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Shahzaib M, Khan UM, Azhar MT, Atif RM, Khan SH, Zaman QU, Rana IA. Phylogenomic curation of Ovate Family Proteins (OFPs) in the U's Triangle of Brassica L. indicates stress-induced growth modulation. PLoS One 2024; 19:e0297473. [PMID: 38277374 PMCID: PMC10817133 DOI: 10.1371/journal.pone.0297473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/06/2024] [Indexed: 01/28/2024] Open
Abstract
The Ovate Family Proteins (OFPs) gene family houses a class of proteins that are involved in regulating plant growth and development. To date, there is no report of the simultaneous functional characterization of this gene family in all members of U's Triangle of Brassica. Here, we retrieved a combined total of 256 OFP protein sequences and analyzed their chromosomal localization, gene structure, conserved protein motif domains, and the pattern of cis-acting regulatory elements. The abundance of light-responsive elements like G-box, MRE, and GT1 motif suggests that OFPs are sensitive to the stimuli of light. The protein-protein interaction network analysis revealed that OFP05 and its orthologous genes were involved in regulating the process of transcriptional repression through their interaction with homeodomain transcription factors like KNAT and BLH. The presence of domains like DNA binding 2 and its superfamily speculated the involvement of OFPs in regulating gene expression. The biotic and abiotic stress, and the tissue-specific expression analysis of the RNA-seq datasets revealed that some of the genes such as BjuOFP30, and BnaOFP27, BolOFP11, and BolOFP10 were highly upregulated in seed coat at the mature stage and roots under various chemical stress conditions respectively which suggests their crucial role in plant growth and development processes. Experimental validation of prominent BnaOFPs such as BnaOFP27 confirmed their involvement in regulating gene expression under salinity, heavy metal, drought, heat, and cold stress. The GO and KEGG pathway enrichment analysis also sheds light on the involvement of OFPs in regulating plant growth and development. These findings have the potential to serve as a forerunner for future studies in terms of functionally diverse analysis of the OFP gene family in Brassica and other plant species.
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Affiliation(s)
- Muhammad Shahzaib
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Faisalabad, Punjab, Pakistan
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad, Faisalabad, Punjab, Pakistan
| | - Uzair Muhammad Khan
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad, Faisalabad, Punjab, Pakistan
| | - Muhammad Tehseen Azhar
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Faisalabad, Punjab, Pakistan
| | - Rana Muhammad Atif
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad, Faisalabad, Punjab, Pakistan
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Faisalabad, Punjab, Pakistan
| | - Sultan Habibullah Khan
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Faisalabad, Punjab, Pakistan
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad, Faisalabad, Punjab, Pakistan
| | - Qamar U. Zaman
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Iqrar Ahmad Rana
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Faisalabad, Punjab, Pakistan
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad, Faisalabad, Punjab, Pakistan
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Deng Z, Yang Z, Liu X, Dai X, Zhang J, Deng K. Genome-Wide Identification and Expression Analysis of C3H Zinc Finger Family in Potato ( Solanum tuberosum L.). Int J Mol Sci 2023; 24:12888. [PMID: 37629069 PMCID: PMC10454627 DOI: 10.3390/ijms241612888] [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: 07/10/2023] [Revised: 08/11/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
Transcription factors containing a CCCH structure (C3H) play important roles in plant growth and development, and their stress response, but research on the C3H gene family in potato has not been reported yet. In this study, we used bioinformatics to identify 50 C3H genes in potato and named them StC3H-1 to StC3H-50 according to their location on chromosomes, and we analyzed their physical and chemical properties, chromosome location, phylogenetic relationship, gene structure, collinearity relationship, and cis-regulatory element. The gene expression pattern analysis showed that many StC3H genes are involved in potato growth and development, and their response to diverse environmental stresses. Furthermore, RT-qPCR data showed that the expression of many StC3H genes was induced by high temperatures, indicating that StC3H genes may play important roles in potato response to heat stress. In addition, Some StC3H genes were predominantly expressed in the stolon and developing tubers, suggesting that these StC3H genes may be involved in the regulation of tuber development. Together, these results provide new information on StC3H genes and will be helpful for further revealing the function of StC3H genes in the heat stress response and tuber development in potato.
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Affiliation(s)
- Zeyi Deng
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (Z.D.); (Z.Y.); (X.L.); (X.D.); (J.Z.)
| | - Zhijiang Yang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (Z.D.); (Z.Y.); (X.L.); (X.D.); (J.Z.)
| | - Xinyan Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (Z.D.); (Z.Y.); (X.L.); (X.D.); (J.Z.)
| | - Xiumei Dai
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (Z.D.); (Z.Y.); (X.L.); (X.D.); (J.Z.)
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Jiankui Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (Z.D.); (Z.Y.); (X.L.); (X.D.); (J.Z.)
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Kexuan Deng
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (Z.D.); (Z.Y.); (X.L.); (X.D.); (J.Z.)
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
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Li C, Li Y, Chu P, Hao-hao Z, Wei Z, Cheng Y, Liu X, Zhao F, Li YJ, Zhang Z, Zheng Y, Mu Z. Effects of salt stress on sucrose metabolism and growth in Chinese rose ( Rosa chinensis). BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2116356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Caihua Li
- Economic Crop Research Laboratory, Economic Crops Institute, Jilin Academy of Agricultural Sciences, Changchun, PR China
| | - Yuhuan Li
- Economic Crop Research Laboratory, Economic Crops Institute, Jilin Academy of Agricultural Sciences, Changchun, PR China
| | - Peiyu Chu
- Laboratory of Economic Crops, Agricultural College, Heilongjiang Bayi Agriculture University, Daqing, PR China
| | - Zhao Hao-hao
- Laboratory of Economic Crops, Agricultural College, Heilongjiang Bayi Agriculture University, Daqing, PR China
| | - Zunmiao Wei
- Economic Crop Research Laboratory, Economic Crops Institute, Jilin Academy of Agricultural Sciences, Changchun, PR China
| | - Yan Cheng
- Economic Crop Research Laboratory, Economic Crops Institute, Jilin Academy of Agricultural Sciences, Changchun, PR China
| | - Xianxian Liu
- Economic Crop Research Laboratory, Economic Crops Institute, Jilin Academy of Agricultural Sciences, Changchun, PR China
| | - Fengzhou Zhao
- Laboratory of Economic Crops, Agricultural College, Heilongjiang Bayi Agriculture University, Daqing, PR China
| | - Yan-jun Li
- Economic Crop Research Laboratory, Economic Crops Institute, Jilin Academy of Agricultural Sciences, Changchun, PR China
| | - Zhiwen Zhang
- Laboratory of Economic Crops, Agricultural College, Heilongjiang Bayi Agriculture University, Daqing, PR China
| | - Yi Zheng
- Economic Crop Research Laboratory, Economic Crops Institute, Jilin Academy of Agricultural Sciences, Changchun, PR China
| | - Zhongsheng Mu
- Economic Crop Research Laboratory, Economic Crops Institute, Jilin Academy of Agricultural Sciences, Changchun, PR China
- Laboratory of Economic Crops, Agricultural College, Heilongjiang Bayi Agriculture University, Daqing, PR China
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