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Tian R, Xie S, Zhang J, Liu H, Li Y, Hu Y, Huang Y, Liu Y. Identification of Morphogenesis-Related NDR Kinase Signaling Network and Its Regulation on Cold Tolerance in Maize. PLANTS (BASEL, SWITZERLAND) 2023; 12:3639. [PMID: 37896102 PMCID: PMC10610150 DOI: 10.3390/plants12203639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 10/13/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023]
Abstract
The MOR (Morphogenesis-related NDR kinase) signaling network, initially identified in yeast, exhibits evolutionary conservation across eukaryotes and plays indispensable roles in the normal growth and development of these organisms. However, the functional role of this network and its associated genes in maize (Zea mays) has remained elusive until now. In this study, we identified a total of 19 maize MOR signaling network genes, and subsequent co-expression analysis revealed that 12 of these genes exhibited stronger associations with each other, suggesting their potential collective regulation of maize growth and development. Further analysis revealed significant co-expression between genes involved in the MOR signaling network and several genes related to cold tolerance. All MOR signaling network genes exhibited significant co-expression with COLD1 (Chilling tolerance divergence1), a pivotal gene involved in the perception of cold stimuli, suggesting that COLD1 may directly transmit cold stress signals to MOR signaling network genes subsequent to the detection of a cold stimulus. The findings indicated that the MOR signaling network may play a crucial role in modulating cold tolerance in maize by establishing an intricate relationship with key cold tolerance genes, such as COLD1. Under low-temperature stress, the expression levels of certain MOR signaling network genes were influenced, with a significant up-regulation observed in Zm00001d010720 and a notable down-regulation observed in Zm00001d049496, indicating that cold stress regulated the MOR signaling network. We identified and analyzed a mutant of Zm00001d010720, which showed a higher sensitivity to cold stress, thereby implicating its involvement in the regulation of cold stress in maize. These findings suggested that the relevant components of the MOR signaling network are also conserved in maize and this signaling network plays a vital role in modulating the cold tolerance of maize. This study offered valuable genetic resources for enhancing the cold tolerance of maize.
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Affiliation(s)
- Ran Tian
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (R.T.); (S.X.); (Y.L.); (Y.H.)
| | - Sidi Xie
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (R.T.); (S.X.); (Y.L.); (Y.H.)
| | - Junjie Zhang
- College of Life Science, Sichuan Agricultural University, Ya’an 625014, China; (J.Z.); (H.L.)
| | - Hanmei Liu
- College of Life Science, Sichuan Agricultural University, Ya’an 625014, China; (J.Z.); (H.L.)
| | - Yangping Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (R.T.); (S.X.); (Y.L.); (Y.H.)
| | - Yufeng Hu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (R.T.); (S.X.); (Y.L.); (Y.H.)
| | - Yubi Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (R.T.); (S.X.); (Y.L.); (Y.H.)
| | - Yinghong Liu
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
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The Importance of a Genome-Wide Association Analysis in the Study of Alternative Splicing Mutations in Plants with a Special Focus on Maize. Int J Mol Sci 2022; 23:ijms23084201. [PMID: 35457019 PMCID: PMC9024592 DOI: 10.3390/ijms23084201] [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: 03/09/2022] [Revised: 04/03/2022] [Accepted: 04/08/2022] [Indexed: 02/01/2023] Open
Abstract
Alternative splicing is an important mechanism for regulating gene expressions at the post-transcriptional level. In eukaryotes, the genes are transcribed in the nucleus to produce pre-mRNAs and alternative splicing can splice a pre-mRNA to eventually form multiple different mature mRNAs, greatly increasing the number of genes and protein diversity. Alternative splicing is involved in the regulation of various plant life activities, especially the response of plants to abiotic stresses and is also an important process of plant growth and development. This review aims to clarify the usefulness of a genome-wide association analysis in the study of alternatively spliced variants by summarizing the application of alternative splicing, genome-wide association analyses and genome-wide association analyses in alternative splicing, as well as summarizing the related research progress.
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Genome-Wide Profiling of Alternative Splicing and Gene Fusion during Rice Black-Streaked Dwarf Virus Stress in Maize (Zea mays L.). Genes (Basel) 2022; 13:genes13030456. [PMID: 35328010 PMCID: PMC8955601 DOI: 10.3390/genes13030456] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/28/2022] [Accepted: 02/28/2022] [Indexed: 12/26/2022] Open
Abstract
Rice black-streaked dwarf virus (RBSDV) causes maize rough dwarf disease (MRDD), which is a viral disease that significantly affects maize yields worldwide. Plants tolerate stress through transcriptional reprogramming at the alternative splicing (AS), transcriptional, and fusion gene (FG) levels. However, it is unclear whether and how AS and FG interfere with transcriptional reprogramming in MRDD. In this study, we performed global profiling of AS and FG on maize response to RBSDV and compared it with transcriptional changes. There are approximately 1.43 to 2.25 AS events per gene in maize infected with RBSDV. GRMZM2G438622 was only detected in four AS modes (A3SS, A5SS, RI, and SE), whereas GRMZM2G059392 showed downregulated expression and four AS events. A total of 106 and 176 FGs were detected at two time points, respectively, including six differentially expressed genes and five differentially spliced genes. The gene GRMZM2G076798 was the only FG that occurred at two time points and was involved in two FG events. Among these, 104 GOs were enriched, indicating that nodulin-, disease resistance-, and chloroplastic-related genes respond to RBSDV stress in maize. These results provide new insights into the mechanisms underlying post-transcriptional and transcriptional regulation of maize response to RBSDV stress.
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Zhang X, Xie S, Han J, Zhou Y, Liu C, Zhou Z, Wang F, Cheng Z, Zhang J, Hu Y, Hao Z, Li M, Zhang D, Yong H, Huang Y, Weng J, Li X. Integrated transcriptome, small RNA, and degradome analysis reveals the complex network regulating starch biosynthesis in maize. BMC Genomics 2019; 20:574. [PMID: 31296166 PMCID: PMC6625009 DOI: 10.1186/s12864-019-5945-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 06/30/2019] [Indexed: 12/18/2022] Open
Abstract
Background Starch biosynthesis in endosperm is a key process influencing grain yield and quality in maize. Although a number of starch biosynthetic genes have been well characterized, the mechanisms by which the expression of these genes is regulated, especially in regard to microRNAs (miRNAs), remain largely unclear. Results Sequence data for small RNAs, degradome, and transcriptome of maize endosperm at 15 and 25 d after pollination (DAP) from inbred lines Mo17 and Ji419, which exhibit distinct starch content and starch granule structure, revealed the mediation of starch biosynthetic pathways by miRNAs. Transcriptome analysis of these two lines indicated that 33 of 40 starch biosynthetic genes were differentially expressed, of which 12 were up-regulated in Ji419 at 15 DAP, one was up-regulated in Ji419 at 25 DAP, 14 were up-regulated in Ji419 at both 15 and 25 DAP, one was down-regulated in Ji419 at 15 DAP, two were down-regulated in Ji419 at 25 DAP, and three were up-regulated in Ji419 at 15 DAP and down-regulated in Ji419 at 25 DAP, compared with Mo17. Through combined analyses of small RNA and degradome sequences, 22 differentially expressed miRNAs were identified, including 14 known and eight previously unknown miRNAs that could target 35 genes. Furthermore, a complex co-expression regulatory network was constructed, in which 19 miRNAs could modulate starch biosynthesis in endosperm by tuning the expression of 19 target genes. Moreover, the potential operation of four miRNA-mediated pathways involving transcription factors, miR169a-NF-YA1-GBSSI/SSIIIa and miR169o-GATA9-SSIIIa/SBEIIb, was validated via analyses of expression pattern, transient transformation assays, and transactivation assays. Conclusion Our results suggest that miRNAs play a critical role in starch biosynthesis in endosperm, and that miRNA-mediated networks could modulate starch biosynthesis in this tissue. These results have provided important insights into the molecular mechanism of starch biosynthesis in developing maize endosperm. Electronic supplementary material The online version of this article (10.1186/s12864-019-5945-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaocong Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sidi Xie
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jienan Han
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agronomy, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Chang Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agronomy, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Zhiqiang Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Feifei Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zixiang Cheng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junjie Zhang
- College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan, China
| | - Yufeng Hu
- College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhuanfang Hao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mingshun Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Degui Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongjun Yong
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yubi Huang
- College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jianfeng Weng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Xinhai Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.
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