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Ni L, Xu Y, Wang Z, Yu C, Hua J, Yin Y, Li H, Gu C. Integrated metabolomics and transcriptomics reveal that HhERF9 positively regulates salt tolerance in Hibiscus hamabo Siebold & Zuccarini. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 213:108843. [PMID: 38879985 DOI: 10.1016/j.plaphy.2024.108843] [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: 03/14/2024] [Revised: 06/01/2024] [Accepted: 06/14/2024] [Indexed: 06/18/2024]
Abstract
Hibiscus hamabo Siebold & Zuccarini is one of the few semi-mangrove plants in the genus Hibiscus that can survive in saline-alkali soil and flooded land, but the mechanism underlying its adaptation to salt soil remains unknown. Here, to uncover this unsolved mystery, we characterized the changes in the accumulation of specific metabolites under salt stress in H. hamabo by integrating physiological, metabolic, and transcriptomic data, and found that osmotic adjustment and abscisic acid (ABA) is highly associated with the salt stress response. Further, a weighted gene co-expression network analysis was performed on the root transcriptome data, which identified three key candidate transcription factors responsive to salt stress. Among them, the expression HhERF9 was significantly upregulated under salt stress and ABA treatment and was involved in regulating the expression of genes related to the salt stress response. Further research indicated that HhERF9 enhances the accumulation of proline and soluble sugars by regulating the expression of genes such as NHX2 and P5CS. These findings provide a reference for improving H. hamabo through targeted genetic engineering and lay a theoretical foundation for its future promotion and cultivation in saline-alkali areas.
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Affiliation(s)
- Longjie Ni
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China; Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China.
| | - Yu Xu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China; Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China.
| | - Zhiquan Wang
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China; Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China.
| | - Chaoguang Yu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China; Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, 210014, China.
| | - Jianfeng Hua
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China; Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, 210014, China.
| | - Yunlong Yin
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China; Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, 210014, China.
| | - Huogen Li
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
| | - Chunsun Gu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China; Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China; Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, 210014, China.
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Li Y, Tao Y, Bai A, Yu Z, Yuan S, Wang H, Liu T, Hou X, Li Y. High expression of ethylene response factor BcERF98 delays the flowering time of non-heading Chinese cabbage. PLANTA 2024; 260:50. [PMID: 38990341 DOI: 10.1007/s00425-024-04479-y] [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: 12/13/2023] [Accepted: 07/02/2024] [Indexed: 07/12/2024]
Abstract
MAIN CONCLUSION BcERF98 is induced by ethylene signaling and inhibits the expression of BcFT by interacting with BcNF-YA2 and BcEIP9, thereby inhibiting plant flowering. Several stresses trigger the accumulation of ethylene, which then transmits the signal to ethylene response factors (ERFs) to participate in the regulation of plant development to adapt to the environment. This study clarifies the function of BcERF98, a homolog of AtERF98, in the regulation of plant flowering time mediated by high concentrations of ethylene. Results indicate that BcERF98 is a nuclear and the cell membrane-localized transcription factor and highly responsive to ethylene signaling. BcERF98 inhibits the expression of BcFT by interacting with BcEIP9 and BcNF-YA2, which are related to flowering time regulation, thereby participating in ethylene-mediated plant late flowering regulation. The results have enriched the theoretical knowledge of flowering regulation in non-heading Chinese cabbage (NHCC), providing the scientific basis and gene reserves for cultivating new varieties of NHCC with different flowering times.
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Affiliation(s)
- Yan Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Yu Tao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Aimei Bai
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Zhanghong Yu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Shuilin Yuan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Haibin Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Tongkun Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Xilin Hou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
- Nanjing Suman Plasma Engineering Research Institute, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ying Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China.
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Luo S, Zheng S, Li Z, Cao J, Wang B, Xu Y, Chong K. Monosaccharide transporter OsMST6 is activated by transcription factor OsERF120 to enhance chilling tolerance in rice seedlings. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4038-4051. [PMID: 38490694 DOI: 10.1093/jxb/erae123] [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: 10/10/2023] [Accepted: 03/15/2024] [Indexed: 03/17/2024]
Abstract
Chilling stress caused by extreme weather is threatening global rice (Oryza sativa L.) production. Identifying components of the signal transduction pathways underlying chilling tolerance in rice would advance molecular breeding. Here, we report that OsMST6, which encodes a monosaccharide transporter, positively regulates the chilling tolerance of rice seedlings. mst6 mutants showed hypersensitivity to chilling, while OsMST6 overexpression lines were tolerant. During chilling stress, OsMST6 transported more glucose into cells to modulate sugar and abscisic acid signaling pathways. We showed that the transcription factor OsERF120 could bind to the DRE/CRT element of the OsMST6 promoter and activate the expression of OsMST6 to positively regulate chilling tolerance. Genetically, OsERF120 was functionally dependent on OsMST6 when promoting chilling tolerance. In summary, OsERF120 and OsMST6 form a new downstream chilling regulatory pathway in rice in response to chilling stress, providing valuable findings for molecular breeding aimed at achieving global food security.
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Affiliation(s)
- Shengtao Luo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuangshuang Zheng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhitao Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Cao
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bo Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunyuan Xu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kang Chong
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Liu Z, Qin GH, Wei SW, Yan LF, Ning ZY, Wang H, Cao Z, Hu KD, Yao GF, Zhang H. PuERF008-PuFAD2 module regulates aroma formation via the fatty acid pathway in response to calcium signaling in 'Nanguo' pear. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 214:108913. [PMID: 38986239 DOI: 10.1016/j.plaphy.2024.108913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 06/14/2024] [Accepted: 07/03/2024] [Indexed: 07/12/2024]
Abstract
Calcium acts as a secondary messenger in plants and is essential for plant growth and development. However, studies on the pathway of aroma synthesis in 'Nanguo' pear (Pyrus ussriensis Maxim.) are scarce. In this study, a bioinformatics analysis of transcriptomic data from calcium-treated 'Nanguo' pear was performed, which identified two fatty acid desaturases, PuFAD2 and PuFAD3, and eight AP2/ERF transcription factors, all exhibiting the same expression patterns. Transient expression experiments showed overexpression of PuFAD2 and PuFAD3 significantly increased the levels of aromatic substrates linoleic acid, hexanal, linolenic acid, and (E)-2-hexenal, but RNAi (RNA interference) had the opposite expression. Promoter sequences analysis revealed that PuFAD2 and PuFAD3 have ERE (estrogen response element) motifs on their promoters. The strongest activation of PuFAD2 by PuERF008 was verified using a dual-luciferase reporting system. Additionally, yeast one-hybrid and electrophoretic mobility shift assays revealed PuERF008 could active PuFAD2. Transient overexpression and RNAi analyses of PuERF008 showed a strong correlation with the expression of PuFAD2. This study provides insights into the process of aroma biosynthesis in 'Nanguo' pear and offers a theoretical basis for elucidating the role of calcium signaling in aroma synthesis.
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Affiliation(s)
- Zhi Liu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui, 230009, PR China.
| | - Gai-Hua Qin
- Key Laboratory of Germplasm Innovation and Utilization of Horticultural Crop (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Institute of Horticultural Research, Anhui Academy of Agricultural Sciences, Hefei, 230031, PR China.
| | - Shu-Wei Wei
- Shandong Institute of Pomology, Tai'an, 271000, PR China.
| | - Long-Fei Yan
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui, 230009, PR China.
| | - Zhi-Yuan Ning
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui, 230009, PR China.
| | - Hong Wang
- Institute of Pomology/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, 210014, Nanjing, PR China.
| | - Zhen Cao
- Key Laboratory of Germplasm Innovation and Utilization of Horticultural Crop (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Institute of Horticultural Research, Anhui Academy of Agricultural Sciences, Hefei, 230031, PR China.
| | - Kang-Di Hu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui, 230009, PR China.
| | - Gai-Fang Yao
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui, 230009, PR China.
| | - Hua Zhang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui, 230009, PR China.
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Ma MM, Zhang HF, Tian Q, Wang HC, Zhang FY, Tian X, Zeng RF, Huang XM. MIKC type MADS-box transcription factor LcSVP2 is involved in dormancy regulation of the terminal buds in evergreen perennial litchi ( Litchi chinensis Sonn.). HORTICULTURE RESEARCH 2024; 11:uhae150. [PMID: 38988620 PMCID: PMC11233856 DOI: 10.1093/hr/uhae150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 05/20/2024] [Indexed: 07/12/2024]
Abstract
SHORT VEGETATIVE PHASE (SVP), a member of the MADS-box transcription factor family, has been reported to regulate bud dormancy in deciduous perennial plants. Previously, three LcSVPs (LcSVP1, LcSVP2 and LcSVP3) were identified from litchi genome, and LcSVP2 was highly expressed in the terminal buds of litchi during growth cessation or dormancy stages and down-regulated during growth stages. In this study, the role of LcSVP2 in governing litchi bud dormancy was examined. LcSVP2 was highly expressed in the shoots, especially in the terminal buds at growth cessation stage, whereas low expression was showed in roots, female flowers and seeds. LcSVP2 was found to be located in the nucleus and have transcription inhibitory activity. Overexpression of LcSVP2 in Arabidopsis thaliana resulted in a later flowering phenotype compared to the wild-type control. Silencing LcSVP2 in growing litchi terminal buds delayed re-entry of dormancy, resulting in significantly lower dormancy rate. The treatment also significantly up-regulated litchi FLOWERING LOCUS T2 (LcFT2). Further study indicates that LcSVP2 interacts with an AP2-type transcription factor, SMALL ORGAN SIZE1 (LcSMOS1). Silencing LcSMOS1 promoted budbreak and delayed bud dormancy. Abscisic acid (200 mg/L), which enforced bud dormancy, induced a short-term increase in the expression of LcSVP2 and LcSMOS1. Our study reveals that LcSVP2 may play a crucial role, likely together with LcSMOS1, in dormancy onset of the terminal bud and may also serve as a flowering repressor in evergreen perennial litchi.
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Fang X, Liu L, Li M, Song H, Zhou Y. WRKY transcription factors modulate flowering time in four Arachis species: a bioinformatics analysis. BMC PLANT BIOLOGY 2024; 24:620. [PMID: 38943100 PMCID: PMC11212391 DOI: 10.1186/s12870-024-05343-7] [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: 05/09/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
Abstract
BACKGROUND WRKY proteins are important transcription factors (TFs) in plants, involved in growth and development and responses to environmental changes. Although WRKY TFs have been studied at the genome level in Arachis genus, including oil crop and turfgrass, their regulatory networks in controlling flowering time remain unclear. The aim of this study was to predict the molecular mechanisms of WRKY TFs regulation flowering time in Arachis genus at the genome level using bioinformatics approaches. RESULTS The flowering-time genes of Arachis genus were retrieved from the flowering-time gene database. The regulatory networks between WRKY TFs and downstream genes in Arachis genus were predicted using bioinformatics tools. The results showed that WRKY TFs were involved in aging, autonomous, circadian clock, hormone, photoperiod, sugar, temperature, and vernalization pathways to modulate flowering time in Arachis duranensis, Arachis ipaensis, Arachis monticola, and Arachis hypogaea cv. Tifrunner. The WRKY TF binding sites in homologous flowering-time genes exhibited asymmetric evolutionary pattern, indicating that the WRKY TFs interact with other transcription factors to modulate flowering time in the four Arachis species. Protein interaction network analysis showed that WRKY TFs interacted with FRUITFULL and APETALA2 to modulate flowering time in the four Arachis species. WRKY TFs implicated in regulating flowering time had low expression levels, whereas their interaction proteins had varying expression patterns in 22 tissues of A. hypogaea cv. Tifrunner. These results indicate that WRKY TFs exhibit antagonistic or synergistic interactions with the associated proteins. CONCLUSIONS This study reveals complex regulatory networks through which WRKY TFs modulate flowering time in the four Arachis species using bioinformatics approaches.
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Affiliation(s)
- Xiao Fang
- School of Animation and Media, Qingdao Agricultural University, 700# Changcheng Road, Qingdao, Shandong, 266019, China
| | - Lubin Liu
- College of Grassland Science, Qingdao Agricultural University, 700# Changcheng Road, Qingdao, Shandong, 266019, China
| | - Meiran Li
- College of Grassland Science, Qingdao Agricultural University, 700# Changcheng Road, Qingdao, Shandong, 266019, China
| | - Hui Song
- College of Grassland Science, Qingdao Agricultural University, 700# Changcheng Road, Qingdao, Shandong, 266019, China.
| | - Yihui Zhou
- School of Animation and Media, Qingdao Agricultural University, 700# Changcheng Road, Qingdao, Shandong, 266019, China.
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7
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Lei C, Dang Z, Zhu M, Zhang M, Wang H, Chen Y, Zhang H. Identification of the ERF gene family of Mangifera indica and the defense response of MiERF4 to Xanthomonas campestris pv. mangiferaeindicae. Gene 2024; 912:148382. [PMID: 38493974 DOI: 10.1016/j.gene.2024.148382] [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: 10/30/2023] [Revised: 03/03/2024] [Accepted: 03/14/2024] [Indexed: 03/19/2024]
Abstract
An important regulatory role for ethylene-responsive transcription factors (ERFs) is in plant growth and development, stress response, and hormone signaling. However, AP2/ERF family genes in mango have not been systematically studied. In this study, a total of 113 AP2/ERF family genes were identified from the mango genome and phylogenetically classified into five subfamilies: AP2 (28 genes), DREB (42 genes), ERF (33 genes), RAV (6 genes), and Soloist (4 genes). Of these, the ERF family, in conjunction with Arabidopsis and rice, forms a phylogenetic tree divided into seven groups, five of which have MiERF members. Analysis of gene structure and cis-elements showed that each MiERF gene contains only one AP2 structural domain, and that MiERF genes contain a large number of cis-elements associated with hormone signaling and stress response. Collinearity tests revealed a high degree of homology between MiERFs and CsERFs. Tissue-specific and stress-responsive expression profiling revealed that MiERF genes are primarily involved in the regulation of reproductive growth and are differentially and positively expressed in response to external hormones and pathogenic bacteria. Physiological results from a gain-of-function analysis of MiERF4 transiently overexpressed in tobacco and mango showed that transient expression of MiERF4 resulted in decreased colony count and callose deposition, as well as varying degrees of response to hormonal signals such as ETH, JA, and SA. Thus, MiERF4 may be involved in the JA/ETH signaling pathway to enhance plant defense against pathogenic bacteria. This study provides a basis for further research on the function and regulation of MiERF genes and lays a foundation for the selection of disease-resistant genes in mango.
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Affiliation(s)
- Chen Lei
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China; Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Zhiguo Dang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Min Zhu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, China
| | - Mengting Zhang
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Huiliang Wang
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Yeyuan Chen
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, China.
| | - He Zhang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China; Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
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Ma L, Shi Q, Ma Q, Wang X, Chen X, Han P, Luo Y, Hu H, Fei X, Wei A. Genome-wide analysis of AP2/ERF transcription factors that regulate fruit development of Chinese prickly ash. BMC PLANT BIOLOGY 2024; 24:565. [PMID: 38879490 PMCID: PMC11179286 DOI: 10.1186/s12870-024-05244-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 06/04/2024] [Indexed: 06/19/2024]
Abstract
BACKGROUND AP2/ERF is a large family of plant transcription factor proteins that play essential roles in signal transduction, plant growth and development, and responses to various stresses. The AP2/ERF family has been identified and verified by functional analysis in various plants, but so far there has been no comprehensive study of these factors in Chinese prickly ash. Phylogenetic, motif, and functional analyses combined with transcriptome analysis of Chinese prickly ash fruits at different developmental stages (30, 60, and 90 days after anthesis) were conducted in this study. RESULTS The analysis identified 146 ZbAP2/ERF genes that could be classified into 15 subgroups. The motif analysis revealed the presence of different motifs or elements in each group that may explain the functional differences between the groups. ZbERF13.2, ZbRAP2-12, and ZbERF2.1 showed high levels of expression in the early stages of fruit development. ZbRAP2-4, and ZbERF3.1 were significantly expressed at the fruit coloring stage (R2 and G2). ZbERF16 were significantly expressed at fruit ripening and expression level increased as the fruit continued to develop. Relative gene expression levels of 6 representative ZbAP2/ERFs assessed by RT-qPCR agreed with transcriptome analysis results. CONCLUSIONS These genes identified by screening can be used as candidate genes that affect fruit development. The results of the analysis can help guide future genetic improvement of Chinese prickly ash and enrich our understanding of AP2/ERF transcription factors and their regulatory functions in plants.
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Affiliation(s)
- Lei Ma
- College of Forestry, Northwest Agriculture and Forestry University, Yangling, Xianyang, 712100, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Xianyang, 712100, China
| | - Qianqian Shi
- College of Forestry, Northwest Agriculture and Forestry University, Yangling, Xianyang, 712100, China
| | - Qin Ma
- College of Forestry, Northwest Agriculture and Forestry University, Yangling, Xianyang, 712100, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Xianyang, 712100, China
| | - Xiaona Wang
- College of Forestry, Northwest Agriculture and Forestry University, Yangling, Xianyang, 712100, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Xianyang, 712100, China
| | - Xin Chen
- College of Forestry, Northwest Agriculture and Forestry University, Yangling, Xianyang, 712100, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Xianyang, 712100, China
| | - Peilin Han
- College of Forestry, Northwest Agriculture and Forestry University, Yangling, Xianyang, 712100, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Xianyang, 712100, China
| | - Yingli Luo
- College of Forestry, Northwest Agriculture and Forestry University, Yangling, Xianyang, 712100, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Xianyang, 712100, China
| | - Haichao Hu
- College of Forestry, Northwest Agriculture and Forestry University, Yangling, Xianyang, 712100, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Xianyang, 712100, China
| | - Xitong Fei
- College of Forestry, Northwest Agriculture and Forestry University, Yangling, Xianyang, 712100, China.
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Xianyang, 712100, China.
| | - Anzhi Wei
- College of Forestry, Northwest Agriculture and Forestry University, Yangling, Xianyang, 712100, China.
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Xianyang, 712100, China.
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Manjarrez LF, Guevara MÁ, de María N, Vélez MD, Cobo-Simón I, López-Hinojosa M, Cabezas JA, Mancha JA, Pizarro A, Díaz-Sala MC, Cervera MT. Maritime Pine Rootstock Genotype Modulates Gene Expression Associated with Stress Tolerance in Grafted Stems. PLANTS (BASEL, SWITZERLAND) 2024; 13:1644. [PMID: 38931075 PMCID: PMC11207801 DOI: 10.3390/plants13121644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 06/06/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024]
Abstract
Climate change-induced hazards, such as drought, threaten forest resilience, particularly in vulnerable regions such as the Mediterranean Basin. Maritime pine (Pinus pinaster Aiton), a model species in Western Europe, plays a crucial role in the Mediterranean forest due to its genetic diversity and ecological plasticity. This study characterizes transcriptional profiles of scion and rootstock stems of four P. pinaster graft combinations grown under well-watered conditions. Our grafting scheme combined drought-sensitive and drought-tolerant genotypes for scions (GAL1056: drought-sensitive scion; and Oria6: drought-tolerant scion) and rootstocks (R1S: drought-sensitive rootstock; and R18T: drought-tolerant rootstock). Transcriptomic analysis revealed expression patterns shaped by genotype provenance and graft combination. The accumulation of differentially expressed genes (DEGs) encoding proteins, involved in defense mechanisms and pathogen recognition, was higher in drought-sensitive scion stems and also increased when grafted onto drought-sensitive rootstocks. DEGs involved in drought tolerance mechanisms were identified in drought-tolerant genotypes as well as in drought-sensitive scions grafted onto drought-tolerant rootstocks, suggesting their establishment prior to drought. These mechanisms were associated with ABA metabolism and signaling. They were also involved in the activation of the ROS-scavenging pathways, which included the regulation of flavonoid and terpenoid metabolisms. Our results reveal DEGs potentially associated with the conifer response to drought and point out differences in drought tolerance strategies. These findings suggest genetic trade-offs between pine growth and defense, which could be relevant in selecting more drought-tolerant Pinus pinaster trees.
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Affiliation(s)
- Lorenzo Federico Manjarrez
- Departamento de Ecología y Genética Forestal, Instituto de Ciencias Forestal (ICIFOR), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria—Consejo Superior de Investigaciones Científicas (INIA–CSIC), 28040 Madrid, Spain; (L.F.M.); (N.d.M.); (M.D.V.); (I.C.-S.); (M.L.-H.); (J.A.C.); (J.A.M.)
| | - María Ángeles Guevara
- Departamento de Ecología y Genética Forestal, Instituto de Ciencias Forestal (ICIFOR), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria—Consejo Superior de Investigaciones Científicas (INIA–CSIC), 28040 Madrid, Spain; (L.F.M.); (N.d.M.); (M.D.V.); (I.C.-S.); (M.L.-H.); (J.A.C.); (J.A.M.)
| | - Nuria de María
- Departamento de Ecología y Genética Forestal, Instituto de Ciencias Forestal (ICIFOR), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria—Consejo Superior de Investigaciones Científicas (INIA–CSIC), 28040 Madrid, Spain; (L.F.M.); (N.d.M.); (M.D.V.); (I.C.-S.); (M.L.-H.); (J.A.C.); (J.A.M.)
| | - María Dolores Vélez
- Departamento de Ecología y Genética Forestal, Instituto de Ciencias Forestal (ICIFOR), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria—Consejo Superior de Investigaciones Científicas (INIA–CSIC), 28040 Madrid, Spain; (L.F.M.); (N.d.M.); (M.D.V.); (I.C.-S.); (M.L.-H.); (J.A.C.); (J.A.M.)
| | - Irene Cobo-Simón
- Departamento de Ecología y Genética Forestal, Instituto de Ciencias Forestal (ICIFOR), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria—Consejo Superior de Investigaciones Científicas (INIA–CSIC), 28040 Madrid, Spain; (L.F.M.); (N.d.M.); (M.D.V.); (I.C.-S.); (M.L.-H.); (J.A.C.); (J.A.M.)
| | - Miriam López-Hinojosa
- Departamento de Ecología y Genética Forestal, Instituto de Ciencias Forestal (ICIFOR), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria—Consejo Superior de Investigaciones Científicas (INIA–CSIC), 28040 Madrid, Spain; (L.F.M.); (N.d.M.); (M.D.V.); (I.C.-S.); (M.L.-H.); (J.A.C.); (J.A.M.)
| | - José Antonio Cabezas
- Departamento de Ecología y Genética Forestal, Instituto de Ciencias Forestal (ICIFOR), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria—Consejo Superior de Investigaciones Científicas (INIA–CSIC), 28040 Madrid, Spain; (L.F.M.); (N.d.M.); (M.D.V.); (I.C.-S.); (M.L.-H.); (J.A.C.); (J.A.M.)
| | - José Antonio Mancha
- Departamento de Ecología y Genética Forestal, Instituto de Ciencias Forestal (ICIFOR), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria—Consejo Superior de Investigaciones Científicas (INIA–CSIC), 28040 Madrid, Spain; (L.F.M.); (N.d.M.); (M.D.V.); (I.C.-S.); (M.L.-H.); (J.A.C.); (J.A.M.)
| | - Alberto Pizarro
- Departamento de Ciencias de la Vida, Universidad de Alcalá (UAH), 28805 Alcalá de Henares, Spain; (A.P.); (M.C.D.-S.)
| | - María Carmen Díaz-Sala
- Departamento de Ciencias de la Vida, Universidad de Alcalá (UAH), 28805 Alcalá de Henares, Spain; (A.P.); (M.C.D.-S.)
| | - María Teresa Cervera
- Departamento de Ecología y Genética Forestal, Instituto de Ciencias Forestal (ICIFOR), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria—Consejo Superior de Investigaciones Científicas (INIA–CSIC), 28040 Madrid, Spain; (L.F.M.); (N.d.M.); (M.D.V.); (I.C.-S.); (M.L.-H.); (J.A.C.); (J.A.M.)
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10
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Yang X, Li X, Wang X, Chen C, Wu D, Cheng Y, Wang Y, Sha L, Kang H, Liu S, Fan X, Chen Y, Zhou Y, Zhang H. Identification and Characterization of LBD Gene Family in Pseudoroegneria libanotica Reveals Functions of PseLBD1 and PseLBD12 in Response to Abiotic Stress. Biochem Genet 2024:10.1007/s10528-024-10859-6. [PMID: 38850375 DOI: 10.1007/s10528-024-10859-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 06/04/2024] [Indexed: 06/10/2024]
Abstract
The lateral organ boundaries domain (LBD) plays a vital role as a transcriptional coactivator within plants, serving as an indispensable function in growth, development, and stress response. In a previous study, we found that the LBD genes of Pseudoroegneria libanotica (a maternal donor for three-quarter of perennial Triticeae species with good stress resistance, holds great significance in exploring its response mechanisms to abiotic stress for the Triticeae tribe) might be involved in responding to drought stress. Therefore, we further identified the LBD gene family in this study. A total of 29 PseLBDs were identified. Among them, 24 were categorized into subclass I, while 5 fell into subclass II. The identification of cis-acting elements reveals the extensive involvement of PseLBDs in various biological processes in P. libanotica. Collinearity analysis indicates that 86% of PseLBDs were single-copy genes and have undergone a single whole-genome duplication event. Transcriptomic differential expression analysis of PseLBDs under drought stress reveals that the most likely candidates for responding to abiotic stress were PseLBD1 and PseLBD12. They have been demonstrated to respond to drought, salt, heavy metal, and heat stress in yeast. Furthermore, it is plausible that functional divergence might have occurred among their orthologous genes in wheat. This study not only establishes a foundation for a deeper understanding of the biological roles of PseLBDs in P. libanotica but also unveils novel potential genes for enhancing the genetic background of crops within Triticeae crops, such as wheat.
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Affiliation(s)
- Xunzhe Yang
- Key Laboratory of Genetic Resources and Crop Improvement, Ministry of Education, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- UWA School of Agriculture and Environment, and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Xiang Li
- College of Grassland Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Xia Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Chen Chen
- Key Laboratory of Genetic Resources and Crop Improvement, Ministry of Education, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Dandan Wu
- Key Laboratory of Genetic Resources and Crop Improvement, Ministry of Education, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Yiran Cheng
- Key Laboratory of Genetic Resources and Crop Improvement, Ministry of Education, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Yi Wang
- Key Laboratory of Genetic Resources and Crop Improvement, Ministry of Education, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Lina Sha
- Key Laboratory of Genetic Resources and Crop Improvement, Ministry of Education, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- College of Grassland Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Houyang Kang
- Key Laboratory of Genetic Resources and Crop Improvement, Ministry of Education, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Songqing Liu
- College of Chemistry and Life Sciences, Chengdu Normal University, Chengdu, 611130, Sichuan, China
| | - Xing Fan
- Key Laboratory of Genetic Resources and Crop Improvement, Ministry of Education, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Yinglong Chen
- UWA School of Agriculture and Environment, and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Yonghong Zhou
- Key Laboratory of Genetic Resources and Crop Improvement, Ministry of Education, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Haiqin Zhang
- Key Laboratory of Genetic Resources and Crop Improvement, Ministry of Education, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China.
- College of Grassland Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China.
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11
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Yu Z, Chen X, Li Y, Shah SHA, Xiao D, Wang J, Hou X, Liu T, Li Y. ETHYLENE RESPONSE FACTOR 070 inhibits flowering in Pak-choi by indirectly impairing BcLEAFY expression. PLANT PHYSIOLOGY 2024; 195:986-1004. [PMID: 38269601 DOI: 10.1093/plphys/kiae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 01/26/2024]
Abstract
APETALA2/ethylene responsive factors respond to ethylene and participate in many biological and physiological processes, such as plant morphogenesis, stress resistance, and hormone signal transduction. Ethylene responsive factor 070 (BcERF070) is important in flowering. However, the underlying molecular mechanisms of BcERF070 in floral transition in response to ethylene signaling have not been fully characterized. Herein, we explored the function of BcERF070 in Pak-choi [Brassica campestris (syn. Brassica rapa) ssp. chinensis]. Ethylene treatment induced BcERF070 expression and delayed flowering in Pak-choi. Silencing of BcERF070 induced flowering in Pak-choi. BcERF070 interacted with major latex protein-like 328 (BcMLP328), which forms a complex with helix-loop-helix protein 30 (BcbHLH30) to enhance the transcriptional activity of BcbHLH30 on LEAFY (BcLFY), ultimately promoting flowering. However, BcERF070 impaired the BcMLP328-BcbHLH30 complex activation of LEAFY (BcLFY), ultimately inhibiting flowering in Pak-choi. BcERF070 directly promoted the expression of the flowering inhibitor gene B-box 29 (BcBBX29) and delayed flowering by reducing FLOWERING LOCUS T (BcFT) expression. These results suggest that BcERF070 mediates ethylene-reduced flowering by impairing the BcMLP328-BcbHLH30 complex activation of BcLFY and by directly promoting the gene expression of the flowering inhibition factor BcBBX29 to repress BcFT expression. The findings contribute to understanding the molecular mechanisms underlying floral transition in response to ethylene in plants.
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Affiliation(s)
- Zhanghong Yu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoshan Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yan Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Sayyed Hamad Ahmad Shah
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Dong Xiao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianjun Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xilin Hou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Tongkun Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ying Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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12
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Li L, Xu JB, Zhu ZW, Ma R, Wu XZ, Geng YK. Genome-wide identification and expression analysis of the SPL transcription factor family and its response to abiotic stress in Pisum sativum L. BMC Genomics 2024; 25:539. [PMID: 38822248 PMCID: PMC11140923 DOI: 10.1186/s12864-024-10262-w] [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: 01/15/2024] [Accepted: 03/27/2024] [Indexed: 06/02/2024] Open
Abstract
Squamous promoter binding protein-like (SPL) genes encode plant-specific transcription factors (TFs) that play essential roles in modulating plant growth, development, and stress response. Pea (Pisum sativum L.) is a coarse grain crop of great importance in food production, biodiversity conservation and molecular genetic research, providing genetic information and nutritional resources for improving agricultural production and promoting human health. However, only limited researches on the structure and functions of SPL genes exist in pea (PsSPLs). In this study, we identified 22 PsSPLs and conducted a genome-wide analysis of their physical characteristics, chromosome distribution, gene structure, phylogenetic evolution and gene expression patterns. As a result, the PsSPLs were unevenly distributed on the seven chromosomes of pea and harbored the SBP domain, which is composed of approximately 76 amino acid residues. The phylogenetic analysis revealed that the PsSPLs clustered into eight subfamilies and showed high homology with SPL genes in soybean. Further analysis showed the presence of segmental duplications in the PsSPLs. The expression patterns of 22 PsSPLs at different tissues, developmental stages and under various stimulus conditions were evaluated by qRT-PCR method. It was found that the expression patterns of PsSPLs from the same subfamily were similar in different tissues, the transcripts of most PsSPLs reached the maximum peak value at 14 days after anthesis in the pod. Abiotic stresses can cause significantly up-regulated PsSPL19 expression with spatiotemporal specificity, in addition, four plant hormones can cause the up-regulated expression of most PsSPLs including PsSPL19 in a time-dependent manner. Therefore, PsSPL19 could be a key candidate gene for signal transduction during pea growth and development, pod formation, abiotic stress and plant hormone response. Our findings should provide insights for the elucidating of development regulation mechanism and breeding for resistance to abiotic stress pea.
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Affiliation(s)
- Long Li
- Minzu University of China, 100010, Beijing, P.R. China
- College of Agronomy, Hebei Agricultural University, 071001, Baoding, P.R. China
| | - Jian Bo Xu
- School of Food and Biological engineering, Zhengzhou University of Light Industry, 450002, Zhengzhou, P.R. China
| | - Zhi Wen Zhu
- School of Food and Biological engineering, Zhengzhou University of Light Industry, 450002, Zhengzhou, P.R. China
| | - Rui Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, 712100, Yangling, Shaanxi, P.R. China
| | - Xiao Zong Wu
- School of Food and Biological engineering, Zhengzhou University of Light Industry, 450002, Zhengzhou, P.R. China.
- Zhengzhou University of Light Industry, 450002, Zhengzhou, P.R. China.
| | - Yu Ke Geng
- Minzu University of China, 100010, Beijing, P.R. China.
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13
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Liang W, Xu Y, Cui X, Li C, Lu S. Genome-Wide Identification and Characterization of miRNAs and Natural Antisense Transcripts Show the Complexity of Gene Regulatory Networks for Secondary Metabolism in Aristolochia contorta. Int J Mol Sci 2024; 25:6043. [PMID: 38892231 PMCID: PMC11172604 DOI: 10.3390/ijms25116043] [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: 04/13/2024] [Revised: 05/26/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
Aristolochia contorta Bunge is an academically and medicinally important plant species. It belongs to the magnoliids, with an uncertain phylogenetic position, and is one of the few plant species lacking a whole-genome duplication (WGD) event after the angiosperm-wide WGD. A. contorta has been an important traditional Chinese medicine material. Since it contains aristolochic acids (AAs), chemical compounds with nephrotoxity and carcinogenicity, the utilization of this plant has attracted widespread attention. Great efforts are being made to increase its bioactive compounds and reduce or completely remove toxic compounds. MicroRNAs (miRNAs) and natural antisense transcripts (NATs) are two classes of regulators potentially involved in metabolism regulation. Here, we report the identification and characterization of 223 miRNAs and 363 miRNA targets. The identified miRNAs include 51 known miRNAs belonging to 20 families and 172 novel miRNAs belonging to 107 families. A negative correlation between the expression of miRNAs and their targets was observed. In addition, we identified 441 A. contorta NATs and 560 NAT-sense transcript (ST) pairs, of which 12 NATs were targets of 13 miRNAs, forming 18 miRNA-NAT-ST modules. Various miRNAs and NATs potentially regulated secondary metabolism through the modes of miRNA-target gene-enzyme genes, NAT-STs, and NAT-miRNA-target gene-enzyme genes, suggesting the complexity of gene regulatory networks in A. contorta. The results lay a solid foundation for further manipulating the production of its bioactive and toxic compounds.
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Affiliation(s)
- Wenjing Liang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource of Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Yayun Xu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource of Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Xinyun Cui
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource of Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Caili Li
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource of Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Shanfa Lu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource of Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
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14
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Dai J, Wang M, Yin H, Han X, Fan Y, Wei Y, Lin J, Liu J. Integrating GC-MS and comparative transcriptome analysis reveals that TsERF66 promotes the biosynthesis of caryophyllene in Toona sinensis tender leaves. FRONTIERS IN PLANT SCIENCE 2024; 15:1378418. [PMID: 38872893 PMCID: PMC11171135 DOI: 10.3389/fpls.2024.1378418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 05/09/2024] [Indexed: 06/15/2024]
Abstract
Introduction The strong aromatic characteristics of the tender leaves of Toona sinensis determine their quality and economic value. Methods and results Here, GC-MS analysis revealed that caryophyllene is a key volatile compound in the tender leaves of two different T. sinensis varieties, however, the transcriptional mechanisms controlling its gene expression are unknown. Comparative transcriptome analysis revealed significant enrichment of terpenoid synthesis pathway genes, suggesting that the regulation of terpenoid synthesis-related gene expression is an important factor leading to differences in aroma between the two varieties. Further analysis of expression levels and genetic evolution revealed that TsTPS18 is a caryophyllene synthase, which was confirmed by transient overexpression in T. sinensis and Nicotiana benthamiana leaves. Furthermore, we screened an AP2/ERF transcriptional factor ERF-IX member, TsERF66, for the potential regulation of caryophyllene synthesis. The TsERF66 had a similar expression trend to that of TsTPS18 and was highly expressed in high-aroma varieties and tender leaves. Exogenous spraying of MeJA also induced the expression of TsERF66 and TsTPS18 and promoted the biosynthesis of caryophyllene. Transient overexpression of TsERF66 in T. sinensis significantly promoted TsTPS18 expression and caryophyllene biosynthesis. Discussion Our results showed that TsERF66 promoted the expression of TsTPS18 and the biosynthesis of caryophyllene in T. sinensis leaves, providing a strategy for improving the aroma of tender leaves.
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Affiliation(s)
| | | | | | | | | | | | | | - Jun Liu
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
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15
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Wei R, Lu Y, Mo Z, Sun Q, Yue P, Xie Z, Ye J, Deng X. CsERF003 enhanced peel coloration by promoting both chlorophyll degradation and carotenoid accumulation in citrus. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112131. [PMID: 38801863 DOI: 10.1016/j.plantsci.2024.112131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/22/2024] [Accepted: 05/18/2024] [Indexed: 05/29/2024]
Abstract
Uneven coloration is a common phenomenon in citrus fruit during the ripening stage, as affects the appearance and economic value of the fruit. The elevated expression of CsERF003 during the degreening process of both lemon and satsuma mandarin peels was reported. In this research, a similar performance of CsERF003 in the pericarp coloration process was also identified by transcriptome analysis of 'Fengjie 72-1' navel orange and Lane Late navel orange. However, the regulatory mechanism of CsERF003 is not clear yet. Overexpression of CsERF003 could deepen the color of citrus callus and promote peel degreening of Newhall navel orange, which was attributed to the upregulation of genes involved in chlorophyll degradation and carotenoid synthesis. Furthermore, CsERF003 acted as an activator to promote the expression of CsLCYE, but couldn't activate the expression of CsLCYB1 and CsLCYB2; CsERF003 could also bind to the promoter of CsSGR to activate its expression. Together, our findings shed light on the regulatory mechanism of CsERF003 in chlorophyll degradation and carotenoid accumulation, particularly in the α-branch of carotenoid metabolism. These insights offer valuable perspectives for the genetic enhancement of peel coloration in citrus.
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Affiliation(s)
- Ranran Wei
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, The College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Yan Lu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, The College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhijing Mo
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, The College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Quan Sun
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, The College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Pengtao Yue
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, The College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Zongzhou Xie
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, The College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Junli Ye
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, The College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiuxin Deng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, The College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China.
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16
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Jiang Y, Shi Y, Xue Y, Hu D, Song X. AP2XII-1 and AP2XI-2 Suppress Schizogony Gene Expression in Toxoplasma gondii. Int J Mol Sci 2024; 25:5527. [PMID: 38791568 PMCID: PMC11122372 DOI: 10.3390/ijms25105527] [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: 03/24/2024] [Revised: 05/10/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Toxoplasma gondii is an intracellular parasite that is important in medicine and veterinary science and undergoes distinct developmental transitions in its intermediate and definitive hosts. The switch between stages of T. gondii is meticulously regulated by a variety of factors. Previous studies have explored the role of the microrchidia (MORC) protein complex as a transcriptional suppressor of sexual commitment. By utilizing immunoprecipitation and mass spectrometry, constituents of this protein complex have been identified, including MORC, Histone Deacetylase 3 (HDAC3), and several ApiAP2 transcription factors. Conditional knockout of MORC or inhibition of HDAC3 results in upregulation of a set of genes associated with schizogony and sexual stages in T. gondii tachyzoites. Here, our focus extends to two primary ApiAP2s (AP2XII-1 and AP2XI-2), demonstrating their significant impact on the fitness of asexual tachyzoites and their target genes. Notably, the targeted disruption of AP2XII-1 and AP2XI-2 resulted in a profound alteration in merozoite-specific genes targeted by the MORC-HDAC3 complex. Additionally, considerable overlap was observed in downstream gene profiles between AP2XII-1 and AP2XI-2, with AP2XII-1 specifically binding to a subset of ApiAP2 transcription factors, including AP2XI-2. These findings reveal an intricate cascade of ApiAP2 regulatory networks involved in T. gondii schizogony development, orchestrated by AP2XII-1 and AP2XI-2. This study provides valuable insights into the transcriptional regulation of T. gondii growth and development, shedding light on the intricate life cycle of this parasitic pathogen.
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Affiliation(s)
- Yucong Jiang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (Y.J.); (Y.X.); (D.H.)
| | - Yuehong Shi
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning 530004, China;
| | - Yingying Xue
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (Y.J.); (Y.X.); (D.H.)
| | - Dandan Hu
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (Y.J.); (Y.X.); (D.H.)
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning 530004, China;
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Nanning 530004, China
| | - Xingju Song
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (Y.J.); (Y.X.); (D.H.)
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning 530004, China;
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Nanning 530004, China
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Fuertes-Aguilar J, Matilla AJ. Transcriptional Control of Seed Life: New Insights into the Role of the NAC Family. Int J Mol Sci 2024; 25:5369. [PMID: 38791407 PMCID: PMC11121595 DOI: 10.3390/ijms25105369] [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: 03/29/2024] [Revised: 05/07/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Transcription factors (TFs) regulate gene expression by binding to specific sequences on DNA through their DNA-binding domain (DBD), a universal process. This update conveys information about the diverse roles of TFs, focusing on the NACs (NAM-ATAF-CUC), in regulating target-gene expression and influencing various aspects of plant biology. NAC TFs appeared before the emergence of land plants. The NAC family constitutes a diverse group of plant-specific TFs found in mosses, conifers, monocots, and eudicots. This update discusses the evolutionary origins of plant NAC genes/proteins from green algae to their crucial roles in plant development and stress response across various plant species. From mosses and lycophytes to various angiosperms, the number of NAC proteins increases significantly, suggesting a gradual evolution from basal streptophytic green algae. NAC TFs play a critical role in enhancing abiotic stress tolerance, with their function conserved in angiosperms. Furthermore, the modular organization of NACs, their dimeric function, and their localization within cellular compartments contribute to their functional versatility and complexity. While most NAC TFs are nuclear-localized and active, a subset is found in other cellular compartments, indicating inactive forms until specific cues trigger their translocation to the nucleus. Additionally, it highlights their involvement in endoplasmic reticulum (ER) stress-induced programmed cell death (PCD) by activating the vacuolar processing enzyme (VPE) gene. Moreover, this update provides a comprehensive overview of the diverse roles of NAC TFs in plants, including their participation in ER stress responses, leaf senescence (LS), and growth and development. Notably, NACs exhibit correlations with various phytohormones (i.e., ABA, GAs, CK, IAA, JA, and SA), and several NAC genes are inducible by them, influencing a broad spectrum of biological processes. The study of the spatiotemporal expression patterns provides insights into when and where specific NAC genes are active, shedding light on their metabolic contributions. Likewise, this review emphasizes the significance of NAC TFs in transcriptional modules, seed reserve accumulation, and regulation of seed dormancy and germination. Overall, it effectively communicates the intricate and essential functions of NAC TFs in plant biology. Finally, from an evolutionary standpoint, a phylogenetic analysis suggests that it is highly probable that the WRKY family is evolutionarily older than the NAC family.
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Affiliation(s)
| | - Angel J. Matilla
- Departamento de Biología Funcional, Universidad de Santiago de Compostela, 14971 Santiago de Compostela, Spain
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Xu S, Chen S, Cai J, Yan T, Tu M, Wang R, Hua S, Jiang L. Genomic and transcriptome analyses reveal potential contributors to erucic acid biosynthesis in seeds of rapeseed (Brassica napus). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:129. [PMID: 38740615 DOI: 10.1007/s00122-024-04642-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/29/2024] [Indexed: 05/16/2024]
Abstract
KEY MESSAGE Through comprehensive genomic and transcriptomic analyses, we identified a set of 23 genes that act up- or downstream of erucic acid content (EAC) production in rapeseed seeds. We selected example genes to showcase the distribution of single nucleotide polymorphisms, haplotypes associated with EAC phenotypes, and the creation of molecular markers differentiating low EAC and high EAC genotypes. Erucic acid content (EAC) is a crucial trait in rapeseed, with low LEAC oil recognized for its health benefits and high EA oil holding industrial value. Despite its significance, the genomic consequences of intensive LEAC-cultivar selection and the genetic basis underlying EA regulation remain largely unexplored. To address this knowledge gap, we conducted selective signal analyses, genome-wide association studies (GWAS), and transcriptome analyses. Our investigation unveiled the genetic footprints resulting from LEAC selection in germplasm populations, drawing attention to specific loci that contribute to enriching diversity. By integrating GWAS and transcriptome analyses, we identified a set of 23 genes that play a significant role in determining EAC in seeds or are downstream consequences of EA-level alterations. These genes have emerged as promising candidates for elucidating the potential mechanisms governing EAC in rapeseed. To exemplify the findings, we selected specific genes to demonstrate the distribution of single nucleotide polymorphisms and haplotypes associated with different EAC phenotypes. Additionally, we showcased to develop molecular markers distinguishing between LEAC and high EAC genotypes.
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Affiliation(s)
- Shiqi Xu
- Institute of Crop Science, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou, 310058, China
| | - Shan Chen
- Institute of Crop Science, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou, 310058, China
| | - Jialing Cai
- Institute of Crop Science, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou, 310058, China
| | - Tao Yan
- Institute of Crop Science, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou, 310058, China
| | - Mengxin Tu
- Institute of Crop Science, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou, 310058, China
| | - Ruisen Wang
- Jaixing Academy of Agricultural Sciences, Jiaxing, 314000, China
| | - Shuijin Hua
- Zhejiang Academy of Agricultural Sciences, Desheng Zhong Road 298, Hangzhou, 310022, China
| | - Lixi Jiang
- Institute of Crop Science, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou, 310058, China.
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19
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Wang C, Pei J, Li H, Zhu X, Zhang Y, Wang Y, Li W, Wang Z, Liu K, Du B, Jiang J, Zhao D. Mechanisms on salt tolerant of Paenibacillus polymyxa SC2 and its growth-promoting effects on maize seedlings under saline conditions. Microbiol Res 2024; 282:127639. [PMID: 38354626 DOI: 10.1016/j.micres.2024.127639] [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: 12/05/2023] [Revised: 02/05/2024] [Accepted: 02/05/2024] [Indexed: 02/16/2024]
Abstract
Soil salinity negatively affects microbial communities, soil fertility, and agricultural productivity and has become a major agricultural problem worldwide. Plant growth-promoting rhizobacteria (PGPR) with salt tolerance can benefit plant growth under saline conditions and diminish the negative effects of salt stress on plants. In this study, we aimed to understand the salt-tolerance mechanism of Paenibacillus polymyxa at the genetic and metabolic levels and elucidate the mechanism of strain SC2 in promoting maize growth under saline conditions. Under salt stress, we found that strain SC2 promoted maize seedling growth, which was accompanied by a significant upregulation of genes encoding for the biosynthesis of peptidoglycan, polysaccharide, and fatty acid, the metabolism of purine and pyrimidine, and the transport of osmoprotectants such as trehalose, glycine betaine, and K+ in strain SC2. To further enhance the salt resistance of strain SC2, three mutants (SC2-11, SC2-13, and SC2-14) with higher capacities for salt resistance and exopolysaccharide synthesis were obtained via atmospheric and room-temperature plasma mutagenesis. In saline-alkaline soil, the mutants showed better promoting effect on maize seedlings than wild-type SC2. The fresh weight of maize seedlings was increased by 68.10% after treatment with SC2-11 compared with that of the control group. The transcriptome analysis of maize roots demonstrated that SC2 and SC2-11 could induce the upregulation of genes related to the plant hormone signal transduction, starch and sucrose metabolism, reactive oxygen species scavenging, and auxin and ethylene signaling under saline-alkaline stress. In addition, various transcription factors, such as zinc finger proteins, ethylene-responsive-element-binding protein, WRKY, myeloblastosis proteins, basic helix-loop-helix proteins, and NAC proteins, were up-regulated in response to abiotic stress. Moreover, the microbial community composition of maize rhizosphere soil after inoculating with strain SC2 was varied from the one after inoculating with mutant SC2-11. Our results provide new insights into the various genes involved in the salt resistance of strain SC2 and a theoretical basis for utilizing P. polymyxa in saline-alkaline environments.
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Affiliation(s)
- Chengqiang Wang
- College of Life Sciences, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-alkali Land, Shandong Key Laboratory of Agricultural Microbiology, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an 271018, China.
| | - Jian Pei
- College of Life Sciences, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-alkali Land, Shandong Key Laboratory of Agricultural Microbiology, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an 271018, China
| | - Hui Li
- College of Life Sciences, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-alkali Land, Shandong Key Laboratory of Agricultural Microbiology, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an 271018, China
| | - Xiuling Zhu
- College of Life Sciences, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-alkali Land, Shandong Key Laboratory of Agricultural Microbiology, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an 271018, China
| | - Yanan Zhang
- College of Life Sciences, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-alkali Land, Shandong Key Laboratory of Agricultural Microbiology, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an 271018, China
| | - Yanjun Wang
- Institute of Wetland Agriculture and Ecology, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Wenjie Li
- College of Life Sciences, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-alkali Land, Shandong Key Laboratory of Agricultural Microbiology, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an 271018, China
| | - Zhongyue Wang
- College of Life Sciences, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-alkali Land, Shandong Key Laboratory of Agricultural Microbiology, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an 271018, China
| | - Kai Liu
- College of Life Sciences, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-alkali Land, Shandong Key Laboratory of Agricultural Microbiology, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an 271018, China
| | - Binghai Du
- College of Life Sciences, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-alkali Land, Shandong Key Laboratory of Agricultural Microbiology, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an 271018, China
| | - Juquan Jiang
- Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin 150030, China.
| | - Dongying Zhao
- College of Life Sciences, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-alkali Land, Shandong Key Laboratory of Agricultural Microbiology, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an 271018, China; College of Life Sciences, Dezhou University, Dezhou 253023, China.
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20
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Fu J, Zhao Y, Zhou Y, Wang Y, Fei Z, Wang W, Wu J, Zhang F, Zhao Y, Li J, Hao J, Niu Y. MrERF039 transcription factor plays an active role in the cold response of Medicago ruthenica as a sugar molecular switch. PLANT, CELL & ENVIRONMENT 2024; 47:1834-1851. [PMID: 38318779 DOI: 10.1111/pce.14845] [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: 05/18/2023] [Revised: 01/21/2024] [Accepted: 01/23/2024] [Indexed: 02/07/2024]
Abstract
Cold stress severely restricts plant development, causing significant agricultural losses. We found a critical transcription factor network in Medicago ruthenica was involved in plant adaptation to low-temperature. APETALA2/ethylene responsive factor (AP2/ERF) transcription factor MrERF039 was transcriptionally induced by cold stress in M. ruthenica. Overexpression of MrERF039 significantly increased the glucose and maltose content, thereby improving the tolerance of M. ruthenica. MrERF039 could bind to the DRE cis-acting element in the MrCAS15A promoter. Additionally, the methyl group of the 14th amino acid in MrERF039 was required for binding. Transcriptome analysis showed that MrERF039 acted as a sugar molecular switch, regulating numerous sugar transporters and sugar metabolism-related genes. In addition, we found that MrERF039 could directly regulate β-amylase gene, UDP glycosyltransferase gene, and C2H2 zinc finger protein gene expression. In conclusion, these findings suggest that high expression of MrERF039 can significantly improve the cold tolerance of M. ruthenica root tissues during cold acclimation. Our results provide a new theoretical basis and candidate genes for breeding new legume forage varieties with high resistance.
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Affiliation(s)
- Jiabin Fu
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Yanyun Zhao
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Yan Zhou
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Yu Wang
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Zhimin Fei
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Waner Wang
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Jiaming Wu
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Feng Zhang
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Yan Zhao
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Jiayu Li
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Jinfeng Hao
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Yiding Niu
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, College of Life Sciences, Inner Mongolia University, Hohhot, China
- Inner Mongolia Academy of Science and Technology, Hohhot, China
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21
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Wei H, Wang X, Wang K, Tang X, Zhang N, Si H. Transcription factors as molecular switches regulating plant responses to drought stress. PHYSIOLOGIA PLANTARUM 2024; 176:e14366. [PMID: 38812034 DOI: 10.1111/ppl.14366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/31/2024]
Abstract
Plants often experience abiotic stress, which severely affects their growth. With the advent of global warming, drought stress has become a pivotal factor affecting crop yield and quality. Increasing numbers of studies have focused on elucidating the molecular mechanisms underlying plant responses to drought stress. As molecular switches, transcription factors (TFs) are key participants in drought-resistance regulatory networks in crops. TFs regulate the transcription of downstream genes and are regulated by various upstream regulatory factors. Therefore, understanding the mechanisms of action of TFs in regulating drought stress can help enhance the adaptive capacity of crops under drought conditions. In this review, we summarize the structural characteristics of several common TFs, their multiple drought-response pathways, and recently employed research strategies. We describe the application of new technologies such as analysis of stress granule dynamics and function, multi-omics data, gene editing, and molecular crosstalk between TFs in drought resistance. This review aims to familiarize readers with the regulatory network of TFs in drought resistance and to provide a reference for examining the molecular mechanisms of drought resistance in plants and improving agronomic traits.
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Affiliation(s)
- Han Wei
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, People's Republic of China
- College of Agronomy, Gansu Agricultural University, Lanzhou, People's Republic of China
| | - Xiao Wang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, People's Republic of China
- College of Agronomy, Gansu Agricultural University, Lanzhou, People's Republic of China
| | - Kaitong Wang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, People's Republic of China
- College of Agronomy, Gansu Agricultural University, Lanzhou, People's Republic of China
| | - Xun Tang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, People's Republic of China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, People's Republic of China
| | - Ning Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, People's Republic of China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, People's Republic of China
| | - Huaijun Si
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, People's Republic of China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, People's Republic of China
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22
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Li B, Zang Y, Song C, Wang X, Wu X, Wang X, Xi Z. VvERF117 positively regulates grape cold tolerance through direct regulation of the antioxidative gene BAS1. Int J Biol Macromol 2024; 268:131804. [PMID: 38670186 DOI: 10.1016/j.ijbiomac.2024.131804] [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: 12/03/2023] [Revised: 03/07/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024]
Abstract
Cold stress significantly threatens grape quality, yield, and geographical distribution. Although ethylene-responsive factors (ERFs) are recognized for their pivotal roles in cold stress, the regulatory mechanisms of many ERFs contributing to tolerance remain unclear. In this study, we identified the cold-responsive gene VvERF117 and elucidated its positive regulatory function in cold tolerance. VvERF117 exhibits transcriptional activity and localizes to the nucleus. VvERF117 overexpression improved cold tolerance in transgenic Arabidopsis, grape calli, and grape leaves, whereas VvERF117 silencing increased cold sensitivity in grape calli and leaves. Furthermore, VvERF117 overexpression remarkably upregulated the expression of several stress-related genes. Importantly, BAS1, encoding a 2-Cys peroxidase (POD), was confirmed as a direct target gene of VvERF117. Meanwhile, compared to the wild-type, POD activity and H2O2 content were remarkably increased and decreased in VvERF117-overexpressing grape calli and leaves, respectively. Conversely, VvERF117 silencing displayed the opposite trend in grape calli and leaves under cold stress. These findings indicate that VvERF117 plays a positive role in cold resistance by, at least in part, enhancing antioxidant capacity through regulating the POD-encoding gene VvBAS1, leading to effective mitigation of reactive oxygen species.
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Affiliation(s)
- Beibei Li
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100
| | - Yushuang Zang
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100
| | - Changze Song
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100
| | - Xuefei Wang
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100
| | - Xueyan Wu
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100
| | - Xianhang Wang
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100.
| | - Zhumei Xi
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100.
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Bian S, Zhao M, Zhang H, Ren Y. Differentially Expressed Genes Identification of Kohlrabi Seedlings ( Brassica oleracea var. caulorapa L.) under Polyethylene Glycol Osmotic Stress and AP2/ERF Transcription Factor Family Analysis. PLANTS (BASEL, SWITZERLAND) 2024; 13:1167. [PMID: 38674577 PMCID: PMC11054715 DOI: 10.3390/plants13081167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/16/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024]
Abstract
Osmotic stress is a condition in which plants do not get enough water due to changes in environmental factors. Plant response to osmotic stress is a complex process involving the interaction of different stress-sensitive mechanisms. Differentially expressed genes and response mechanisms of kohlrabi have not been reported under osmotic stress. A total of 196,642 unigenes and 33,040 differentially expressed unigenes were identified in kohlrabi seedlings under polyethylene glycol osmotic stress. AP2/ERF, NAC and eight other transcription factor family members with a high degree of interaction with CAT and SOD antioxidant enzyme activity were identified. Subsequently, 151 AP2/ERF genes were identified and analyzed. Twelve conserved motifs were searched and all AP2/ERF genes were clustered into four groups. A total of 149 AP2/ERF genes were randomly distributed on the chromosome, and relative expression level analysis showed that BocAP2/ERF genes of kohlrabi have obvious specificity in different tissues. This study lays a foundation for explaining the osmotic stress resistance mechanism of kohlrabi and provides a theoretical basis for the functional analysis of BocAP2/ERF transcription factor family members.
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Affiliation(s)
- Shuanling Bian
- State Key Laboratory of Plateau Ecology and Agriculture, Laboratory of Research and Utilization of Germplasm Resources in Qinghai-Tibet Plateau, Qinghai University, Xining 810016, China; (S.B.); (H.Z.)
| | - Mengliang Zhao
- State Key Laboratory of Plateau Ecology and Agriculture, Laboratory of Research and Utilization of Germplasm Resources in Qinghai-Tibet Plateau, Qinghai University, Xining 810016, China; (S.B.); (H.Z.)
| | - Huijuan Zhang
- State Key Laboratory of Plateau Ecology and Agriculture, Laboratory of Research and Utilization of Germplasm Resources in Qinghai-Tibet Plateau, Qinghai University, Xining 810016, China; (S.B.); (H.Z.)
| | - Yanjing Ren
- State Key Laboratory of Plateau Ecology and Agriculture, Laboratory of Research and Utilization of Germplasm Resources in Qinghai-Tibet Plateau, Qinghai University, Xining 810016, China; (S.B.); (H.Z.)
- Key Laboratory of Germplasm Resources Protection and Genetic Improvement of the Qinghai-Tibet Plateau in Ministry of Agriculture and Rural, Xining 810016, China
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Awan MJA, Farooq MA, Naqvi RZ, Karamat U, Bukhari SAR, Waqas MAB, Mahmood MA, Buzdar MI, Rasheed A, Amin I, Saeed NA, Mansoor S. Deciphering the differential expression patterns of yield-related negative regulators in hexaploid wheat cultivars and hybrids at different growth stages. Mol Biol Rep 2024; 51:537. [PMID: 38642174 DOI: 10.1007/s11033-024-09454-0] [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: 12/12/2023] [Accepted: 03/18/2024] [Indexed: 04/22/2024]
Abstract
BACKGROUND Hexaploid bread wheat underwent a series of polyploidization events through interspecific hybridizations that conferred adaptive plasticity and resulted in duplication and neofunctionalization of major agronomic genes. The genetic architecture of polyploid wheat not only confers adaptive plasticity but also offers huge genetic diversity. However, the contribution of different gene copies (homeologs) encoded from different subgenomes (A, B, D) at different growth stages remained unexplored. METHODS In this study, hybrid of elite cultivars of wheat were developed via reciprocal crosses (cytoplasm swapping) and phenotypically evaluated. We assessed differential expression profiles of yield-related negative regulators in these cultivars and their F1 hybrids and identified various cis-regulatory signatures by employing bioinformatics tools. Furthermore, the preferential expression patterns of the syntenic triads encoded from A, B, and D subgenomes were assessed to decipher their functional redundancy at six different growth stages. RESULTS Hybrid progenies showed better heterosis such as up to 17% increase in the average number of grains and up to 50% increase in average thousand grains weight as compared to mid-parents. Based on the expression profiling, our results indicated significant dynamic transcriptional expression patterns, portraying the different homeolog-dominance at the same stage in the different cultivars and their hybrids. Albeit belonging to same syntenic triads, a dynamic trend was observed in the regulatory signatures of these genes that might be influencing their expression profiles. CONCLUSION These findings can substantially contribute and provide insights for the selective introduction of better cultivars into traditional and hybrid breeding programs which can be harnessed for the improvement of future wheat.
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Affiliation(s)
- Muhammad Jawad Akbar Awan
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Muhammad Awais Farooq
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Rubab Zahra Naqvi
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Umer Karamat
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Sayyad Ali Raza Bukhari
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
- Department of Biotechnology, University of Sargodha, Sargodha, Pakistan
| | - Muhammad Abu Bakar Waqas
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Muhammad Arslan Mahmood
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Muhammad Ismail Buzdar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Awais Rasheed
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS) & CIMMYT-China office, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Nasir A Saeed
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan.
- International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan.
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Gentile D, Serino G, Frugis G. CRF transcription factors in the trade-off between abiotic stress response and plant developmental processes. Front Genet 2024; 15:1377204. [PMID: 38694876 PMCID: PMC11062136 DOI: 10.3389/fgene.2024.1377204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 04/04/2024] [Indexed: 05/04/2024] Open
Abstract
Climate change-induced environmental stress significantly affects crop yield and quality. In response to environmental stressors, plants use defence mechanisms and growth suppression, creating a resource trade-off between the stress response and development. Although stress-responsive genes have been widely engineered to enhance crop stress tolerance, there is still limited understanding of the interplay between stress signalling and plant growth, a research topic that can provide promising targets for crop genetic improvement. This review focuses on Cytokinin Response Factors (CRFs) transcription factor's role in the balance between abiotic stress adaptation and sustained growth. CRFs, known for their involvement in cytokinin signalling and abiotic stress responses, emerge as potential targets for delaying senescence and mitigating yield penalties under abiotic stress conditions. Understanding the molecular mechanisms regulated by CRFs paves the way for decoupling stress responses from growth inhibition, thus allowing the development of crops that can adapt to abiotic stress without compromising development. This review highlights the importance of unravelling CRF-mediated pathways to address the growing need for resilient crops in the face of evolving climatic conditions.
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Affiliation(s)
- Davide Gentile
- Institute of Agricultural Biology and Biotechnology (IBBA), National Research Council (CNR), Rome, Italy
- Department of Biology and Biotechnology ‘Charles Darwin’, Sapienza University of Rome, Rome, Italy
| | - Giovanna Serino
- Department of Biology and Biotechnology ‘Charles Darwin’, Sapienza University of Rome, Rome, Italy
| | - Giovanna Frugis
- Institute of Agricultural Biology and Biotechnology (IBBA), National Research Council (CNR), Rome, Italy
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Meng HX, Wang YZ, Yao XL, Xie XR, Dong S, Yuan X, Li X, Gao L, Yang G, Chu X, Wang JG. Reactive oxygen species (ROS) modulate nitrogen signaling using temporal transcriptome analysis in foxtail millet. PLANT MOLECULAR BIOLOGY 2024; 114:37. [PMID: 38602592 DOI: 10.1007/s11103-024-01435-y] [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: 08/29/2023] [Accepted: 02/26/2024] [Indexed: 04/12/2024]
Abstract
Reactive oxygen species (ROS) is a chemically reactive chemical substance containing oxygen and a natural by-product of normal oxygen metabolism. Excessive ROS affect the growth process of crops, which will lead to the decrease of yield. Nitrogen, as a critical nutrient element in plants and plays a vital role in plant growth and crop production. Nitrate is the primary nitrogen source available to plants in agricultural soil and various natural environments. However, the molecular mechanism of ROS-nitrate crosstalk is still unclear. In this study, we used the foxtail millet (Setaria italica L.) as the material to figure it out. Here, we show that excessive NaCl inhibits nitrate-promoted plant growth and nitrogen use efficiency (NUE). NaCl induces ROS accumulation in roots, and ROS inhibits nitrate-induced gene expression in a short time. Surprisingly, low concentration ROS slight promotes and high concentration of ROS inhibits foxtail millet growth under long-term H2O2 treatment. These results may open a new perspective for further exploration of ROS-nitrate signaling pathway in plants.
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Affiliation(s)
- Hui-Xin Meng
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, China
| | - Yu-Ze Wang
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, China
| | - Xin-Li Yao
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, China
| | - Xin-Ran Xie
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, China
| | - Shuqi Dong
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, China
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), Shanxi Agricultural University, Taigu, 030801, China
| | - Xiangyang Yuan
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, China
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), Shanxi Agricultural University, Taigu, 030801, China
| | - Xiaorui Li
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, China
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), Shanxi Agricultural University, Taigu, 030801, China
| | - Lulu Gao
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, China
| | - Guanghui Yang
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, China.
| | - Xiaoqian Chu
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, China.
| | - Jia-Gang Wang
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, China.
- Hou Ji Laboratory in Shanxi Province, Shanxi Agricultural University, Taigu, 030801, China.
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Zeng Q, Gu J, Cai M, Wang Y, Xie Q, Han Y, Zhang S, Lu L, Chen Y, Zeng Y, Chen T. Genome-Wide Identification and Expression Analysis of TGA Family Genes Associated with Abiotic Stress in Sunflowers ( Helianthus annuus L.). Int J Mol Sci 2024; 25:4097. [PMID: 38612905 PMCID: PMC11012525 DOI: 10.3390/ijms25074097] [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: 03/09/2024] [Revised: 03/31/2024] [Accepted: 04/04/2024] [Indexed: 04/14/2024] Open
Abstract
Sunflower (Helianthus annuus L.) is an important, substantial global oil crop with robust resilience to drought and salt stresses. The TGA (TGACG motif-binding factor) transcription factors, belonging to the basic region leucine zipper (bZIP) family, have been implicated in orchestrating multiple biological processes. Despite their functional significance, a comprehensive investigation of the TGA family's abiotic stress tolerance in sunflowers remains elusive. In the present study, we identified 14 TGA proteins in the sunflower genome, which were unequally distributed across 17 chromosomes. Employing phylogenetic analysis encompassing 149 TGA members among 13 distinct species, we revealed the evolutionary conservation of TGA proteins across the plant kingdom. Collinearity analysis suggested that both HaTGA01 and HaTGA03 were generated due to HaTGA08 gene duplication. Notably, qRT-PCR analysis demonstrated that HaTGA04, HaTGA05, and HaTGA14 genes were remarkably upregulated under ABA, MeJA, and salt treatments, whereas HaTGA03, HaTGA06, and HaTGA07 were significantly repressed. This study contributes valuable perspectives on the potential roles of the HaTGA gene family under various stress conditions in sunflowers, thereby enhancing our understanding of TGA gene family dynamics and function within this agriculturally significant species.
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Affiliation(s)
- Qinzong Zeng
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China;
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China; (J.G.); (M.C.); (Y.W.); (Q.X.); (Y.H.); (S.Z.); (L.L.); (Y.C.)
| | - Jiafeng Gu
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China; (J.G.); (M.C.); (Y.W.); (Q.X.); (Y.H.); (S.Z.); (L.L.); (Y.C.)
| | - Maohong Cai
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China; (J.G.); (M.C.); (Y.W.); (Q.X.); (Y.H.); (S.Z.); (L.L.); (Y.C.)
| | - Yingwei Wang
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China; (J.G.); (M.C.); (Y.W.); (Q.X.); (Y.H.); (S.Z.); (L.L.); (Y.C.)
| | - Qinyu Xie
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China; (J.G.); (M.C.); (Y.W.); (Q.X.); (Y.H.); (S.Z.); (L.L.); (Y.C.)
| | - Yuliang Han
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China; (J.G.); (M.C.); (Y.W.); (Q.X.); (Y.H.); (S.Z.); (L.L.); (Y.C.)
| | - Siqi Zhang
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China; (J.G.); (M.C.); (Y.W.); (Q.X.); (Y.H.); (S.Z.); (L.L.); (Y.C.)
| | - Lingyue Lu
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China; (J.G.); (M.C.); (Y.W.); (Q.X.); (Y.H.); (S.Z.); (L.L.); (Y.C.)
| | - Youheng Chen
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China; (J.G.); (M.C.); (Y.W.); (Q.X.); (Y.H.); (S.Z.); (L.L.); (Y.C.)
| | - Youling Zeng
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China;
| | - Tao Chen
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China; (J.G.); (M.C.); (Y.W.); (Q.X.); (Y.H.); (S.Z.); (L.L.); (Y.C.)
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Wang X, Yuan W, Yuan X, Jiang C, An Y, Chen N, Huang L, Lu M, Zhang J. Comparative analysis of PLATZ transcription factors in six poplar species and analysis of the role of PtrPLATZ14 in leaf development. Int J Biol Macromol 2024; 263:130471. [PMID: 38417753 DOI: 10.1016/j.ijbiomac.2024.130471] [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: 12/07/2023] [Revised: 02/13/2024] [Accepted: 02/25/2024] [Indexed: 03/01/2024]
Abstract
Plant AT-rich sequence and zinc-binding (PLATZ) proteins are a class of plant-specific transcription factor that play a crucial role in plant growth, development, and stress response. However, the evolutionary relationship of the PLATZ gene family across the Populus genus and the biological functions of the PLATZ protein require further investigation. In this study, we identified 133 PLATZ genes from six Populus species belonging to four Populus sections. Synteny analysis of the PLATZ gene family indicated that whole genome duplication events contributed to the expansion of the PLATZ family. Among the nine paralogous pairs, the protein structure of PtrPLATZ14/18 pair exhibited significant differences with others. Through gene expression patterns and co-expression networks, we discovered divergent expression patterns and sub-networks, and found that the members of pair PtrPLATZ14/18 might play different roles in the regulation of macromolecule biosynthesis and modification. Furthermore, we found that PtrPLATZ14 regulates poplar leaf development by affecting cell size control genes PtrGRF/GIF and PtrTCP. In conclusion, our study provides a theoretical foundation for exploring the evolution relationships and functions of the PLATZ gene family within Populus species and provides insights into the function and potential mechanism of PtrPLATZ14 in leaf morphology that were diverse across the Populus genus.
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Affiliation(s)
- Xiaqin Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China.
| | - Wenya Yuan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Xuening Yuan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Cheng Jiang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China.
| | - Yi An
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China.
| | - Ningning Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Lichao Huang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China.
| | - Mengzhu Lu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China.
| | - Jin Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China.
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29
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Fick A, Swart V, Bombarely A, van den Berg N. Comparative transcriptional analysis of Persea americana MYB, WRKY and AP2/ERF transcription factors following Phytophthora cinnamomi infection. MOLECULAR PLANT PATHOLOGY 2024; 25:e13453. [PMID: 38590150 PMCID: PMC11002358 DOI: 10.1111/mpp.13453] [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: 09/11/2023] [Revised: 03/07/2024] [Accepted: 03/20/2024] [Indexed: 04/10/2024]
Abstract
Plant cells undergo extensive transcriptional reprogramming following pathogen infection, with these reprogramming patterns becoming more complex when pathogens, such as hemibiotrophs, exhibit different lifestyles. These transcriptional changes are often orchestrated by MYB, WRKY and AP2/ERF transcription factors (TFs), which modulate both growth and defence-related gene expression. Transcriptional analysis of defence-related genes in avocado (Persea americana) infected with Phytophthora cinnamomi indicated differential immune response activation when comparing a partially resistant and susceptible rootstock. This study identified 226 MYB, 82 WRKY, and 174 AP2/ERF TF-encoding genes in avocado, using a genome-wide approach. Phylogenetic analysis revealed substantial sequence conservation within TF groups underscoring their functional significance. RNA-sequencing analysis in a partially resistant and susceptible avocado rootstock infected with P. cinnamomi was indicative of an immune response switch occurring in either rootstock after 24 and 6 h post-inoculation, respectively. Different clusters of co-expressed TF genes were observed at these times, suggesting the activation of necrotroph-related immune responses at varying intervals between the two rootstocks. This study aids our understanding of avocado immune response activation following P. cinnamomi infection, and the role of the TFs therein, elucidating the transcriptional reprogramming disparities between partially resistant and susceptible rootstocks.
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Affiliation(s)
- Alicia Fick
- Department of Biochemistry, Genetics and MicrobiologyUniversity of PretoriaPretoriaGautengSouth Africa
- Hans Merensky Chair in Avocado Research, Forestry and Agricultural Biotechnology InstituteUniversity of PretoriaPretoriaGautengSouth Africa
| | - Velushka Swart
- Department of Biochemistry, Genetics and MicrobiologyUniversity of PretoriaPretoriaGautengSouth Africa
- Hans Merensky Chair in Avocado Research, Forestry and Agricultural Biotechnology InstituteUniversity of PretoriaPretoriaGautengSouth Africa
| | - Aureliano Bombarely
- Instituto de Biología Molecular y Celular de PlantasConsejo Superior de Investigaciones Científicas‐Universitat Politècnica de València (IBMCP‐CSIC‐UPV)ValenciaSpain
| | - Noëlani van den Berg
- Department of Biochemistry, Genetics and MicrobiologyUniversity of PretoriaPretoriaGautengSouth Africa
- Hans Merensky Chair in Avocado Research, Forestry and Agricultural Biotechnology InstituteUniversity of PretoriaPretoriaGautengSouth Africa
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30
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Song Z, Wang R, Zhang H, Tong Z, Yuan C, Li Y, Huang C, Zhao L, Wang Y, Di Y, Sui X. Comparative transcriptome analysis reveals nicotine metabolism is a critical component for enhancing stress response intensity of innate immunity system in tobacco. FRONTIERS IN PLANT SCIENCE 2024; 15:1338169. [PMID: 38595766 PMCID: PMC11003474 DOI: 10.3389/fpls.2024.1338169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 03/05/2024] [Indexed: 04/11/2024]
Abstract
The pyridine alkaloid nicotine acts as one of best-studied plant resistant traits in tobacco. Previous research has shown that NtERF199 and NtERF189, acting as master regulators within the NIC1 and NIC2 locus, quantitatively contribute to nicotine accumulation levels in N. tabacum. Genome editing-created Nic1(Nterf199) and Nic2 (Nterf189) double mutant provides an ideal platform for precisely dissecting the defensive role of nicotine and the connection between the nicotine biosynthetic pathway with other putative metabolic networks. Taking this advantage, we performed a comparative transcriptomic analysis to reevaluate the potential physiological and metabolic changes in response to nicotine synthesis defect by comparing the nic1nic2 and NIC1NIC2 plants. Our findings revealed that nicotine reduction could systematically diminishes the expression intensities of genes associated with stimulus perception, signal transduction and regulation, as well as secondary metabolic flux. Consequently, this global expression reduction might compromise tobacco adaptions to environmental fitness, herbivore resistances, and plant growth and development. The up-regulation of a novel set of stress-responsive and metabolic pathway genes might signify a newly established metabolic reprogramming to tradeoff the detrimental effect of nicotine loss. These results offer additional compelling evidence regarding nicotine's critical defensive role in nature and highlights the tight link between nicotine biosynthesis and gene expression levels of quantitative resistance-related genes for better environmental adaptation.
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Affiliation(s)
- Zhongbang Song
- National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| | - Ruixue Wang
- National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
- College of Resources and Environmental Science, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Hongbo Zhang
- Plant Functional Component Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, Shandong, China
| | - Zhijun Tong
- National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| | - Cheng Yuan
- National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| | - Yong Li
- National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| | - Changjun Huang
- National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| | - Lu Zhao
- National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| | - Yuehu Wang
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yingtong Di
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Xueyi Sui
- National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
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31
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Zhang X, Fan R, Yu Z, Du X, Yang X, Wang H, Xu W, Yu X. Genome-wide identification of GATA transcription factors in tetraploid potato and expression analysis in differently colored potato flesh. FRONTIERS IN PLANT SCIENCE 2024; 15:1330559. [PMID: 38576788 PMCID: PMC10991705 DOI: 10.3389/fpls.2024.1330559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/04/2024] [Indexed: 04/06/2024]
Abstract
The GATA gene family belongs to a kind of transcriptional regulatory protein featuring a zinc finger motif, which is essential for plant growth and development. However, the identification of the GATA gene family in tetraploid potato is still not performed. In the present research, a total of 88 GATA genes in the tetraploid potato C88.v1 genome were identified by bioinformatics methods. These StGATA genes had an uneven distribution on 44 chromosomes, and the corresponding StGATA proteins were divided into four subfamilies (I-IV) based on phylogenetic analysis. The cis-elements of StGATA genes were identified, including multiple cis-elements related to light-responsive and hormone-responsive. The collinearity analysis indicates that segmental duplication is a key driving force for the expansion of GATA gene family in tetraploid potato, and that the GATA gene families of tetraploid potato and Arabidopsis share a closer evolutionary relationship than rice. The transcript profiling analysis showed that all 88 StGATA genes had tissue-specific expression, indicating that the StGATA gene family members participate in the development of multiple potato tissues. The RNA-seq analysis was also performed on the tuber flesh of two potato varieties with different color, and 18 differentially expressed GATA transcription factor genes were screened, of which eight genes were validated through qRT-PCR. In this study, we identified and characterized StGATA transcription factors in tetraploid potato for the first time, and screened differentially expressed genes in potato flesh with different color. It provides a theoretical basis for further understanding the StGATA gene family and its function in anthocyanin biosynthesis.
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Affiliation(s)
| | | | | | | | | | | | | | - Xiaoxia Yu
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
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Li L, Liu S, Wang Y, Shang Y, Qi Z, Lin H, Niu L. Transcriptomic Analysis of Self-Incompatibility in Alfalfa. PLANTS (BASEL, SWITZERLAND) 2024; 13:875. [PMID: 38592914 PMCID: PMC10975240 DOI: 10.3390/plants13060875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/12/2024] [Accepted: 03/15/2024] [Indexed: 04/11/2024]
Abstract
Alfalfa (Medicago sativa L.) is an important forage crop worldwide, but molecular genetics and breeding research in this species are hindered by its self-incompatibility (SI). Although the mechanisms underlying SI have been extensively studied in other plant families, SI in legumes, including alfalfa, remains poorly understood. Here, we determined that self-pollinated pollen tubes could germinate on the stigma of alfalfa, grow through the style, and reach the ovarian cavity, but the ovules collapsed ~48 h after self-pollination. A transcriptomic analysis of dissected pistils 24 h after self-pollination identified 941 differently expressed genes (DEGs), including 784 upregulated and 157 downregulated genes. A gene ontology (GO) analysis showed that the DEGs were highly enriched in functions associated with the regulation of pollen tube growth and pollen germination. A Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that pentose and glucuronate interconversion, plant hormone signal transduction, the spliceosome, and ribosomes might play important roles in SI. Our co-expression analysis showed that F-box proteins, serine/threonine protein kinases, calcium-dependent protein kinases (CDPKs), bHLHs, bZIPs, and MYB-related family proteins were likely involved in the SI response. Our study provides a catalog of candidate genes for further study to understand SI in alfalfa and related legumes.
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Affiliation(s)
- Lulu Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.L.)
- School of Life Sciences, Inner Mongolia University, Hohhot 010021, China;
| | - Sinan Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.L.)
| | - Yulu Wang
- College of Life Science, Shanxi University, Taiyuan 030006, China;
| | - Yangzhou Shang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.L.)
| | - Zhi Qi
- School of Life Sciences, Inner Mongolia University, Hohhot 010021, China;
| | - Hao Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.L.)
| | - Lifang Niu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.L.)
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Yang T, Zhao X, Bai J, Lv W, Chen Q, Hu J, Liu G, Zhao Y, Zhou H, Zhao M, Zheng H. Transcriptome analysis of genes involved in the pathogenesis mechanism of potato virus Y in potato cultivar YouJin. Front Microbiol 2024; 15:1353814. [PMID: 38511006 PMCID: PMC10951100 DOI: 10.3389/fmicb.2024.1353814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 02/07/2024] [Indexed: 03/22/2024] Open
Abstract
Introduction Potatoes (Solanum tuberosum L.) can be infected by various viruses, but out of all of viruses, the potato virus Y (PVY) is the most detrimental. Research shows that the potato cultivar YouJin is especially vulnerable to PVY and displays severe symptoms, including leaf vein chlorosis, curled leaf margins, large necrotic spots on the leaf blades, and the growth of small new leaves. Methods PVY infection in potato cultivar YouJin was confirmed through symptom observation, RT-PCR, and Western blot analysis. Transcriptome sequencing was used to analyze the genes associated with PVY pathogenesis in this cultivar. Result Transcriptome analysis of differential genes was conducted in this study to examine the pathogenesis of PVY on YouJin. The results showed that 1,949 genes were differentially regulated, including 853 upregulated genes and 1,096 downregulated genes. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that carbohydrate synthesis and metabolism pathways were suppressed, and electron transferase and hydrolase activities were reduced. Moreover, there were increased expression levels of protein kinase genes. By focusing on plant-pathogen interaction pathways, six core genes all upregulating the WARK family of transcription factors were obtained. Additionally, a constructed PPI network revealed the identification of key modular differential genes, such as downregulated photosynthesis-related protein genes and upregulated AP2/ERF-ERF transcription factors. Functional network enrichment analysis revealed that PVY infection limited RNA metabolism, glutathionylation, and peroxiredoxin activity while triggering the expression of associated defense genes in YouJin. After analyzing the above, 26 DEGs were screened and 12 DEGs were confirmed via RT-qPCR. Conclusion These results establish a hypothetical framework for clarifying the pathogenesis of PVY in the YouJin variety of potatoes, which will help design the disease resistance of YouJin.
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Affiliation(s)
- Tianqi Yang
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Xingyue Zhao
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Jinjiang Bai
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Wenxia Lv
- Inner Mongolia Zhongjia Agricultural Biotechnology Co., Siziwang Banner, China
| | - Qi Chen
- Siziwang Banner Agricultural and Livestock Products Quality and Safety Inspection and Testing Station, Siziwang Banner, China
| | - Jun Hu
- Inner Mongolia Zhongjia Agricultural Biotechnology Co., Siziwang Banner, China
| | - Guangjing Liu
- Inner Mongolia Zhongjia Agricultural Biotechnology Co., Siziwang Banner, China
| | - Yuanzheng Zhao
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Hongyou Zhou
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of the Development and Resource Utilization of Biological Pesticide in Inner Mongolia, Hohhot, China
| | - Mingmin Zhao
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of the Development and Resource Utilization of Biological Pesticide in Inner Mongolia, Hohhot, China
| | - Hongli Zheng
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
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34
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Shu P, Li Y, Sheng J, Shen L. Recent Advances in Dissecting the Function of Ethylene in Interaction between Host and Pathogen. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:4552-4563. [PMID: 38379128 DOI: 10.1021/acs.jafc.3c07978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Pathogens influence the growth and development of plants, resulting in detrimental damage to their yields and quality. Ethylene, a gaseous phytohormone, serves a pivotal function in modulating diverse physiological processes in plants, including defense mechanisms against pathogen invasion. Ethylene biosynthesis is involved in both plants and pathogens. Recent empirical research elucidates the intricate interactions and regulatory mechanisms between ethylene and pathogens across various plant species. In this review, we provide a comprehensive overview of the latest findings concerning ethylene's role and its regulatory networks in host-pathogen interactions. Additionally, we explore the crosstalk between ethylene and other phytohormones. Points regarding ethylene emission and its modulation by pathogens are also emphasized. Moreover, we also discuss potential unresolved issues in the field that warrant further investigation.
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Affiliation(s)
- Pan Shu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China
| | - Yujing Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China
| | - Jiping Sheng
- School of Agricultural Economics and Rural Development, Renmin University of China, Beijing 100872, P. R. China
| | - Lin Shen
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China
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Wang Y, Wang Y, Pan A, Miao Q, Han Y, Liu Z, Yu F. CaERF1- mediated ABA signal positively regulates camptothecin biosynthesis by activating the iridoid pathway in Camptotheca acuminata. Int J Biol Macromol 2024; 261:129560. [PMID: 38246434 DOI: 10.1016/j.ijbiomac.2024.129560] [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: 08/29/2023] [Revised: 01/13/2024] [Accepted: 01/15/2024] [Indexed: 01/23/2024]
Abstract
Camptotheca acuminata is one of the primary sources of camptothecin (CPT), which is widely used in the treatment of human malignancies because of its inhibitory activity against DNA topoisomerase I. Although several transcription factors have been identified for regulating CPT biosynthesis in other species, such as Ophiorrhiza pumila, the specific regulatory components controlling CPT biosynthesis in C. acuminata have yet to be definitively determined. In this study, CaERF1, an DREB subfamily of the APETALA2/ethylene response factors (AP2ERFs), was identified in C. acuminata. The transient overexpression and silencing of CaERF1 in C. acuminata leaves confirmed that it positively regulates the accumulation of CPT by inducing the expression of CaCYC1 and CaG8O in the iridoid pathway. Results of transient transcriptional activity assay and yeast one-hybrid assays have showed that CaERF1 transcriptionally activates the expression of CaCYC1 and CaG8O by binding to RAA and CEI elements in the promoter regions of these two genes. Furthermore, the expression of CaCYC1 and CaG8O in CaERF1-silenced leaves was less sensitive to ABA treatment, indicating that CaERF1 is a crucial component involved in ABA-regulated CPT biosynthesis in C. acuminata.
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Affiliation(s)
- Yanyan Wang
- School of Biological Engineering, Dalian Polytechnic University, Dalian 116034, China
| | - Yang Wang
- School of Biological Engineering, Dalian Polytechnic University, Dalian 116034, China
| | - AiKun Pan
- School of Biological Engineering, Dalian Polytechnic University, Dalian 116034, China
| | - Qi Miao
- School of Biological Engineering, Dalian Polytechnic University, Dalian 116034, China
| | - Yuqian Han
- School of Biological Engineering, Dalian Polytechnic University, Dalian 116034, China
| | - Zhiwen Liu
- School of Biological Engineering, Dalian Polytechnic University, Dalian 116034, China
| | - Fang Yu
- School of Biological Engineering, Dalian Polytechnic University, Dalian 116034, China; College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China.
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Zhang S, Yu Z, Sun L, Liang S, Xu F, Li S, Zheng X, Yan L, Huang Y, Qi X, Ren H. T2T reference genome assembly and genome-wide association study reveal the genetic basis of Chinese bayberry fruit quality. HORTICULTURE RESEARCH 2024; 11:uhae033. [PMID: 38495030 PMCID: PMC10940123 DOI: 10.1093/hr/uhae033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 01/23/2024] [Indexed: 03/19/2024]
Abstract
Chinese bayberry (Myrica rubra or Morella rubra; 2n = 16) produces fruit with a distinctive flavor, high nutritional, and economic value. However, previous versions of the bayberry genome lack sequence continuity. Moreover, to date, no large-scale germplasm resource association analysis has examined the allelic and genetic variations determining fruit quality traits. Therefore, in this study, we assembled a telomere-to-telomere (T2T) gap-free reference genome for the cultivar 'Zaojia' using PacBio HiFi long reads. The resulting 292.60 Mb T2T genome, revealed 8 centromeric regions, 15 telomeres, and 28 345 genes. This represents a substantial improvement in the genome continuity and integrity of Chinese bayberry. Subsequently, we re-sequenced 173 accessions, identifying 6 649 674 single nucleotide polymorphisms (SNPs). Further, the phenotypic analyses of 29 fruit quality-related traits enabled a genome-wide association study (GWAS), which identified 1937 SNPs and 1039 genes significantly associated with 28 traits. An SNP cluster pertinent to fruit color was identified on Chr6: 3407532 to 5 153 151 bp region, harboring two MYB genes (MrChr6G07650 and MrChr6G07660), exhibiting differential expression in extreme phenotype transcriptomes, linked to anthocyanin synthesis. An adjacent, closely linked gene, MrChr6G07670 (MLP-like protein), harbored an exonic missense variant and was shown to increase anthocyanin production in tobacco leaves tenfold. This SNP cluster, potentially a quantitative trait locus (QTL), collectively regulates bayberry fruit color. In conclusion, our study presented a complete reference genome, uncovered a suite of allelic variations related to fruit-quality traits, and identified functional genes that could be harnessed to enhance fruit quality and breeding efficiency of bayberries.
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Affiliation(s)
- Shuwen Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, 298 Desheng Road, Shangcheng District, Hangzhou 310021, Zhejiang, China
| | - Zheping Yu
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, 298 Desheng Road, Shangcheng District, Hangzhou 310021, Zhejiang, China
| | - Li Sun
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, 298 Desheng Road, Shangcheng District, Hangzhou 310021, Zhejiang, China
| | - Senmiao Liang
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, 298 Desheng Road, Shangcheng District, Hangzhou 310021, Zhejiang, China
| | - Fei Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, 298 Desheng Road, Shangcheng District, Hangzhou 310021, Zhejiang, China
| | - Sujuan Li
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, 298 Desheng Road, Shangcheng District, Hangzhou 310021, Zhejiang, China
| | - Xiliang Zheng
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, 298 Desheng Road, Shangcheng District, Hangzhou 310021, Zhejiang, China
| | - Lijv Yan
- Linhai Specialty and Technology Extension Station, 219 Dongfang Avenue, Linhai 317000, Zhejiang, China
| | - Yinghong Huang
- Jiangsu Taihu Evergreen Fruit Tree Technology Promotion Center, Dongshan Town, Wuzhong District, Suzhou 215107, Jiangsu, China
| | - Xingjiang Qi
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, 298 Desheng Road, Shangcheng District, Hangzhou 310021, Zhejiang, China
- Xianghu Laboratory, 168 Gengwen Road, Xiaoshan District, Hangzhou 311231, Zhejiang, China
| | - Haiying Ren
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, 298 Desheng Road, Shangcheng District, Hangzhou 310021, Zhejiang, China
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Han Y, Zhang J, Zhang S, Xiang L, Lei Z, Huang Q, Wang H, Chen T, Cai M. DcERF109 regulates shoot branching by participating in strigolactone signal transduction in Dendrobium catenatum. PHYSIOLOGIA PLANTARUM 2024; 176:e14286. [PMID: 38618752 DOI: 10.1111/ppl.14286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/14/2024] [Accepted: 03/26/2024] [Indexed: 04/16/2024]
Abstract
Shoot branching fundamentally influences plant architecture and agricultural yield. However, research on shoot branching in Dendrobium catenatum, an endangered medicinal plant in China, remains limited. In this study, we identified a transcription factor DcERF109 as a key player in shoot branching by regulating the expression of strigolactone (SL) receptors DWARF 14 (D14)/ DECREASED APICAL DOMINANCE 2 (DAD2). The treatment of D. catenatum seedlings with GR24rac/TIS108 revealed that SL can significantly repress the shoot branching in D. catenatum. The expression of DcERF109 in multi-branched seedlings is significantly higher than that of single-branched seedlings. Ectopic expression in Arabidopsis thaliana demonstrated that overexpression of DcERF109 resulted in significant shoot branches increasing and dwarfing. Molecular and biochemical assays demonstrated that DcERF109 can directly bind to the promoters of AtD14 and DcDAD2.2 to inhibit their expression, thereby positively regulating shoot branching. Inhibition of DcERF109 by virus-induced gene silencing (VIGS) resulted in decreased shoot branching and improved DcDAD2.2 expression. Moreover, overexpression of DpERF109 in A. thaliana, the homologous gene of DcERF109 in Dendrobium primulinum, showed similar phenotypes to DcERF109 in shoot branch and plant height. Collectively, these findings shed new insights into the regulation of plant shoot branching and provide a theoretical basis for improving the yield of D. catenatum.
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Affiliation(s)
- Yuliang Han
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, China
| | - Juncheng Zhang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, China
| | - Siqi Zhang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, China
| | - Lijun Xiang
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, China
| | - Zhonghua Lei
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, China
| | - Qixiu Huang
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, China
| | - Huizhong Wang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, China
| | - Tao Chen
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, China
| | - Maohong Cai
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, China
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Zhang Y, Xiao W, Wang M, Khan M, Liu JH. A C2H2-type zinc finger protein ZAT12 of Poncirus trifoliata acts downstream of CBF1 to regulate cold tolerance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1317-1329. [PMID: 38017362 DOI: 10.1111/tpj.16562] [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: 07/15/2023] [Revised: 09/21/2023] [Accepted: 11/14/2023] [Indexed: 11/30/2023]
Abstract
The Cys2/His2 (C2H2)-type zinc finger family has been reported to regulate multiple aspects of plant development and abiotic stress response. However, the role of C2H2-type zinc finger proteins in cold tolerance remains largely unclear. Through RNA-sequence analysis, a cold-responsive zinc finger protein, named as PtrZAT12, was identified and isolated from trifoliate orange (Poncirus trifoliata L. Raf.), a cold-hardy plant closely related to citrus. Furthermore, we found that PtrZAT12 was markedly induced by various abiotic stresses, especially cold stress. PtrZAT12 is a nuclear protein, and physiological analysis suggests that overexpression of PtrZAT12 conferred enhanced cold tolerance in transgenic tobacco (Nicotiana tabacum) plants, while knockdown of PtrZAT12 by virus-induced gene silencing (VIGS) increased the cold sensitivity of trifoliate orange and repressed expression of genes involved in stress tolerance. The promoter of PtrZAT12 harbors a DRE/CRT cis-acting element, which was verified to be specifically bound by PtrCBF1 (Poncirus trifoliata C-repeat BINDING FACTOR1). VIGS-mediated silencing of PtrCBF1 reduced the relative expression levels of PtrZAT12 and decreased the cold resistance of trifoliate orange. Based on these results, we propose that PtrZAT12 is a direct target of CBF1 and plays a positive role in modulation of cold stress tolerance. The knowledge gains new insight into a regulatory module composed of CBF1-ZAT12 in response to cold stress and advances our understanding of cold stress response in plants.
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Affiliation(s)
- Yang Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Key Laboratory of Germplasm Innovation and Utilization of Fruit Trees, Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Wei Xiao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Min Wang
- College of Life Sciences, Gannan Normal University, Ganzhou, 341000, China
| | - Madiha Khan
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ji-Hong Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
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39
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Quiroz LF, Gondalia N, Brychkova G, McKeown PC, Spillane C. Haploid rhapsody: the molecular and cellular orchestra of in vivo haploid induction in plants. THE NEW PHYTOLOGIST 2024; 241:1936-1949. [PMID: 38180262 DOI: 10.1111/nph.19523] [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: 09/19/2023] [Accepted: 12/11/2023] [Indexed: 01/06/2024]
Abstract
In planta haploid induction (HI), which reduces the chromosome number in the progeny after fertilization, has garnered increasing attention for its significant potential in crop breeding and genetic research. Despite the identification of several natural and synthetic HI systems in different plant species, the molecular and cellular mechanisms underlying these HI systems remain largely unknown. This review synthesizes the current understanding of HI systems in plants (with a focus on genes and molecular mechanisms involved), including the molecular and cellular interactions which orchestrate the HI process. As most HI systems can function across taxonomic boundaries, we particularly discuss the evidence for conserved mechanisms underlying the process. These include mechanisms involved in preserving chromosomal integrity, centromere function, gamete communication and/or fusion, and maintenance of karyogamy. While significant discoveries and advances on haploid inducer systems have arisen over the past decades, we underscore gaps in understanding and deliberate on directions for further research for a more comprehensive understanding of in vivo HI processes in plants.
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Affiliation(s)
- Luis Felipe Quiroz
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, Galway, H91 REW4, Ireland
| | - Nikita Gondalia
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, Galway, H91 REW4, Ireland
| | - Galina Brychkova
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, Galway, H91 REW4, Ireland
| | - Peter C McKeown
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, Galway, H91 REW4, Ireland
| | - Charles Spillane
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, Galway, H91 REW4, Ireland
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40
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Xiao S, Yang D, Li F, Tian X, Li Z. The EIN3/EIL-ERF9-HAK5 transcriptional cascade positively regulates high-affinity K + uptake in Gossypium hirsutum. THE NEW PHYTOLOGIST 2024; 241:2090-2107. [PMID: 38168024 DOI: 10.1111/nph.19500] [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: 08/18/2023] [Accepted: 12/06/2023] [Indexed: 01/05/2024]
Abstract
High-affinity K+ (HAK) transporters play essential roles in facilitating root K+ uptake in higher plants. Our previous studies revealed that GhHAK5a, a member of the HAK family, is crucial for K+ uptake in upland cotton. Nevertheless, the precise regulatory mechanism governing the expression of GhHAK5a remains unclear. The yeast one-hybrid screening was performed to identify the transcription factors responsible for regulating GhHAK5a, and ethylene response factor 9 (GhERF9) was identified as a potential candidate. Subsequent dual-luciferase and electrophoretic mobility shift assays confirmed that GhERF9 binds directly to the GhHAK5a promoter, thereby activating its expression. Silencing of GhERF9 decreased the expression of GhHAK5a and exacerbated K+ deficiency symptoms in leaves, also decreased K+ uptake rate and K+ content in roots. Additionally, it was observed that the application of ethephon (an ethylene-releasing reagent) resulted in a significant upregulation of GhERF9 and GhHAK5a, accompanied by an increased rate of K+ uptake. Expectedly, GhEIN3b and GhEIL3c, the two key components involved in ethylene signaling, bind directly to the GhERF9 promoter. These findings provide valuable insights into the molecular mechanisms underlying the expression of GhHAK5a and ethylene-mediated K+ uptake and suggest a potential strategy to genetically enhance cotton K+ uptake by exploiting the EIN3/EILs-ERF9-HAK5 module.
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Affiliation(s)
- Shuang Xiao
- State Key Laboratory of Plant Environmental Resilience, Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan Xilu, Haidian District, Beijing, 100193, China
| | - Doudou Yang
- State Key Laboratory of Plant Environmental Resilience, Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan Xilu, Haidian District, Beijing, 100193, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Fangjun Li
- State Key Laboratory of Plant Environmental Resilience, Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan Xilu, Haidian District, Beijing, 100193, China
| | - Xiaoli Tian
- State Key Laboratory of Plant Environmental Resilience, Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan Xilu, Haidian District, Beijing, 100193, China
| | - Zhaohu Li
- State Key Laboratory of Plant Environmental Resilience, Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan Xilu, Haidian District, Beijing, 100193, China
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Liu X, Zhang W, Tang N, Chen Z, Rao S, Cheng H, Luo C, Ye J, Cheng S, Xu F. Genomic-wide identification and expression analysis of AP2/ERF transcription factors in Zanthoxylum armatum reveals the candidate genes for the biosynthesis of terpenoids. THE PLANT GENOME 2024; 17:e20422. [PMID: 38129947 DOI: 10.1002/tpg2.20422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/25/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023]
Abstract
Terpenoids are the main active components in the Zanthoxylum armatum leaves, which have extensive medicinal value. The Z. armatum leaf is the main by-product in the Z. armatum industry. However, the transcription factors involved in the biosynthesis of terpenoids are rarely reported. This study was performed to identify and classify the APETALA2/ethylene-responsive factor (AP2/ERF) gene family of Z. armatum. The chromosome distribution, gene structure, conserved motifs, and cis-acting elements of the promoter of the species were also comprehensively analyzed. A total of 214 ZaAP2/ERFs were identified. From the obtained transcriptome and terpenoid content data, four candidate ZaAP2/ERFs involved in the biosynthesis of terpenoids were selected via correlation and weighted gene co-expression network analysis. A phylogenetic tree was constructed using 13 AP2/ERFs related to the biosynthesis of terpenoids in other plants. ZaERF063 and ZaERF166 showed close evolutionary relationships with the ERFs in other plant species and shared a high AP2-domain sequence similarity with the two closest AP2/ERF proteins, namelySmERF8 from Salvia miltiorrhiza and AaERF4 from Artemisia annua. Further investigation into the effects of methyl jasmonate (MeJA) treatment on the content of terpenoids in Z. armatum leaves revealed that MeJA significantly induced the upregulation of ZaERF166 and led to a significant increase in the terpenoids content in Z. armatum leaves, indicating that ZaERF166 might be involved in the accumulation of terpenoids of Z. armatum. Results will be beneficial for the functional characterization of AP2/ERFs in Z. armatum and establishment of the theoretical foundation to increase the production of terpenoids via the manipulation of the regulatory elements and strengthen the development and utilization of Z. armatum leaves.
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Affiliation(s)
- Xiaomeng Liu
- School of Modern Industry for Selenium Science and Engineering, National R&D Center for Se-rich Agricultural Products Processing Technology, Wuhan Polytechnic University, Wuhan, China
| | - Weiwei Zhang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, China
| | - Ning Tang
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, China
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing, China
| | - Zexiong Chen
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, China
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing, China
| | - Shen Rao
- School of Modern Industry for Selenium Science and Engineering, National R&D Center for Se-rich Agricultural Products Processing Technology, Wuhan Polytechnic University, Wuhan, China
| | - Hua Cheng
- School of Modern Industry for Selenium Science and Engineering, National R&D Center for Se-rich Agricultural Products Processing Technology, Wuhan Polytechnic University, Wuhan, China
| | | | - Jiabao Ye
- College of Horticulture and Gardening, Yangtze University, Jingzhou, China
| | - Shuiyuan Cheng
- School of Modern Industry for Selenium Science and Engineering, National R&D Center for Se-rich Agricultural Products Processing Technology, Wuhan Polytechnic University, Wuhan, China
| | - Feng Xu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, China
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Li M, Li J, Zhang Y, Zhai Y, Chen Y, Lin L, Peng J, Zheng H, Chen J, Yan F, Lu Y. Integrated ATAC-seq and RNA-seq data analysis identifies transcription factors related to rice stripe virus infection in Oryza sativa. MOLECULAR PLANT PATHOLOGY 2024; 25:e13446. [PMID: 38502176 PMCID: PMC10950023 DOI: 10.1111/mpp.13446] [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: 01/15/2024] [Revised: 02/29/2024] [Accepted: 03/03/2024] [Indexed: 03/20/2024]
Abstract
Animal studies have shown that virus infection causes changes in host chromatin accessibility, but little is known about changes in chromatin accessibility of plants infected by viruses and its potential impact. Here, rice infected by rice stripe virus (RSV) was used to investigate virus-induced changes in chromatin accessibility. Our analysis identified a total of 6462 open- and 3587 closed-differentially accessible chromatin regions (DACRs) in rice under RSV infection by ATAC-seq. Additionally, by integrating ATAC-seq and RNA-seq, 349 up-regulated genes in open-DACRs and 126 down-regulated genes in closed-DACRs were identified, of which 34 transcription factors (TFs) were further identified by search of upstream motifs. Transcription levels of eight of these TFs were validated by reverse transcription-PCR. Importantly, four of these TFs (OsWRKY77, OsWRKY28, OsZFP12 and OsERF91) interacted with RSV proteins and are therefore predicted to play important roles in RSV infection. This is the first application of ATAC-seq and RNA-seq techniques to analyse changes in rice chromatin accessibility caused by RSV infection. Integrating ATAC-seq and RNA-seq provides a new approach to select candidate TFs in response to virus infection.
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Affiliation(s)
- Miaomiao Li
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Jing Li
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Yan Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Yushan Zhai
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Yi Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Lin Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Jiejun Peng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Hongying Zheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Jianping Chen
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Fei Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Yuwen Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Plant VirologyNingbo UniversityNingboChina
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Xu L, Lan Y, Lin M, Zhou H, Ying S, Chen M. Genome-Wide Identification and Transcriptional Analysis of AP2/ERF Gene Family in Pearl Millet ( Pennisetum glaucum). Int J Mol Sci 2024; 25:2470. [PMID: 38473718 DOI: 10.3390/ijms25052470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 03/14/2024] Open
Abstract
The apetala2/ethylene response factor (AP2/ERF) gene family plays a crucial role in regulating plant growth and development and responding to different abiotic stresses (e.g., drought, heat, cold, and salinity). However, the knowledge of the ERF family in pearl millet remains limited. Here, a total of 167 high-confidence PgERF genes are identified and divided into five subgroups based on gene-conserved structure and phylogenetic analysis. Forty-one pairs of segmental duplication are found using collinear analysis. Nucleotide substitution analysis reveals these duplicated pairs are under positive purification, indicating they are actively responding to natural selection. Comprehensive transcriptomic analysis reveals that PgERF genesare preferentially expressed in the imbibed seeds and stem (tilling stage) and respond to heat, drought, and salt stress. Prediction of the cis-regulatory element by the PlantCARE program indicates that PgERF genes are involved in responses to environmental stimuli. Using reverse transcription quantitative real-time PCR (RT-qPCR), expression profiles of eleven selected PgERF genes are monitored in various tissues and during different abiotic stresses. Transcript levels of each PgERF gene exhibit significant changes during stress treatments. Notably, the PgERF7 gene is the only candidate that can be induced by all adverse conditions. Furthermore, four PgERF genes (i.e., PgERF22, PgERF37, PgERF88, and PgERF155) are shown to be involved in the ABA-dependent signaling pathway. These results provide useful bioinformatic and transcriptional information for understanding the roles of the pearl millet ERF gene family in adaptation to climate change.
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Affiliation(s)
- Liang Xu
- College of Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524091, China
| | - Ying Lan
- College of Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524091, China
| | - Miaohong Lin
- College of Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524091, China
| | - Hongkai Zhou
- College of Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524091, China
| | - Sheng Ying
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48823, USA
| | - Miao Chen
- College of Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524091, China
- Shenzhen Institute, Guangdong Ocean University, Shenzhen 518120, China
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Le Berre M, Tubiana T, Reuterswärd Waldner P, Lazar N, Li de la Sierra I, Santos JM, Llinás M, Nessler S. Structural characterization of the ACDC domain from ApiAP2 proteins of the malaria parasite. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.09.579679. [PMID: 38370614 PMCID: PMC10871335 DOI: 10.1101/2024.02.09.579679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
The Apicomplexan AP2 (ApiAP2) proteins are the best characterized family of DNA-binding proteins in the malaria parasite. Apart from the AP2 DNA-binding domain, there is little sequence similarity between ApiAP2 proteins and no other functional domains have been extensively characterized. One protein domain, which is present in a subset of the ApiAP2 proteins, is the conserved AP2-coincident domain mostly at the C-terminus (ACDC domain). Here we solved for the first time the crystal structure of the ACDC domain from two distinct Plasmodium falciparum ApiAP2 proteins and one orthologue from P. vivax , revealing a non-canonical four-helix bundle. Despite little sequence conservation between the ACDC domains from the two proteins, the structures are remarkably similar and do not resemble that of any other known protein domains. Due to their unique protein architecture and lack of homologues in the human genome, we performed in silico docking calculations against a library of known antimalarial compounds and we identified a small molecule that can potentially bind to any Apicomplexan ACDC domain within a pocket highly conserved amongst ApiAP2 proteins. Inhibitors based on this compound would disrupt the function of the ACDC domain and thus of the ApiAP2 proteins containing it, providing a new therapeutic window for targeting the malaria parasite and other Apicomplexans.
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Shao Y, Zhou Y, Yang L, Mu D, Wilson IW, Zhang Y, Zhu L, Liu X, Luo L, He J, Qiu D, Tang Q. Genome-wide identification of GATA transcription factor family and the effect of different light quality on the accumulation of terpenoid indole alkaloids in Uncaria rhynchophylla. PLANT MOLECULAR BIOLOGY 2024; 114:15. [PMID: 38329633 DOI: 10.1007/s11103-023-01400-1] [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: 06/08/2023] [Accepted: 11/07/2023] [Indexed: 02/09/2024]
Abstract
Uncaria rhynchophylla is an evergreen vine plant, belonging to the Rubiaceae family, that is rich in terpenoid indole alkaloids (TIAs) that have therapeutic effects on hypertension and Alzheimer's disease. GATA transcription factors (TF) are a class of transcription regulators that participate in the light response regulation, chlorophyll synthesis, and metabolism, with the capability to bind to GATA cis-acting elements in the promoter region of target genes. Currently the charactertics of GATA TFs in U. rhynchophylla and how different light qualities affect the expression of GATA and key enzyme genes, thereby affecting the changes in U. rhynchophylla alkaloids have not been investigated. In this study, 25 UrGATA genes belonging to four subgroups were identified based on genome-wide analysis. Intraspecific collinearity analysis revealed that only segmental duplications were identified among the UrGATA gene family. Collinearity analysis of GATA genes between U. rhynchophylla and four representative plant species, Arabidopsis thaliana, Oryza sativa, Coffea Canephora, and Catharanthus roseus was also performed. U. rhynchophylla seedlings grown in either red lights or under reduced light intensity had altered TIAs content after 21 days. Gene expression analysis reveal a complex pattern of expression from the 25 UrGATA genes as well as a number of key TIA enzyme genes. UrGATA7 and UrGATA8 were found to have similar expression profiles to key enzyme TIA genes in response to altered light treatments, implying that they may be involved in the regulation TIA content. In this research, we comprehensively analyzed the UrGATA TFs, and offered insight into the involvement of UrGATA TFs from U. rhynchophylla in TIAs biosynthesis.
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Affiliation(s)
- Yingying Shao
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, 410128, Changsha, China
| | - Yu Zhou
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, 410128, Changsha, China
| | - Li Yang
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, 410128, Changsha, China
| | - Detian Mu
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, 410128, Changsha, China.
| | - Iain W Wilson
- CSIRO Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Yao Zhang
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, 410128, Changsha, China
| | - Lina Zhu
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, 410128, Changsha, China
| | - Xinghui Liu
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, 410128, Changsha, China
| | - Ling Luo
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, 410128, Changsha, China
| | - Jialong He
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, 410128, Changsha, China
| | - Deyou Qiu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, 100091, Beijing, China
| | - Qi Tang
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, 410128, Changsha, China.
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Liu G, Liu F, Pan L, Wang H, Lu Y, Liu C, Yu S, Hu X. Agronomic, physiological and transcriptional characteristics provide insights into fatty acid biosynthesis in yellowhorn ( Xanthoceras sorbifolium Bunge) during fruit ripening. Front Genet 2024; 15:1325484. [PMID: 38356698 PMCID: PMC10864670 DOI: 10.3389/fgene.2024.1325484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 01/19/2024] [Indexed: 02/16/2024] Open
Abstract
Yellowhorn (Xanthoceras sorbifolium Bunge) is an oil-bearing tree species in northern China. In this study, we used yellowhorn from Heilongjiang to analyze the morphological and physiological changes of fruit development and conducted transcriptome sequencing. The results showed that the fruit experienced relatively slow growth from fertilization to DAF20 (20 days after flowering). From DAF40 to DAF60, the fruit entered an accelerated development stage, with a rapid increase in both transverse and longitudinal diameters, and the kernel contour developed completely at DAF40. From DAF60 to DAF80, the transverse and vertical diameters of the fruit developed slowly, and the overall measures remained stable until maturity. The soluble sugar, starch, and anthocyanin content gradually accumulated until reaching a peak at DAF80 and then rapidly decreased. RNA-seq analysis revealed differentially expressed genes (DEGs) in the seed coat and kernel, implying that seed components have different metabolite accumulation mechanisms. During the stages of seed kernel development, k-means clustering separated the DEGs into eight sub-classes, indicating gene expression shifts during the fruit ripening process. In subclass 8, the fatty acid biosynthesis pathway was enriched, suggesting that this class was responsible for lipid accumulation in the kernel. WGCNA revealed ten tissue-specific modules for the 12 samples among 20 modules. We identified 54 fatty acid biosynthesis pathway genes across the genome, of which 14 was quantified and confirmed by RT-qPCR. Most genes in the plastid synthesis stage showed high expression during the DAF40-DAF60 period, while genes in the endoplasmic reticulum synthesis stage showed diverse expression patterns. EVM0012847 (KCS) and EVM0002968 (HCD) showed similar high expression in the early stages and low expression in the late stages. EVM0022385 (HCD) exhibited decreased expression from DAF40 to DAF60 and then increased from DAF60 to DAF100. EVM0000575 (KCS) was increasingly expressed from DAF40 to DAF60 and then decreased from DAF60 to DAF100. Finally, we identified transcription factors (TFs) (HB-other, bHLH and ARF) that were predicted to bind to fatty acid biosynthesis pathway genes with significant correlations. These results are conducive to promoting the transcriptional regulation of lipid metabolism and the genetic improvement in terms of high lipid content of yellowhorn.
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Affiliation(s)
- Guan Liu
- State Key Laboratory of Tree Genetics and Breeding, College of Forestry, Northeast Forestry University, Harbin, China
- College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Fengjiao Liu
- College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Lin Pan
- College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Hanhui Wang
- State Key Laboratory of Tree Genetics and Breeding, College of Forestry, Northeast Forestry University, Harbin, China
| | - Yanan Lu
- State Key Laboratory of Tree Genetics and Breeding, College of Forestry, Northeast Forestry University, Harbin, China
| | - Changhua Liu
- College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Song Yu
- State Key Laboratory of Tree Genetics and Breeding, College of Forestry, Northeast Forestry University, Harbin, China
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, China
| | - Xiaohang Hu
- College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
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Zhang H, Wang X, Yang Z, Bai Y, Chen L, Wu T. Transcriptome analysis reveals the potential mechanism of the response to scale insects in Camellia sasanqua Thunb. BMC Genomics 2024; 25:106. [PMID: 38267855 PMCID: PMC10807073 DOI: 10.1186/s12864-024-09980-y] [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: 11/29/2023] [Accepted: 01/06/2024] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND Camellia sasanqua Thunb. is an essential woody ornamental plant. Our continuous observation found that scale insects often infest C. sasanqua all year round in Kunming, China, resulting in poor growth. Scientifically preventing and controlling the infestation of scale insects should be paid attention to, and the mechanism of scale insects influencing C. sasanqua should be used as the research basis. RESULTS The scale insect was identified as Pseudaulacaspis sasakawai Takagi. We analyzed transcriptome sequencing data from leaves of C. sasanqua infested with scale insects. A total of 1320 genes were either up-regulated or down-regulated and differed significantly in response to scale insects. GO (Gene Ontology) annotation analysis showed that the pathway of catalytic activity, binding, membrane part, cell part, and cellular process were affected. KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis showed that most DEGs (differentially expressed genes) involved in plant hormone signal transduction, MAPK signaling pathway, flavonoid biosynthesis, tropane, piperidine and pyridine alkaloid biosynthesis. We also observed that the expression of galactose metabolism and carotenoid biosynthesis were significantly influenced. In addition, qRT-PCR (quantitative real-time PCR) validated the expression patterns of DEGs, which showed an excellent agreement with the transcriptome sequencing. CONCLUSIONS Our transcriptomic analysis revealed that the C. sasanqua had an intricate resistance strategy to cope with scale insect attacks. After sensing the attack signal of scale insects, C. sasanqua activated the early signal MAPK (mitogen-activated protein kinase) to activate further transcription factors and Auxin, ET, JA, ABA, and other plant hormone signaling pathways, ultimately leading to the accumulation of lignin, scopolin, flavonoids and other secondary metabolites, produces direct and indirect resistance to scale insects. Our results suggested that it provided some potential resources of defense genes that would benefit the following resistance breeding in C. sasanqua to scale insects.
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Affiliation(s)
- Hongye Zhang
- School of Landscape Architecture and Horticulture Sciences, Southwest Forestry University, Kunming, 650224, China
| | - Xubo Wang
- Yunnan Biodiversity Research Institute, Southwest Forestry University, Kunming, 650224, China
| | - Ziyun Yang
- School of Landscape Architecture and Horticulture Sciences, Southwest Forestry University, Kunming, 650224, China
| | - Yan Bai
- School of Landscape Architecture and Horticulture Sciences, Southwest Forestry University, Kunming, 650224, China
| | - Longqing Chen
- School of Landscape Architecture and Horticulture Sciences, Southwest Forestry University, Kunming, 650224, China
| | - Tian Wu
- School of Landscape Architecture and Horticulture Sciences, Southwest Forestry University, Kunming, 650224, China.
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Tang Q, Wei S, Zheng X, Tu P, Tao F. APETALA2/ethylene-responsive factors in higher plant and their roles in regulation of plant stress response. Crit Rev Biotechnol 2024:1-19. [PMID: 38267262 DOI: 10.1080/07388551.2023.2299769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 11/30/2023] [Indexed: 01/26/2024]
Abstract
Plants, anchored throughout their life cycles, face a unique set of challenges from fluctuating environments and pathogenic assaults. Central to their adaptative mechanisms are transcription factors (TFs), particularly the AP2/ERF superfamily-one of the most extensive TF families unique to plants. This family plays instrumental roles in orchestrating diverse biological processes ranging from growth and development to secondary metabolism, and notably, responses to both biotic and abiotic stresses. Distinguished by the presence of the signature AP2 domain or its responsiveness to ethylene signals, the AP2/ERF superfamily has become a nexus of research focus, with increasing literature elucidating its multifaceted roles. This review provides a synoptic overview of the latest research advancements on the AP2/ERF family, spanning its taxonomy, structural nuances, prevalence in higher plants, transcriptional and post-transcriptional dynamics, and the intricate interplay in DNA-binding and target gene regulation. Special attention is accorded to the ethylene response factor B3 subgroup protein Pti5 and its role in stress response, with speculative insights into its functionalities and interaction matrix in tomatoes. The overarching goal is to pave the way for harnessing these TFs in the realms of plant genetic enhancement and novel germplasm development.
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Affiliation(s)
- Qiong Tang
- College of Standardization, China Jiliang University, Hangzhou, China
| | - Sishan Wei
- College of Standardization, China Jiliang University, Hangzhou, China
| | - Xiaodong Zheng
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, China
| | - Pengcheng Tu
- Department of Environmental Health, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Fei Tao
- College of Standardization, China Jiliang University, Hangzhou, China
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Joshi P, Soni P, Sharma V, Manohar SS, Kumar S, Sharma S, Pasupuleti J, Vadez V, Varshney RK, Pandey MK, Puppala N. Genome-Wide Mapping of Quantitative Trait Loci for Yield-Attributing Traits of Peanut. Genes (Basel) 2024; 15:140. [PMID: 38397130 PMCID: PMC10888419 DOI: 10.3390/genes15020140] [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: 11/14/2023] [Revised: 01/09/2024] [Accepted: 01/19/2024] [Indexed: 02/25/2024] Open
Abstract
Peanuts (Arachis hypogaea L.) are important high-protein and oil-containing legume crops adapted to arid to semi-arid regions. The yield and quality of peanuts are complex quantitative traits that show high environmental influence. In this study, a recombinant inbred line population (RIL) (Valencia-C × JUG-03) was developed and phenotyped for nine traits under two environments. A genetic map was constructed using 1323 SNP markers spanning a map distance of 2003.13 cM. Quantitative trait loci (QTL) analysis using this genetic map and phenotyping data identified seventeen QTLs for nine traits. Intriguingly, a total of four QTLs, two each for 100-seed weight (HSW) and shelling percentage (SP), showed major and consistent effects, explaining 10.98% to 14.65% phenotypic variation. The major QTLs for HSW and SP harbored genes associated with seed and pod development such as the seed maturation protein-encoding gene, serine-threonine phosphatase gene, TIR-NBS-LRR gene, protein kinase superfamily gene, bHLH transcription factor-encoding gene, isopentyl transferase gene, ethylene-responsive transcription factor-encoding gene and cytochrome P450 superfamily gene. Additionally, the identification of 76 major epistatic QTLs, with PVE ranging from 11.63% to 72.61%, highlighted their significant role in determining the yield- and quality-related traits. The significant G × E interaction revealed the existence of the major role of the environment in determining the phenotype of yield-attributing traits. Notably, the seed maturation protein-coding gene in the vicinity of major QTLs for HSW can be further investigated to develop a diagnostic marker for HSW in peanut breeding. This study provides understanding of the genetic factor governing peanut traits and valuable insights for future breeding efforts aimed at improving yield and quality.
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Affiliation(s)
- Pushpesh Joshi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (P.J.); (V.S.); (S.S.M.); (J.P.); (R.K.V.)
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut 250004, India;
| | - Pooja Soni
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (P.J.); (V.S.); (S.S.M.); (J.P.); (R.K.V.)
| | - Vinay Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (P.J.); (V.S.); (S.S.M.); (J.P.); (R.K.V.)
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut 250004, India;
| | - Surendra S. Manohar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (P.J.); (V.S.); (S.S.M.); (J.P.); (R.K.V.)
| | - Sampath Kumar
- Agricultural Research Station, Andhra Pradesh Agricultural University, Anantapur 515591, India;
| | - Shailendra Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut 250004, India;
| | - Janila Pasupuleti
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (P.J.); (V.S.); (S.S.M.); (J.P.); (R.K.V.)
| | - Vincent Vadez
- Institut de Recherche pour le Development (IRD), Université de Montpellier, Unité Mixte de Recherche Diversité et Adaptation des Espèces (UMR DIADE), 34394 Montpellier, France;
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (P.J.); (V.S.); (S.S.M.); (J.P.); (R.K.V.)
- Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
| | - Manish K. Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (P.J.); (V.S.); (S.S.M.); (J.P.); (R.K.V.)
| | - Naveen Puppala
- Agricultural Science Center at Clovis, New Mexico State University, Clovis, NM 88101, USA
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Su J, Zhan N, Cheng X, Song S, Dong T, Ge X, Duan H. Genome-Wide Analysis of Cotton MYB Transcription Factors and the Functional Validation of GhMYB in Response to Drought Stress. PLANT & CELL PHYSIOLOGY 2024; 65:79-94. [PMID: 37847105 DOI: 10.1093/pcp/pcad125] [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: 06/29/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 10/18/2023]
Abstract
MYB transcription factors play important roles during abiotic stress responses in plants. However, little is known about the accurate systematic analysis of MYB genes in the four cotton species, Gossypium hirsutum, G. barbadense, G. arboreum and G. raimondii. Herein, we performed phylogenetic analysis and showed that cotton MYBs and Arabidopsis MYBs were clustered in the same subfamilies for each species. The identified cotton MYBs were distributed unevenly on chromosomes in various densities for each species, wherein genome-wide tandem and segment duplications were the main driving force of MYB family expansion. Synteny analysis suggested that the abundant collinearity pairs of MYBs were identified between G. hirsutum and the other three species, and that they might have undergone strong purification selection. Characteristics of conserved motifs, along with their consensus sequence, promoter cis elements and gene structure, revealed that MYB proteins might be highly conserved in the same subgroups for each species. Subsequent analysis of differentially expressed genes and expression patterns indicated that most GhMYBs might be involved in response to drought (especially) and salt stress, which was supported by the expression levels of nine GhMYBs using real-time quantitative PCR. Finally, we performed a workflow that combined virus-induced gene silencing and the heterologous transformation of Arabidopsis, which confirmed the positive roles of GhMYBs under drought conditions, as validated by determining the drought-tolerant phenotypes, damage index and/or water loss rate. Collectively, our findings not only expand our understanding of the relationships between evolution and function of MYB genes, but they also provide candidate genes for cotton breeding.
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Affiliation(s)
- Jiuchang Su
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
- Henan International Joint Laboratory of Aquatic Toxicology and Health Protection, College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Na Zhan
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Xiaoru Cheng
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Shanglin Song
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Tianyu Dong
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Xiaoyang Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Hongying Duan
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
- Henan International Joint Laboratory of Aquatic Toxicology and Health Protection, College of Life Sciences, Henan Normal University, Xinxiang 453007, China
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