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Liu H, Liu Z, Qin A, Zhou Y, Sun S, Liu Y, Hu M, Yang J, Sun X. Mitochondrial ATP Synthase beta-Subunit Affects Plastid Retrograde Signaling in Arabidopsis. Int J Mol Sci 2024; 25:7829. [PMID: 39063070 PMCID: PMC11277312 DOI: 10.3390/ijms25147829] [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: 05/21/2024] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
Plastid retrograde signaling plays a key role in coordinating the expression of plastid genes and photosynthesis-associated nuclear genes (PhANGs). Although plastid retrograde signaling can be substantially compromised by mitochondrial dysfunction, it is not yet clear whether specific mitochondrial factors are required to regulate plastid retrograde signaling. Here, we show that mitochondrial ATP synthase beta-subunit mutants with decreased ATP synthase activity are impaired in plastid retrograde signaling in Arabidopsis thaliana. Transcriptome analysis revealed that the expression levels of PhANGs were significantly higher in the mutants affected in the AT5G08670 gene encoding the mitochondrial ATP synthase beta-subunit, compared to wild-type (WT) seedlings when treated with lincomycin (LIN) or norflurazon (NF). Further studies indicated that the expression of nuclear genes involved in chloroplast and mitochondrial retrograde signaling was affected in the AT5G08670 mutant seedlings treated with LIN. These changes might be linked to the modulation of some transcription factors (TFs), such as LHY (Late Elongated Hypocotyl), PIF (Phytochrome-Interacting Factors), MYB, WRKY, and AP2/ERF (Ethylene Responsive Factors). These findings suggest that the activity of mitochondrial ATP synthase significantly influences plastid retrograde signaling.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Xuwu Sun
- State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China; (H.L.); (Z.L.); (A.Q.); (Y.Z.); (S.S.); (Y.L.); (M.H.); (J.Y.)
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Rehman A, Tian C, Li X, Wang X, Li H, He S, Jiao Z, Qayyum A, Du X, Peng Z. GhiPLATZ17 and GhiPLATZ22, zinc-dependent DNA-binding transcription factors, promote salt tolerance in upland cotton. PLANT CELL REPORTS 2024; 43:140. [PMID: 38740586 DOI: 10.1007/s00299-024-03178-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: 01/29/2024] [Accepted: 02/19/2024] [Indexed: 05/16/2024]
Abstract
KEY MESSAGE The utilization of transcriptome analysis, functional validation, VIGS, and DAB techniques have provided evidence that GhiPLATZ17 and GhiPLATZ22 play a pivotal role in improving the salt tolerance of upland cotton. PLATZ (Plant AT-rich sequences and zinc-binding proteins) are known to be key regulators in plant growth, development, and response to salt stress. In this study, we comprehensively analyzed the PLATZ family in ten cotton species in response to salinity stress. Gossypium herbaceum boasts 25 distinct PLATZ genes, paralleled by 24 in G. raimondii, 25 in G. arboreum, 46 in G. hirsutum, 48 in G. barbadense, 43 in G. tomentosum, 67 in G. mustelinum, 60 in G. darwinii, 46 in G. ekmanianum, and a total of 53 PLATZ genes attributed to G. stephensii. The PLATZ gene family shed light on the hybridization and allopolyploidy events that occurred during the evolutionary history of allotetraploid cotton. Ka/Ks analysis suggested that the PLATZ gene family underwent intense purifying selection during cotton evolution. Analysis of synteny and gene collinearity revealed a complex pattern of segmental and dispersed duplication events to expand PLATZ genes in cotton. Cis-acting elements and gene expressions revealed that GhiPLATZ exhibited salt stress resistance. Transcriptome analysis, functional validation, virus-induced gene silencing (VIGS), and diaminobenzidine staining (DAB) demonstrated that GhiPLATZ17 and GhiPLATZ22 enhance salt tolerance in upland cotton. The study can potentially advance our understanding of identifying salt-resistant genes in cotton.
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Affiliation(s)
- Abdul Rehman
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450001, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, 455000, Henan, China
| | - Chunyan Tian
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450001, China
| | - Xiawen Li
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450001, China
| | - Xiaoyang Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, 455000, Henan, China
| | - Hongge Li
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450001, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, 455000, Henan, China
| | - Shoupu He
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450001, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, 455000, Henan, China
| | - Zhen Jiao
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450001, China
| | - Abdul Qayyum
- Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan, 66000, Pakistan
| | - Xiongming Du
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450001, China.
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, 455000, Henan, China.
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572025, China.
| | - Zhen Peng
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450001, China.
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, 455000, Henan, China.
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572025, China.
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Sun M, Yan H, Zhang A, Jin Y, Lin C, Luo L, Wu B, Fan Y, Tian S, Cao X, Wang Z, Luo J, Yang Y, Jia J, Zhou P, Tang Q, Jones CS, Varshney RK, Srivastava RK, He M, Xie Z, Wang X, Feng G, Nie G, Huang D, Zhang X, Zhu F, Huang L. Milletdb: a multi-omics database to accelerate the research of functional genomics and molecular breeding of millets. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2348-2357. [PMID: 37530223 PMCID: PMC10579705 DOI: 10.1111/pbi.14136] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 07/01/2023] [Accepted: 07/17/2023] [Indexed: 08/03/2023]
Abstract
Millets are a class of nutrient-rich coarse cereals with high resistance to abiotic stress; thus, they guarantee food security for people living in areas with extreme climatic conditions and provide stress-related genetic resources for other crops. However, no platform is available to provide a comprehensive and systematic multi-omics analysis for millets, which seriously hinders the mining of stress-related genes and the molecular breeding of millets. Here, a free, web-accessible, user-friendly millets multi-omics database platform (Milletdb, http://milletdb.novogene.com) has been developed. The Milletdb contains six millets and their one related species genomes, graph-based pan-genomics of pearl millet, and stress-related multi-omics data, which enable Milletdb to be the most complete millets multi-omics database available. We stored GWAS (genome-wide association study) results of 20 yield-related trait data obtained under three environmental conditions [field (no stress), early drought and late drought] for 2 years in the database, allowing users to identify stress-related genes that support yield improvement. Milletdb can simplify the functional genomics analysis of millets by providing users with 20 different tools (e.g., 'Gene mapping', 'Co-expression', 'KEGG/GO Enrichment' analysis, etc.). On the Milletdb platform, a gene PMA1G03779.1 was identified through 'GWAS', which has the potential to modulate yield and respond to different environmental stresses. Using the tools provided by Milletdb, we found that the stress-related PLATZs TFs (transcription factors) family expands in 87.5% of millet accessions and contributes to vegetative growth and abiotic stress responses. Milletdb can effectively serve researchers in the mining of key genes, genome editing and molecular breeding of millets.
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Affiliation(s)
- Min Sun
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Haidong Yan
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
- School of Plant and Environmental SciencesVirginia TechBlacksburgVirginiaUSA
- Department of GeneticsUniversity of GeorgiaAthensGeorgiaUSA
| | - Aling Zhang
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Yarong Jin
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Chuang Lin
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Lin Luo
- College of Life SciencesFujian Agriculture and Forestry UniversityFujianChina
| | - Bingchao Wu
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Yuhang Fan
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Shilin Tian
- Novogene Bioinformatics InstituteBeijingChina
- Department of Ecology, Hubei Key Laboratory of Cell Homeostasis, College of Life SciencesWuhan UniversityWuhanChina
| | | | - Zan Wang
- College of Grassland Science and TechnologyChina Agricultural UniversityBeijingChina
| | - Jinchan Luo
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Yuchen Yang
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Jiyuan Jia
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Puding Zhou
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Qianzi Tang
- College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Chris Stephen Jones
- Feed and Forage DevelopmentInternational Livestock Research InstituteNairobiKenya
| | - Rajeev K. Varshney
- Center of Excellence in Genomics and Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
- Murdoch's Centre for Crop and Food Innovation, Food Futures InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Rakesh K. Srivastava
- Center of Excellence in Genomics and Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
| | - Min He
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduSichuanChina
| | - Zheni Xie
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
- College of Agro‐Grassland ScienceNanjing Agricultural UniversityNanjingChina
| | - Xiaoshan Wang
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Guangyan Feng
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Gang Nie
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Dejun Huang
- Herbivorous Livestock Research InstituteChongqing Academy of Animal SciencesChongqingChina
| | - Xinquan Zhang
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Fangjie Zhu
- College of Life SciencesFujian Agriculture and Forestry UniversityFujianChina
| | - Linkai Huang
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduSichuanChina
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Zhang X, Lan Y, Wang L, Liu H, Jiang N, He W, Yan H, Wu M, Xiang Y. Whole-genome identification and multiple abiotic stresses expression pattern profiling analysis of PLATZ transcription factor family members in Pecan (Carya illinoensis). Int J Biol Macromol 2023; 248:125959. [PMID: 37495003 DOI: 10.1016/j.ijbiomac.2023.125959] [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: 03/10/2023] [Revised: 07/03/2023] [Accepted: 07/13/2023] [Indexed: 07/28/2023]
Abstract
Plant AT-rich sequence and zinc-binding (PLATZ), as a plant-specific transcription factor, have been identified and studied in a variety of plants. However, there are no reports about PLATZ proteins in Carya illinoensis (pecan). Here, 24 C. illinoensis CiPLATZs have been identified and divided into 4 groups. Gene structure, motif composition, conserved domain and cis-acting elements analysis indicated that the PLATZ gene family was highly conserved. Transcriptome data combined with qRT-PCR analysis revealed that CiPLATZ6, CiPLATZ12, CiPLATZ13, CiPLATZ14 and CiPLATZ23 were highly expressed in multiple tissues of C. illinoensis and strongly responded to drought, salt and heat stress. Among them, CiPLATZ6, CiPLATZ12 and CiPLATZ23 were all located in the nucleus and had no transcriptional autoactivation ability in yeast cells, and acted as transcriptional suppressors in plants. In addition, the CiPLATZ23-overexpressing transgenic Arabidopsis thaliana showed enhanced tolerance to drought. Measurements of physiological indicators and analysis of stress-related genes expression levels in transgenic A. thaliana were used to support this conclusion. The results of this study are helpful to understand the structural feature and function of CiPLATZs, and provide candidate genes for molecular breeding of drought tolerance of C. illinoensis.
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Affiliation(s)
- Xiaoyue Zhang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China
| | - Yangang Lan
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China
| | - Linna Wang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China
| | - Hongxia Liu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China
| | - Nianqin Jiang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China
| | - Wei He
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China
| | - Hanwei Yan
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China
| | - Min Wu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China
| | - Yan Xiang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China.
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5
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Qi J, Wang H, Wu X, Noman M, Wen Y, Li D, Song F. Genome-wide characterization of the PLATZ gene family in watermelon (Citrullus lanatus L.) with putative functions in biotic and abiotic stress response. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107854. [PMID: 37356384 DOI: 10.1016/j.plaphy.2023.107854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/19/2023] [Accepted: 06/18/2023] [Indexed: 06/27/2023]
Abstract
Plant AT-rich sequence and zinc-binding (PLATZ) proteins are plant-specific transcription factors involved in growth, development, and stress responses. Here, we conducted a genome-wide characterization of the watermelon ClPLATZ family and examined its expression responsiveness to defense hormones and pathogen infection along with putative functions in biotic and abiotic stress responses. The watermelon genome contains 12 putative ClPLATZ genes, encoding proteins with a characteristic PLATZ domain, and their promoters contain various cis-elements related to plant growth, development, phytohormones and stress response. The ClPLATZ genes, except ClPLATZ6, are differentially expressed in response to defense hormones (e.g., salicylic acid and methyl jasmonate) and fungal infections caused by Fusarium oxysporum f. sp. niveum and Stagonosporopsis cucurbitacearum. Most ClPLATZ proteins interact with other proteins (viz., ClDP, ClRPT2a, and ClRPC53). Among ClPLATZ proteins, ClPLATZ8, 9, 10, and 11 are predominately localized in the nucleus. ClPLATZ3 and 8 positively, but ClPLATZ11 negatively regulate resistance against Pseudomonas syringe pv. tomato DC3000 in transgenic Arabidopsis lines. ClPLATZ8 and 11 positively regulate stress tolerance to NaCl and mannitol during seed germination in transgenic Arabidopsis. In conclusion, the characterization of the ClPLATZ family provides insights into the biological functions of ClPLATZ genes in growth, development, and stress response in watermelon. Further, the involvement of certain ClPLATZ genes in biotic and abiotic stress response in transgenic Arabidopsis suggests their potential application in engineering stress-tolerant crops.
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Affiliation(s)
- Jiahui Qi
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Hui Wang
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Xinyi Wu
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Muhammad Noman
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Ya Wen
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Dayong Li
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Fengming Song
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
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Zhang L, Yang T, Wang Z, Zhang F, Li N, Jiang W. Genome-Wide Identification and Expression Analysis of the PLATZ Transcription Factor in Tomato. PLANTS (BASEL, SWITZERLAND) 2023; 12:2632. [PMID: 37514247 PMCID: PMC10384190 DOI: 10.3390/plants12142632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/07/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023]
Abstract
The PLATZ (plant AT protein and zinc-binding protein) transcription factor family is involved in the regulation of plant growth and development and plant stress response. In this study, 24 SlPLATZs were identified from the cultivated tomato genome and classified into four groups based on the similarity of conserved patterns among members of the same subfamily. Fragment duplication was an important way to expand the SlPLATZ gene family in tomatoes, and the sequential order of tomato PLATZ genes in the evolution of monocotyledonous and dicotyledonous plants and the roles they played were hypothesized. Expression profiles based on quantitative real-time reverse transcription PCR showed that SlPLATZ was involved in the growth of different tissues in tomatoes. SlPLATZ21 acts mainly in the leaves. SlPLATZ9, SlPLATZ21, and SlPLATZ23 were primarily involved in the red ripening, expanding, and mature green periods of fruit, respectively. In addition, SlPLATZ1 was found to play an important role in salt stress. This study will lay the foundation for the analysis of the biological functions of SlPLATZ genes and will also provide a theoretical basis for the selection and breeding of new tomato varieties and germplasm innovation.
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Affiliation(s)
- Lifang Zhang
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Tao Yang
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Zepeng Wang
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Fulin Zhang
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Ning Li
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Weijie Jiang
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Li J, Zhao Y, Zhang Y, Ye F, Hou Z, Zhang Y, Hao L, Li G, Shao J, Tan M. Genome-wide analysis of MdPLATZ genes and their expression during axillary bud outgrowth in apple (Malus domestica Borkh.). BMC Genomics 2023; 24:329. [PMID: 37322464 DOI: 10.1186/s12864-023-09399-x] [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: 01/29/2023] [Accepted: 05/23/2023] [Indexed: 06/17/2023] Open
Abstract
BACKGROUND Branching is a plastic character that affects plant architecture and spatial structure. The trait is controlled by a variety of plant hormones through coordination with environmental signals. Plant AT-rich sequence and zinc-binding protein (PLATZ) is a transcription factor that plays an important role in plant growth and development. However, systematic research on the role of the PLATZ family in apple branching has not been conducted previously. RESULTS In this study, a total of 17 PLATZ genes were identified and characterized from the apple genome. The 83 PLATZ proteins from apple, tomato, Arabidopsis, rice, and maize were classified into three groups based on the topological structure of the phylogenetic tree. The phylogenetic relationships, conserved motifs, gene structure, regulatory cis-acting elements, and microRNAs of the MdPLATZ family members were predicted. Expression analysis revealed that MdPLATZ genes exhibited distinct expression patterns in different tissues. The expression patterns of the MdPLATZ genes were systematically investigated in response to treatments that impact apple branching [thidazuron (TDZ) and decapitation]. The expression of MdPLATZ1, 6, 7, 8, 9, 15, and 16 was regulated during axillary bud outgrowth based on RNA-sequencing data obtained from apple axillary buds treated by decapitation or exogenous TDZ application. Quantitative real-time PCR analysis showed that MdPLATZ6 was strongly downregulated in response to the TDZ and decapitation treatments, however, MdPLATZ15 was significantly upregulated in response to TDZ, but exhibited little response to decapitation. Furthermore, the co-expression network showed that PLATZ might be involved in shoot branching by regulating branching-related genes or mediating cytokinin or auxin pathway. CONCLUSION The results provide valuable information for further functional investigation of MdPLATZ genes in the control of axillary bud outgrowth in apple.
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Affiliation(s)
- Jiuyang Li
- College of Horticulture, Hebei Agricultural University, Hebei, 071000, China
| | - Yongliang Zhao
- College of Horticulture, Hebei Agricultural University, Hebei, 071000, China
| | - Yaohui Zhang
- College of Horticulture, Hebei Agricultural University, Hebei, 071000, China
| | - Feng Ye
- College of Horticulture, Hebei Agricultural University, Hebei, 071000, China
| | - Zhengcun Hou
- College of Horticulture, Hebei Agricultural University, Hebei, 071000, China
| | - Yuhang Zhang
- College of Horticulture, Hebei Agricultural University, Hebei, 071000, China
| | - Longjie Hao
- College of Horticulture, Hebei Agricultural University, Hebei, 071000, China
| | - Guofang Li
- College of Horticulture, Hebei Agricultural University, Hebei, 071000, China
| | - Jianzhu Shao
- College of Horticulture, Hebei Agricultural University, Hebei, 071000, China.
| | - Ming Tan
- College of Horticulture, Hebei Agricultural University, Hebei, 071000, China.
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8
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Boatwright JL, Sapkota S, Kresovich S. Functional genomic effects of indels using Bayesian genome-phenome wide association studies in sorghum. Front Genet 2023; 14:1143395. [PMID: 37065477 PMCID: PMC10102435 DOI: 10.3389/fgene.2023.1143395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/20/2023] [Indexed: 04/03/2023] Open
Abstract
High-throughput genomic and phenomic data have enhanced the ability to detect genotype-to-phenotype associations that can resolve broad pleiotropic effects of mutations on plant phenotypes. As the scale of genotyping and phenotyping has advanced, rigorous methodologies have been developed to accommodate larger datasets and maintain statistical precision. However, determining the functional effects of associated genes/loci is expensive and limited due to the complexity associated with cloning and subsequent characterization. Here, we utilized phenomic imputation of a multi-year, multi-environment dataset using PHENIX which imputes missing data using kinship and correlated traits, and we screened insertions and deletions (InDels) from the recently whole-genome sequenced Sorghum Association Panel for putative loss-of-function effects. Candidate loci from genome-wide association results were screened for potential loss of function using a Bayesian Genome-Phenome Wide Association Study (BGPWAS) model across both functionally characterized and uncharacterized loci. Our approach is designed to facilitate in silico validation of associations beyond traditional candidate gene and literature-search approaches and to facilitate the identification of putative variants for functional analysis and reduce the incidence of false-positive candidates in current functional validation methods. Using this Bayesian GPWAS model, we identified associations for previously characterized genes with known loss-of-function alleles, specific genes falling within known quantitative trait loci, and genes without any previous genome-wide associations while additionally detecting putative pleiotropic effects. In particular, we were able to identify the major tannin haplotypes at the Tan1 locus and effects of InDels on the protein folding. Depending on the haplotype present, heterodimer formation with Tan2 was significantly affected. We also identified major effect InDels in Dw2 and Ma1, where proteins were truncated due to frameshift mutations that resulted in early stop codons. These truncated proteins also lost most of their functional domains, suggesting that these indels likely result in loss of function. Here, we show that the Bayesian GPWAS model is able to identify loss-of-function alleles that can have significant effects upon protein structure and folding as well as multimer formation. Our approach to characterize loss-of-function mutations and their functional repercussions will facilitate precision genomics and breeding by identifying key targets for gene editing and trait integration.
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Affiliation(s)
- J. Lucas Boatwright
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
- *Correspondence: J. Lucas Boatwright,
| | - Sirjan Sapkota
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
| | - Stephen Kresovich
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
- Feed the Future Innovation Lab for Crop Improvement, Cornell University, Ithaca, NY, United States
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Genome-wide identification of PLATZ genes related to cadmium tolerance in Populus trichocarpa and characterization of the role of PtPLATZ3 in phytoremediation of cadmium. Int J Biol Macromol 2023; 228:732-743. [PMID: 36563811 DOI: 10.1016/j.ijbiomac.2022.12.176] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/03/2022] [Accepted: 12/10/2022] [Indexed: 12/24/2022]
Abstract
Plant AT-rich sequence and zinc-binding (PLATZ) proteins are a class of plant-specific zinc finger transcription factors that perform critical functions in plant development and resistance. However, the function of PLATZs in heavy metal tolerance has not yet been investigated. Moreover, only a few PLATZ proteins have been functionally characterized in tree species. In this study, we identified 18 PtPLATZ genes in Populus trichocarpa, an important woody model plant, and classified them into five groups. PtPLATZ genes attributed to the same clade usually possess similar exon-intron structures containing two or three introns, as well as a similar motif composition. Furthermore, chromosomal location analysis indicated an uneven distribution of PtPLATZ genes on 13 of the 19 Populus chromosomes. Promoter cis-acting element prediction and gene expression analysis showed that PtPLATZ genes were highly responsive to heavy metal stress. Heterologous yeast expression revealed that PtPLATZ1, PtPLATZ2, PtPLATZ3, PtPLATZ4, PtPLATZ8 and PtPLATZ9 are significantly involved in Cd tolerance. In addition, transgenic expression of PtPLATZ3 significantly enhanced Cd tolerance and accumulation, slowed the decline in chlorophyll content, maintained membrane integrity in Populus, and increased the expression of genes related to Cd tolerance and accumulation. In conclusion, our results suggest the potential of PtPLATZ3 to improve Cd tolerance and accumulation in Populus, which is of great significance for phytoremediation.
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Genome-Wide Identification and Phylogenetic and Expression Analyses of the PLATZ Gene Family in Medicago sativa L. Int J Mol Sci 2023; 24:ijms24032388. [PMID: 36768707 PMCID: PMC9916490 DOI: 10.3390/ijms24032388] [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: 12/12/2022] [Revised: 01/10/2023] [Accepted: 01/18/2023] [Indexed: 01/27/2023] Open
Abstract
The PLATZ family is a novel class of plant-specific zinc finger transcription factors with important roles in plant growth and development and abiotic stress responses. PLATZ members have been identified in many plants, including Oryza sativa, Zea mays, Triticum aestivum, Fagopyrum tataricum, and Arabidopsis thaliana; however, due to the complexity of the alfalfa reference genome, the members of the PLATZ gene family in alfalfa (Medicago sativa L.) have not been systematically identified and analyzed. In this study, 55 Medicago sativa PLATZ genes (MsPLATZs) were identified in the alfalfa "Xinjiangdaye" reference genome. Basic bioinformatic analysis was performed, including the characterization of sequence lengths, protein molecular weights, genomic positions, and conserved motifs. Expression analysis reveals that 7 MsPLATZs are tissue-specifically expressed, and 10 MsPLATZs are expressed in all examined tissues. The transcriptomic expression of these genes is obvious, indicating that these MsPLATZs have different functions in the growth and development of alfalfa. Based on transcriptome data analysis and real-time quantitative PCR (RT-qPCR), we identified 22, 22, and 21 MsPLATZ genes that responded to salt, cold, and drought stress, respectively, with 20 MsPLATZs responding to all three stresses. This study lays a foundation for further exploring the functions of MsPLATZs, and provides ideas for the improvement of alfalfa varieties and germplasm innovation.
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Wai AH, Rahman MM, Waseem M, Cho LH, Naing AH, Jeon JS, Lee DJ, Kim CK, Chung MY. Comprehensive Genome-Wide Analysis and Expression Pattern Profiling of PLATZ Gene Family Members in Solanum Lycopersicum L. under Multiple Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11223112. [PMID: 36432841 PMCID: PMC9697139 DOI: 10.3390/plants11223112] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 05/29/2023]
Abstract
PLATZ (plant AT-rich sequence and zinc-binding) family proteins with two conserved zinc-dependent DNA-binding motifs are transcription factors specific to the plant kingdom. The functions of PLATZ proteins in growth, development, and adaptation to multiple abiotic stresses have been investigated in various plant species, but their role in tomato has not been explored yet. In the present work, 20 non-redundant Solanum lycopersicum PLATZ (SlPLATZ) genes with three segmentally duplicated gene pairs and four tandemly duplicated gene pairs were identified on eight tomato chromosomes. The comparative modeling and gene ontology (GO) annotations of tomato PLATZ proteins indicated their probable roles in defense response, transcriptional regulation, and protein metabolic processes as well as their binding affinity for various ligands, including nucleic acids, peptides, and zinc. SlPLATZ10 and SlPLATZ17 were only expressed in 1 cm fruits and flowers, respectively, indicating their preferential involvement in the development of these organs. The expression of SlPLATZ1, SlPLATZ12, and SlPLATZ19 was up- or down-regulated following exposure to various abiotic stresses, whereas that of SlPLATZ11 was induced under temperature stresses (i.e., cold and heat stress), revealing their probable function in the abiotic stress tolerance of tomato. Weighted gene co-expression network analysis corroborated the aforementioned findings by spotlighting the co-expression of several stress-associated genes with SlPLATZ genes. Confocal fluorescence microscopy revealed the localization of SlPLATZ−GFP fusion proteins in the nucleus, hinting at their functions as transcription factors. These findings provide a foundation for a better understanding of the structure and function of PLATZ genes and should assist in the selection of potential candidate genes involved in the development and abiotic stress adaptation in tomato.
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Affiliation(s)
- Antt Htet Wai
- Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon 57922, Republic of Korea
- Department of Biology, Yangon University of Education, Kamayut Township 11041, Yangon Region, Myanmar
| | - Md Mustafizur Rahman
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Muhammad Waseem
- Department of Botany, University of Narowal, Narowal 51600, Pakistan
| | - Lae-Hyeon Cho
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang-si 50463, Gyeongsangnam-do, Republic of Korea
| | - Aung Htay Naing
- Department of Horticulture, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jong-Seong Jeon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Do-jin Lee
- Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon 57922, Republic of Korea
| | - Chang-Kil Kim
- Department of Horticulture, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Mi-Young Chung
- Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon 57922, Republic of Korea
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12
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Wu Z, Qiu H, Tian Z, Liu C, Qin M, Li W, Yang P, Wen Y, Tian B, Wei F, Zhou Z, Lei Z, Hou J. Uncovering the genetic basis of gluten aggregation parameters by genome-wide association analysis in wheat (Triticum aestivum L.) using GlutoPeak. BMC PLANT BIOLOGY 2022; 22:493. [PMID: 36271339 PMCID: PMC9585721 DOI: 10.1186/s12870-022-03874-5] [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: 03/11/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Numerous studies have shown that gluten aggregation properties directly affect the processing quality of wheat, however, the genetic basis of gluten aggregation properties were rarely reported. RESULTS To explore the genetic basis of gluten aggregation properties in wheat, an association population consisted with 207 wheat genotypes were constructed for evaluating nine parameters of aggregation properties on GlutoPeak across three-year planting seasons. A total of 940 significant SNPs were detected for 9 GlutoPeak parameters through genome-wide association analysis (GWAS). Finally, these SNPs were integrated to 68 non-redundant QTL distributed on 20 chromosomes and 54 QTL was assigned as pleiotropic loci which accounting for multiple parameters of gluten aggregation property. Furthermore, the peak SNPs representing 54 QTL domonstrated additive effect on all the traits. There was a significant positive correlation between the number of favorable alleles and the phenotypic values of each parameter. Peak SNPs of two novel QTL, q3AL.2 and q4DL, which contributing to both PMT (peak maximum time) and A3 (area from the first minimum to torque 15 s before the maximum torque) parameters, were selected for KASP (Kompetitive Allele Specific PCR) markers development and the KASP markers can be used for effectively evaluating the quality of gluten aggregation properties in the association population. CONCLUSION The rapid and efficient GlutoPeak method for gluten measurement can be used for early selection of wheat breeding. This study revealed the genetic loci related to GlutoPeak parameters in association population, which would be helpful to develop wheat elite lines with improved gluten aggregation through molecular marker-assisted breeding.
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Affiliation(s)
- Zhengqing Wu
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Postgraduate T & R Base of Zhengzhou University, Zhengzhou, 450002, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Hongxia Qiu
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Postgraduate T & R Base of Zhengzhou University, Zhengzhou, 450002, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Zhaoran Tian
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Postgraduate T & R Base of Zhengzhou University, Zhengzhou, 450002, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Congcong Liu
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Postgraduate T & R Base of Zhengzhou University, Zhengzhou, 450002, China
| | - Maomao Qin
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Postgraduate T & R Base of Zhengzhou University, Zhengzhou, 450002, China
| | - Wenxu Li
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Postgraduate T & R Base of Zhengzhou University, Zhengzhou, 450002, China
| | - Pan Yang
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Postgraduate T & R Base of Zhengzhou University, Zhengzhou, 450002, China
| | - Yao Wen
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Baoming Tian
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Postgraduate T & R Base of Zhengzhou University, Zhengzhou, 450002, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Fang Wei
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Postgraduate T & R Base of Zhengzhou University, Zhengzhou, 450002, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Zhengfu Zhou
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Postgraduate T & R Base of Zhengzhou University, Zhengzhou, 450002, China.
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China.
- Shennong Laboratory, Zhengzhou, 450002, Henan, China.
| | - Zhensheng Lei
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Postgraduate T & R Base of Zhengzhou University, Zhengzhou, 450002, China.
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China.
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.
- Shennong Laboratory, Zhengzhou, 450002, Henan, China.
| | - Jinna Hou
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Postgraduate T & R Base of Zhengzhou University, Zhengzhou, 450002, China.
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China.
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13
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Thabet SG, Alomari DZ, Börner A, Brinch-Pedersen H, Alqudah AM. Elucidating the genetic architecture controlling antioxidant status and ionic balance in barley under salt stress. PLANT MOLECULAR BIOLOGY 2022; 110:287-300. [PMID: 35918559 DOI: 10.1007/s11103-022-01302-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
Association genetic analysis empowered us to identify candidate genes underlying natural variation of morpho-physiological, antioxidants, and grain yield-related traits in barley. Novel intriguing genomic regions were identified and dissected. Salinity stress is one of the abiotic stresses that influence the morpho-physiological, antioxidants, and yield-related traits in crop plants. The plants of a core set of 138 diverse barley accessions were analyzed after exposure to salt stress under field conditions during the reproductive phase. A genome-wide association scan (GWAS) was then conducted using 19,276 single nucleotide polymorphisms (SNPs) to uncover the genetic basis of morpho-physiological and grain-related traits. A wide range of responses to salt stress by the accessions was explored in the current study. GWAS detected 263 significantly associated SNPs with the antioxidants, K+/Na+ content ratio, and agronomic traits. Five genomic regions harbored interesting putative candidate genes within LD ± 1.2 Mbp. Choromosome 2H harbored many candidate genes associated with the antioxidants ascorbic acid (AsA) and glutathione (GSH), such as superoxide dismutase (SOD), ascorbate peroxidase (APX), and glutathione reductase (GR), under salt stress. Markedly, an A:C SNP at 153,773,211 bp on chromosome 7H is located inside the gene HORVU.MOREX.r3.7HG0676830 (153,772,300-153,774,057 bp) that was annotated as L-gulonolactone oxidase, regulating the natural variation of SOD_S and APX_S. The allelic variation at this SNP reveals a negative selection of accessions carrying the C allele, predominantly found in six-rowed spring landraces originating from Far-, Near-East, and central Asia carrying photoperiod sensitive alleles having lower activity of enzymatic antioxidants. The SNP-trait associations detected in the current study constitute a benchmark for developing molecular selection tools for antioxidant compound selection in barley.
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Affiliation(s)
- Samar G Thabet
- Department of Botany, Faculty of Science, Fayoum University, 63514, Fayoum, Egypt
| | - Dalia Z Alomari
- Department of Agroecology, Aarhus University, Flakkebjerg, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr 3, 06466, Seeland, Germany
| | - Henrik Brinch-Pedersen
- Department of Agroecology, Aarhus University, Flakkebjerg, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Ahmad M Alqudah
- Department of Agroecology, Aarhus University, Flakkebjerg, Forsøgsvej 1, 4200, Slagelse, Denmark.
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14
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Zhang K, Lan Y, Wu M, Wang L, Liu H, Xiang Y. PhePLATZ1, a PLATZ transcription factor in moso bamboo (Phyllostachys edulis), improves drought resistance of transgenic Arabidopsis thaliana. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 186:121-134. [PMID: 35835078 DOI: 10.1016/j.plaphy.2022.07.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 06/20/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
Drought is one of the most serious environmental stresses. Plant AT-rich sequence and zinc-binding (PLATZ) proteins perform indispensable functions to regulate plant growth and development and to respond to environmental stress. In this present study, we identified PhePLATZ1 in moso bamboo and found that its expression was up-regulated in response to 20% PEG-6000 and abscisic acid (ABA) treatments. Next, transgenic PhePLATZ1-overexpressing Arabidopsis lines were generated. Overexpression of PhePLATZ1 improved drought stress resistance of transgenic plants by mediating osmotic regulation, enhancing water retention capacity and reducing membrane and oxidative damage. These findings were corroborated by analysing physiological indicators including chlorophyll, relative water content, leaf water loss rate, electrolyte leakage, H2O2, proline, malondialdehyde content and the enzyme activities of peroxidase and catalase. Subsequent seed germination and seedling root length experiments that included exposure to exogenous ABA treatments showed that ABA sensitivity decreased in transgenic plants relative to wild-type plants. Moreover, transgenic PhePLATZ1-overexpressing plants promoted stomatal closure in response to ABA treatment, suggesting that PhePLATZ1 might play a positive regulatory role in the drought resistance of plants via the ABA signaling pathway. In addition, the transgenic PhePLATZ1-OE plants showed altered expression of some stress-related genes when grown under drought conditions. Taken together, these findings improve our understanding of the drought response of moso bamboo and provide a key candidate gene for the molecular breeding of this species for drought tolerance.
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Affiliation(s)
- Kaimei Zhang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China.
| | - Yangang Lan
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China.
| | - Min Wu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China.
| | - Linna Wang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China.
| | - Hongxia Liu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China.
| | - Yan Xiang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China.
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15
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Guo X, Fu Y, Lee YJ, Chern M, Li M, Cheng M, Dong H, Yuan Z, Gui L, Yin J, Qing H, Zhang C, Pu Z, Liu Y, Li W, Li W, Qi P, Chen G, Jiang Q, Ma J, Chen X, Wei Y, Zheng Y, Wu Y, Liu B, Wang J. The PGS1 basic helix-loop-helix protein regulates Fl3 to impact seed growth and grain yield in cereals. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1311-1326. [PMID: 35315196 PMCID: PMC9241376 DOI: 10.1111/pbi.13809] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 03/11/2022] [Indexed: 05/02/2023]
Abstract
Plant transcription factors (TFs), such as basic helix-loop-helix (bHLH) and AT-rich zinc-binding proteins (PLATZ), play critical roles in regulating the expression of developmental genes in cereals. We identified the bHLH protein TaPGS1 (T. aestivum Positive Regulator of Grain Size 1) specifically expressed in the seeds at 5-20 days post-anthesis in wheat. TaPGS1 was ectopically overexpressed (OE) in wheat and rice, leading to increased grain weight (up to 13.81% in wheat and 18.55% in rice lines) and grain size. Carbohydrate and total protein levels also increased. Scanning electron microscopy results indicated that the starch granules in the endosperm of TaPGS1 OE wheat and rice lines were smaller and tightly embedded in a proteinaceous matrix. Furthermore, TaPGS1 was bound directly to the E-box motif at the promoter of the PLATZ TF genes TaFl3 and OsFl3 and positively regulated their expression in wheat and rice. In rice, the OsFl3 CRISPR/Cas9 knockout lines showed reduced average thousand-grain weight, grain width, and grain length in rice. Our results reveal that TaPGS1 functions as a valuable trait-associated gene for improving cereal grain yield.
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Affiliation(s)
- Xiaojiang Guo
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
- Department of Plant BiologyUniversity of CaliforniaDavisCAUSA
| | - Yuxin Fu
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
- National Key Laboratory of Plant Molecular GeneticsCAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina
| | | | - Mawsheng Chern
- Department of Plant PathologyUniversity of CaliforniaDavisCAUSA
| | - Maolian Li
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Mengping Cheng
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Huixue Dong
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Zhongwei Yuan
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Lixuan Gui
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Junjie Yin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Hai Qing
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Chengbi Zhang
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Zhien Pu
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Yujiao Liu
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Weitao Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Wei Li
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Pengfei Qi
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Guoyue Chen
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Qiantao Jiang
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Jian Ma
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Xuewei Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Yuming Wei
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
- Ministry of Education Key Laboratory for Crop Genetic Resources and Improvement in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Youliang Zheng
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
- Ministry of Education Key Laboratory for Crop Genetic Resources and Improvement in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Yongrui Wu
- National Key Laboratory of Plant Molecular GeneticsCAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina
| | - Bo Liu
- Department of Plant BiologyUniversity of CaliforniaDavisCAUSA
| | - Jirui Wang
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
- Ministry of Education Key Laboratory for Crop Genetic Resources and Improvement in Southwest ChinaSichuan Agricultural UniversityChengduChina
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16
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Li J, Feng S, Zhang Y, Xu L, Luo Y, Yuan Y, Yang Q, Feng B. Genome-wide identification and expression analysis of the plant-specific PLATZ gene family in Tartary buckwheat (Fagopyrum tataricum). BMC PLANT BIOLOGY 2022; 22:160. [PMID: 35365087 PMCID: PMC8974209 DOI: 10.1186/s12870-022-03546-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 03/22/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND Plant AT-rich sequence and zinc-binding (PLATZ) proteins belong to a novel class of plant-specific zinc-finger-dependent DNA-binding proteins that play essential roles in plant growth and development. Although the PLATZ gene family has been identified in several species, systematic identification and characterization of this gene family has not yet been carried out for Tartary buckwheat, which is an important medicinal and edible crop with high nutritional value. The recent completion of Tartary buckwheat genome sequencing has laid the foundation for this study. RESULTS A total of 14 FtPLATZ proteins were identified in Tartary buckwheat and were classified into four phylogenetic groups. The gene structure and motif composition were similar within the same group, and evident distinctions among different groups were detected. Gene duplication, particularly segmental duplication, was the main driving force in the evolution of FtPLATZs. Synteny analysis revealed that Tartary buckwheat shares more orthologous PLATZ genes with dicotyledons, particularly soybean. In addition, the expression of FtPLATZs in different tissues and developmental stages of grains showed evident specificity and preference. FtPLATZ3 may be involved in the regulation of grain size, and FtPLATZ4 and FtPLATZ11 may participate in root development. Abundant and variable hormone-responsive cis-acting elements were distributed in the promoter regions of FtPLATZs, and almost all FtPLATZs were significantly regulated after exogenous hormone treatments, particularly methyl jasmonate treatment. Moreover, FtPLATZ6 was significantly upregulated under all exogenous hormone treatments, which may indicate that this gene plays a critical role in the hormone response of Tartary buckwheat. CONCLUSIONS This study lays a foundation for further exploration of the function of FtPLATZ proteins and their roles in the growth and development of Tartary buckwheat and contributes to the genetic improvement of Tartary buckwheat.
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Affiliation(s)
- Jing Li
- State Key Laboratory of Crop Stress Biology for Arid Areas / College of Agronomy, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Shan Feng
- School of Mathematics and Statistics, Northwestern Polytechnical University, Xi'an, 710129, Shaanxi, China
| | - Yuchuan Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas / College of Agronomy, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Lei Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas / College of Agronomy, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Yan Luo
- State Key Laboratory of Crop Stress Biology for Arid Areas / College of Agronomy, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Yuhao Yuan
- State Key Laboratory of Crop Stress Biology for Arid Areas / College of Agronomy, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Qinghua Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas / College of Agronomy, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Baili Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas / College of Agronomy, Northwest A & F University, Yangling, 712100, Shaanxi, China.
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Han X, Rong H, Tian Y, Qu Y, Xu M, Xu LA. Genome-Wide Identification of PLATZ Transcription Factors in Ginkgo biloba L. and Their Expression Characteristics During Seed Development. FRONTIERS IN PLANT SCIENCE 2022; 13:946194. [PMID: 35812908 PMCID: PMC9262033 DOI: 10.3389/fpls.2022.946194] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/07/2022] [Indexed: 05/20/2023]
Abstract
Plant AT-rich protein and zinc-binding protein (PLATZ) is a class of plant-specific zinc-dependent DNA-binding protein that binds to A/T-rich DNA sequences. PLATZ plays an important role in seed development, water tolerance, and cell proliferation in early plant growth. In this study, 11 GbPLATZs were identified from the ginkgo genome with complete PLATZ-conserved domains, which represents a smaller number compared with angiosperms. Multi-species phylogenetic analysis showed that PLATZ genes were conserved in seed plants, and the 11 members were represented by four groups, among which groups I and II were closely related. Analysis of gene structures, sequence module characteristics, and expression patterns showed that GbPLATZs were similar within and differed between groups. RNA-seq and qRT-PCR results showed that GbPLATZs had distinct expression patterns. Most genes were associated with seed development, among which six genes were highly related. Subcellular localization experiments showed that six GbPLATZ proteins related to seed development were localized in the nucleus, suggesting that they might function as traditional transcription factors. This study provides a basis for understanding the structural differentiation, evolutionary characteristics, expression profile, and potential functions of PLATZ transcription factors in Ginkgo biloba.
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