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Lu Y, Liu D, Kong X, Song Y, Jing L. Pangenome characterization and analysis of the NAC gene family reveals genes for Sclerotinia sclerotiorum resistance in sunflower (Helianthus annuus). BMC Genom Data 2024; 25:39. [PMID: 38693490 PMCID: PMC11064331 DOI: 10.1186/s12863-024-01227-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 04/22/2024] [Indexed: 05/03/2024] Open
Abstract
BACKGROUND Sunflower (Helianthus annuus) is one of the most important economic crops in oilseed production worldwide. The different cultivars exhibit variability in their resistance genes. The NAC transcription factor (TF) family plays diverse roles in plant development and stress responses. With the completion of the H. annuus genome sequence, the entire complement of genes coding for NACs has been identified. However, the reference genome of a single individual cannot cover all the genetic information of the species. RESULTS Considering only a single reference genome to study gene families will miss many meaningful genes. A pangenome-wide survey and characterization of the NAC genes in sunflower species were conducted. In total, 139 HaNAC genes are identified, of which 114 are core and 25 are variable. Phylogenetic analysis of sunflower NAC proteins categorizes these proteins into 16 subgroups. 138 HaNACs are randomly distributed on 17 chromosomes. SNP-based haplotype analysis shows haplotype diversity of the HaNAC genes in wild accessions is richer than in landraces and modern cultivars. Ten HaNAC genes in the basal stalk rot (BSR) resistance quantitative trait loci (QTL) are found. A total of 26 HaNAC genes are differentially expressed in response to Sclerotinia head rot (SHR). A total of 137 HaNAC genes are annotated in Gene Ontology (GO) and are classified into 24 functional groups. GO functional enrichment analysis reveals that HaNAC genes are involved in various functions of the biological process. CONCLUSIONS We identified NAC genes in H. annuus (HaNAC) on a pangenome-wide scale and analyzed S. sclerotiorum resistance-related NACs. This study provided a theoretical basis for further genomic improvement targeting resistance-related NAC genes in sunflowers.
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Affiliation(s)
- Yan Lu
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Dongqi Liu
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiangjiu Kong
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Yang Song
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Lan Jing
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China.
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2
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Zhang S, Han Y, Zeng Q, Wang C, Wang H, Zhang J, Cai M, Lu J, Chen T. Whole-Transcriptome Sequencing Reveals the Global Molecular Responses and NAC Transcription Factors Involved in Drought Stress in Dendrobium catenatum. Antioxidants (Basel) 2024; 13:94. [PMID: 38247518 PMCID: PMC10812421 DOI: 10.3390/antiox13010094] [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: 11/26/2023] [Revised: 01/05/2024] [Accepted: 01/10/2024] [Indexed: 01/23/2024] Open
Abstract
Dendrobium catenatum is a highly drought-tolerant herb, which usually grows on cliffs or in the branches of trees, yet the underlying molecular mechanisms for its tolerance remain poorly understood. We conducted a comprehensive study utilizing whole-transcriptome sequencing approaches to investigate the molecular response to extreme drought stress in D. catenatum. A large number of differentially expressed mRNAs, lncRNAs, and circRNAs have been identified, and the NAC transcription factor family was highly enriched. Meanwhile, 46 genes were significantly up-regulated in the ABA-activated signaling pathway. In addition to the 89 NAC family members accurately identified in this study, 32 members were found to have different expressions between the CK and extreme drought treatment. They may regulate drought stress through both ABA-dependent and ABA-independent pathways. Moreover, the 32 analyzed differentially expressed DcNACs were found to be predominantly expressed in the floral organs and roots. The ceRNA regulatory network showed that DcNAC87 is at the core of the ceRNA network and is regulated by miR169, miR393, and four lncRNAs. These investigations provided valuable information on the role of NAC transcription factors in D. catenatum's response to drought stress.
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Affiliation(s)
| | | | | | | | | | | | | | - Jiangjie Lu
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China; (S.Z.); (Y.H.); (Q.Z.); (C.W.); (H.W.); (J.Z.); (M.C.)
| | - Tao Chen
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China; (S.Z.); (Y.H.); (Q.Z.); (C.W.); (H.W.); (J.Z.); (M.C.)
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3
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Gao J, Ma G, Chen J, Gichovi B, Cao L, Liu Z, Chen L. The B3 gene family in Medicago truncatula: Genome-wide identification and the response to salt stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108260. [PMID: 38096733 DOI: 10.1016/j.plaphy.2023.108260] [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: 09/06/2023] [Revised: 11/08/2023] [Accepted: 12/03/2023] [Indexed: 02/15/2024]
Abstract
The B3 family genes constitute a pivotal group of transcription factors that assume diverse roles in the growth, development, and response to both biotic and abiotic stresses in plants. Medicago truncatula is a diploid plant with a relatively small genome, adopted as a model species for legumes genetics and functional genomic research. In this study, 173 B3 genes were identified in the M. truncatula genome, and classified into seven subgroups by phylogenetic analysis. Collinearity analysis revealed that 18 MtB3 gene pairs arose from segmented replication events. Analysis of expression patterns disclosed that 61 MtB3s exhibited a spectrum of expression profiles across various tissues and in the response to salt stress, indicating their potential involvement in salt stress signaling response. Among these genes, MtB3-53 exhibited tissue-specific differential expression and demonstrated a rapid response to salt stress induction. Overexpression of MtB3-53 gene in Arabidopsis improves salt stress tolerance by increasing plant biomass and chlorophyll content, while reducing leaf cell membrane damage. Moreover, salt treatment resulted in more up-regulation of AtABF1, AtABI3, AtHKT1, AtKIN1, AtNHX1, and AtRD29A in MtB3-53 transgenic Arabidopsis plants compared to the wild type, providing evidences that MtB3-53 enhances plant salt tolerance not only by modulating ion homeostasis but also by stimulating the production of antioxidants, which leads to the alleviation of cellular damage caused by salt stress. In conclusion, this study provides a fundamental basis for future investigations into the B3 gene family and its capacity to regulate plant responses to environmental stressors.
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Affiliation(s)
- Jing Gao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China; State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan, 430074, China.
| | - Guangjing Ma
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China; State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan, 430074, China.
| | - Junjie Chen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074, China; State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan, 430074, China.
| | - Bancy Gichovi
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China; State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan, 430074, China.
| | - Liwen Cao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074, China; Academician Workstation of Agricultural High-tech Industrial Area of the Yellow River Delta, National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying, 257300, China; State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan, 430074, China.
| | - Zhihao Liu
- Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Normal University, Huangshi, 435002, China.
| | - Liang Chen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074, China; Academician Workstation of Agricultural High-tech Industrial Area of the Yellow River Delta, National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying, 257300, China; State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan, 430074, China.
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4
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Pan Y, Zhuang Y, Liu T, Chen H, Wang L, Varshney RK, Zhuang W, Wang X. Deciphering peanut complex genomes paves a way to understand its origin and domestication. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2173-2181. [PMID: 37523347 PMCID: PMC10579718 DOI: 10.1111/pbi.14125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 06/12/2023] [Accepted: 07/01/2023] [Indexed: 08/02/2023]
Abstract
Peanut (Arachis) is a key oil and protein crop worldwide with large genome. The genomes of diploid and tetraploid peanuts have been sequenced, which were compared to decipher their genome structures, evolutionary, and life secrets. Genome sequencing efforts showed that different cultivars, although Bt homeologs being more privileged in gene retention and gene expression. This subgenome bias, extended to sequence variation and point mutation, might be related to the long terminal repeat (LTR) explosions after tetraploidization, especially in At subgenomes. Except that, whole-genome sequences revealed many important genes, for example, fatty acids and triacylglycerols pathway, NBS-LRR (nucleotide-binding site-leucine-rich repeats), and seed size decision genes, were enriched after recursive polyploidization. Each ancestral polyploidy, with old ones having occurred hundreds of thousand years ago, has thousands of duplicated genes in extant genomes, contributing to genetic novelty. Notably, although full genome sequences are available, the actual At subgenome ancestor has still been elusive, highlighted with new debate about peanut origin. Although being an orphan crop lagging behind other crops in genomic resources, the genome sequencing achievement has laid a solid foundation for advancing crop enhancement and system biology research of peanut.
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Affiliation(s)
- Yuxin Pan
- Center for Genomics and Computational BiologyCollege of Life Science, and College of ScienceNorth China University of Science and TechnologyTangshanHebeiChina
| | - Yuhui Zhuang
- Fujian Provincial Key Laboratory of Plant Molecular and Cell BiologyOil Crops Research InstituteState Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Tao Liu
- Center for Genomics and Computational BiologyCollege of Life Science, and College of ScienceNorth China University of Science and TechnologyTangshanHebeiChina
| | - Hua Chen
- Fujian Provincial Key Laboratory of Plant Molecular and Cell BiologyOil Crops Research InstituteState Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Lihui Wang
- Fujian Provincial Key Laboratory of Plant Molecular and Cell BiologyOil Crops Research InstituteState Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Rajeev K. Varshney
- State Agricultural Biotechnology Centre, and Centre for Crop & Food InnovationFood Futures InstituteMurdoch UniversityMurdochWest AustraliaAustralia
| | - Weijian Zhuang
- Fujian Provincial Key Laboratory of Plant Molecular and Cell BiologyOil Crops Research InstituteState Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Xiyin Wang
- Center for Genomics and Computational BiologyCollege of Life Science, and College of ScienceNorth China University of Science and TechnologyTangshanHebeiChina
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5
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Wang Q, Hu F, Yao Z, Zhao X, Chu G, Ye J. Comprehensive genomic characterisation of the NAC transcription factor family and its response to drought stress in Eucommia ulmoides. PeerJ 2023; 11:e16298. [PMID: 37901460 PMCID: PMC10601904 DOI: 10.7717/peerj.16298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/23/2023] [Indexed: 10/31/2023] Open
Abstract
The NAC transcription factor family enhances plant adaptation to environmental challenges by participating in signalling pathways triggered by abiotic stressors and hormonal cues. We identified 69 NAC genes in the Eucommia ulmoides genome and renamed them according to their chromosomal distribution. These EuNAC proteins were clustered into 13 sub-families and distributed on 16 chromosomes and 2 scaffolds. The gene structures suggested that the number of exons varied from two to eight among these EuNACs, with a multitude of them containing three exons. Duplicated events resulted in a large gene family; 12 and four pairs of EuNACs were the result of segmental and tandem duplicates, respectively. The drought-stress response pattern of 12 putative EuNACs was observed under drought treatment, revealing that these EuNACs could play crucial roles in mitigating the effects of drought stress responses and serve as promising candidate genes for genetic engineering aimed at enhancing the drought stress tolerance of E. ulmoides. This study provides insight into the evolution, diversity, and characterisation of NAC genes in E. ulmoides and will be helpful for future characterisation of putative EuNACs associated with water deficit.
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Affiliation(s)
- Qi Wang
- Laboratory of Forestry Department, Agricultural College, Shihezi University, Shihezi, China
| | - FengCheng Hu
- Lveyang County Forest Tree Seedling Workstation, Forestry Bureau of Lveyang County, Lveyang, China
| | - ZhaoQun Yao
- Laboratory of Plant Protection Department, Agricultural College, Shihezi University, Shihezi, China
| | - XinFeng Zhao
- Lveyang County Forest Tree Seedling Workstation, Forestry Bureau of Lveyang County, Lveyang, China
| | - GuangMing Chu
- Laboratory of Forestry Department, Agricultural College, Shihezi University, Shihezi, China
| | - Jing Ye
- Laboratory of Forestry Department, Agricultural College, Shihezi University, Shihezi, China
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6
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Bouzroud S, Henkrar F, Fahr M, Smouni A. Salt stress responses and alleviation strategies in legumes: a review of the current knowledge. 3 Biotech 2023; 13:287. [PMID: 37520340 PMCID: PMC10382465 DOI: 10.1007/s13205-023-03643-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 05/21/2023] [Indexed: 08/01/2023] Open
Abstract
Salinity is one of the most significant environmental factors limiting legumes development and productivity. Salt stress disturbs all developmental stages of legumes and affects their hormonal regulation, photosynthesis and biological nitrogen fixation, causing nutritional imbalance, plant growth inhibition and yield losses. At the molecular level, salt stress exposure involves large number of factors that are implicated in stress perception, transduction, and regulation of salt responsive genes' expression through the intervention of transcription factors. Along with the complex gene network, epigenetic regulation mediated by non-coding RNAs, and DNA methylation events are also involved in legumes' response to salinity. Different alleviation strategies can increase salt tolerance in legume plants. The most promising ones are Plant Growth Promoting Rhizobia, Arbuscular Mycorrhizal Fungi, seed and plant's priming. Genetic manipulation offers an effective approach for improving salt tolerance. In this review, we present a detailed overview of the adverse effect of salt stress on legumes and their molecular responses. We also provide an overview of various ameliorative strategies that have been implemented to mitigate/overcome the harmful effects of salt stress on legumes.
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Affiliation(s)
- Sarah Bouzroud
- Equipe de Microbiologie et Biologie Moléculaire, Centre de Biotechnologie Végétale et Microbienne Biodiversité et Environnement, Faculté des Sciences, Université Mohammed V de Rabat, 10000 Rabat, Morocco
| | - Fatima Henkrar
- Laboratoire de Biotechnologie et Physiologie Végétales, Centre de Biotechnologie Végétale et Microbienne Biodiversité et Environnement, Faculté des Sciences, Université Mohammed V de Rabat, 10000 Rabat, Morocco
- Laboratoire Mixte International Activité Minière Responsable “LMI-AMIR”, IRD/UM5R/INAU, 10000 Rabat, Morocco
| | - Mouna Fahr
- Laboratoire de Biotechnologie et Physiologie Végétales, Centre de Biotechnologie Végétale et Microbienne Biodiversité et Environnement, Faculté des Sciences, Université Mohammed V de Rabat, 10000 Rabat, Morocco
- Laboratoire Mixte International Activité Minière Responsable “LMI-AMIR”, IRD/UM5R/INAU, 10000 Rabat, Morocco
| | - Abdelaziz Smouni
- Laboratoire de Biotechnologie et Physiologie Végétales, Centre de Biotechnologie Végétale et Microbienne Biodiversité et Environnement, Faculté des Sciences, Université Mohammed V de Rabat, 10000 Rabat, Morocco
- Laboratoire Mixte International Activité Minière Responsable “LMI-AMIR”, IRD/UM5R/INAU, 10000 Rabat, Morocco
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7
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Abdul Aziz M, Masmoudi K. Insights into the Transcriptomics of Crop Wild Relatives to Unravel the Salinity Stress Adaptive Mechanisms. Int J Mol Sci 2023; 24:9813. [PMID: 37372961 DOI: 10.3390/ijms24129813] [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: 04/19/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 06/29/2023] Open
Abstract
The narrow genomic diversity of modern cultivars is a major bottleneck for enhancing the crop's salinity stress tolerance. The close relatives of modern cultivated plants, crop wild relatives (CWRs), can be a promising and sustainable resource to broaden the diversity of crops. Advances in transcriptomic technologies have revealed the untapped genetic diversity of CWRs that represents a practical gene pool for improving the plant's adaptability to salt stress. Thus, the present study emphasizes the transcriptomics of CWRs for salinity stress tolerance. In this review, the impacts of salt stress on the plant's physiological processes and development are overviewed, and the transcription factors (TFs) regulation of salinity stress tolerance is investigated. In addition to the molecular regulation, a brief discussion on the phytomorphological adaptation of plants under saline environments is provided. The study further highlights the availability and use of transcriptomic resources of CWR and their contribution to pangenome construction. Moreover, the utilization of CWRs' genetic resources in the molecular breeding of crops for salinity stress tolerance is explored. Several studies have shown that cytoplasmic components such as calcium and kinases, and ion transporter genes such as Salt Overly Sensitive 1 (SOS1) and High-affinity Potassium Transporters (HKTs) are involved in the signaling of salt stress, and in mediating the distribution of excess Na+ ions within the plant cells. Recent comparative analyses of transcriptomic profiling through RNA sequencing (RNA-Seq) between the crops and their wild relatives have unraveled several TFs, stress-responsive genes, and regulatory proteins for generating salinity stress tolerance. This review specifies that the use of CWRs transcriptomics in combination with modern breeding experimental approaches such as genomic editing, de novo domestication, and speed breeding can accelerate the CWRs utilization in the breeding programs for enhancing the crop's adaptability to saline conditions. The transcriptomic approaches optimize the crop genomes with the accumulation of favorable alleles that will be indispensable for designing salt-resilient crops.
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Affiliation(s)
- Mughair Abdul Aziz
- Integrative Agriculture Department, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain 15551, United Arab Emirates
| | - Khaled Masmoudi
- Integrative Agriculture Department, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain 15551, United Arab Emirates
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Kapazoglou A, Gerakari M, Lazaridi E, Kleftogianni K, Sarri E, Tani E, Bebeli PJ. Crop Wild Relatives: A Valuable Source of Tolerance to Various Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12020328. [PMID: 36679041 PMCID: PMC9861506 DOI: 10.3390/plants12020328] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 05/27/2023]
Abstract
Global climate change is one of the major constraints limiting plant growth, production, and sustainability worldwide. Moreover, breeding efforts in the past years have focused on improving certain favorable crop traits, leading to genetic bottlenecks. The use of crop wild relatives (CWRs) to expand genetic diversity and improve crop adaptability seems to be a promising and sustainable approach for crop improvement in the context of the ongoing climate challenges. In this review, we present the progress that has been achieved towards CWRs exploitation for enhanced resilience against major abiotic stressors (e.g., water deficiency, increased salinity, and extreme temperatures) in crops of high nutritional and economic value, such as tomato, legumes, and several woody perennial crops. The advances in -omics technologies have facilitated the elucidation of the molecular mechanisms that may underlie abiotic stress tolerance. Comparative analyses of whole genome sequencing (WGS) and transcriptomic profiling (RNA-seq) data between crops and their wild relative counterparts have unraveled important information with respect to the molecular basis of tolerance to abiotic stressors. These studies have uncovered genomic regions, specific stress-responsive genes, gene networks, and biochemical pathways associated with resilience to adverse conditions, such as heat, cold, drought, and salinity, and provide useful tools for the development of molecular markers to be used in breeding programs. CWRs constitute a highly valuable resource of genetic diversity, and by exploiting the full potential of this extended allele pool, new traits conferring abiotic-stress tolerance may be introgressed into cultivated varieties leading to superior and resilient genotypes. Future breeding programs may greatly benefit from CWRs utilization for overcoming crop production challenges arising from extreme environmental conditions.
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Affiliation(s)
- Aliki Kapazoglou
- Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Department of Vitis, Hellenic Agricultural Organization-Dimitra (ELGO-Dimitra), Sofokli Venizelou 1, Lykovrysi, 14123 Athens, Greece
| | - Maria Gerakari
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Efstathia Lazaridi
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Konstantina Kleftogianni
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Efi Sarri
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Eleni Tani
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Penelope J. Bebeli
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
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Shen Q, Qian Z, Wang T, Zhao X, Gu S, Rao X, Lyu S, Zhang R, He L, Li F. Genome-wide identification and expression analysis of the NAC transcription factor family in Saccharum spontaneum under different stresses. PLANT SIGNALING & BEHAVIOR 2022; 17:2088665. [PMID: 35730557 PMCID: PMC9225438 DOI: 10.1080/15592324.2022.2088665] [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] [Indexed: 05/15/2023]
Abstract
The NAC (NAM, ATAF1/2, and CUC2) transcription factor family is one of the largest families unique to plants and is involved in plant growth and development, organs, morphogenesis, and stress responses. The NAC family has been identified in many plants. As the main source of resistance genes for sugarcane breeding, the NAC gene family in the wild species Saccharum spontaneum has not been systematically studied. In this study, 115 SsNAC genes were identified in the S. spontaneum genome, and these genes were heterogeneously distributed on 25 chromosomes. Phylogenetic analysis divided the SsNAC family members into 18 subgroups, and the gene structure and conserved motif analysis further supported the phylogenetic classification. Four groups of tandemly duplicated genes and nine pairs of segmentally duplicated genes were detected. The SsNAC gene has different expression patterns at different developmental stages of stems and leaves. Further qRT-PCR analysis showed that drought, low-temperature, salinity, pathogenic fungi, and other stresses as well as abscisic acid (ABA) and methyl jasmonate (MeJA) treatments significantly induced the expression of 12 SsNAC genes, indicating that these genes may play a key role in the resistance of S. spontaneum to biotic and abiotic stresses. In summary, the results from this study provide comprehensive information on the NAC transcription factor family, providing a reference for further functional studies of the SsNAC gene.
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Affiliation(s)
- Qingqing Shen
- Sugarcane Research Institute, Yunnan Agricultural University, Kunming, Yunnan, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Zhenfeng Qian
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Tianju Wang
- Institute for Bio-resources Research and Development of Central Yunnan Plateau, Chuxiong Normal University, Chuxiong, China
| | - Xueting Zhao
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Shujie Gu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Xibing Rao
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Shaozhi Lyu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Rongqiong Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Lilian He
- Sugarcane Research Institute, Yunnan Agricultural University, Kunming, Yunnan, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
- CONTACT Lilian He Sugarcane Research Institute, Yunnan Agricultural University, Kunming, China
| | - Fusheng Li
- Sugarcane Research Institute, Yunnan Agricultural University, Kunming, Yunnan, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
- Key Laboratory for Crop Production and Smart Agriculture of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan, China
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Liu Y, Shen Y, Liang M, Zhang X, Xu J, Shen Y, Chen Z. Identification of Peanut AhMYB44 Transcription Factors and Their Multiple Roles in Drought Stress Responses. PLANTS (BASEL, SWITZERLAND) 2022; 11:3522. [PMID: 36559634 PMCID: PMC9788490 DOI: 10.3390/plants11243522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/13/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
MYB transcription factors (TFs) comprise a large gene family that plays an important role in plant growth, development, stress responses, and defense regulation. However, their functions in peanut remain to be further elucidated. Here, we identified six AhMYB44 genes (AhMYB44-01/11, AhMYB44-05/15, and AhMYB44-06/16) in cultivated peanut. They are typical R2R3-MYB TFs and have many similarities but different expression patterns in response to drought stress, suggesting different functions under drought stress. Homologous genes with higher expression in each pair were selected for further study. All of them were nuclear proteins and had no self-transactivation activity. In addition, we compared the performances of different lines at germination, seedling, and adult stages under drought stress. After drought treatment, the overexpression of AhMYB44-11 transgenic plants resulted in the longest root length at the seedling stage. Levels of proline, soluble sugar and chlorophyll, and expression levels of stress-related genes, including P5CS1, RD29A, CBF1, and COR15A, were higher than those of the wild type (WT) at the adult stage. While the overexpression of AhMYB44-16 significantly increased the drought sensitivity of plants at all stages, with differential ABA content, the expression levels of the ABA-related genes PP2CA and ABI1 were significantly upregulated and those of ABA1 and ABA2 were significantly downregulated compared with the WT. AhMYB44-05 showed similar downregulated expression as AhMYB44-16 under drought stress, but its overexpression in Arabidopsis did not significantly affect the drought resistance of transgenic plants. Based on the results, we propose that AhMYB44-11 plays a role as a positive factor in drought tolerance by increasing the transcription abundance of stress-related genes and the accumulation of osmolytes, while AhMYB44-16 negatively regulates drought tolerance through its involvement in ABA-dependent stress response pathways.
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Affiliation(s)
| | | | | | | | | | - Yi Shen
- Correspondence: (Y.S.); (Z.C.)
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11
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Du Z, You S, Yang D, Tao Y, Zhu Y, Sun W, Chen Z, Li J. Comprehensive analysis of the NAC transcription factor gene family in Kandelia obovata reveals potential members related to chilling tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:1048822. [PMID: 36466244 PMCID: PMC9714628 DOI: 10.3389/fpls.2022.1048822] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/03/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Kandelia obovata is an important mangrove species extensively distributed in Eastern Asia that is susceptible to low-temperature stress. NAC (NAM, ATAF1/2 and CUC2) domain proteins are transcription factors (TFs) that play various roles in plant growth and development and in the plant response to environmental stresses. Nevertheless, genome-wide analyses of K. obovata NAC genes (KoNACs) and their responses to chilling stress have rarely been studied. METHODS The KoNAC gene family was identified and characterized using bioinformatic analysis, the subcellular location of some NAC proteins was confirmed using confocal microscopy analysis, and the KoNACs that responded to chilling stress were screened using RNA-seq and qRT-PCR analysis. RESULTS A total of 79 KoNACs were identified, and they were unequally distributed across all 18 chromosomes of K. obovata. The KoNAC proteins could be divided into 16 subgroups according to the phylogenetic tree based on NAC family members of Arabidopsis thaliana. The KoNACs exhibited greater synteny with A. thaliana sequences than with Oryza sativa sequences, indicating that KoNACs underwent extensive evolution after the divergence of dicotyledons and monocotyledons. Segmental duplication was the main driving force of the expansions of KoNAC genes. Confocal microscopy analysis verified that the four randomly selected KoNACs localized to the nucleus, indicating the accuracy of the bioinformatic predictions. Tissue expression pattern analysis demonstrated that some KoNAC genes showed tissue-specific expression, suggesting that these KoNACs might be important for plant development and growth. Additionally, the expression levels of 19 KoNACs were significantly (15 positively and 4 negatively) induced by cold treatment, demonstrating that these KoNACs might play important roles during cold stress responses and might be candidate genes for the genetic engineering of K. obovata with enhanced chilling stress tolerance. Coexpression network analysis revealed that 381 coexpressed pairs (between 13 KoNACs and 284 other genes) were significantly correlated. CONCLUSIONS Seventy-nine KoNACs were identified in K. obovata, nineteen of which displayed chilling-induced expression patterns. These genes may serve as candidates for functional analyses of KoNACs engaged in chilling stress. Our results lay the foundation for evolutionary analyses of KoNACs and their molecular mechanisms in response to environmental stress.
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Affiliation(s)
- Zhaokui Du
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Shixian You
- Section of Maritime Space and Island Management, Yuhuan Municipal Bureau of Natural Resources and Planning, Yuhuan, China
| | - Dang Yang
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Yutian Tao
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Yunxiao Zhu
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Wen Sun
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Zhengman Chen
- Department of Security Production Management, Taizhou Circular Economy Development Co., Ltd., Taizhou, China
| | - Junmin Li
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
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12
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Venkatesh B, Vennapusa AR, Kumar NJ, Jayamma N, Reddy BM, Johnson AMA, Madhusudan KV, Pandurangaiah M, Kiranmai K, Sudhakar C. Co-expression of stress-responsive regulatory genes, MuNAC4, MuWRKY3 and MuMYB96 associated with resistant-traits improves drought adaptation in transgenic groundnut ( Arachis hypogaea l.) plants. FRONTIERS IN PLANT SCIENCE 2022; 13:1055851. [PMID: 36466254 PMCID: PMC9709484 DOI: 10.3389/fpls.2022.1055851] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/28/2022] [Indexed: 05/24/2023]
Abstract
Groundnut, cultivated under rain-fed conditions is prone to yield losses due to intermittent drought stress. Drought tolerance is a complex phenomenon and multiple gene expression required to maintain the cellular tolerance. Transcription factors (TFs) regulate many functional genes involved in tolerance mechanisms. In this study, three stress-responsive regulatory TFs cloned from horse gram, (Macrotyloma uniflorum (Lam) Verdc.), MuMYB96, involved in cuticular wax biosynthesis; MuWRKY3, associated with anti-oxidant defense mechanism and MuNAC4, tangled with lateral root development were simultaneously expressed to enhance drought stress resistance in groundnut (Arachis hypogaea L.). The multigene transgenic groundnut lines showed reduced ROS production, membrane damage, and increased superoxide dismutase (SOD) and ascorbate peroxidase (APX) enzyme activity, evidencing improved antioxidative defense mechanisms under drought stress. Multigene transgenic plants showed lower proline content, increased soluble sugars, epicuticular wax content and higher relative water content suggesting higher maintenance of tissue water status compared to wildype and mock plants. The scanning electron microscopy (SEM) analysis showed a substantial increase in deposition of cuticular waxes and variation in stomatal number in multigene transgenic lines compared to wild type and mock plants. The multigene transgenic plants showed increased growth of lateral roots, chlorophyll content, and stay-green nature in drought stress compared to wild type and mock plants. Expression analysis of transgenes, MuMYB96, MuWRKY3, and MuNAC4 and their downstream target genes, KCS6, KCR1, APX3, CSD1, LBD16 and DBP using qRT-PCR showed a two- to four-fold increase in transcript levels in multigene transgenic groundnut plants over wild type and mock plants under drought stress. Our study demonstrate that introducing multiple genes with simultaneous expression of genes is a viable option to improve stress tolerance and productivity under drought stress.
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Affiliation(s)
- Boya Venkatesh
- Plant Molecular Biology Laboratory, Department of Botany, Sri Krishnadevaraya University, Anantapuram, India
| | - Amaranatha R. Vennapusa
- Department of Agriculture and Natural Resources, Delaware State University, Dover, DE, United States
| | - Nulu Jagadeesh Kumar
- Plant Molecular Biology Laboratory, Department of Botany, Sri Krishnadevaraya University, Anantapuram, India
| | - N. Jayamma
- Plant Molecular Biology Laboratory, Department of Botany, Sri Krishnadevaraya University, Anantapuram, India
| | - B. Manohara Reddy
- Department of Botany, Government College (Autonomous), Anantapuram, India
| | | | - K. V. Madhusudan
- Department of Botany, Government College, Cluster University, Kurnool, India
| | - Merum Pandurangaiah
- Plant Molecular Biology Laboratory, Department of Botany, Sri Krishnadevaraya University, Anantapuram, India
| | - K. Kiranmai
- Plant Molecular Biology Laboratory, Department of Botany, Sri Krishnadevaraya University, Anantapuram, India
| | - Chinta Sudhakar
- Plant Molecular Biology Laboratory, Department of Botany, Sri Krishnadevaraya University, Anantapuram, India
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13
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Genome-Wide Identification of Membrane-Bound Fatty Acid Desaturase Genes in Three Peanut Species and Their Expression in Arachis hypogaea during Drought Stress. Genes (Basel) 2022; 13:genes13101718. [PMID: 36292603 PMCID: PMC9601973 DOI: 10.3390/genes13101718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 09/17/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022] Open
Abstract
As a crop irrigated primarily by rain, the quality and yield of peanuts are significantly limited by drought. To date, many studies have indicated that fatty acid desaturase (FAD) genes enhance plant tolerance to drought stresses. In this study, 16, 15, and 31 FADs were identified in Arachis duranensis, Arachis ipaensis, and Arachis hypogaea, respectively. All the FADs were divided into four subfamilies, which had relatively conserved gene structures, motifs, and domains. The synteny relationships and chromosomal position analysis showed that the FADs in subgenome pairs, A. duranensis-A. hypogaea (AA) and A. ipaensis-A. hypogaea (BB), were homologous, and their physical locations were consistent. The Ka/Ks results indicated that nine FAD genes underwent a purifying selection, and Ah|FAD3.2 experienced positive selection during tetraploid peanut speciation. Various cis-acting elements related to hormone signaling and stress responsiveness in promoters and the predicted miRNA targeting Ah|FADs suggested that these genes play crucial roles in drought tolerance. The expression profiles of Ah|FADs in 22 tissues and drought-tolerant and -sensitive cultivars under drought stress suggested that 4 and 6 FADs were putative genes related to oil accumulation and drought, respectively. These findings will help provide insight into the potential functional roles of the FAD genes, which may aid in dealing with plant drought stress.
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14
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Song H, Liu Y, Dong G, Zhang M, Wang Y, Xin J, Su Y, Sun H, Yang M. Genome-Wide Characterization and Comprehensive Analysis of NAC Transcription Factor Family in Nelumbo nucifera. Front Genet 2022; 13:901838. [PMID: 35754820 PMCID: PMC9214227 DOI: 10.3389/fgene.2022.901838] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/17/2022] [Indexed: 11/18/2022] Open
Abstract
NAC (NAM, ATAF, and CUC) is a ubiquitously expressed plant-specific transcription factor (TF) family which is involved in the regulation of various biological processes. However, a systematic characterization of NAC gene family is yet to be reported in lotus. Here, 82 NnNAC genes which included five predicted membrane-bound NAC proteins were identified in the lotus genome. Phylogenetic analysis revealed seven-subfamily clusters (I–VII) of NnNAC proteins, with homologous gene pairs displaying similar conserved motifs and gene structure characteristics. Transactivation assay of NnNAC proteins revealed an extensive transcriptional activation capacity which is mediated by the highly divergent C-terminal activation domain (AD). Expression analysis of NnNAC genes in lotus tissues showed high transcript levels in root, stamen, petal and seed coat. In addition, 30 and 29 differentially expressed NnNAC candidate genes putatively involved in lotus seed development and response to complete submergence stress, respectively, were identified. Overall, our study provides potentially useful candidate gene resources for future molecular breeding of lotus varieties with novel agronomic traits.
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Affiliation(s)
- Heyun Song
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yanling Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | | | - Minghua Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuxin Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jia Xin
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yanyan Su
- Amway (China) Botanical R&D Centre, Wuxi, China
| | - Heng Sun
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Mei Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
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15
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Li Q, Qin Y, Hu X, Jin L, Li G, Gong Z, Xiong X, Wang W. Physiology and Gene Expression Analysis of Potato ( Solanum tuberosum L.) in Salt Stress. PLANTS (BASEL, SWITZERLAND) 2022; 11:1565. [PMID: 35736717 PMCID: PMC9229698 DOI: 10.3390/plants11121565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
The production of potato (Solanum tuberosum L.) faces a severe challenge due to the salinization of arable land worldwide. The cultivation of salt-tolerant potatoes is of great significance to ensure food security. In this study, two cultivars of 'Longshu 5' and 'Qingshu 9' were compared for physiological responses to salt stress, and then the salt tolerance of the two cultivars were assessed via principal component analysis. Furthermore, the Na+, K+, and Ca2+ flux of the cultivars under salt stress was recorded. Finally, the expression levels of ion transport-related genes and transcription factors in salt-tolerant cultivars were explored under NaCl stress. The results showed that the seven physiological indicators of salt tolerance were differed between the cultivars. Interestingly, soluble protein and sugar were early responsive to salt stress than proline in the salt-tolerance cultivar. Peroxidase and superoxide dismutase activity were significantly different in 'Longshu 5' under NaCl stress and without being significantly different in 'Qingshu9'. In addition, the salt tolerance of 'Longshu 5' was more tolerant than 'Qingshu 9' based on principal component evaluation. Meanwhile, the strong efflux of Na+, the stability of K+, and the high absorption of Ca2+ in 'Longshu 5' indicated salt adaption mechanisms in the salt-tolerant potato. In addition, we found that ion transport-related genes and transcription factors, such as StSOS1, StNHX4, StAKT1, StNAC24, and StCYP707A, played a role in the salt tolerance of 'Longshu 5'. In conclusion, the salt-tolerant potato can regulate physiological substances to adapt to salt stress, and ion transport related genes and transcription factors play a role in improving salt tolerance.
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Affiliation(s)
- Qing Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Root and Tuber Crops, Ministry of Agriculture, Beijing 100081, China; (Q.L.); (L.J.); (G.L.)
- College of Horticulture, Hunan Agricultural University, Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education Changsha, Hunan Provincial Engineering Research Center for Potatoes, Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Key Laboratory for Vegetable Biology of Hunan Province, Changsha 410128, China; (Y.Q.); (X.H.)
| | - Yuzhi Qin
- College of Horticulture, Hunan Agricultural University, Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education Changsha, Hunan Provincial Engineering Research Center for Potatoes, Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Key Laboratory for Vegetable Biology of Hunan Province, Changsha 410128, China; (Y.Q.); (X.H.)
| | - Xinxi Hu
- College of Horticulture, Hunan Agricultural University, Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education Changsha, Hunan Provincial Engineering Research Center for Potatoes, Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Key Laboratory for Vegetable Biology of Hunan Province, Changsha 410128, China; (Y.Q.); (X.H.)
| | - Liping Jin
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Root and Tuber Crops, Ministry of Agriculture, Beijing 100081, China; (Q.L.); (L.J.); (G.L.)
| | - Guangcun Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Root and Tuber Crops, Ministry of Agriculture, Beijing 100081, China; (Q.L.); (L.J.); (G.L.)
| | - Zhenping Gong
- Tangshan Academy of Agricultural Sciences, Tangshan 063001, China;
| | - Xingyao Xiong
- College of Horticulture, Hunan Agricultural University, Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education Changsha, Hunan Provincial Engineering Research Center for Potatoes, Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Key Laboratory for Vegetable Biology of Hunan Province, Changsha 410128, China; (Y.Q.); (X.H.)
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Wanxing Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Root and Tuber Crops, Ministry of Agriculture, Beijing 100081, China; (Q.L.); (L.J.); (G.L.)
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16
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Genome-Wide Identification of the NAC Gene Family in Zanthoxylum bungeanum and Their Transcriptional Responses to Drought Stress. Int J Mol Sci 2022; 23:ijms23094769. [PMID: 35563160 PMCID: PMC9103986 DOI: 10.3390/ijms23094769] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/22/2022] [Accepted: 04/22/2022] [Indexed: 12/13/2022] Open
Abstract
NAC (NAM, ATAF1/2, and CUC2) transcription factors (TFs) are one of the largest plant-specific TF families and play a pivotal role in adaptation to abiotic stresses. The genome-wide analysis of NAC TFs is still absent in Zanthoxylum bungeanum. Here, 109 ZbNAC proteins were identified from the Z. bungeanum genome and were classified into four groups with Arabidopsis NAC proteins. The 109 ZbNAC genes were unevenly distributed on 46 chromosomes and included 4 tandem duplication events and 17 segmental duplication events. Synteny analysis of six species pairs revealed the closely phylogenetic relationship between Z. bungeanum and C. sinensis. Twenty-four types of cis-elements were identified in the ZbNAC promoters and were classified into three types: abiotic stress, plant growth and development, and response to phytohormones. Co-expression network analysis of the ZbNACs revealed 10 hub genes, and their expression levels were validated by real-time quantitative polymerase chain reaction (qRT-PCR). Finally, ZbNAC007, ZbNAC018, ZbNAC047, ZbNAC072, and ZbNAC079 were considered the pivotal NAC genes for drought tolerance in Z. bungeanum. This study represented the first genome-wide analysis of the NAC family in Z. bungeanum, improving our understanding of NAC proteins and providing useful information for molecular breeding of Z. bungeanum.
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17
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Sun S, Li X, Gao S, Nie N, Zhang H, Yang Y, He S, Liu Q, Zhai H. A Novel WRKY Transcription Factor from Ipomoea trifida, ItfWRKY70, Confers Drought Tolerance in Sweet Potato. Int J Mol Sci 2022; 23:686. [PMID: 35054868 PMCID: PMC8775875 DOI: 10.3390/ijms23020686] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/03/2022] [Accepted: 01/06/2022] [Indexed: 01/27/2023] Open
Abstract
WRKY transcription factors are one of the important families in plants, and have important roles in plant growth, abiotic stress responses, and defense regulation. In this study, we isolated a WRKY gene, ItfWRKY70, from the wild relative of sweet potato Ipomoea trifida (H.B.K.) G. Don. This gene was highly expressed in leaf tissue and strongly induced by 20% PEG6000 and 100 μM abscisic acid (ABA). Subcellar localization analyses indicated that ItfWRKY70 was localized in the nucleus. Overexpression of ItfWRKY70 significantly increased drought tolerance in transgenic sweet potato plants. The content of ABA and proline, and the activity of SOD and POD were significantly increased, whereas the content of malondialdehyde (MDA) and H2O2 were decreased in transgenic plants under drought stress. Overexpression of ItfWRKY70 up-regulated the genes involved in ABA biosynthesis, stress-response, ROS-scavenging system, and stomatal aperture in transgenic plants under drought stress. Taken together, these results demonstrated that ItfWRKY70 plays a positive role in drought tolerance by accumulating the content of ABA, regulating stomatal aperture and activating the ROS scavenging system in sweet potato.
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Affiliation(s)
- Sifan Sun
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China; (S.S.); (X.L.); (S.G.); (N.N.); (H.Z.); (Y.Y.); (S.H.); (Q.L.)
| | - Xu Li
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China; (S.S.); (X.L.); (S.G.); (N.N.); (H.Z.); (Y.Y.); (S.H.); (Q.L.)
| | - Shaopei Gao
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China; (S.S.); (X.L.); (S.G.); (N.N.); (H.Z.); (Y.Y.); (S.H.); (Q.L.)
| | - Nan Nie
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China; (S.S.); (X.L.); (S.G.); (N.N.); (H.Z.); (Y.Y.); (S.H.); (Q.L.)
| | - Huan Zhang
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China; (S.S.); (X.L.); (S.G.); (N.N.); (H.Z.); (Y.Y.); (S.H.); (Q.L.)
| | - Yufeng Yang
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China; (S.S.); (X.L.); (S.G.); (N.N.); (H.Z.); (Y.Y.); (S.H.); (Q.L.)
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Postgraduate T&R Base of Zhengzhou University, Zhengzhou 450000, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450000, China
| | - Shaozhen He
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China; (S.S.); (X.L.); (S.G.); (N.N.); (H.Z.); (Y.Y.); (S.H.); (Q.L.)
| | - Qingchang Liu
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China; (S.S.); (X.L.); (S.G.); (N.N.); (H.Z.); (Y.Y.); (S.H.); (Q.L.)
| | - Hong Zhai
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China; (S.S.); (X.L.); (S.G.); (N.N.); (H.Z.); (Y.Y.); (S.H.); (Q.L.)
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18
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Zhou H, Liang X, Feng N, Zheng D, Qi D. Effect of uniconazole to soybean seed priming treatment under drought stress at VC stage. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 224:112619. [PMID: 34403945 DOI: 10.1016/j.ecoenv.2021.112619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 06/13/2023]
Abstract
Studying the mechanism of drought stress in soybean root at vegetative cotyledon (VC) stage by soaking seeds with uniconazole revealed new insights into soybean stress physiology. Therefore, a completely random pot experiments with different time gradients for water cut-off (24, 48, 72, 96 and 120 h, respectively) were carried out with uniconazole (0.4 mgL-1) with respect to morphological, microscopic, ultramicroscopic, physiological, and molecular studies on varieties Hefeng55 (H50, drought tolerant variety) and Kenfeng16 (K16, drought susceptible variety). Results revealed that uniconazole effectively alleviated the inhibition on root growth caused by drought stress, increased the number of root tips, significantly reduced lignification of vessels, alleviated the damage of mitochondria and nucleus caused by drought stress, further strengthened osmotic adjustment system and antioxidant system, especially when the soil moisture content was less than 14%, broke expression restriction of IAA due to drought stress, and inhibited GA3 generation; finally, we found that high-intensity drought stress significantly increased the expression levels of GmNAC003, GmNAC004, GmNAC015, GmNAC020, GmHK07, GmRR01, GmRR02 and GmRR16 genes relating to drought tolerance, while uniconazole had a significant inhibitory effect on GmNAC003, GmNAC004, GmNAC015, GmNAC020, GmRR01, GmRR02 and GmRR16 genes. Our results provided a reference for the mechanism of drought resistance in legume and the effect of uniconazole on alleviating drought stress.
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Affiliation(s)
- Hang Zhou
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524000, China; Shenzhen Reseach Institute of Guangdong Ocean University, Shenzhen 518108, China
| | - Xiaoyan Liang
- College of Agronomy, Heilongjiang Bayi Agricultural University, Daqing 163000, China
| | - Naijie Feng
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524000, China; Shenzhen Reseach Institute of Guangdong Ocean University, Shenzhen 518108, China.
| | - Dianfeng Zheng
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524000, China; Shenzhen Reseach Institute of Guangdong Ocean University, Shenzhen 518108, China.
| | - Deqiang Qi
- College of Agronomy, Heilongjiang Bayi Agricultural University, Daqing 163000, China
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Zhao N, Cui S, Li X, Liu B, Deng H, Liu Y, Hou M, Yang X, Mu G, Liu L. Transcriptome and Co-expression Network Analyses Reveal Differential Gene Expression and Pathways in Response to Severe Drought Stress in Peanut ( Arachis hypogaea L.). Front Genet 2021; 12:672884. [PMID: 33995498 PMCID: PMC8120245 DOI: 10.3389/fgene.2021.672884] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/06/2021] [Indexed: 01/23/2023] Open
Abstract
Drought is one of the major abiotic stress factors limiting peanut production. It causes the loss of pod yield during the pod formation stage. Here, one previously identified drought-tolerant cultivar, "L422" of peanut, was stressed by drought (35 ± 5%) at pod formation stage for 5, 7, and 9 days. To analyze the drought effects on peanut, we conducted physiological and transcriptome analysis in leaves under well-watered (CK1, CK2, and CK3) and drought-stress conditions (T1, T2, and T3). By transcriptome analysis, 3,586, 6,730, and 8,054 differentially expressed genes (DEGs) were identified in "L422" at 5 days (CK1 vs T1), 7 days (CK2 vs T2), and 9 days (CK3 vs T3) of drought stress, respectively, and 2,846 genes were common DEGs among the three-time points. Furthermore, the result of weighted gene co-expression network analysis (WGCNA) revealed one significant module that was closely correlated between drought stress and physiological data. A total of 1,313 significantly up-/down-regulated genes, including 61 transcription factors, were identified in the module at three-time points throughout the drought stress stage. Additionally, six vital metabolic pathways, namely, "MAPK signaling pathway-plant," "flavonoid biosynthesis," "starch and sucrose metabolism," "phenylpropanoid biosynthesis," "glutathione metabolism," and "plant hormone signal transduction" were enriched in "L422" under severe drought stress. Nine genes responding to drought tolerance were selected for quantitative real-time PCR (qRT-PCR) verification and the results agreed with transcriptional profile data, which reveals the reliability and accuracy of transcriptome data. Taken together, these findings could lead to a better understanding of drought tolerance and facilitate the breeding of drought-resistant peanut cultivars.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Lifeng Liu
- State Key Laboratory for Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
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