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Fang Y, Wang L, Liu K, Wu H, Zheng Y, Duan Y, Feng S, Wang Y. Genome-wide investigation of HD-ZIP gene family and functional characterization of BnaHDZ149 and BnaHDZ22 in salt and drought response in Brassica napus L. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112130. [PMID: 38795751 DOI: 10.1016/j.plantsci.2024.112130] [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: 04/01/2024] [Revised: 05/08/2024] [Accepted: 05/18/2024] [Indexed: 05/28/2024]
Abstract
HD-ZIP proteins comprise a plant-specific transcription factor family, which play pivotal roles in plant development and adaptation to ever-changing environment. Although HD-ZIP family members have been identified in some plant species, so far our knowledge about HD-ZIP genes in rapeseed is still limited. In this study, 178 Brassica napus HD-ZIP (BnaHDZ) family members were identified in the rapeseed genome. The phylogenetic relationship, chromosomal locations, intron-exon structures, motif composition, and expression patterns of the BnaHDZ members were analyzed. The BnaHDZ family can be phylogenetically divided into four categories (Ⅰ, Ⅱ, Ⅲ and Ⅳ). Genome-wide transcriptome analysis revealed that most of the HD-ZIP I members respond to at least one abiotic stress. Two closely homologous stress-responsive HD-ZIP Ⅰ genes, BnaHDZ22 and BnaHDZ149, were identified to be involved in drought and salt responses, and selected for further functional characterization. Overexpressing BnaHDZ149 in rapeseed increased salt sensitivity of the transgenic plants, whereas overexpressing BnaHDZ22 increased sensitivity of the transgenic plants to polyethylene glycol (PEG)-simulated drought stress. This research provides not only a comprehensive landscape of BnaHDZ genes, but also a theoretical basis for elucidating the molecular mechanism of the abiotic stress responses of the HD-ZIP family in rapeseed.
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Affiliation(s)
- Yujie Fang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu 225009, China.
| | - Lu Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Kuan Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Han Wu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Yuqian Zheng
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Yujing Duan
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Shanshan Feng
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Youping Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu 225009, China.
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Fu C, Zhou Y, Liu A, Chen R, Yin L, Li C, Mao H. Genome-wide association study for seedling heat tolerance under two temperature conditions in bread wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2024; 24:430. [PMID: 38773371 PMCID: PMC11107014 DOI: 10.1186/s12870-024-05116-2] [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: 11/22/2023] [Accepted: 05/08/2024] [Indexed: 05/23/2024]
Abstract
BACKGROUND As the greenhouse effect intensifies, global temperatures are steadily increasing, posing a challenge to bread wheat (Triticum aestivum L.) production. It is imperative to comprehend the mechanism of high temperature tolerance in wheat and implement breeding programs to identify and develop heat-tolerant wheat germplasm and cultivars. RESULTS To identify quantitative trait loci (QTL) related to heat stress tolerance (HST) at seedling stage in wheat, a panel of 253 wheat accessions which were re-sequenced used to conduct genome-wide association studies (GWAS) using the factored spectrally transformed linear mixed models (FaST-LMM). For most accessions, the growth of seedlings was found to be inhibited under heat stress. Analysis of the phenotypic data revealed that under heat stress conditions, the main root length, total root length, and shoot length of seedlings decreased by 47.46%, 49.29%, and 15.19%, respectively, compared to those in normal conditions. However, 17 varieties were identified as heat stress tolerant germplasm. Through GWAS analysis, a total of 115 QTLs were detected under both heat stress and normal conditions. Furthermore, 15 stable QTL-clusters associated with heat response were identified. By combining gene expression, haplotype analysis, and gene annotation information within the physical intervals of the 15 QTL-clusters, two novel candidate genes, TraesCS4B03G0152700/TaWRKY74-B and TraesCS4B03G0501400/TaSnRK3.15-B, were responsive to temperature and identified as potential regulators of HST in wheat at the seedling stage. CONCLUSIONS This study conducted a detailed genetic analysis and successfully identified two genes potentially associated with HST in wheat at the seedling stage, laying a foundation to further dissect the regulatory mechanism underlying HST in wheat under high temperature conditions. Our finding could serve as genomic landmarks for wheat breeding aimed at improving adaptation to heat stress in the face of climate change.
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Affiliation(s)
- Chao Fu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ying Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ankui Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Rui Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Li Yin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Cong Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hailiang Mao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
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Wang Y, Wang H, Yu C, Yan X, Chu J, Jiang B, Zhu J. Comprehensive bioinformation analysis of homeodomain-leucine zipper gene family and expression pattern of HD-Zip I under abiotic stress in Salix suchowensis. BMC Genomics 2024; 25:182. [PMID: 38360569 PMCID: PMC10870566 DOI: 10.1186/s12864-024-10067-x] [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: 09/11/2023] [Accepted: 01/30/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND Homeodomain-leucine zipper (HD-Zip) transcription factors are plant-specific and play important roles in plant defense against environmental stresses. Identification and functional studies have been carried out in model plants such as rice, Arabidopsis thaliana, and poplar, but comprehensive analysis on the HD-Zip family of Salix suchowensis have not been reported. RESULTS A total of 55 HD-Zip genes were identified in the willow genome, unevenly distributed on 18 chromosomes except for chromosome 19. And segmental duplication events containing SsHD-Zip were detected on all chromosomes except chromosomes 13 and 19. The SsHD-Zip were classified into 4 subfamilies subfamilies (I-IV) according to the evolutionary analysis, and members of each subfamily shared similar domain structure and gene structure. The combination of GO annotation and promoter analysis showed that SsHD-Zip genes responded to multiple abiotic stresses. Furthermore, the results of qPCR analysis showed that the SsHD-Zip I gene exhibited different degrees of expression under salt stress, PEG treatment and heat treatment. Moreover, there was a synergistic effect between SsHD-Zip I genes under stress conditions based on coregulatory networks analysis. CONCLUSIONS In this study, HD-Zip transcription factors were systematically identified and analyzed at the whole genome level. These results preliminarily clarified the structural characteristics and related functions of willow HD-Zip family members, and it was found that SsHox34, SsHox36 and SsHox51 genes were significantly involved in the response to various stresses. Together, these findings laid the foundation for further research on the resistance functions of willow HD-Zip genes.
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Affiliation(s)
- Yujiao Wang
- Department of Cotton Research Institute, Anhui Academy of Agricultural Sciences, 230001, Hefei, China
| | - Hongjuan Wang
- Department of Cotton Research Institute, Anhui Academy of Agricultural Sciences, 230001, Hefei, China
| | - Chun Yu
- Department of Cotton Research Institute, Anhui Academy of Agricultural Sciences, 230001, Hefei, China
| | - Xiaoming Yan
- Department of Cotton Research Institute, Anhui Academy of Agricultural Sciences, 230001, Hefei, China
| | - Jiasong Chu
- Department of Cotton Research Institute, Anhui Academy of Agricultural Sciences, 230001, Hefei, China
| | - Benli Jiang
- Department of Cotton Research Institute, Anhui Academy of Agricultural Sciences, 230001, Hefei, China.
| | - Jiabao Zhu
- Department of Cotton Research Institute, Anhui Academy of Agricultural Sciences, 230001, Hefei, China.
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Jiao P, Jiang Z, Miao M, Wei X, Wang C, Liu S, Guan S, Ma Y. Zmhdz9, an HD-Zip transcription factor, promotes drought stress resistance in maize by modulating ABA and lignin accumulation. Int J Biol Macromol 2024; 258:128849. [PMID: 38113999 DOI: 10.1016/j.ijbiomac.2023.128849] [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: 09/26/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 12/21/2023]
Abstract
Maize is the largest crop in the world in terms of both planting area and total yield, and it plays a crucial role in ensuring global food and feed security. However, in recent years, with climate deterioration, environmental changes, and the scarcity of freshwater resources, drought has become a serious limiting factor for maize yield and quality. Drought stress-induced signals undergo a series of transmission processes to regulate the expression of specific genes, thereby affecting the drought tolerance of plants at the tissue, cellular, physiological and biochemical levels. Therefore, in this study we investigated the HD-Zip transcription factor gene Zmhdz9, and yeast activation experiments demonstrated that Zmhdz9 exhibited transcriptional activation activity. Under drought stress, high abscisic acid (ABA) and lignin levels significantly improved drought resistance in maize. Yeast two-hybrid, bimolecular fluorescence complementation (BIFC) and pull-down experiments showed that Zmhdz9 interacted with ZmWRKY120 and ZmTCP9, respectively. Overexpression of Zmhdz9 and gene editing of ZmWRKY120 or ZmTCP9 improved maize drought resistance, indicating their importance in the drought stress response. Furthermore, Zmhdz9 promoted the direct transcription of ZmWRKY120 in the W-box, activating elements of the ZmNCED1 promoter, which encodes a key enzyme in ABA biosynthesis. Additionally, Zmhdz9 promoted direct transcription of ZmTCP9 in the GGTCA motif, activating elements of the ZmKNOX8 promoter, which encodes a key enzyme in lignin synthesis. This study showed that the regulation of ABA and lignin by Zmhdz9 is essential for drought stress resistance in maize.
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Affiliation(s)
- Peng Jiao
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China; Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Zhenzhong Jiang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Ming Miao
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China; Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Xiaotong Wei
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China; Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Chunlai Wang
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China; Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Siyan Liu
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China; Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Shuyan Guan
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China; Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Jilin Agricultural University, Changchun 130118, China.
| | - Yiyong Ma
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China; Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Jilin Agricultural University, Changchun 130118, China.
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Hoheneder F, Steidele CE, Messerer M, Mayer KFX, Köhler N, Wurmser C, Heß M, Gigl M, Dawid C, Stam R, Hückelhoven R. Barley shows reduced Fusarium head blight under drought and modular expression of differentially expressed genes under combined stress. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6820-6835. [PMID: 37668551 DOI: 10.1093/jxb/erad348] [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: 02/15/2023] [Accepted: 09/04/2023] [Indexed: 09/06/2023]
Abstract
Plants often face simultaneous abiotic and biotic stress conditions; however, physiological and transcriptional responses under such combined stress conditions are still not fully understood. Spring barley (Hordeum vulgare) is susceptible to Fusarium head blight (FHB), which is strongly affected by weather conditions. We therefore studied the potential influence of drought on FHB severity and plant responses in three varieties of different susceptibility. We found strongly reduced FHB severity in susceptible varieties under drought. The number of differentially expressed genes (DEGs) and strength of transcriptomic regulation reflected the concentrations of physiological stress markers such as abscisic acid or fungal DNA contents. Infection-related gene expression was associated with susceptibility rather than resistance. Weighted gene co-expression network analysis revealed 18 modules of co-expressed genes that reflected the pathogen- or drought-response in the three varieties. A generally infection-related module contained co-expressed genes for defence, programmed cell death, and mycotoxin detoxification, indicating that the diverse genotypes used a similar defence strategy towards FHB, albeit with different degrees of success. Further, DEGs showed co-expression in drought- or genotype-associated modules that correlated with measured phytohormones or the osmolyte proline. The combination of drought stress with infection led to the highest numbers of DEGs and resulted in a modular composition of the single-stress responses rather than a specific transcriptional output.
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Affiliation(s)
- Felix Hoheneder
- Chair of Phytopathology, TUM School of Life Sciences, HEF World Agricultural Systems Center, Technical University of Munich, Emil-Ramann Str. 2, 85354 Freising-Weihenstephan, Germany
| | - Christina E Steidele
- Chair of Phytopathology, TUM School of Life Sciences, HEF World Agricultural Systems Center, Technical University of Munich, Emil-Ramann Str. 2, 85354 Freising-Weihenstephan, Germany
| | - Maxim Messerer
- Plant Genome and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Nikolai Köhler
- Chair of Phytopathology, TUM School of Life Sciences, HEF World Agricultural Systems Center, Technical University of Munich, Emil-Ramann Str. 2, 85354 Freising-Weihenstephan, Germany
- LipiTUM, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof Forum 3, 85354 Freising-Weihenstephan, Germany
| | - Christine Wurmser
- Chair of Animal Physiology and Immunology, TUM School of Life Sciences, Technical University of Munich, Weihenstephaner Berg 3/I, 85354 Freising-Weihenstephan, Germany
| | - Michael Heß
- Chair of Phytopathology, TUM School of Life Sciences, HEF World Agricultural Systems Center, Technical University of Munich, Emil-Ramann Str. 2, 85354 Freising-Weihenstephan, Germany
| | - Michael Gigl
- Chair of Food Chemistry and Molecular Sensory Science, TUM School of Life Sciences, Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising-Weihenstephan, Germany
| | - Corinna Dawid
- Chair of Food Chemistry and Molecular Sensory Science, TUM School of Life Sciences, Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising-Weihenstephan, Germany
| | - Remco Stam
- Chair of Phytopathology, TUM School of Life Sciences, HEF World Agricultural Systems Center, Technical University of Munich, Emil-Ramann Str. 2, 85354 Freising-Weihenstephan, Germany
- Institute of Phytopathology, Christian Albrecht University of Kiel, Hermann-Rodewald-Straße 9, 24118 Kiel, Germany
| | - Ralph Hückelhoven
- Chair of Phytopathology, TUM School of Life Sciences, HEF World Agricultural Systems Center, Technical University of Munich, Emil-Ramann Str. 2, 85354 Freising-Weihenstephan, Germany
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Mao H, Jiang C, Tang C, Nie X, Du L, Liu Y, Cheng P, Wu Y, Liu H, Kang Z, Wang X. Wheat adaptation to environmental stresses under climate change: Molecular basis and genetic improvement. MOLECULAR PLANT 2023; 16:1564-1589. [PMID: 37671604 DOI: 10.1016/j.molp.2023.09.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/19/2023] [Accepted: 09/01/2023] [Indexed: 09/07/2023]
Abstract
Wheat (Triticum aestivum) is a staple food for about 40% of the world's population. As the global population has grown and living standards improved, high yield and improved nutritional quality have become the main targets for wheat breeding. However, wheat production has been compromised by global warming through the more frequent occurrence of extreme temperature events, which have increased water scarcity, aggravated soil salinization, caused plants to be more vulnerable to diseases, and directly reduced plant fertility and suppressed yield. One promising option to address these challenges is the genetic improvement of wheat for enhanced resistance to environmental stress. Several decades of progress in genomics and genetic engineering has tremendously advanced our understanding of the molecular and genetic mechanisms underlying abiotic and biotic stress responses in wheat. These advances have heralded what might be considered a "golden age" of functional genomics for the genetic improvement of wheat. Here, we summarize the current knowledge on the molecular and genetic basis of wheat resistance to abiotic and biotic stresses, including the QTLs/genes involved, their functional and regulatory mechanisms, and strategies for genetic modification of wheat for improved stress resistance. In addition, we also provide perspectives on some key challenges that need to be addressed.
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Affiliation(s)
- Hude Mao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Cong Jiang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chunlei Tang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Linying Du
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuling Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Peng Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yunfeng Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Huiquan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Xiaojie Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China.
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Guo Y, Wang G, Guo X, Chi S, Yu H, Jin K, Huang H, Wang D, Wu C, Tian J, Chen J, Bao Y, Zhang W, Deng Z. Genetic dissection of protein and starch during wheat grain development using QTL mapping and GWAS. FRONTIERS IN PLANT SCIENCE 2023; 14:1189887. [PMID: 37377808 PMCID: PMC10291175 DOI: 10.3389/fpls.2023.1189887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/18/2023] [Indexed: 06/29/2023]
Abstract
Protein, starch, and their components are important for wheat grain yield and end-products, which are affected by wheat grain development. Therefore, QTL mapping and a genome-wide association study (GWAS) of grain protein content (GPC), glutenin macropolymer content (GMP), amylopectin content (GApC), and amylose content (GAsC) were performed on wheat grain development at 7, 14, 21, and 28 days after anthesis (DAA) in two environments using a recombinant inbred line (RIL) population of 256 stable lines and a panel of 205 wheat accessions. A total of 29 unconditional QTLs, 13 conditional QTLs, 99 unconditional marker-trait associations (MTAs), and 14 conditional MTAs significantly associated (p < 10-4) with four quality traits were found to be distributed on 15 chromosomes, with the phenotypic variation explained (PVE) ranging from 5.35% to 39.86%. Among these genomic variations, three major QTLs [QGPC3B, QGPC2A, and QGPC(S3|S2)3B] and SNP clusters on the 3A and 6B chromosomes were detected for GPC, and the SNP TA005876-0602 was stably expressed during the three periods in the natural population. The QGMP3B locus was detected five times in three developmental stages in two environments with 5.89%-33.62% PVE, and SNP clusters for GMP content were found on the 3A and 3B chromosomes. For GApC, the QGApC3B.1 locus had the highest PVE of 25.69%, and SNP clusters were found on chromosomes 4A, 4B, 5B, 6B, and 7B. Four major QTLs of GAsC were detected at 21 and 28 DAA. Most interestingly, both QTL mapping and GWAS analysis indicated that four chromosomes (3B, 4A, 6B, and 7A) were mainly involved in the development of protein, GMP, amylopectin, and amylose synthesis. Of these, the wPt-5870-wPt-3620 marker interval on chromosome 3B seemed to be most important because it played an important role in the synthesis of GMP and amylopectin before 7 DAA, in the synthesis of protein and GMP from 14 to 21 DAA, and in the development of GApC and GAsC from 21 to 28 DAA. Using the annotation information of IWGSC Chinese Spring RefSeq v1.1 genome assembly, we predicted 28 and 69 candidate genes for major loci from QTL mapping and GWAS, respectively. Most of them have multiple effects on protein and starch synthesis during grain development. These results provide new insights and information for the potential regulatory network between grain protein and starch synthesis.
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Affiliation(s)
- Yingxin Guo
- State Key Laboratory of Wheat Breeding, Group of Wheat Quality and Molecular Breeding, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, China
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan, Shandong, China
| | - Guanying Wang
- State Key Laboratory of Wheat Breeding, Group of Wheat Quality and Molecular Breeding, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, China
| | - Xin Guo
- State Key Laboratory of Wheat Breeding, Group of Wheat Quality and Molecular Breeding, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, China
- Taiyuan Agro-Tech Extension and Service Center, Taiyuan, Shanxi, China
| | - Songqi Chi
- State Key Laboratory of Wheat Breeding, Group of Wheat Quality and Molecular Breeding, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, China
| | - Hui Yu
- State Key Laboratory of Wheat Breeding, Group of Wheat Quality and Molecular Breeding, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, China
| | - Kaituo Jin
- State Key Laboratory of Wheat Breeding, Group of Wheat Quality and Molecular Breeding, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, China
| | - Heting Huang
- State Key Laboratory of Wheat Breeding, Group of Wheat Quality and Molecular Breeding, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, China
| | - Dehua Wang
- State Key Laboratory of Wheat Breeding, Group of Wheat Quality and Molecular Breeding, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, China
| | - Chongning Wu
- State Key Laboratory of Wheat Breeding, Group of Wheat Quality and Molecular Breeding, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, China
| | - Jichun Tian
- R&D Department, Shandong Huatian Agricultural Technology Co., Ltd, Feicheng, Shandong, China
| | - Jiansheng Chen
- State Key Laboratory of Wheat Breeding, Group of Wheat Quality and Molecular Breeding, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, China
| | - Yinguang Bao
- State Key Laboratory of Wheat Breeding, Group of Wheat Quality and Molecular Breeding, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, China
| | - Weidong Zhang
- State Key Laboratory of Wheat Breeding, Group of Wheat Quality and Molecular Breeding, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, China
| | - Zhiying Deng
- State Key Laboratory of Wheat Breeding, Group of Wheat Quality and Molecular Breeding, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, China
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Baek W, Bae Y, Lim CW, Lee SC. Pepper homeobox abscisic acid signalling-related transcription factor 1, CaHAT1, plays a positive role in drought response. PLANT, CELL & ENVIRONMENT 2023. [PMID: 37128851 DOI: 10.1111/pce.14597] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 03/15/2023] [Accepted: 04/17/2023] [Indexed: 05/03/2023]
Abstract
Abscisic acid (ABA) signalling triggers drought resistance mediated by SNF1-related kinase 2s (SnRK2s), which transmits stress signals through the phosphorylation of several downstream factors. However, these kinases and their downstream targets remain elusive in pepper plants. This study aimed to isolate interacting partners of CaSnRK2.6, a homologue of Arabidopsis SnRK2.6/OST1. Among the candidate proteins, we identified a homeodomain-leucine zipper (HD-Zip) class II protein and named it CaHAT1 (Capsicum annuum homeobox ABA signalling related- transcription factor 1). CaHAT1-silenced pepper and -overexpression (OE) transgenic Arabidopsis plants were generated to investigate the in vivo function of CaHAT1 in drought response. Following the application of drought stress, CaHAT1-silenced pepper plants exhibited drought-sensitive phenotypes with reduced ABA-mediated stomatal closure and lower expression of stress-responsive genes compared with control plants. In contrast, CaHAT1-OE transgenic Arabidopsis plants showed the opposite phenotypes, including increased drought resistance and ABA sensitivity. CaHAT1, particularly its N-terminal consensus sequences, was directly phosphorylated by CaSnRK2.6. Furthermore, CaSnRK2.6 kinase activity and CaSnRK2.6-mediated CaHAT1 phosphorylation levels were enhanced by treatment with ABA and drought stress. Taken together, our results indicated that CaHAT1, which is the target protein of CaSnRK2.6, is a positive regulator of drought stress response. This study advances our understanding of CaHAT1-CaSnRK2.6 mediated defence mechanisms in pepper plants against drought stress.
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Affiliation(s)
- Woonhee Baek
- Department of Life Science (BK21 program), Chung-Ang University, Seoul, Korea
| | - Yeongil Bae
- Department of Life Science (BK21 program), Chung-Ang University, Seoul, Korea
| | - Chae Woo Lim
- Department of Life Science (BK21 program), Chung-Ang University, Seoul, Korea
| | - Sung Chul Lee
- Department of Life Science (BK21 program), Chung-Ang University, Seoul, Korea
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9
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Urbanavičiūtė I, Bonfiglioli L, Pagnotta MA. Phenotypic and Genotypic Diversity of Roots Response to Salt in Durum Wheat Seedlings. PLANTS (BASEL, SWITZERLAND) 2023; 12:412. [PMID: 36679125 PMCID: PMC9865824 DOI: 10.3390/plants12020412] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/03/2023] [Accepted: 01/11/2023] [Indexed: 06/17/2023]
Abstract
Soil salinity is a serious threat to food production now and in the near future. In this study, the root system of six durum wheat genotypes, including one highly salt-tolerant (J. Khetifa) used as a check genotype, was evaluated, by a high-throughput phenotyping system, under control and salt conditions at the seedling stage. Genotyping was performed using 11 SSR markers closely linked with genome regions associated with root traits. Based on phenotypic cluster analysis, genotypes were grouped differently under control and salt conditions. Under control conditions, genotypes were clustered mainly due to a root angle, while under salt stress, genotypes were grouped according to their capacity to maintain higher roots length, volume, and surface area, as J. Khetifa, Sebatel, and Azeghar. SSR analysis identified a total of 42 alleles, with an average of about three alleles per marker. Moreover, quite a high number of Private alleles in total, 18 were obtained. The UPGMA phenogram of the Nei (1972) genetic distance clusters for 11 SSR markers and all phenotypic data under control conditions discriminate genotypes almost into the same groups. The study revealed as the combination of high-throughput systems for phenotyping with SSR markers for genotyping it's a useful tool to provide important data for the selection of suitable parental lines for salt-tolerance breeding. Nevertheless, the narrow root angle, which is an important trait in drought tolerance, is not a good indicator of salt tolerance. Instated for salt tolerance is more important the amount of roots.
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10
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Fang ZT, Kapoor R, Datta A, Liu S, Stull MA, Seitz PG, Johnson CD, Okumoto S. Transcriptome Analysis of Developing Grains from Wheat Cultivars TAM 111 and TAM 112 Reveal Cultivar-Specific Regulatory Networks. Int J Mol Sci 2022; 23:ijms232012660. [PMID: 36293517 PMCID: PMC9604430 DOI: 10.3390/ijms232012660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/20/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022] Open
Abstract
Wheat flour's end-use quality is tightly linked to the quantity and composition of storage proteins in the endosperm. TAM 111 and TAM 112 are two popular cultivars grown in the Southern US Great Plains with significantly different protein content. To investigate regulatory differences, transcriptome data were analyzed from developing grains at early- and mid-filling stages. At the mid-filling stage, TAM 111 preferentially upregulated starch metabolism-related pathways compared to TAM 112, whereas amino acid metabolism and transporter-related pathways were over-represented in TAM 112. Elemental analyses also indicated a higher N percentage in TAM 112 at the mid-filling stage. To explore the regulatory variation, weighted correlation gene network was constructed from publicly available RNAseq datasets to identify the modules differentially regulated in TAM 111 and TAM 112. Further, the potential transcription factors (TFs) regulating those modules were identified using graphical least absolute shrinkage and selection operator (GLASSO). Homologs of the OsNF-Y family members with known starch metabolism-related functions showed higher connectivities in TAM 111. Multiple TFs with high connectivity in TAM 112 had predicted functions associated with ABA response in grain. These results will provide novel targets for breeders to explore and further our understanding in mechanisms regulating grain development.
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Affiliation(s)
- Ze-Tian Fang
- Department of Soil and Crop Sciences, Texas A&M AgriLife Research, Texas A&M University, College Station, TX 77843, USA
| | - Rajan Kapoor
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Aniruddha Datta
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Shuyu Liu
- Texas A&M AgriLife Research Center, 6500 Amarillo Blvd W, Amarillo, TX 79106, USA
| | - Matthew A. Stull
- Texas A&M AgriLife Genomics and Bioinformatics Service, College Station, TX 77845, USA
| | - Paige G. Seitz
- Department of Soil and Crop Sciences, Texas A&M AgriLife Research, Texas A&M University, College Station, TX 77843, USA
| | - Charles D. Johnson
- Texas A&M AgriLife Genomics and Bioinformatics Service, College Station, TX 77845, USA
| | - Sakiko Okumoto
- Department of Soil and Crop Sciences, Texas A&M AgriLife Research, Texas A&M University, College Station, TX 77843, USA
- Correspondence:
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11
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Li Y, Yang Z, Zhang Y, Guo J, Liu L, Wang C, Wang B, Han G. The roles of HD-ZIP proteins in plant abiotic stress tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:1027071. [PMID: 36311122 PMCID: PMC9598875 DOI: 10.3389/fpls.2022.1027071] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/26/2022] [Indexed: 05/31/2023]
Abstract
Homeodomain leucine zipper (HD-ZIP) proteins are plant-specific transcription factors that contain a homeodomain (HD) and a leucine zipper (LZ) domain. The highly conserved HD binds specifically to DNA and the LZ mediates homodimer or heterodimer formation. HD-ZIP transcription factors control plant growth, development, and responses to abiotic stress by regulating downstream target genes and hormone regulatory pathways. HD-ZIP proteins are divided into four subclasses (I-IV) according to their sequence conservation and function. The genome-wide identification and expression profile analysis of HD-ZIP proteins in model plants such as Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) have improved our understanding of the functions of the different subclasses. In this review, we mainly summarize and discuss the roles of HD-ZIP proteins in plant response to abiotic stresses such as drought, salinity, low temperature, and harmful metals. HD-ZIP proteins mainly mediate plant stress tolerance by regulating the expression of downstream stress-related genes through abscisic acid (ABA) mediated signaling pathways, and also by regulating plant growth and development. This review provides a basis for understanding the roles of HD-ZIP proteins and potential targets for breeding abiotic stress tolerance in plants.
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12
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Overexpression of McHB7 Transcription Factor from Mesembryanthemum crystallinum Improves Plant Salt Tolerance. Int J Mol Sci 2022; 23:ijms23147879. [PMID: 35887227 PMCID: PMC9318261 DOI: 10.3390/ijms23147879] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/10/2022] [Accepted: 07/15/2022] [Indexed: 02/06/2023] Open
Abstract
Mesembryanthemum crystallinum (common ice plant) is one of the facultative halophyte plants, and it serves as a model for investigating the molecular mechanisms underlying its salt stress response and tolerance. Here we cloned one of the homeobox transcription factor (TF) genes, McHB7, from the ice plant, which has 60% similarity with the Arabidopsis AtHB7. Overexpression of the McHB7 in Arabidopsis (OE) showed that the plants had significantly elevated relative water content (RWC), chlorophyll content, superoxide dismutase (SOD), and peroxidase (POD) activities after salt stress treatment. Our proteomic analysis identified 145 proteins to be significantly changed in abundance, and 66 were exclusively increased in the OE plants compared to the wild type (WT). After salt treatment, 979 and 959 metabolites were significantly increased and decreased, respectively, in the OE plants compared to the WT. The results demonstrate that the McHB7 can improve photosynthesis, increase the leaf chlorophyll content, and affect the TCA cycle by regulating metabolites (e.g., pyruvate) and proteins (e.g., citrate synthase). Moreover, McHB7 modulates the expression of stress-related proteins (e.g., superoxide dismutase, dehydroascorbate reductase, and pyrroline-5-carboxylate synthase B) to scavenge reactive oxygen species and enhance plant salt tolerance.
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13
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Yu M, Wang X, Zhou H, Yu Y, Wei F, Zhang S, Song T, Wang Y, Zhang X. Identification of the yield traits related haplotype combinations of transcription factor genes TaHDZ34 in common wheat. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:34. [PMID: 37312965 PMCID: PMC10248608 DOI: 10.1007/s11032-022-01298-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
A predominant objective in wheat breeding is improving yield-related traits. The homeodomain-leucine zipper (HD-Zip) transcription factor plays a significant role in plant growth and development. In this study, we cloned all homeologs of TaHDZ34, which is a member of the HD-Zip class IV transcription factor family in wheat (Triticum aestivum L.). Sequence polymorphism analysis showed that TaHDZ-A34, TaHDZ-B34, and TaHDZ-D34 formed five, six, and six haplotypes, respectively, and the genes were divided into two main haplotype groups. We also developed functional molecular markers. The TaHDZ34 genes were divided into eight main haplotype combinations. Association analysis and distinct population validation preliminarily indicated that TaHDZ34 genes modulate grain number per spike, effective spikelet number per spike, thousand kernel weight, and flag leaf area per plant in wheat. Hap-ABD was the most effective haplotype combination of TaHDZ34. Subcellular localization showed that TaHDZ-A34 was localized to the nucleus. The interacting proteins of TaHDZ-A34 were involved in protein synthesis/degradation, energy production and transportation, and photosynthesis. Geographic distribution and frequencies of TaHDZ34 haplotype combinations suggested that Hap-Abd and Hap-AbD were preferentially selected in Chinese wheat breeding programs. The high-yield-related haplotype combination Hap-ABD provided beneficial genetic resources for the marker-assisted selection of new wheat cultivars. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01298-5.
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Affiliation(s)
- Ming Yu
- College of Agronomy, Northwest A & F University, Yangling, 712100 Shaanxi China
| | - Xiaolong Wang
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi’an, 710162 Shaanxi China
| | - Hongwei Zhou
- College of Agronomy, Northwest A & F University, Yangling, 712100 Shaanxi China
| | - Yang Yu
- College of Agronomy, Northwest A & F University, Yangling, 712100 Shaanxi China
| | - Fan Wei
- College of Agronomy, Northwest A & F University, Yangling, 712100 Shaanxi China
| | - Shuangxing Zhang
- College of Agronomy, Northwest A & F University, Yangling, 712100 Shaanxi China
| | - Tianqi Song
- College of Agronomy, Northwest A & F University, Yangling, 712100 Shaanxi China
| | - Yukun Wang
- College of Agronomy, Northwest A & F University, Yangling, 712100 Shaanxi China
| | - Xiaoke Zhang
- College of Agronomy, Northwest A & F University, Yangling, 712100 Shaanxi China
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Sharif R, Raza A, Chen P, Li Y, El-Ballat EM, Rauf A, Hano C, El-Esawi MA. HD-ZIP Gene Family: Potential Roles in Improving Plant Growth and Regulating Stress-Responsive Mechanisms in Plants. Genes (Basel) 2021; 12:genes12081256. [PMID: 34440430 PMCID: PMC8394574 DOI: 10.3390/genes12081256] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/06/2021] [Accepted: 08/12/2021] [Indexed: 12/11/2022] Open
Abstract
Exploring the molecular foundation of the gene-regulatory systems underlying agronomic parameters or/and plant responses to both abiotic and biotic stresses is crucial for crop improvement. Thus, transcription factors, which alone or in combination directly regulated the targeted gene expression levels, are appropriate players for enlightening agronomic parameters through genetic engineering. In this regard, homeodomain leucine zipper (HD-ZIP) genes family concerned with enlightening plant growth and tolerance to environmental stresses are considered key players for crop improvement. This gene family containing HD and LZ domain belongs to the homeobox superfamily. It is further classified into four subfamilies, namely HD-ZIP I, HD-ZIP II, HD-ZIP III, and HD-ZIP IV. The first HD domain-containing gene was discovered in maize cells almost three decades ago. Since then, with advanced technologies, these genes were functionally characterized for their distinct roles in overall plant growth and development under adverse environmental conditions. This review summarized the different functions of HD-ZIP genes in plant growth and physiological-related activities from germination to fruit development. Additionally, the HD-ZIP genes also respond to various abiotic and biotic environmental stimuli by regulating defense response of plants. This review, therefore, highlighted the various significant aspects of this important gene family based on the recent findings. The practical application of HD-ZIP biomolecules in developing bioengineered plants will not only mitigate the negative effects of environmental stresses but also increase the overall production of crop plants.
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Affiliation(s)
- Rahat Sharif
- Department of Horticulture, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China;
- College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Ali Raza
- Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agriculture Science (CAAS), Wuhan 430062, China
| | - Peng Chen
- College of Life Science, Northwest A&F University, Yangling 712100, China;
| | - Yuhong Li
- College of Horticulture, Northwest A&F University, Yangling 712100, China
- Correspondence: (Y.L.); (M.A.E.-E.)
| | - Enas M. El-Ballat
- Botany Department, Faculty of Science, Tanta University, Tanta 31527, Egypt;
| | - Abdur Rauf
- Department of Chemistry, University of Swabi, Anbar 23430, Pakistan;
| | - Christophe Hano
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), INRAE USC1328, Université d’Orléans, 28000 Chartres, France;
| | - Mohamed A. El-Esawi
- Botany Department, Faculty of Science, Tanta University, Tanta 31527, Egypt;
- Correspondence: (Y.L.); (M.A.E.-E.)
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15
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Öztürk Gökçe ZN, Aksoy E, Bakhsh A, Demirel U, Çalışkan S, Çalışkan ME. Combined drought and heat stresses trigger different sets of miRNAs in contrasting potato cultivars. Funct Integr Genomics 2021; 21:489-502. [PMID: 34241734 DOI: 10.1007/s10142-021-00793-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/31/2021] [Accepted: 06/08/2021] [Indexed: 12/17/2022]
Abstract
MicroRNAs are small, non-coding RNAs that are responsible for regulation of gene expression during plant growth and development. Although there are many studies on miRNAs in other plants, little work has been done to understand the role of miRNAs in abiotic stress tolerance in potatoes. This study investigates changes in miRNA profiles of two different potato cultivars (tolerant, Unica and susceptible, Russet Burbank) in response to heat, drought and their combination. Transcriptomic studies revealed that miRNA profiles depend on the susceptibility and tolerance of the cultivar and also the stress conditions. Large number of miRNAs were expressed in Unica, whereas Russet Burbank indicated lesser number of changes in miRNA expression. Physiological and transcriptional results clearly supported that Unica cultivar is tolerant to combined drought and heat stress compared to Russet Burbank. Moreover, psRNATarget analysis predicted that major miRNAs identified were targeting genes playing important roles in response to drought and heat stress and their important roles in genetic and post-transcriptional regulation, root development, auxin responses and embryogenesis were also observed. This study focused on eight miRNAs (Novel_8, Novel_9, Novel_105, miR156d-3p, miR160a-5p, miR162a-3p, miR172b-3p and miR398a-5p) and their putative targets where results indicate that they may play a vital role at different post-transcriptional levels against drought and heat stresses. We suggest that miRNA overexpression in plants can lead to increased tolerance against abiotic stresses; furthermore, there should be more emphasis on the studies to investigate the role of miRNAs in combined abiotic stress in plants.
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Affiliation(s)
- Zahide Neslihan Öztürk Gökçe
- Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Department of Agricultural Genetic Engineering, Niğde Ömer Halisdemir University, 51240, Niğde, Turkey.
| | - Emre Aksoy
- Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Department of Agricultural Genetic Engineering, Niğde Ömer Halisdemir University, 51240, Niğde, Turkey
| | - Allah Bakhsh
- Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Department of Agricultural Genetic Engineering, Niğde Ömer Halisdemir University, 51240, Niğde, Turkey
| | - Ufuk Demirel
- Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Department of Agricultural Genetic Engineering, Niğde Ömer Halisdemir University, 51240, Niğde, Turkey
| | - Sevgi Çalışkan
- Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Department of Agricultural Genetic Engineering, Niğde Ömer Halisdemir University, 51240, Niğde, Turkey
| | - Mehmet Emin Çalışkan
- Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Department of Agricultural Genetic Engineering, Niğde Ömer Halisdemir University, 51240, Niğde, Turkey
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16
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Perotti MF, Arce AL, Chan RL. The underground life of homeodomain-leucine zipper transcription factors. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4005-4021. [PMID: 33713412 DOI: 10.1093/jxb/erab112] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 03/08/2021] [Indexed: 06/12/2023]
Abstract
Roots are the anchorage organs of plants, responsible for water and nutrient uptake, exhibiting high plasticity. Root architecture is driven by the interactions of biomolecules, including transcription factors and hormones that are crucial players regulating root plasticity. Multiple transcription factor families are involved in root development; some, such as ARFs and LBDs, have been well characterized, whereas others remain less well investigated. In this review, we synthesize the current knowledge about the involvement of the large family of homeodomain-leucine zipper (HD-Zip) transcription factors in root development. This family is divided into four subfamilies (I-IV), mainly according to structural features, such as additional motifs aside from HD-Zip, as well as their size, gene structure, and expression patterns. We explored and analyzed public databases and the scientific literature regarding HD-Zip transcription factors in Arabidopsis and other species. Most members of the four HD-Zip subfamilies are expressed in specific cell types and several individuals from each group have assigned functions in root development. Notably, a high proportion of the studied proteins are part of intricate regulation pathways involved in primary and lateral root growth and development.
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Affiliation(s)
- María Florencia Perotti
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, FBCB, Colectora Ruta Nacional 168 km 0, 3000 Santa Fe,Argentina
| | - Agustín Lucas Arce
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, FBCB, Colectora Ruta Nacional 168 km 0, 3000 Santa Fe,Argentina
| | - Raquel Lía Chan
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, FBCB, Colectora Ruta Nacional 168 km 0, 3000 Santa Fe,Argentina
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17
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Zhou Y, Zhong T, Wei W, Wu Z, Yang A, Liu N, Wang M, Zhang X. Single START-domain protein Mtsp17 is involved in transcriptional regulation in Mycobacterium smegmatis. PLoS One 2021; 16:e0249379. [PMID: 33857164 PMCID: PMC8049324 DOI: 10.1371/journal.pone.0249379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 03/17/2021] [Indexed: 11/19/2022] Open
Abstract
Tuberculosis caused by the pathogen Mycobacterium tuberculosis (MTB), remains a significant threat to global health. Elucidating the mechanisms of essential MTB genes provides an important theoretical basis for drug exploitation. Gene mtsp17 is essential and is conserved in the Mycobacterium genus. Although Mtsp17 has a structure closely resembling typical steroidogenic acute regulatory protein-related lipid transfer (START) family proteins, its biological function is different. This study characterizes the transcriptomes of Mycobacterium smegmatis to explore the consequences of mtsp17 downregulation on gene expression. Suppression of the mtsp17 gene resulted in significant down-regulation of 3% and upregulation of 1% of all protein-coding genes. Expression of desA1, an essential gene involved in mycolic acid synthesis, and the anti-SigF antagonist MSMEG_0586 were down-regulated in the conditional Mtsp17 knockout mutant and up-regulated in the Mtsp17 over-expression strain. Trends in the changes of 70 of the 79 differentially expressed genes (Log2 fold change > 1.5) in the conditional Mtsp17 knockout strain were the same as in the SigF knockout strain. Our data suggest that Mtsp17 is likely an activator of desA1 and Mtsp17 regulates the SigF regulon by SigF regulatory pathways through the anti-SigF antagonist MSMEG_0586. Our findings indicate the role of Mtsp17 may be in transcriptional regulation, provide new insights into the molecular mechanisms of START family proteins, and uncover a new node in the regulatory network of mycobacteria.
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Affiliation(s)
- Ying Zhou
- Department of Bone and Joint Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Tianying Zhong
- Guangdong Province Green and High Performance Novel Materials Engineering Research Center, Jiangmen Polytechnic, Jiangmen, China
| | - Wenjing Wei
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
| | - Zhuhua Wu
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
| | - Anping Yang
- School of Medicine, Foshan University, Foshan, Guangdong, China
| | - Ning Liu
- Department of Bone and Joint Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
- * E-mail: (NL); (MW); (XZ)
| | - Ming Wang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- * E-mail: (NL); (MW); (XZ)
| | - Xiaoli Zhang
- School of Medicine, Foshan University, Foshan, Guangdong, China
- * E-mail: (NL); (MW); (XZ)
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18
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Gao Y, Liu H, Zhang K, Li F, Wu M, Xiang Y. A moso bamboo transcription factor, Phehdz1, positively regulates the drought stress response of transgenic rice. PLANT CELL REPORTS 2021; 40:187-204. [PMID: 33098450 DOI: 10.1007/s00299-020-02625-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 10/08/2020] [Indexed: 05/16/2023]
Abstract
78 HD-Zip family genes in Phyllostachys edulis were analyzed. Overexpression of Phehdz1 can improve the drought tolerance of transgenic rice and affect its secondary metabolism. Many studies suggested homeodomain-leucine zipper (HD-Zip) transcription factors are important regulators of plant growth and development, signal transduction, and responses to environmental stresses. In this study, 78 moso bamboo (Phyllostachys edulis) HD-Zip genes were investigated and classified into four subfamilies (HD-Zip I-IV). Additionally, Phehdz1 (HD-Zip I gene) was isolated and confirmed to be highly expressed in the roots. A quantitative real-time PCR analysis indicated Phehdz1 expression was significantly induced by drought, high salinity, and abscisic acid (ABA). A transient expression assay proved that Phehdz1 was localized in the nucleus of tobacco cells. Moreover, it could bind to the core region encoded by the H-box sequence (CAATAATTG) in yeast. In response to mannitol treatments, the Phehdz1-overexpressing transgenic rice had a higher germination rate and longer shoots than the wild-type controls. Moreover, Phehdz1-overexpressing rice plants had a higher survival rate as well as higher relative water and proline contents, but a lower malondialdehyde content, than the WT plants after a 30% polyethylene glycol 6000 treatment. Accordingly, the overexpression of Phehdz1 enhances the drought tolerance of transgenic rice. Many of the differentially expressed genes identified by a transcriptome analysis are involved in MAPK signal transduction and the biosynthesis of secondary metabolites. Thus, the overexpression of Phehdz1 enhances the drought stress tolerance of transgenic rice, while also potentially modulating the expression of metabolism-related genes.
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Affiliation(s)
- Yameng Gao
- National Engineering Laboratory of Crop Stress Resistance Breeding, College of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Huanlong Liu
- National Engineering Laboratory of Crop Stress Resistance Breeding, College of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Kaimei Zhang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Fei Li
- 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
- National Engineering Laboratory of Crop Stress Resistance Breeding, College of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China.
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Zhang J, Wu J, Guo M, Aslam M, Wang Q, Ma H, Li S, Zhang X, Cao S. Genome-wide characterization and expression profiling of Eucalyptus grandis HD-Zip gene family in response to salt and temperature stress. BMC PLANT BIOLOGY 2020; 20:451. [PMID: 33004006 PMCID: PMC7528242 DOI: 10.1186/s12870-020-02677-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 09/24/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND The HD-Zip transcription factors are unique to plants and play an essential role in plant growth, development and stress responses. The HD-Zip transcription factor family consists of a highly conserved homeodomain (HD) and a leucine zipper domain (LZ) domain. Although the HD-Zip gene family has been extensively studied in many plant species, a systematic study of the Eucalyptus HD-Zip family has not been reported until today. Here, we systematically identified 40 HD-Zip genes in Eucalyptus (Eucalyptus grandis). Besides, we comprehensively analyzed the HD-Zips of Eucalyptus by studying the homology, conserved protein regions, gene structure, 3D structure of the protein, location of the genes on the chromosomes and the expression level of the genes in different tissues. RESULTS The HD-Zip family in Eucalyptus has four subfamilies, which is consistent with other plants such as Arabidopsis and rice. Moreover, genes that are in the same group tend to have similar exon-intron structures, motifs, and protein structures. Under salt stress and temperature stress, the Eucalyptus HD-Zip transcription factors show a differential expression pattern. CONCLUSIONS Our findings reveal the response of HD-Zip transcription factors under salt and temperature stresses, laying a foundation for future analysis of Eucalyptus HD-Zip transcription factors.
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Affiliation(s)
- Jiashuo Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Jinzhang Wu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Mingliang Guo
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Mohammad Aslam
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Qi Wang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Huayan Ma
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Shubin Li
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Xingtan Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Shijiang Cao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
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Kumar A, Saripalli G, Jan I, Kumar K, Sharma PK, Balyan HS, Gupta PK. Meta-QTL analysis and identification of candidate genes for drought tolerance in bread wheat ( Triticum aestivum L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:1713-1725. [PMID: 32801498 PMCID: PMC7415061 DOI: 10.1007/s12298-020-00847-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/30/2020] [Accepted: 07/03/2020] [Indexed: 05/18/2023]
Abstract
Meta-QTL (MQTL) analysis for drought tolerance was undertaken in bread wheat to identify consensus and robust MQTLs using 340 known QTLs from 11 earlier studies; 13 MQTLs located on 6 chromosomes (1D, 3B, 5A, 6D, 7A and 7D) were identified, with maximum of 4 MQTLs on chromosome 5A. Mean confidence intervals for MQTLs were much narrower (mean, 6.01 cM; range 2.07-19.46 cM), relative to those in original QTLs (mean, 13.6 cM; range, 1.0-119.1 cM). Two MQTLs, namely MQTL4 and MQTL12, were major MQTLs with potential for use in marker-assisting breeding. As many as 228 candidate genes (CGs) were also identified using 6 of the 13 MQTLs. In-silico expression analysis of these 228 CGs allowed identification of 14 important CGs, with + 3 to - 8 fold change in expression under drought (relative to normal conditions) in a tolerant cv. named TAM107. These CGs encoded proteins belonging to the following families: NAD-dependent epimerase/dehydratase, protein kinase, NAD(P)-binding domain protein, heat shock protein 70 (Hsp70), glycosyltransferase 2-like, etc. Important MQTLs and CGs identified in the present study should prove useful for future molecular breeding and for the study of molecular basis of drought tolerance in cereals in general and wheat in particular.
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Affiliation(s)
- Anuj Kumar
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 India
| | - Gautam Saripalli
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 India
| | - Irfat Jan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 India
| | - Kuldeep Kumar
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 India
| | - P. K. Sharma
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 India
| | - H. S. Balyan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 India
| | - P. K. Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 India
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The HD-ZIP II Transcription Factors Regulate Plant Architecture through the Auxin Pathway. Int J Mol Sci 2020; 21:ijms21093250. [PMID: 32375344 PMCID: PMC7246542 DOI: 10.3390/ijms21093250] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/29/2020] [Accepted: 05/02/2020] [Indexed: 11/17/2022] Open
Abstract
The homeodomain-leucine zipper (HD-ZIP) family transcription factors play important roles in plant growth and development. However, the underlying mechanisms remain largely unclear. Here we found that ATHB2, encoding a HD-ZIP transcription factor, is an early auxin responsive gene. Phenotypic analyses show that overexpression of ATHB2 impairs plant architecture, including reduced plant height and small leaves, and also reduces auxin response in leaves when grown in soil. Simultaneously, the seedlings with chemical induction of ATHB2 exhibit abnormal root gravitropism, a typical auxin-related phenotype. We further show that the auxin response pattern is altered in roots of the inducible ATHB2 seedlings. Consistently, the transcript levels of some auxin biosynthetic and transport genes are significantly decreased in these transgenic seedlings. Further, protein and promoter sequence analyses in common wheat showed that the HD-ZIP II subfamily transcription factors have highly conserved motifs and most of these encoding gene promoters contain the canonical auxin-responsive elements. Expression analyses confirm that some of these HD-ZIP II genes are indeed regulated by auxin in wheat. Together, our results suggest that the HD-ZIP II subfamily transcription factors regulate plant development possibly through the auxin pathway in plants.
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