martin Fellner
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University and Institute of Experimental Botany AS CR, Šlechtitelů 27, Olomouc-Holice, Czech Republic
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