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Hamid R, Jacob F, Ghorbanzadeh Z, Khayam Nekouei M, Zeinalabedini M, Mardi M, Sadeghi A, Kumar S, Ghaffari MR. Genomic insights into CKX genes: key players in cotton fibre development and abiotic stress responses. PeerJ 2024; 12:e17462. [PMID: 38827302 PMCID: PMC11144395 DOI: 10.7717/peerj.17462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 05/05/2024] [Indexed: 06/04/2024] Open
Abstract
Cytokinin oxidase/dehydrogenase (CKX), responsible for irreversible cytokinin degradation, also controls plant growth and development and response to abiotic stress. While the CKX gene has been studied in other plants extensively, its function in cotton is still unknown. Therefore, a genome-wide study to identify the CKX gene family in the four cotton species was conducted using transcriptomics, quantitative real-time PCR (qRT-PCR) and bioinformatics. As a result, in G. hirsutum and G. barbadense (the tetraploid cotton species), 87 and 96 CKX genes respectively and 62 genes each in G. arboreum and G. raimondii, were identified. Based on the evolutionary studies, the cotton CKX gene family has been divided into five distinct subfamilies. It was observed that CKX genes in cotton have conserved sequence logos and gene family expansion was due to segmental duplication or whole genome duplication (WGD). Collinearity and multiple synteny studies showed an expansion of gene families during evolution and purifying selection pressure has been exerted. G. hirsutum CKX genes displayed multiple exons/introns, uneven chromosomal distribution, conserved protein motifs, and cis-elements related to growth and stress in their promoter regions. Cis-elements related to resistance, physiological metabolism and hormonal regulation were identified within the promoter regions of the CKX genes. Expression analysis under different stress conditions (cold, heat, drought and salt) revealed different expression patterns in the different tissues. Through virus-induced gene silencing (VIGS), the GhCKX34A gene was found to improve cold resistance by modulating antioxidant-related activity. Since GhCKX29A is highly expressed during fibre development, we hypothesize that the increased expression of GhCKX29A in fibres has significant effects on fibre elongation. Consequently, these results contribute to our understanding of the involvement of GhCKXs in both fibre development and response to abiotic stress.
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Affiliation(s)
- Rasmieh Hamid
- Department of Plant Breeding, Cotton Research Institute of Iran (CRII), Agricultural Research, Education and Extension Organization (AREEO), Gorgan, Golestan, Iran
| | - Feba Jacob
- Centre for Plant Biotechnology and Molecular Biology, Kerala Agricultural University, Thrissur, Kerala, India
| | - Zahra Ghorbanzadeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Alborz, Iran
| | | | - Mehrshad Zeinalabedini
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Alborz, Iran
| | - Mohsen Mardi
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Alborz, Iran
| | - Akram Sadeghi
- Department of Microbial Biotechnology and Biosafety, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Alborrz, Iran
| | - Sushil Kumar
- Agricultural Biotechnology, Anand agricultural University, Anand, Gujarat, India
| | - Mohammad Reza Ghaffari
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Alborz, Iran
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Hamid R, Ghorbanzadeh Z, Jacob F, Nekouei MK, Zeinalabedini M, Mardi M, Sadeghi A, Ghaffari MR. Decoding drought resilience: a comprehensive exploration of the cotton Eceriferum (CER) gene family and its role in stress adaptation. BMC PLANT BIOLOGY 2024; 24:468. [PMID: 38811873 PMCID: PMC11134665 DOI: 10.1186/s12870-024-05172-8] [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: 01/20/2024] [Accepted: 05/20/2024] [Indexed: 05/31/2024]
Abstract
BACKGROUND The cuticular wax serves as a primary barrier that protects plants from environmental stresses. The Eceriferum (CER) gene family is associated with wax production and stress resistance. RESULTS In a genome-wide identification study, a total of 52 members of the CER family were discovered in four Gossypium species: G. arboreum, G. barbadense, G. raimondii, and G. hirsutum. There were variations in the physicochemical characteristics of the Gossypium CER (GCER) proteins. Evolutionary analysis classified the identified GCERs into five groups, with purifying selection emerging as the primary evolutionary force. Gene structure analysis revealed that the number of conserved motifs ranged from 1 to 15, and the number of exons varied from 3 to 13. Closely related GCERs exhibited similar conserved motifs and gene structures. Analyses of chromosomal positions, selection pressure, and collinearity revealed numerous fragment duplications in the GCER genes. Additionally, nine putative ghr-miRNAs targeting seven G. hirsutum CER (GhCER) genes were identified. Among them, three miRNAs, including ghr-miR394, ghr-miR414d, and ghr-miR414f, targeted GhCER09A, representing the most targeted gene. The prediction of transcription factors (TFs) and the visualization of the regulatory TF network revealed interactions with GhCER genes involving ERF, MYB, Dof, bHLH, and bZIP. Analysis of cis-regulatory elements suggests potential associations between the CER gene family of cotton and responses to abiotic stress, light, and other biological processes. Enrichment analysis demonstrated a robust correlation between GhCER genes and pathways associated with cutin biosynthesis, fatty acid biosynthesis, wax production, and stress response. Localization analysis showed that most GCER proteins are localized in the plasma membrane. Transcriptome and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) expression assessments demonstrated that several GhCER genes, including GhCER15D, GhCER04A, GhCER06A, and GhCER12D, exhibited elevated expression levels in response to water deficiency stress compared to control conditions. The functional identification through virus-induced gene silencing (VIGS) highlighted the pivotal role of the GhCER04A gene in enhancing drought resistance by promoting increased tissue water retention. CONCLUSIONS This investigation not only provides valuable evidence but also offers novel insights that contribute to a deeper understanding of the roles of GhCER genes in cotton, their role in adaptation to drought and other abiotic stress and their potential applications for cotton improvement.
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Affiliation(s)
- Rasmieh Hamid
- Department of Plant Breeding, Cotton Research Institute of Iran (CRII), Agricultural Research, Education and Extension Organization (AREEO), Gorgan, Iran
| | - Zahra Ghorbanzadeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Feba Jacob
- Centre for Plant Biotechnology and Molecular Biology, Kerala Agricultural University, Thrissur, India
| | | | - Mehrshad Zeinalabedini
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Mohsen Mardi
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Akram Sadeghi
- Department of Microbial Biotechnology and Biosafety, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Mohammad Reza Ghaffari
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.
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Jiao Y, Zhao F, Geng S, Li S, Su Z, Chen Q, Yu Y, Qu Y. Genome-Wide and Expression Pattern Analysis of the DVL Gene Family Reveals GhM_A05G1032 Is Involved in Fuzz Development in G. hirsutum. Int J Mol Sci 2024; 25:1346. [PMID: 38279348 PMCID: PMC10816595 DOI: 10.3390/ijms25021346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/18/2024] [Accepted: 01/20/2024] [Indexed: 01/28/2024] Open
Abstract
DVL is one of the small polypeptides which plays an important role in regulating plant growth and development, tissue differentiation, and organ formation in the process of coping with stress conditions. So far, there has been no comprehensive analysis of the expression profile and function of the cotton DVL gene. According to previous studies, a candidate gene related to the development of fuzz was screened, belonging to the DVL family, and was related to the development of trichomes in Arabidopsis thaliana. However, the comprehensive identification and systematic analysis of DVL in cotton have not been conducted. In this study, we employed bioinformatics approaches to conduct a novel analysis of the structural characteristics, phylogenetic tree, gene structure, expression pattern, evolutionary relationship, and selective pressure of the DVL gene family members in four cotton species. A total of 117 DVL genes were identified, including 39 members in G. hirsutum. Based on the phylogenetic analysis, the DVL protein sequences were categorized into five distinct subfamilies. Additionally, we successfully mapped these genes onto chromosomes and visually represented their gene structure information. Furthermore, we predicted the presence of cis-acting elements in DVL genes in G. hirsutum and characterized the repeat types of DVL genes in the four cotton species. Moreover, we computed the Ka/Ks ratio of homologous genes across the four cotton species and elucidated the selective pressure acting on these homologous genes. In addition, we described the expression patterns of the DVL gene family using RNA-seq data, verified the correlation between GhMDVL3 and fuzz development through VIGS technology, and found that some DVL genes may be involved in resistance to biotic and abiotic stress conditions through qRT-PCR technology. Furthermore, a potential interaction network was constructed by WGCNA, and our findings demonstrated the potential of GhM_A05G1032 to interact with numerous genes, thereby playing a crucial role in regulating fuzz development. This research significantly contributed to the comprehension of DVL genes in upland cotton, thereby establishing a solid basis for future investigations into the functional aspects of DVL genes in cotton.
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Affiliation(s)
- Yang Jiao
- Cotton Research Institute, Xinjiang Academy of Agriculture and Reclamation Science, Shihezi 832000, China; (Y.J.); (F.Z.)
- College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China; (S.G.); (S.L.); (Z.S.); (Q.C.)
| | - Fuxiang Zhao
- Cotton Research Institute, Xinjiang Academy of Agriculture and Reclamation Science, Shihezi 832000, China; (Y.J.); (F.Z.)
| | - Shiwei Geng
- College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China; (S.G.); (S.L.); (Z.S.); (Q.C.)
| | - Shengmei Li
- College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China; (S.G.); (S.L.); (Z.S.); (Q.C.)
| | - Zhanlian Su
- College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China; (S.G.); (S.L.); (Z.S.); (Q.C.)
| | - Quanjia Chen
- College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China; (S.G.); (S.L.); (Z.S.); (Q.C.)
| | - Yu Yu
- Cotton Research Institute, Xinjiang Academy of Agriculture and Reclamation Science, Shihezi 832000, China; (Y.J.); (F.Z.)
| | - Yanying Qu
- College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China; (S.G.); (S.L.); (Z.S.); (Q.C.)
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