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Cong L, Shi YK, Gao XY, Zhao XF, Zhang HQ, Zhou FL, Zhang HJ, Ma BQ, Zhai R, Yang CQ, Wang ZG, Ma FW, Xu LF. Transcription factor PbNAC71 regulates xylem and vessel development to control plant height. PLANT PHYSIOLOGY 2024; 195:395-409. [PMID: 38198215 DOI: 10.1093/plphys/kiae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/13/2023] [Accepted: 12/08/2023] [Indexed: 01/12/2024]
Abstract
Dwarfism is an important agronomic trait in fruit breeding programs. However, the germplasm resources required to generate dwarf pear (Pyrus spp.) varieties are limited. Moreover, the mechanisms underlying dwarfism remain unclear. In this study, "Yunnan" quince (Cydonia oblonga Mill.) had a dwarfing effect on "Zaosu" pear. Additionally, the dwarfism-related NAC transcription factor gene PbNAC71 was isolated from pear trees comprising "Zaosu" (scion) grafted onto "Yunnan" quince (rootstock). Transgenic Nicotiana benthamiana and pear OHF-333 (Pyrus communis) plants overexpressing PbNAC71 exhibited dwarfism, with a substantially smaller xylem and vessel area relative to the wild-type controls. Yeast one-hybrid, dual-luciferase, chromatin immunoprecipitation-qPCR, and electrophoretic mobility shift assays indicated that PbNAC71 downregulates PbWalls are thin 1 expression by binding to NAC-binding elements in its promoter. Yeast two-hybrid assays showed that PbNAC71 interacts with the E3 ubiquitin ligase PbRING finger protein 217 (PbRNF217). Furthermore, PbRNF217 promotes the ubiquitin-mediated degradation of PbNAC71 by the 26S proteasome, thereby regulating plant height as well as xylem and vessel development. Our findings reveal a mechanism underlying pear dwarfism and expand our understanding of the molecular basis of dwarfism in woody plants.
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Affiliation(s)
- Liu Cong
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Yi-Ke Shi
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Xin-Yi Gao
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Xiao-Fei Zhao
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Hai-Qi Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Feng-Li Zhou
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Hong-Juan Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Bai-Quan Ma
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Rui Zhai
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Cheng-Quan Yang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Zhi-Gang Wang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Feng-Wang Ma
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Ling-Fei Xu
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province 712100, China
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Deng Z, Yang Z, Liu X, Dai X, Zhang J, Deng K. Genome-Wide Identification and Expression Analysis of C3H Zinc Finger Family in Potato ( Solanum tuberosum L.). Int J Mol Sci 2023; 24:12888. [PMID: 37629069 PMCID: PMC10454627 DOI: 10.3390/ijms241612888] [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: 07/10/2023] [Revised: 08/11/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
Transcription factors containing a CCCH structure (C3H) play important roles in plant growth and development, and their stress response, but research on the C3H gene family in potato has not been reported yet. In this study, we used bioinformatics to identify 50 C3H genes in potato and named them StC3H-1 to StC3H-50 according to their location on chromosomes, and we analyzed their physical and chemical properties, chromosome location, phylogenetic relationship, gene structure, collinearity relationship, and cis-regulatory element. The gene expression pattern analysis showed that many StC3H genes are involved in potato growth and development, and their response to diverse environmental stresses. Furthermore, RT-qPCR data showed that the expression of many StC3H genes was induced by high temperatures, indicating that StC3H genes may play important roles in potato response to heat stress. In addition, Some StC3H genes were predominantly expressed in the stolon and developing tubers, suggesting that these StC3H genes may be involved in the regulation of tuber development. Together, these results provide new information on StC3H genes and will be helpful for further revealing the function of StC3H genes in the heat stress response and tuber development in potato.
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Affiliation(s)
- Zeyi Deng
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (Z.D.); (Z.Y.); (X.L.); (X.D.); (J.Z.)
| | - Zhijiang Yang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (Z.D.); (Z.Y.); (X.L.); (X.D.); (J.Z.)
| | - Xinyan Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (Z.D.); (Z.Y.); (X.L.); (X.D.); (J.Z.)
| | - Xiumei Dai
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (Z.D.); (Z.Y.); (X.L.); (X.D.); (J.Z.)
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Jiankui Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (Z.D.); (Z.Y.); (X.L.); (X.D.); (J.Z.)
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Kexuan Deng
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (Z.D.); (Z.Y.); (X.L.); (X.D.); (J.Z.)
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
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Xia F, Liang X, Tan L, Sun W, Dai X, Yan H. Genome-Wide Identification, Evolution and Expression Profile Analysis of NAC Transcription Factor in Simmondsia chinensis. Curr Issues Mol Biol 2023; 45:5422-5436. [PMID: 37504260 PMCID: PMC10378596 DOI: 10.3390/cimb45070344] [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: 05/10/2023] [Revised: 06/16/2023] [Accepted: 06/25/2023] [Indexed: 07/29/2023] Open
Abstract
NAC transcription factors (TFs) are one of the largest plant-specific gene families and play important roles in plant growth, development, and the biotic and abiotic stress response. Although the sequencing of Jojoba (Simmondsia chinensis) has been completed, the genome-wide identification and analysis of its NAC TFs has not been reported. In this study, a total of 57 genes were identified in Jojoba, which were divided into eight groups based on phylogenetic analysis. The genes clustered in the same groups have a similar gene structure and motif distribution. Based on the analysis of cis-elements in NAC TFs, nine cis-acting elements were identified in the promoter region that involved in light response, hormonal response, and stress response. Synteny analysis showed a greater collinearity between Jojoba and V. vinifera than Arabidopsis thaliana. The 24 genes in the Jojoba NAC TFs are derived from fragment replication, which may be the main source of NAC amplification. Gene expression analysis identified seven genes that were highly expressed in seeds. The differential expression analysis of NAC TFs in cotyledon and embryonic axis tissues showed that the expression of 10 genes was up-regulated and 1 gene was down-regulated. This study provides more information on the classification, gene structure, conserved motif, and evolution of NAC TFs in Jojoba, facilitating further exploration of their specific functional analysis in Jojoba seed development.
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Affiliation(s)
- Fan Xia
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China
| | - Xiaoyu Liang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China
| | - Lina Tan
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China
| | - Wen Sun
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China
| | - Xiaogang Dai
- Key Laboratory of Tree Breeding & Germplasm Improvement, Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Hanwei Yan
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China
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Xu Y, Li P, Ma F, Huang D, Xing W, Wu B, Sun P, Xu B, Song S. Characterization of the NAC Transcription Factor in Passion Fruit ( Passiflora edulis) and Functional Identification of PeNAC-19 in Cold Stress. PLANTS (BASEL, SWITZERLAND) 2023; 12:1393. [PMID: 36987081 PMCID: PMC10051797 DOI: 10.3390/plants12061393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/07/2023] [Accepted: 03/13/2023] [Indexed: 06/19/2023]
Abstract
The NAC (NAM, ATAF and CUC) gene family plays an important role in plant development and abiotic stress response. However, up to now, the identification and research of the NAC (PeNAC) family members of passion fruit are still lacking. In this study, 25 PeNACs were identified from the passion fruit genome, and their functions under abiotic stress and at different fruit-ripening stages were analyzed. Furthermore, we analyzed the transcriptome sequencing results of PeNACs under four various abiotic stresses (drought, salt, cold and high temperature) and three different fruit-ripening stages, and verified the expression results of some genes by qRT-PCR. Additionally, tissue-specific analysis showed that most PeNACs were mainly expressed in flowers. In particular, PeNAC-19 was induced by four various abiotic stresses. At present, low temperatures have seriously endangered the development of passion fruit cultivation. Therefore, PeNAC-19 was transformed into tobacco, yeast and Arabidopsis to study their function of resisting low temperature. The results show that PeNAC-19 responded to cold stress significantly in tobacco and Arabidopsis, and could improve the low temperature tolerance of yeast. This study not only improved the understanding of the PeNAC gene family characteristics and evolution, but also provided new insights into the regulation of the PeNAC gene at different stages of fruit maturation and abiotic stresses.
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Affiliation(s)
- Yi Xu
- State Key Laboratory of Biological Breeding for Tropical Crops, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Germplasm Repository of Passiflora, Hainan Province, Hainan 571101, China
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya 571101, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 571101, China
| | - Pengfei Li
- College of Tropical Crops, Yunnan Agricultural University, Kunming 650201, China
| | - Funing Ma
- State Key Laboratory of Biological Breeding for Tropical Crops, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Germplasm Repository of Passiflora, Hainan Province, Hainan 571101, China
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya 571101, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 571101, China
| | - Dongmei Huang
- State Key Laboratory of Biological Breeding for Tropical Crops, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Germplasm Repository of Passiflora, Hainan Province, Hainan 571101, China
| | - Wenting Xing
- State Key Laboratory of Biological Breeding for Tropical Crops, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Germplasm Repository of Passiflora, Hainan Province, Hainan 571101, China
| | - Bin Wu
- State Key Laboratory of Biological Breeding for Tropical Crops, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Germplasm Repository of Passiflora, Hainan Province, Hainan 571101, China
| | - Peiguang Sun
- State Key Laboratory of Biological Breeding for Tropical Crops, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Germplasm Repository of Passiflora, Hainan Province, Hainan 571101, China
| | - Binqiang Xu
- State Key Laboratory of Biological Breeding for Tropical Crops, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Germplasm Repository of Passiflora, Hainan Province, Hainan 571101, China
| | - Shun Song
- State Key Laboratory of Biological Breeding for Tropical Crops, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Germplasm Repository of Passiflora, Hainan Province, Hainan 571101, China
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya 571101, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 571101, China
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Liu J, Qiao Y, Li C, Hou B. The NAC transcription factors play core roles in flowering and ripening fundamental to fruit yield and quality. FRONTIERS IN PLANT SCIENCE 2023; 14:1095967. [PMID: 36909440 PMCID: PMC9996081 DOI: 10.3389/fpls.2023.1095967] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
Fruits are derived from flowers and play an important role in human food, nutrition, and health. In general, flowers determine the crop yield, and ripening affects the fruit quality. Although transcription factors (TFs) only account for a small part of plant transcriptomes, they control the global gene expression and regulation. The plant-specific NAC (NAM, ATAF, and CUC) TFs constitute a large family evolving concurrently with the transition of both aquatic-to-terrestrial plants and vegetative-to-reproductive growth. Thus, NACs play an important role in fruit yield and quality by determining shoot apical meristem (SAM) inflorescence and controlling ripening. The present review focuses on the various properties of NACs together with their function and regulation in flower formation and fruit ripening. Hitherto, we have a better understanding of the molecular mechanisms of NACs in ripening through abscisic acid (ABA) and ethylene (ETH), but how NACs regulate the expression of the inflorescence formation-related genes is largely unknown. In the future, we should focus on the analysis of NAC redundancy and identify the pivotal regulators of flowering and ripening. NACs are potentially vital manipulation targets for improving fruit quantity and quality.
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Affiliation(s)
- Jianfeng Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuyuan Qiao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cui Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bingzhu Hou
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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Lee MH, Park J, Kim KH, Kim KM, Kang CS, Lee GE, Choi JY, Shon J, Ko JM, Choi C. Genome-Wide Association Study of Arabinoxylan Content from a 562 Hexaploid Wheat Collection. PLANTS (BASEL, SWITZERLAND) 2023; 12:184. [PMID: 36616313 PMCID: PMC9823421 DOI: 10.3390/plants12010184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 06/17/2023]
Abstract
The selection of wheat varieties with high arabinoxylan (AX) levels could effectively improve the daily consumption of dietary fiber. However, studies on the selection of markers for AX levels are scarce. This study analyzed AX levels in 562 wheat genotypes collected from 46 countries using a GWAS with the BLINK model in the GAPIT3. Wheat genotypes were classified into eight subpopulations that exhibited high genetic differentiation based on 31,926 SNP loci. Eight candidate genes were identified, among which those encoding F-box domain-containing proteins, disease resistance protein RPM1, and bZIP transcription factor 29 highly correlated with AX levels. The AX level was higher in the adenine allele than in the guanine alleles of these genes in the wheat collection. In addition, the AX level was approximately 10% higher in 3 adenine combinations than 2 guanine, 1 adenine, and 3 guanine combinations in genotypes of three genes (F-box domain-containing proteins, RPM1, and bZIP transcription factor 29). The adenine allele, present in 97.46% of AX-95086356 SNP, exhibited a high correlation with AX levels following classification by country. Notably, the East Asian wheat genotypes contain high adenine alleles in three genes. These results highlight the potential of these three SNPs to serve as selectable markers for high AX content.
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Meng L, Chen S, Li D, Huang M, Zhu S. Genome-Wide Characterization and Evolutionary Expansion of Poplar NAC Transcription Factors and Their Tissue-Specific Expression Profiles under Drought. Int J Mol Sci 2022; 24:ijms24010253. [PMID: 36613699 PMCID: PMC9820422 DOI: 10.3390/ijms24010253] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022] Open
Abstract
The NAC (NAM, ATAF1/2 and CUC2) is a large gene family of plant-specific transcription factors that play a pivotal role in various physiological processes and abiotic stresses. Due to the lack of genome-wide characterization, intraspecific and interspecific synteny, and drought-responsive expression pattern of NAC genes in poplar, the functional characterization of drought-related NAC genes have been scarcely reported in Populus species. Here, we identified a total of 170 NAC domain-containing genes in the P. trichocarpa genome, 169 of which were unevenly distributed on its nineteen chromosomes. These NAC genes were phylogenetically divided into twenty subgroups, some of which exhibited a similar pattern of exon-intron architecture. The synteny and Ka/Ks analysis indicated that the expansion of NAC genes in poplar was mainly due to gene duplication events occurring before and after the divergence of Populus and Salix. Ten PdNAC (P. deltoids × P. euramericana cv.'Nanlin895') genes were randomly selected and cloned. Their drought-responsive expression profiles showed a tissue-specific pattern. The transcription factor PdNAC013 was verified to be localized in the nucleus. Our research results provide genomic information for the expansion of NAC genes in the poplar genome, and for further characterizing putative poplar NAC genes associated with water-deficit.
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Affiliation(s)
- Lu Meng
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Siyuan Chen
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Dawei Li
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Minren Huang
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Sheng Zhu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Correspondence: or
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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: 0] [Impact Index Per Article: 0] [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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Genome-Wide Identification and Expression Analysis of the NAC Gene Family in Alfalfa Revealed Its Potential Roles in Response to Multiple Abiotic Stresses. Int J Mol Sci 2022; 23:ijms231710015. [PMID: 36077414 PMCID: PMC9456191 DOI: 10.3390/ijms231710015] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/16/2022] [Accepted: 08/23/2022] [Indexed: 01/19/2023] Open
Abstract
NAC (NAM, ATAF1/2, and CUC2) transcription factors compose one of the largest families of plant-specific transcription factors; they are widely involved in plant growth and development and have especially important roles in improving stress resistance in plants. However, NAC gene family members in alfalfa (Medicago sativa L.) have not been systematically identified and analyzed genome-wide due to the complexity of the alfalfa reference genome. In this study, a total of 421 M. sativa NAC genes (MsNACs) were identified from the alfalfa “Xinjiangdaye” reference genome. Basic bioinformatics analysis, including characterization of sequence length, protein molecular weight and genome position and conserved motif analysis, was conducted. Expression analysis showed that 47 MsNACs had tissue-specific expression, and 64 MsNACs were expressed in all tissues. The transcriptomic profiles of the genes were very different, indicating that these MsNACs have various functions in alfalfa growth and development. We identified 25, 42 and 47 MsNACs that respond to cold, drought and salt stress based on transcriptome data analysis and real-time quantitative PCR (RT−qPCR). Furthermore, 22 MsNACs were found to respond to both salt and drought stress, and 15 MsNACs were found to respond to cold, salt and drought stress. The results of this study could provide valuable information for further functional analysis of MsNACs and for the improvement of stress resistance in alfalfa.
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Tariq R, Hussain A, Tariq A, Khalid MHB, Khan I, Basim H, Ingvarsson PK. Genome-wide analyses of the mung bean NAC gene family reveals orthologs, co-expression networking and expression profiling under abiotic and biotic stresses. BMC PLANT BIOLOGY 2022; 22:343. [PMID: 35836131 PMCID: PMC9284730 DOI: 10.1186/s12870-022-03716-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/28/2022] [Indexed: 05/03/2023]
Abstract
BACKGROUND Mung bean is a short-duration and essential food crop owing to its cash prominence in Asia. Mung bean seeds are rich in protein, fiber, antioxidants, and phytonutrients. The NAC transcription factors (TFs) family is a large plant-specific family, participating in tissue development regulation and abiotic and biotic stresses. RESULTS In this study, we perform genome-wide comparisons of VrNAC with their homologs from Arabidopsis. We identified 81 NAC transcription factors (TFs) in mung bean genome and named as per their chromosome location. A phylogenetic analysis revealed that VrNACs are broadly distributed in nine groups. Moreover, we identified 20 conserved motifs across the VrNACs highlighting their roles in different biological process. Based on the gene structure of the putative VrNAC and segmental duplication events might be playing a vital role in the expansion of mung bean genome. A comparative phylogenetic analysis of mung bean NAC together with homologs from Arabidopsis allowed us to classify NAC genes into 13 groups, each containing several orthologs and paralogs. Gene ontology (GO) analysis categorized the VrNACs into biological process, cellular components and molecular functions, explaining the functions in different plant physiology processes. A gene co-expression network analysis identified 173 genes involved in the transcriptional network of putative VrNAC genes. We also investigated how miRNAs potentially target VrNACs and shape their interactions with proteins. VrNAC1.4 (Vradi01g03390.1) was targeted by the Vra-miR165 family, including 9 miRNAs. Vra-miR165 contributes to leaf development and drought tolerance. We also performed qRT-PCR on 22 randomly selected VrNAC genes to assess their expression patterns in the NM-98 genotype, widely known for being tolerant to drought and bacterial leaf spot disease. CONCLUSIONS This genome-wide investigation of VrNACs provides a unique resource for further detailed investigations aimed at predicting orthologs functions and what role the play under abiotic and biotic stress, with the ultimate aim to improve mung bean production under diverse environmental conditions.
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Affiliation(s)
- Rezwan Tariq
- Department of Plant Protection, Akdeniz University, 07070, Antalya, Turkey
| | - Ammara Hussain
- Department of Biotechnology, University of Okara, Punjab, 56300, Pakistan
| | - Arslan Tariq
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Muhammad Hayder Bin Khalid
- College of agronomy, Sichuan Agricultural University, Ya'an, China
- National Research Center of intercropping, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Imran Khan
- State Key Laboratory of Grassland Agro-Ecosystem, Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou, 730020, China
| | - Huseyin Basim
- Department of Plant Protection, Akdeniz University, 07070, Antalya, Turkey.
| | - Pär K Ingvarsson
- Linnean Centre for Plan Biology, Department of Plant Biology, Swedish University of Agricultural Sciences, SE75007, Uppsala, Sweden.
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11
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Genome-Wide Identification and Analysis of bZIP Gene Family and Resistance of TaABI5 ( TabZIP96) under Freezing Stress in Wheat ( Triticum aestivum). Int J Mol Sci 2022; 23:ijms23042351. [PMID: 35216467 PMCID: PMC8874521 DOI: 10.3390/ijms23042351] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/02/2022] [Accepted: 02/15/2022] [Indexed: 01/07/2023] Open
Abstract
The basic leucine zipper (bZIP) regulates plant growth and responds to stress as a key transcription factor of the Abscisic acid (ABA) signaling pathway. In this study, TabZIP genes were identified in wheat and the gene structure, physicochemical properties, cis-acting elements, and gene collinearity were analyzed. RNA-Seq and qRT-PCR analysis showed that ABA and abiotic stress induced most TabZIP genes expression. The ectopic expression of TaABI5 up-regulated the expression of several cold-responsive genes in Arabidopsis. Physiological indexes of seedlings of different lines under freezing stress showed that TaABI5 enhanced the freezing tolerance of plants. Subcellular localization showed that TaABI5 is localized in the nucleus. Furthermore, TaABI5 physically interacted with cold-resistant transcription factor TaICE1 in yeast two-hybrid system. In conclusion, this study identified and analyzed members of the TabZIP gene family in wheat. It proved for the first time that the gene TaABI5 affected the cold tolerance of transgenic plants and was convenient for us to understand the cold resistance molecular mechanism of TaABI5. These results will provide a new inspiration for further study on improving plant abiotic stress resistance.
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12
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HuNAC20 and HuNAC25, Two Novel NAC Genes from Pitaya, Confer Cold Tolerance in Transgenic Arabidopsis. Int J Mol Sci 2022; 23:ijms23042189. [PMID: 35216304 PMCID: PMC8876859 DOI: 10.3390/ijms23042189] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/11/2022] [Accepted: 02/11/2022] [Indexed: 11/21/2022] Open
Abstract
NAC transcription factors are one of the largest families of transcriptional regulators in plants, and members of the gene family play vital roles in regulating plant growth and development processes including biotic/abiotic stress responses. However, little information is available about the NAC family in pitaya. In this study, we conducted a genome-wide analysis and a total of 64 NACs (named HuNAC1-HuNAC64) were identified in pitaya (Hylocereus). These genes were grouped into fifteen subgroups with diversities in gene proportions, exon–intron structures, and conserved motifs. Genome mapping analysis revealed that HuNAC genes were unevenly scattered on all eleven chromosomes. Synteny analysis indicated that the segmental duplication events played key roles in the expansion of the pitaya NAC gene family. Expression levels of these HuNAC genes were analyzed under cold treatments using qRT-PCR. Four HuNAC genes, i.e., HuNAC7, HuNAC20, HuNAC25, and HuNAC30, were highly induced by cold stress. HuNAC7, HuNAC20, HuNAC25, and HuNAC30 were localized exclusively in the nucleus. HuNAC20, HuNAC25, and HuNAC30 were transcriptional activators while HuNAC7 was a transcriptional repressor. Overexpression of HuNAC20 and HuNAC25 in Arabidopsis thaliana significantly enhanced tolerance to cold stress through decreasing ion leakage, malondialdehyde (MDA), and H2O2 and O2− accumulation, accompanied by upregulating the expression of cold-responsive genes (AtRD29A, AtCOR15A, AtCOR47, and AtKIN1). This study presents comprehensive information on the understanding of the NAC gene family and provides candidate genes to breed new pitaya cultivars with tolerance to cold conditions through genetic transformation.
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13
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Liu GS, Li HL, Grierson D, Fu DQ. NAC Transcription Factor Family Regulation of Fruit Ripening and Quality: A Review. Cells 2022; 11:cells11030525. [PMID: 35159333 PMCID: PMC8834055 DOI: 10.3390/cells11030525] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/27/2022] [Accepted: 01/31/2022] [Indexed: 01/18/2023] Open
Abstract
The NAC transcription factor (TF) family is one of the largest plant-specific TF families and its members are involved in the regulation of many vital biological processes during plant growth and development. Recent studies have found that NAC TFs play important roles during the ripening of fleshy fruits and the development of quality attributes. This review focuses on the advances in our understanding of the function of NAC TFs in different fruits and their involvement in the biosynthesis and signal transduction of plant hormones, fruit textural changes, color transformation, accumulation of flavor compounds, seed development and fruit senescence. We discuss the theoretical basis and potential regulatory models for NAC TFs action and provide a comprehensive view of their multiple roles in modulating different aspects of fruit ripening and quality.
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Affiliation(s)
- Gang-Shuai Liu
- Laboratory of Fruit Biology, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China; (G.-S.L.); (H.-L.L.)
| | - Hong-Li Li
- Laboratory of Fruit Biology, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China; (G.-S.L.); (H.-L.L.)
| | - Donald Grierson
- Laboratory of Fruit Quality Biology, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China;
- Plant Sciences Division, School of Biosciences, Sutton Bonington Campus, University of Nottingham, Loughborough LE12 5RD, UK
| | - Da-Qi Fu
- Laboratory of Fruit Biology, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China; (G.-S.L.); (H.-L.L.)
- Correspondence:
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14
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Wang R, Xue Y, Fan J, Yao JL, Qin M, Lin T, Lian Q, Zhang M, Li X, Li J, Sun M, Song B, Zhang J, Zhao K, Chen X, Hu H, Fei Z, Xue C, Wu J. A systems genetics approach reveals PbrNSC as a regulator of lignin and cellulose biosynthesis in stone cells of pear fruit. Genome Biol 2021; 22:313. [PMID: 34776004 PMCID: PMC8590786 DOI: 10.1186/s13059-021-02531-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 10/29/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Stone cells in fruits of pear (Pyrus pyrifolia) negatively influence fruit quality because their lignified cell walls impart a coarse and granular texture to the fruit flesh. RESULTS We generate RNA-seq data from the developing fruits of 206 pear cultivars with a wide range of stone cell contents and use a systems genetics approach to integrate co-expression networks and expression quantitative trait loci (eQTLs) to characterize the regulatory mechanisms controlling lignocellulose formation in the stone cells of pear fruits. Our data with a total of 35,897 expressed genes and 974,404 SNPs support the identification of seven stone cell formation modules and the detection of 139,515 eQTLs for 3229 genes in these modules. Focusing on regulatory factors and using a co-expression network comprising 39 structural genes, we identify PbrNSC as a candidate regulator of stone cell formation. We then verify the function of PbrNSC in regulating lignocellulose formation using both pear fruit and Arabidopsis plants and further show that PbrNSC can transcriptionally activate multiple target genes involved in secondary cell wall formation. CONCLUSIONS This study generates a large resource for studying stone cell formation and provides insights into gene regulatory networks controlling the formation of stone cell and lignocellulose.
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Affiliation(s)
- Runze Wang
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yongsong Xue
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jing Fan
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, 430072, China
| | - Jia-Long Yao
- The New Zealand Institute for Plant & Food Research Limited, Auckland, 1025, New Zealand
| | - Mengfan Qin
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tao Lin
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
- College of Horticulture, China Agricultural University, Beijing, 100083, China
| | - Qun Lian
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Mingyue Zhang
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China
| | - Xiaolong Li
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Jiaming Li
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Manyi Sun
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bobo Song
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiaying Zhang
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kejiao Zhao
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xu Chen
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hongju Hu
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, 430072, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA.
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA.
| | - Cheng Xue
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China.
| | - Jun Wu
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
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15
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Zhang H, Xu J, Chen H, Jin W, Liang Z. Characterization of NAC family genes in Salvia miltiorrhiza and NAC2 potentially involved in the biosynthesis of tanshinones. PHYTOCHEMISTRY 2021; 191:112932. [PMID: 34454170 DOI: 10.1016/j.phytochem.2021.112932] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 08/22/2021] [Accepted: 08/23/2021] [Indexed: 06/13/2023]
Abstract
The NAC (NAM, ATAF, and CUC) family members are specific transcription factors in plants. The large family is involved in many plant growth and developmental processes, as well as in abiotic/biotic stress responses. It has been well studied in the genomes of various plants, including Arabidopsis thaliana, tomato, and quinoa. However, identification and functional studies of NAC family members in medicinal Salvia miltiorrhiza are limited. Here, we systematically identified 84 NAC genes and named them according to their gene IDs in the recently sequenced genome. The phylogeny of NAC family protein sequences was analyzed using bioinformatics methods, which divided them into nine subfamilies. Then, their chromosomal locations, gene structures and conserved domains were analyzed comprehensively. To further investigate the regulatory functions of NACs in S. miltiorrhiza, we analyzed the response of 10 selected NAC genes to methyl jasmonate and used NAC2 for transgenic experiments. The overexpression of Sm-NAC2 decreased the tanshinone I and IIA contents by 56% and 62%, respectively. However, Sm-NAC2-RNAi promoted the accumulation of four tanshinones, tanshinone I, tanshinone IIA, cryptotanshinone, and dihydrotanshinone I, which increased 3.68-, 4.1-, 3.13- and 5.9- fold, respectively, compared with wild type. In the tanshinone biosynthetic pathways, the overexpression of Sm-NAC2 down-regulated CYP76AH1, and the silencing of Sm-NAC2 up-regulated the expression levels of HMGR1, DXS2, KSL2, and CYP76AH1. This study provides information on the evolution of Sm-NAC genes and their possible functions, and it lays a foundation for further research into the NAC family-associated regulation of tanshinone biosynthesis.
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Affiliation(s)
- Haihua Zhang
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Jinfeng Xu
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Haimin Chen
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Weibo Jin
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| | - Zongsuo Liang
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
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16
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Gao Y, Yang Q, Yan X, Wu X, Yang F, Li J, Wei J, Ni J, Ahmad M, Bai S, Teng Y. High-quality genome assembly of 'Cuiguan' pear (Pyrus pyrifolia) as a reference genome for identifying regulatory genes and epigenetic modifications responsible for bud dormancy. HORTICULTURE RESEARCH 2021; 8:197. [PMID: 34465760 PMCID: PMC8408243 DOI: 10.1038/s41438-021-00632-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 06/09/2021] [Accepted: 06/13/2021] [Indexed: 05/26/2023]
Abstract
Dormancy-associated MADS-box (DAM) genes serve as crucial regulators of the endodormancy cycle in rosaceous plants. Although pear DAM genes have been identified previously, the lack of a high-quality reference genome and techniques to study gene function have prevented accurate genome-wide analysis and functional verification of such genes. Additionally, the contribution of other genes to the regulation of endodormancy release remains poorly understood. In this study, a high-quality genome assembly for 'Cuiguan' pear (Pyrus pyrifolia), which is a leading cultivar with a low chilling requirement cultivated in China, was constructed using PacBio and Hi-C technologies. Using this genome sequence, we revealed that pear DAM genes were tandemly clustered on Chr8 and Chr15 and were differentially expressed in the buds between 'Cuiguan' and the high-chilling-requirement cultivar 'Suli' during the dormancy cycle. Using a virus-induced gene silencing system, we determined the repressive effects of DAM genes on bud break. Several novel genes potentially involved in the regulation of endodormancy release were identified by RNA sequencing and H3K4me3 chromatin immunoprecipitation sequencing analyses of 'Suli' buds during artificial chilling using the new reference genome. Our findings enrich the knowledge of the regulatory mechanism underlying endodormancy release and chilling requirements and provide a foundation for the practical regulation of dormancy release in fruit trees as an adaptation to climate change.
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Affiliation(s)
- Yuhao Gao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Qinsong Yang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Key Laboratory for Silviculture and Conservation, Ministry of Education, Beijing Forestry University, Haidian District, Beijing, 100083, China
| | - Xinhui Yan
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Xinyue Wu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Feng Yang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jianzhao Li
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- College of Agriculture, Ludong University, Yantai, Shandong, 264025, China
| | - Jia Wei
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Junbei Ni
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Mudassar Ahmad
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Songling Bai
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Yuanwen Teng
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Hainan Institute of Zhejiang University, Sanya, Hainan, 572000, China
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17
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Jiang L, Sun Q, Wang Y, Chang P, Kong H, Luo C, He X. Genome-wide identification and characterization of NAC genes in Brassica juncea var. tumida. PeerJ 2021; 9:e11212. [PMID: 33996278 PMCID: PMC8106399 DOI: 10.7717/peerj.11212] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 03/15/2021] [Indexed: 01/05/2023] Open
Abstract
Background NAC (NAM, ATAF1/2, and CUC2) transcription factors play an important role in plant growth and development. However, in tumorous stem mustard (Brassica juncea var. tumida), one of the economically important crops cultivated in southwest China and some southeast Asian countries, reports on the identification of NAC family genes are lacking. In this study, we conducted a genome-wide investigation of the NAC family genes in B. juncea var. tumida, based on its recently published genome sequence data. Methods The NAC genes were identified in B. juncea var. tumida using the bioinformatics approach on the whole genome level. Additionally, the expression of BjuNAC genes was analyzed under high- and low-temperature stresses by quantitative real-time PCR (qRT-PCR). Results A total of 300 BjuNAC genes were identified, of which 278 were mapped to specific chromosomes. Phylogenetic analysis of B. juncea var. tumida, Brassica rapa, Brassica nigra, rice and Arabidopsis thaliana NAC proteins revealed that all NAC genes were divided into 18 subgroups. Furthermore, gene structure analysis showed that most of the NAC genes contained two or three exons. Conserved motif analysis revealed that BjuNAC genes contain a conserved NAM domain. Additionally, qRT-PCR data indicated that thirteen BjuNAC genes with a varying degree of up-regulation during high-temperature stress. Conversely, four BjuNAC genes (BjuNAC006, BjuNAC083, BjuNAC170 and BjuNAC223) were up-regulated and two BjuNAC genes (BjuNAC074 and BjuNAC295) down-regulated under low temperature, respectively. Together, the results of this study provide a strong foundation for future investigation of the biological function of NAC genes in B. juncea var. tumida.
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Affiliation(s)
- Longxing Jiang
- Chongqing Key Laboratory on Big Data for Bio Intelligence, College of Bioinformation, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Quan Sun
- Chongqing Key Laboratory on Big Data for Bio Intelligence, College of Bioinformation, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Yu Wang
- Chongqing Key Laboratory on Big Data for Bio Intelligence, College of Bioinformation, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Pingan Chang
- Chongqing Key Laboratory on Big Data for Bio Intelligence, College of Bioinformation, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Haohuan Kong
- Chongqing Key Laboratory on Big Data for Bio Intelligence, College of Bioinformation, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Changshu Luo
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
| | - Xiaohong He
- Chongqing Key Laboratory on Big Data for Bio Intelligence, College of Bioinformation, Chongqing University of Posts and Telecommunications, Chongqing, China
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18
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Li P, Peng Z, Xu P, Tang G, Ma C, Zhu J, Shan L, Wan S. Genome-Wide Identification of NAC Transcription Factors and Their Functional Prediction of Abiotic Stress Response in Peanut. Front Genet 2021; 12:630292. [PMID: 33767732 PMCID: PMC7985091 DOI: 10.3389/fgene.2021.630292] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 02/08/2021] [Indexed: 11/25/2022] Open
Abstract
The NAC transcription factor (TF) is one of the most significant TFs in plants and is widely involved in plant growth, development, and responses to biotic and abiotic stresses. To date, there are no systematic studies on the NAC family in peanuts. Herein, 132 AhNACs were identified from the genome of cultivated peanut, and they were classified into eight subgroups (I–VIII) based on phylogenetic relationships with Arabidopsis NAC proteins and their conserved motifs. These genes were unevenly scattered on all 20 chromosomes, among which 116 pairs of fragment duplication events and 1 pair of tandem duplications existed. Transcriptome analysis showed that many AhNAC genes responded to drought and abscisic acid (ABA) stresses, especially most of the members in groups IV, VII, and VIII, which were expressed at larger differential levels under polyethylene glycol (PEG) and/or ABA treatment in roots or leaves. Furthermore, 20 of them selected in response to PEG and ABA treatment were evaluated by quantitative real-time polymerase chain reaction. The results showed that these genes significantly responded to drought and ABA in roots and/or leaves. This study was helpful for guiding the functional characterization and improvement of drought-resistant germplasms in peanuts.
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Affiliation(s)
- Pengxiang Li
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China.,College of Life Science, Shandong Normal University, Jinan, China
| | - Zhenying Peng
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Pingli Xu
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Guiying Tang
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Changle Ma
- College of Life Science, Shandong Normal University, Jinan, China
| | - Jieqiong Zhu
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China.,College of Life Science, Shandong Normal University, Jinan, China
| | - Lei Shan
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China.,College of Life Science, Shandong Normal University, Jinan, China
| | - Shubo Wan
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China.,College of Life Science, Shandong Normal University, Jinan, China
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19
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Ma J, Yuan M, Sun B, Zhang D, Zhang J, Li C, Shao Y, Liu W, Jiang L. Evolutionary Divergence and Biased Expression of NAC Transcription Factors in Hexaploid Bread Wheat ( Triticum aestivum L.). PLANTS 2021; 10:plants10020382. [PMID: 33671285 PMCID: PMC7922369 DOI: 10.3390/plants10020382] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/08/2021] [Accepted: 02/15/2021] [Indexed: 11/16/2022]
Abstract
The NAC genes, a large plant-specific family of transcription factors, regulate a wide range of pathways involved in development and response to biotic and abiotic stress. In this study, the NAC transcription factors were identified in 27 green plants, and the results showed that NAC transcription factors in plants undergo an appearance stage from water to land and a number expansion stage from gymnosperm to angiosperm. Investigating the evolutionary process of the NAC transcription factors from diploid species to hexaploid wheat revealed that tandem replications during the polyploidization process is an important event for increasing the number of NAC transcription factors in wheat. Then, the molecular characteristics, phylogenetic relationships, and expression patterns of 462 NAC transcription factors of hexaploid wheat (TaNACs) were analyzed. The protein structure results showed that TaNAC was relatively conservative at the N-terminal that contains five subdomains. All these TaNACs were divided into Group I and Group II by phylogenetic analysis, and the TaNACs in Group I should undergo strong artificial selection based on single nucleotide polymorphism (SNP) analysis. Through genome synteny and phylogenetic analysis, these TaNACs were classified into 88 groups and 9 clusters. The biased expression results of these TaNACs showed that there are 24 groups and 67 groups of neofunctionalization genes under biotic and abiotic stress, respectively, and 16 groups and 59 groups of subfunctionalization genes. This shows that neofunctionalization plays an important role in coping with different stresses. Our study provides new insights into the evolution of NAC transcription factors in hexaploid wheat.
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Affiliation(s)
- Jianhui Ma
- College of Life Science, Henan Normal University, Xinxiang 453007, China; (J.M.); (M.Y.); (B.S.); (D.Z.); (C.L.); (Y.S.)
| | - Meng Yuan
- College of Life Science, Henan Normal University, Xinxiang 453007, China; (J.M.); (M.Y.); (B.S.); (D.Z.); (C.L.); (Y.S.)
| | - Bo Sun
- College of Life Science, Henan Normal University, Xinxiang 453007, China; (J.M.); (M.Y.); (B.S.); (D.Z.); (C.L.); (Y.S.)
| | - Daijing Zhang
- College of Life Science, Henan Normal University, Xinxiang 453007, China; (J.M.); (M.Y.); (B.S.); (D.Z.); (C.L.); (Y.S.)
| | - Jie Zhang
- Collaborative Innovation Center of Henan Grain Crops, Agronomy College, Henan Agricultural University, Zhengzhou 450002, China;
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Chunxi Li
- College of Life Science, Henan Normal University, Xinxiang 453007, China; (J.M.); (M.Y.); (B.S.); (D.Z.); (C.L.); (Y.S.)
| | - Yun Shao
- College of Life Science, Henan Normal University, Xinxiang 453007, China; (J.M.); (M.Y.); (B.S.); (D.Z.); (C.L.); (Y.S.)
| | - Wei Liu
- Collaborative Innovation Center of Henan Grain Crops, Agronomy College, Henan Agricultural University, Zhengzhou 450002, China;
- Correspondence: (W.L.); (L.J.)
| | - Lina Jiang
- College of Life Science, Henan Normal University, Xinxiang 453007, China; (J.M.); (M.Y.); (B.S.); (D.Z.); (C.L.); (Y.S.)
- Correspondence: (W.L.); (L.J.)
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Jia D, Jiang Z, Fu H, Chen L, Liao G, He Y, Huang C, Xu X. Genome-wide identification and comprehensive analysis of NAC family genes involved in fruit development in kiwifruit (Actinidia). BMC PLANT BIOLOGY 2021; 21:44. [PMID: 33451304 PMCID: PMC7811246 DOI: 10.1186/s12870-020-02798-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 12/16/2020] [Indexed: 05/02/2023]
Abstract
BACKGROUND NAC transcription factors (TFs) are plant-specific proteins encoded by a large gene family. They play important roles in diverse biological processes, such as plant growth and development, leaf senescence, and responses to biotic or abiotic stresses. Functions of a number of NAC TFs have been identified mainly in model plants. However, very few studies on NAC TFs have been conducted in the fruit tree of kiwifruit. RESULTS Genome-wide NAC genes were identified and their phylogeny, genomic structure, chromosomal location, synteny relationships, protein properties and conserved motifs were analyzed. In addition, the fruit developmental process was evaluated in a new kiwifruit cultivar of Actinidia eriantha 'Ganlu 1'. And expressions for all those NAC genes were analyzed by quantitative real-time PCR method in fruits of 'Ganlu 1' during its developmental process. Our research identified 142 NAC TFs which could be phylogenetically divided into 23 protein subfamilies. The genomic structures of those NAC genes indicated that their exons were between one and ten. Analysis of chromosomal locations suggested that 116 out of 142 NACs distributed on all the 29 kiwifruit chromosomes. In addition, genome-wide gene expression analysis showed that expressions of 125 out of 142 NAC genes could be detected in fruit samples. CONCLUSION Our comprehensive study provides novel information on NAC genes and expression patterns in kiwifruit fruit. This research would be helpful for future functional identification of NAC genes involved in kiwifruit fruit development.
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Affiliation(s)
- Dongfeng Jia
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China
- Institute of Kiwifruit, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China
| | - Zhiqiang Jiang
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China
- Institute of Kiwifruit, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China
| | - Haihui Fu
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China
| | - Lu Chen
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China
- Institute of Kiwifruit, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China
| | - Guanglian Liao
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China
- Institute of Kiwifruit, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China
| | - Yanqun He
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China
- Institute of Kiwifruit, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China
| | - Chunhui Huang
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China.
- Institute of Kiwifruit, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China.
| | - Xiaobiao Xu
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China.
- Institute of Kiwifruit, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China.
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21
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Munir N, Yukun C, Xiaohui C, Nawaz MA, Iftikhar J, Rizwan HM, Xu S, Yuling L, Xuhan X, Zhongxiong L. Genome-wide identification and comprehensive analyses of NAC transcription factor gene family and expression patterns during somatic embryogenesis in Dimocarpus longan Lour. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 157:169-184. [PMID: 33120109 DOI: 10.1016/j.plaphy.2020.10.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 10/06/2020] [Indexed: 05/23/2023]
Abstract
The NAM, ATAF1/2, and CUC2 form a huge plant-specific gene family of NAC TFs that are involved in the growth, development, and regulation of biotic and abiotic stress responses. Although the draft genome of longan (Dimocarpus longan Lour.) has been published, however the comprehensive data regarding the functions, evolution, and expression patterns of the NAC family are still unavailable. In this study, a comprehensive analysis of the NAC transcription factor family in longan was performed, and a total of 114 NAC genes were found. We investigated the NAC gene family exploring the phylogeny, domain conservation, intron/exon, motifs, cis-regulatory elements, protein-protein interaction, and expression profiles of RNA-seq samples in different tissues and early somatic embryogenesis of longan. Phylogenetic analysis showed that the genes with similar gene structure and motif distribution were clustered in the same group. Cis-element identification indicates the possible role of NAC genes in biological and physiological processes. Protein-protein interaction identified the DlNACs homologous with Arabidopsis proteins. We further investigated the expression pattern of DlNAC genes in different tissues (pulp, stem, large fruit, young fruit, and flower) during somatic embryogenesis at embryogenic callus (EC), incomplete compact pro-embryogenic cultures (ICpEC), and globular embryos (GE) stages. The qRT-PCR results showed that the DlNAC genes were expressed higher at EC and GE stage compared with ICpEC stage. In conclusion, our results provide insight into the evolution, diversity, and characterization of NAC genes in the longan and provide a base for understanding their biological roles and molecular mechanisms in plants.
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Affiliation(s)
- Nigarish Munir
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chen Yukun
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chen Xiaohui
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Muhammad Azher Nawaz
- Department of Horticulture, College of Agriculture, University of Sargodha, Sargodha, 40100, Pakistan
| | - Junaid Iftikhar
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hafiz Muhammad Rizwan
- Institute of Subtropical Fruit, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shen Xu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lin Yuling
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xu Xuhan
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Institute de la Recherché Interdisciplinary de Toulouse, IRIT-ARI, 31300, Toulouse, France.
| | - Lai Zhongxiong
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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22
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Liu M, Sun W, Ma Z, Yu G, Li J, Wang Y, Wang X. Comprehensive multiomics analysis reveals key roles of NACs in plant growth and development and its environmental adaption mechanism by regulating metabolite pathways. Genomics 2020; 112:4897-4911. [PMID: 32916257 DOI: 10.1016/j.ygeno.2020.08.038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/13/2020] [Accepted: 08/27/2020] [Indexed: 01/17/2023]
Abstract
Abnormal environmental conditions induce polyploidization and exacerbate vulnerability to agricultural production. Polyploidization is a pivotal event for plant adaption to stress and the expansion of transcription factors. NACs play key roles in plant stress resistance and growth and development, but the adaptive mechanism of NACs during plant polyploidization remain to be explored. Here, we identified and analyzed NACs from 15 species and found that the expansion of NACs was contributed by polyploidization. The regulatory networks were systematically analyzed based on polyomics. NACs might influence plant phenotypes and were correlated with amino acids acting as nitrogen source, indicating that NACs play a vital role in plant development. More importantly, in quinoa and Arabidopsis thaliana, NACs enabled plants to resist stress by regulating flavonoid pathways, and the universality was further confirmed by the Arabidopsis population. Our study provides a cornerstone for future research into improvement of important agronomic traits by transcription factors in a changing global environment.
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Affiliation(s)
- Moyang Liu
- Shanghai Jiao Tong University, School of Agriculture and Biology, Joint Center for Single Cell Biology, Shanghai, China.
| | - Wenjun Sun
- Sichuan Agricultural University, College of Life Science, Ya'an, China.
| | - Zhaotang Ma
- Sichuan Agricultural University, State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Major Crop Diseases and Rice Research Institute, Chengdu, China.
| | - Guolong Yu
- Shanghai Jiao Tong University, School of Agriculture and Biology, Joint Center for Single Cell Biology, Shanghai, China.
| | - Jiahao Li
- Shanghai Jiao Tong University, School of Agriculture and Biology, Joint Center for Single Cell Biology, Shanghai, China.
| | - Yudong Wang
- Shanghai Jiao Tong University, School of Agriculture and Biology, Joint Center for Single Cell Biology, Shanghai, China.
| | - Xu Wang
- Shanghai Jiao Tong University, School of Agriculture and Biology, Joint Center for Single Cell Biology, Shanghai, China.
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23
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Jin JF, Wang ZQ, He QY, Wang JY, Li PF, Xu JM, Zheng SJ, Fan W, Yang JL. Genome-wide identification and expression analysis of the NAC transcription factor family in tomato (Solanum lycopersicum) during aluminum stress. BMC Genomics 2020; 21:288. [PMID: 32264854 PMCID: PMC7140551 DOI: 10.1186/s12864-020-6689-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/19/2020] [Indexed: 01/28/2023] Open
Abstract
Background The family of NAC proteins (NAM, ATAF1/2, and CUC2) represent a class of large plant-specific transcription factors. However, identification and functional surveys of NAC genes of tomato (Solanum lycopersicum) remain unstudied, despite the tomato genome being decoded for several years. This study aims to identify the NAC gene family and investigate their potential roles in responding to Al stress. Results Ninety-three NAC genes were identified and named in accordance with their chromosome location. Phylogenetic analysis found SlNACs are broadly distributed in 5 groups. Gene expression analysis showed that SlNACs had different expression levels in various tissues and at different fruit development stages. Cycloheximide treatment and qRT-PCR analysis indicated that SlNACs may aid regulation of tomato in response to Al stress, 19 of which were significantly up- or down-regulated in roots of tomato following Al stress. Conclusion This work establishes a knowledge base for further studies on biological functions of SlNACs in tomato and will aid in improving agricultural traits of tomato in the future.
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Affiliation(s)
- Jian Feng Jin
- State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Biology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhan Qi Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000, China
| | - Qi Yu He
- State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Biology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jia Yi Wang
- State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Biology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Peng Fei Li
- State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Biology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ji Ming Xu
- State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Biology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Shao Jian Zheng
- State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Biology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Wei Fan
- College of Resources and Environment, Yunnan Agricultural University, Kunming, 650201, China
| | - Jian Li Yang
- State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Biology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
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24
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Li M, Cheng C, Zhang X, Zhou S, Wang C, Ma C, Yang S. PpNAC187 Enhances Lignin Synthesis in 'Whangkeumbae' Pear ( Pyrus pyrifolia) 'Hard-End' Fruit. Molecules 2019; 24:E4338. [PMID: 31783586 PMCID: PMC6930614 DOI: 10.3390/molecules24234338] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 11/23/2019] [Accepted: 11/25/2019] [Indexed: 11/16/2022] Open
Abstract
A disorder in pears that is known as 'hard-end' fruit affects the appearance, edible quality, and market value of pear fruit. RNA-Seq was carried out on the calyx end of 'Whangkeumbae' pear fruit with and without the hard-end symptom to explore the mechanism underlying the formation of hard-end. The results indicated that the genes in the phenylpropanoid pathway affecting lignification were up-regulated in hard-end fruit. An analysis of differentially expressed genes (DEGs) identified three NAC transcription factors, and RT-qPCR analysis of PpNAC138, PpNAC186, and PpNAC187 confirmed that PpNAC187 gene expression was correlated with the hard-end disorder in pear fruit. A transient increase in PpNAC187 was observed in the calyx end of 'Whangkeumbae' fruit when they began to exhibit hard-end symptom. Concomitantly, the higher level of PpCCR and PpCOMT transcripts was observed, which are the key genes in lignin biosynthesis. Notably, lignin content in the stem and leaf tissues of transgenic tobacco overexpressing PpNAC187 was significantly higher than in the control plants that were transformed with an empty vector. Furthermore, transgenic tobacco overexpressing PpNAC187 had a larger number of xylem vessel elements. The results of this study confirmed that PpNAC187 functions in inducing lignification in pear fruit during the development of the hard-end disorder.
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Affiliation(s)
- Mingtong Li
- College of Horticulture, Qingdao Agricultural University, No. 700 Changcheng Road, Chengyang, Qingdao 266109, China; (M.L.); (C.C.); (X.Z.); (C.W.); (C.M.)
| | - Chenxia Cheng
- College of Horticulture, Qingdao Agricultural University, No. 700 Changcheng Road, Chengyang, Qingdao 266109, China; (M.L.); (C.C.); (X.Z.); (C.W.); (C.M.)
| | - Xinfu Zhang
- College of Horticulture, Qingdao Agricultural University, No. 700 Changcheng Road, Chengyang, Qingdao 266109, China; (M.L.); (C.C.); (X.Z.); (C.W.); (C.M.)
| | - Suping Zhou
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John Merritt Blvd, Nashville, TN 37209, USA;
| | - Caihong Wang
- College of Horticulture, Qingdao Agricultural University, No. 700 Changcheng Road, Chengyang, Qingdao 266109, China; (M.L.); (C.C.); (X.Z.); (C.W.); (C.M.)
| | - Chunhui Ma
- College of Horticulture, Qingdao Agricultural University, No. 700 Changcheng Road, Chengyang, Qingdao 266109, China; (M.L.); (C.C.); (X.Z.); (C.W.); (C.M.)
| | - Shaolan Yang
- College of Horticulture, Qingdao Agricultural University, No. 700 Changcheng Road, Chengyang, Qingdao 266109, China; (M.L.); (C.C.); (X.Z.); (C.W.); (C.M.)
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25
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Genome-Wide Investigation of the NAC Gene Family and Its Potential Association with the Secondary Cell Wall in Moso Bamboo. Biomolecules 2019; 9:biom9100609. [PMID: 31615151 PMCID: PMC6843218 DOI: 10.3390/biom9100609] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/09/2019] [Accepted: 10/13/2019] [Indexed: 01/20/2023] Open
Abstract
NAC (NAM, ATAF, and CUC) transcription factors (TFs) are implicated in the transcriptional regulation of diverse processes and have been characterized in a number of plant species. However, NAC TFs are still not well understood in bamboo, especially their potential association with the secondary cell wall (SCW). Here, 94 PeNACs were identified and characterized in moso bamboo (Phyllostachys edulis). Based on their gene structures and conserved motifs, the PeNACs were divided into 11 groups according to their homologs in Arabidopsis. PeNACs were expressed variously in different tissues of moso bamboo, suggesting their functional diversity. Fifteen PeNACs associated with the SCW were selected for co-expression analysis and validation. It was predicted that 396 genes were co-expressed with the 15 PeNACs, in which 16 and 55 genes were involved in the lignin catabolic process and cellulose biosynthetic process respectively. As the degree of lignification in the growing bamboo shoots increased, all 15 PeNACs were upregulated with a trend of rising first and then decreasing except PeNAC37, which increased continuously. These results indicated that these PeNACs might play important roles in SCW biosynthesis and lignification in bamboo shoots. Seven of 15 PeNACs had been found positively co-expressed with seven PeMYBs, and they had similar expression patterns with those of the PeMYBs in bamboo shoots. The targeted sites of miR164 were found in 16 PeNACs, of which three PeNACs associated with SCW were validated to have an opposite expression trend to that of miR164 in growing bamboo shoots. In addition, three PeNACs were selected and verified to have self-activation activities. These results provide comprehensive information of the NAC gene family in moso bamboo, which will be helpful for further functional studies of PeNACs to reveal the molecular regulatory mechanisms of bamboo wood property.
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26
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Su X, Zhao Y, Wang H, Li G, Cheng X, Jin Q, Cai Y. Transcriptomic analysis of early fruit development in Chinese white pear (Pyrus bretschneideri Rehd.) and functional identification of PbCCR1 in lignin biosynthesis. BMC PLANT BIOLOGY 2019; 19:417. [PMID: 31604417 PMCID: PMC6788021 DOI: 10.1186/s12870-019-2046-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 09/20/2019] [Indexed: 05/02/2023]
Abstract
BACKGROUND The content of stone cells and lignin is one of the key factors affecting the quality of pear fruit. In a previous study, we determined the developmental regularity of stone cells and lignin in 'Dangshan Su' pear fruit 15-145 days after pollination (DAP). However, the development of fruit stone cells and lignin before 15 DAP has not been heavily researched. RESULTS In this study, we found that primordial stone cells began to appear at 7 DAP and that the fruit had formed a large number of stone cells at 15 DAP. Subsequently, transcriptome sequencing was performed on fruits at 0, 7, and 15 DAP and identified 3834 (0 vs. 7 DAP), 4049 (7 vs. 15 DAP) and 5763 (0 vs. 15 DAP) DEGs. During the 7-15 DAP period, a large number of key enzyme genes essential for lignin biosynthesis are gradually up-regulated, and their expression pattern is consistent with the accumulation of lignin in this period. Further analysis found that the biosynthesis of S-type lignin in 'Dangshan Su' pear does not depend on the catalytic activity of PbSAD but is primarily generated by the catalytic activity of caffeoyl-CoA through CCoAOMT, CCR, F5H, and CAD. We cloned PbCCR1, 2 and analysed their functions in Chinese white pear lignin biosynthesis. PbCCR1 and 2 have a degree of functional redundancy; both demonstrate the ability to participate in lignin biosynthesis. However, PbCCR1 may be the major gene for lignin biosynthesis, while PbCCR2 has little effect on lignin biosynthesis. CONCLUSIONS Our results revealed that 'Dangshan Su' pear began to form a large number of stone cells and produce lignin after 7 DAP and mainly accumulated materials from 0 to 7 DAP. PbCCR1 is mainly involved in the biosynthesis of lignin in 'Dangshan Su' pear and plays a positive role in lignin biosynthesis.
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Affiliation(s)
- Xueqiang Su
- School of Life Science, Anhui Agricultural University, Hefei, Anhui China
| | - Yu Zhao
- School of Life Science, Anhui Agricultural University, Hefei, Anhui China
| | - Han Wang
- School of Life Science, Anhui Agricultural University, Hefei, Anhui China
| | - Guohui Li
- School of Life Science, Anhui Agricultural University, Hefei, Anhui China
| | - Xi Cheng
- School of Life Science, Anhui Agricultural University, Hefei, Anhui China
| | - Qing Jin
- School of Life Science, Anhui Agricultural University, Hefei, Anhui China
| | - Yongping Cai
- School of Life Science, Anhui Agricultural University, Hefei, Anhui China
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Comparative transcriptome and metabolite profiling of four tissues from Alisma orientale (Sam.) Juzep reveals its inflorescence developmental and medicinal characteristics. Sci Rep 2019; 9:12310. [PMID: 31444376 PMCID: PMC6707231 DOI: 10.1038/s41598-019-48806-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 08/13/2019] [Indexed: 12/11/2022] Open
Abstract
Alisma orientale (Sam.) Juzep (A. orientale) is an important medicinal plant in traditional Chinese medicine. In this study, de novo RNA-seq of A. orientale was performed based on the cDNA libraries from four different tissues, roots, leaves, scapes and inflorescences. A total of 41,685 unigenes were assembled, 25,024 unigene functional annotations were obtained by searching against the five public sequence databases, and 3,411 simple sequence repeats in A. orientale were reported for the first time. 15,402 differentially expressed genes were analysed. The morphological characteristics showed that compared to the other tissues, the leaves had more chlorophyll, the scapes had more vascular bundles, and the inflorescences contained more starch granules and protein. In addition, the metabolic profiles of eight kinds of alisols metabolite profiling, which were measured by ultra-Performance liquid chromatography-triple quadrupole-mass spectrometry showed that alisol B 23-acetate and alisol B were the major components of the four tissues at amounts of 0.068~0.350 mg/g and 0.046~0.587 mg/g, respectively. In addition, qRT-PCR validated that farnesyl pyrophosphate synthase and 3-hydroxy-3-methylglutaryl-CoA reductase should be considered the critical candidate genes involved in alisol biosynthesis. These transcriptome and metabolic profiles of A. orientale may help clarify the molecular mechanisms underlying the medicinal characteristics of A. orientale.
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28
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Ahmad M, Li J, Yang Q, Jamil W, Teng Y, Bai S. Phylogenetic, Molecular, and Functional Characterization of PpyCBF Proteins in Asian Pears ( Pyrus pyrifolia). Int J Mol Sci 2019; 20:ijms20092074. [PMID: 31035490 PMCID: PMC6539064 DOI: 10.3390/ijms20092074] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 04/23/2019] [Accepted: 04/24/2019] [Indexed: 11/16/2022] Open
Abstract
C-repeat binding factor/dehydration-responsive element (CBF/DRE) transcription factors (TFs) participate in a variety of adaptive mechanisms, and are involved in molecular signaling and abiotic stress tolerance in plants. In pear (Pyrus pyrifolia) and other rosaceous crops, the independent evolution of CBF subfamily members requires investigation to understand the possible divergent functions of these proteins. In this study, phylogenetic analysis divided six PpyCBFs from the Asian pear genome into three clades/subtypes, and collinearity and phylogenetic analyses suggested that PpyCBF3 was the mother CBF. All PpyCBFs were found to be highly expressed in response to low temperature, salt, drought, and abscisic acid (ABA) as well as bud endodormancy, similar to PpyCORs (PpyCOR47, PpyCOR15A, PpyRD29A, and PpyKIN). Transcript levels of clade II PpyCBFs during low temperature and ABA treatments were higher than those of clades I and III. Ectopic expression of PpyCBF2 and PpyCBF3 in Arabidopsis enhanced its tolerance against abiotic stresses, especially to low temperature in the first case and salt and drought stresses in the latter, and resulted in lower reactive oxygen species (ROS) and antioxidant gene activities compared with the wild type. The increased expression of endogenous ABA-dependent and -independent genes during normal conditions in PpyCBF2- and PpyCBF3-overexpressing Arabidopsis lines suggested that PpyCBFs were involved in both ABA-dependent and -independent pathways. All PpyCBFs, especially the mother CBF, had high transactivation activities with 6XCCGAC binding elements. Luciferase and Y1H assays revealed the existence of phylogenetically and promoter-dependent conserved CBF-COR cascades in the pear. The presence of a previously identified CCGA binding site, combined with the results of mutagenesis of the CGACA binding site of the PpyCOR15A promoter, indicated that CGA was a core binding element of PpyCBFs. In conclusion, PpyCBF TFs might operate redundantly via both ABA-dependent and -independent pathways, and are strongly linked to abiotic stress signaling and responses in the Asian pear.
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Affiliation(s)
- Mudassar Ahmad
- Department of Horticulture, Zhejiang University, Hangzhou 310058, Zhejiang, China.
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, the Ministry of Agriculture of China, Hangzhou 310058, Zhejiang, China.
- Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Hangzhou 310058, Zhejiang, China.
| | - Jianzhao Li
- Department of Horticulture, Zhejiang University, Hangzhou 310058, Zhejiang, China.
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, the Ministry of Agriculture of China, Hangzhou 310058, Zhejiang, China.
- Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Hangzhou 310058, Zhejiang, China.
| | - Qinsong Yang
- Department of Horticulture, Zhejiang University, Hangzhou 310058, Zhejiang, China.
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, the Ministry of Agriculture of China, Hangzhou 310058, Zhejiang, China.
- Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Hangzhou 310058, Zhejiang, China.
| | - Wajeeha Jamil
- Department of Horticulture, Zhejiang University, Hangzhou 310058, Zhejiang, China.
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, the Ministry of Agriculture of China, Hangzhou 310058, Zhejiang, China.
- Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Hangzhou 310058, Zhejiang, China.
| | - Yuanwen Teng
- Department of Horticulture, Zhejiang University, Hangzhou 310058, Zhejiang, China.
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, the Ministry of Agriculture of China, Hangzhou 310058, Zhejiang, China.
- Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Hangzhou 310058, Zhejiang, China.
| | - Songling Bai
- Department of Horticulture, Zhejiang University, Hangzhou 310058, Zhejiang, China.
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, the Ministry of Agriculture of China, Hangzhou 310058, Zhejiang, China.
- Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Hangzhou 310058, Zhejiang, China.
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