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Fang Y, Wang L, Liu K, Wu H, Zheng Y, Duan Y, Feng S, Wang Y. Genome-wide investigation of HD-ZIP gene family and functional characterization of BnaHDZ149 and BnaHDZ22 in salt and drought response in Brassica napus L. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112130. [PMID: 38795751 DOI: 10.1016/j.plantsci.2024.112130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/08/2024] [Accepted: 05/18/2024] [Indexed: 05/28/2024]
Abstract
HD-ZIP proteins comprise a plant-specific transcription factor family, which play pivotal roles in plant development and adaptation to ever-changing environment. Although HD-ZIP family members have been identified in some plant species, so far our knowledge about HD-ZIP genes in rapeseed is still limited. In this study, 178 Brassica napus HD-ZIP (BnaHDZ) family members were identified in the rapeseed genome. The phylogenetic relationship, chromosomal locations, intron-exon structures, motif composition, and expression patterns of the BnaHDZ members were analyzed. The BnaHDZ family can be phylogenetically divided into four categories (Ⅰ, Ⅱ, Ⅲ and Ⅳ). Genome-wide transcriptome analysis revealed that most of the HD-ZIP I members respond to at least one abiotic stress. Two closely homologous stress-responsive HD-ZIP Ⅰ genes, BnaHDZ22 and BnaHDZ149, were identified to be involved in drought and salt responses, and selected for further functional characterization. Overexpressing BnaHDZ149 in rapeseed increased salt sensitivity of the transgenic plants, whereas overexpressing BnaHDZ22 increased sensitivity of the transgenic plants to polyethylene glycol (PEG)-simulated drought stress. This research provides not only a comprehensive landscape of BnaHDZ genes, but also a theoretical basis for elucidating the molecular mechanism of the abiotic stress responses of the HD-ZIP family in rapeseed.
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Affiliation(s)
- Yujie Fang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu 225009, China.
| | - Lu Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Kuan Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Han Wu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Yuqian Zheng
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Yujing Duan
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Shanshan Feng
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Youping Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu 225009, China.
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Wu C, Xiao S, Zhang X, Ren W, Shangguan X, Li S, Zuo D, Cheng H, Zhang Y, Wang Q, Lv L, Li P, Song G. GhHDZ76, a cotton HD-Zip transcription factor, involved in regulating the initiation and early elongation of cotton fiber development in G. hirsutum. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 345:112132. [PMID: 38788903 DOI: 10.1016/j.plantsci.2024.112132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 05/26/2024]
Abstract
In this study, the whole HD-Zip family members of G. hirsutum were identified, and GhHDZ76 was classified into the HD-Zip IV subgroup. GhHDZ76 was predominantly expressed in the 0-5 DPA of fiber development stage and localized in the nucleus. Overexpression of GhHDZ76 significantly increased the length and density of trichomes in Arabidopsis thaliana. The fiber length of GhHDZ76 knockout lines by CRISPR/Cas9 was significantly shorter than WT at the early elongation and mature stage, indicating that GhHDZ76 positively regulate the fiber elongation. Scanning electron microscopy showed that the number of ovule surface protrusion of 0 DPA of GhHDZ76 knockout lines was significantly lower than WT, suggesting that GhHDZ76 can also promote the initiation of fiber development. The transcript level of GhWRKY16, GhRDL1, GhEXPA1 and GhMYB25 genes related to fiber initiation and elongation in GhHDZ76 knockout lines were significantly decreased. Yeast two-hybrid and Luciferase complementation imaging (LCI) assays showed that GhHDZ76 can interact with GhWRKY16 directly. As a transcription factor, GhHDZ76 has transcriptional activation activity, which could bind to L1-box elements of the promoters of GhRDL1 and GhEXPA1. Double luciferase reporter assay showed that the GhWRKY16 could enhance the transcriptional activity of GhHDZ76 to pGhRDL1, but it did not promote the transcriptional activity of GhHDZ76 to pGhEXPA1. GhHDZ76 protein may also promote the transcriptional activity of GhWRKY16 to the downstream target gene GhMYB25. Our results provided a new gene resource for fiber development and a theoretical basis for the genetic improvement of cotton fiber quality.
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Affiliation(s)
- Cuicui Wu
- Cotton Research Institute of Shanxi Agricultural University, Yuncheng 044000, China
| | - Shuiping Xiao
- Jiangxi Provincial Key Laboratory of Plantation and High Valued Utilization of Specialty Fruit Tree and Tea, Economic Crops Research Institute of Jiangxi Province, Nanchang 330000, China
| | - Xianliang Zhang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang 455000, China; Western Research Institute, Chinese Academy of Agricultural Sciences (CAAS), changji 831100, China
| | - Wenbin Ren
- Cotton Research Institute of Shanxi Agricultural University, Yuncheng 044000, China
| | - Xiaoxia Shangguan
- Cotton Research Institute of Shanxi Agricultural University, Yuncheng 044000, China
| | - Shuyan Li
- Anyang Institute of Technology, Anyang 455000, China
| | - Dongyun Zuo
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Hailiang Cheng
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Youping Zhang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Qiaolian Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Limin Lv
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Pengbo Li
- Cotton Research Institute of Shanxi Agricultural University, Yuncheng 044000, China.
| | - Guoli Song
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang 455000, China.
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Liu Y, Yang L, Ma Y, Zhou Y, Zhang S, Liu Q, Ma F, Liu C. The HD-Zip I transcription factor MdHB-7 negatively regulates resistance to Glomerella leaf spot in apple. JOURNAL OF PLANT PHYSIOLOGY 2024; 299:154277. [PMID: 38843655 DOI: 10.1016/j.jplph.2024.154277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 03/01/2024] [Accepted: 05/29/2024] [Indexed: 06/17/2024]
Abstract
Glomerella leaf spot (GLS), caused by Colletotrichum fructicola (Cf), has been one of the main fungal diseases afflicting apple-producing areas across the world for many years, and it has led to substantial reductions in apple output and quality. HD-Zip transcription factors have been identified in several species, and they are involved in the immune response of plants to various types of biotic stress. In this study, inoculation of MdHB-7 overexpressing (MdHB-7-OE) and interference (MdHB-7-RNAi) transgenic plants with Cf revealed that MdHB-7, which encodes an HD-Zip transcription factor, adversely affects GLS resistance. The SA content and the expression of SA pathway-related genes were lower in MdHB-7-OE plants than in 'GL-3' plants; the content of ABA and the expression of ABA biosynthesis genes were higher in MdHB-7-OE plants than in 'GL-3' plants. Further analysis indicated that the content of phenolics and chitinase and β-1, 3 glucanase activities were lower and H2O2 accumulation was higher in MdHB-7-OE plants than in 'GL-3' plants. The opposite patterns were observed in MdHB-7-RNAi apple plants. Overall, our results indicate that MdHB-7 plays a negative role in regulating defense against GLS in apple, which is likely achieved by altering the content of SA, ABA, polyphenols, the activities of defense-related enzymes, and the content of H2O2.
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Affiliation(s)
- Yuerong Liu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Lulu Yang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yongxin Ma
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yufei Zhou
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shangyu Zhang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qianwei Liu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Fengwang Ma
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Changhai Liu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Xu H, Teng H, Zhang B, Liu W, Sui Y, Yan X, Wang Z, Cui H, Zhang H. NtHD9 modulates plant salt tolerance by regulating the formation of glandular trichome heads in Nicotiana tabacum. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 212:108765. [PMID: 38795550 DOI: 10.1016/j.plaphy.2024.108765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/13/2024] [Accepted: 05/21/2024] [Indexed: 05/28/2024]
Abstract
Salt stress is one of the main abiotic factor affecting plant growth. We have previously identified a key gene (NtHD9) in Nicotiana tabacum L. that positively regulates the formation of long glandular trichomes (LGTs). Here, we verified that both abiotic stress (aphids, drought and salt stress) could restore the phenotype lacking LGTs in NtHD9-knockout (NtHD9-KO) plants. The abiotic stress response assays indicated that NtHD9 is highly sensitive to salt stress. Compared with cultivated tobacco "K326" (CK) plants, NtHD9-overexpressing (NtHD9-OE) plants with more LGTs exhibited stronger salt tolerance, whereas NtHD9-KO with no LGTs showed weaker tolerance to salt. The densities and sizes of the glandular heads gradually increased with increasing NaCl concentrations in NtHD9-KO plants. Mineral element determination showed that leaves and trichomes of NtHD9-OE plants accumulated less Na+ but had higher K+ contents under salt stress, thus maintaining ion homeostasis in plants, which could contribute to a robust photosynthetic and antioxidant system under salt stress. Therefore, NtHD9-OE plants maintained a larger leaf area and root length under high-salt conditions than CK and NtHD9-KO plants. We verified that NtHD9 could individually interact with NtHD5, NtHD7, NtHD12, and NtJAZ10 proteins. Salt stress led to an increase in jasmonic acid (JA) levels and activated the expression of NtHDs while inhibiting the expression of NtJAZ. This study suggests that the glandular heads play an important role in plant resistance to salt stress. The activation of JA signaling leading to JAZ protein degradation may be key factors regulating the glandular heads development under salt stress.
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Affiliation(s)
- Hanchi Xu
- Key Laboratory for Cultivation of Tobacco Industry, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450046, China
| | - Huanyu Teng
- Key Laboratory for Cultivation of Tobacco Industry, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450046, China
| | - Bokai Zhang
- Key Laboratory for Cultivation of Tobacco Industry, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450046, China
| | - Wei Liu
- Key Laboratory for Cultivation of Tobacco Industry, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yalin Sui
- Key Laboratory for Cultivation of Tobacco Industry, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xiaoxiao Yan
- Key Laboratory for Cultivation of Tobacco Industry, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450046, China
| | - Zhaojun Wang
- Key Laboratory for Cultivation of Tobacco Industry, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450046, China
| | - Hong Cui
- Key Laboratory for Cultivation of Tobacco Industry, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450046, China.
| | - Hongying Zhang
- Key Laboratory for Cultivation of Tobacco Industry, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450046, China.
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Ye YY, Liu DD, Tang RJ, Gong Y, Zhang CY, Mei P, Ma CL, Chen JD. Bulked Segregant RNA-Seq Reveals Different Gene Expression Patterns and Mutant Genes Associated with the Zigzag Pattern of Tea Plants ( Camellia sinensis). Int J Mol Sci 2024; 25:4549. [PMID: 38674133 PMCID: PMC11049935 DOI: 10.3390/ijms25084549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/05/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
The unique zigzag-patterned tea plant is a rare germplasm resource. However, the molecular mechanism behind the formation of zigzag stems remains unclear. To address this, a BC1 genetic population of tea plants with zigzag stems was studied using histological observation and bulked segregant RNA-seq. The analysis revealed 1494 differentially expressed genes (DEGs) between the upright and zigzag stem groups. These DEGs may regulate the transduction and biosynthesis of plant hormones, and the effects on the phenylpropane biosynthesis pathways may cause the accumulation of lignin. Tissue sections further supported this finding, showing differences in cell wall thickness between upright and curved stems, potentially due to lignin accumulation. Additionally, 262 single-nucleotide polymorphisms (SNPs) across 38 genes were identified as key SNPs, and 5 genes related to zigzag stems were identified through homologous gene function annotation. Mutations in these genes may impact auxin distribution and content, resulting in the asymmetric development of vascular bundles in curved stems. In summary, we identified the key genes associated with the tortuous phenotype by using BSR-seq on a BC1 population to minimize genetic background noise.
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Affiliation(s)
| | | | | | | | | | | | - Chun-Lei Ma
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou 310008, China; (Y.-Y.Y.); (D.-D.L.); (R.-J.T.); (Y.G.); (C.-Y.Z.); (P.M.)
| | - Jie-Dan Chen
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou 310008, China; (Y.-Y.Y.); (D.-D.L.); (R.-J.T.); (Y.G.); (C.-Y.Z.); (P.M.)
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Shen L, Liu Y, Zhang L, Sun Z, Wang Z, Jiao Y, Shen K, Guo Z. A transcriptional atlas identifies key regulators and networks for the development of spike tissues in barley. Cell Rep 2023; 42:113441. [PMID: 37971941 DOI: 10.1016/j.celrep.2023.113441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 07/06/2023] [Accepted: 10/31/2023] [Indexed: 11/19/2023] Open
Abstract
Grain number and size determine grain yield in crops and are closely associated with spikelet fertility and grain filling in barley (Hordeum vulgare). Abortion of spikelet primordia within individual barley spikes causes a 30%-50% loss in the potential number of grains during development from the awn primordium stage to the tipping stage, after that grain filling is the primary factor regulating grain size. To identify transcriptional signatures associated with spike development, we use a six-rowed barley cultivar (Morex) to develop a spatiotemporal transcriptome atlas containing 255 samples covering 17 stages and 5 positions along the spike. We identify several fundamental regulatory networks, in addition to key regulators of spike development and morphology. Specifically, we show HvGELP96, encoding a GDSL domain-containing protein, as a regulator of spikelet fertility and grain number. Our transcriptional atlas offers a powerful resource to answer fundamental questions in spikelet development and degeneration in barley.
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Affiliation(s)
- Liping Shen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China
| | - Yangyang Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lili Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Zhiwen Sun
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ziying Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuannian Jiao
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
| | - Kuocheng Shen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zifeng Guo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China; China National Botanical Garden, Beijing 100093, China.
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Bai Y, Zhou Y, Lei Q, Wang Y, Pu G, Liu Z, Chen X, Liu Q. Analysis of the HD-Zip I transcription factor family in Salvia miltiorrhiza and functional research of SmHD-Zip12 in tanshinone synthesis. PeerJ 2023; 11:e15510. [PMID: 37397009 PMCID: PMC10312201 DOI: 10.7717/peerj.15510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 05/15/2023] [Indexed: 07/04/2023] Open
Abstract
Background The homeodomain-leucine zipper I (HD-Zip I) transcription factor is a plant-specific protein that plays an essential role in the abiotic stress response of plants. Research on the HD-Zip I family in Salvia miltiorrhiza is still lacking. Methods and Results In this study, a total of 25 SmHD-Zip I proteins were identified. Their characterizations, phylogenetic relationships, conserved motifs, gene structures, and cis-elements were analyzed comprehensively using bioinformatics methods. Expression profiling revealed that SmHD-Zip I genes exhibited distinctive tissue-specific patterns and divergent responses to ABA, PEG, and NaCl stresses. SmHD-Zip12 responded the most strongly to ABA, PEG, and NaCl, so it was used for transgenic experiments. The overexpression of SmHD-Zip12 significantly increased the content of cryptotanshinone, dihydrotanshinone I, tanshinone I, and tanshinone IIA by 2.89-fold, 1.85-fold, 2.14-fold, and 8.91-fold compared to the wild type, respectively. Moreover, in the tanshinone biosynthetic pathways, the overexpression of SmHD-Zip12 up-regulated the expression levels of SmAACT, SmDXS, SmIDS, SmGGPPS, SmCPS1, SmCPS2, SmCYP76AH1, SmCYP76AH3, and SmCYP76AK1 compared with the wild type. Conclusions This study provides information the possible functions of the HD-Zip I family and lays a theoretical foundation for clarifying the functional mechanism of the SmHD-Zip12 gene in regulating the synthesis of tanshinone in S. miltiorrhiza.
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Affiliation(s)
- Yanhong Bai
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Ying Zhou
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Qiaoqi Lei
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Yu Wang
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Gaobin Pu
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Zhenhua Liu
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Xue Chen
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Qian Liu
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
- LiShizhen College of Traditional Chinese Medicine, Huanggang Normal University, Huanggang, Hubei, China
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Wang Z, Wu X, Zhang B, Xiao Y, Guo J, Liu J, Chen Q, Peng F. Genome-wide identification, bioinformatics and expression analysis of HD-Zip gene family in peach. BMC PLANT BIOLOGY 2023; 23:122. [PMID: 36864374 PMCID: PMC9979464 DOI: 10.1186/s12870-023-04061-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 01/12/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND HD-Zips (Homeodomain-Leucine Zippers) are a class of plant-specific transcription factors that play multiple roles in plant growth and development. Although some functions of HD-Zip transcription factor have been reported in several plants, it has not been comprehensively studied in peach, especially during adventitious root formation of peach cuttings. RESULTS In this study, 23 HD-Zip genes distributed on 6 chromosomes were identified from the peach (Prunus persica) genome, and named PpHDZ01-23 according to their positions on the chromosomes. These 23 PpHDZ transcription factors all contained a homeomorphism box domain and a leucine zipper domain, were divided into 4 subfamilies(I-IV) according to the evolutionary analysis, and their promoters contained many different cis-acting elements. Spatio-temporal expression pattern showed that these genes were expressed in many tissues with different levels, and they had distinct expression pattern during adventitious root formation and development. CONCLUSION Our results showed the roles of PpHDZs on root formation, which is helpful to better understand the classification and function of peach HD-Zip genes.
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Affiliation(s)
- Zhe Wang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, 271000, Tai'an, China
| | - Xuelian Wu
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, 271000, Tai'an, China
| | - Binbin Zhang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, 271000, Tai'an, China
| | - Yuansong Xiao
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, 271000, Tai'an, China
| | - Jian Guo
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, 271000, Tai'an, China
| | - Jin Liu
- Agricultural Technical Service Center of Yiyuan County, 256100, Zibo, China
| | - Qiuju Chen
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, 271000, Tai'an, China.
- Agricultural Technical Service Center of Yiyuan County, 256100, Zibo, China.
| | - Futian Peng
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, 271000, Tai'an, China.
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Genomewide identification and analysis of the OSCA gene family in barley (Hordeum vulgare L.). J Genet 2022. [DOI: 10.1007/s12041-022-01375-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Genome-Wide Identification and Expression Profile of the HD-Zip Transcription Factor Family Associated with Seed Germination and Abiotic Stress Response in Miscanthus sinensis. Genes (Basel) 2022; 13:genes13122256. [PMID: 36553523 PMCID: PMC9777646 DOI: 10.3390/genes13122256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 11/21/2022] [Accepted: 11/27/2022] [Indexed: 12/05/2022] Open
Abstract
Miscanthus sinensis is an ornamental grass, non-food bioenergy crop, and forage with high feeding value. It can adapt to many kinds of soil conditions due to its high level of resistance to various abiotic stresses. However, a low level of seed germination restricts the utilization and application of M. sinensis. It is reported that the Homeodomain-leucine zipper (HD-Zip) gene family participates in plant growth and development and ability to cope with outside environment stresses, which may potentially regulate seed germination and stress resistance in M. sinensis. In this study, a complete overview of M. sinensis HD-Zip genes was conducted, including gene structure, conserved motifs, chromosomal distribution, and gene duplication patterns. A total of 169 members were identified, and the HD-Zip proteins were divided into four subgroups. Inter-chromosomal evolutionary analysis revealed that four pairs of tandem duplicate genes and 72 segmental duplications were detected, suggesting the possible role of gene replication events in the amplification of the M. sinensis HD-Zip gene family. There was an uneven distribution of HD-Zip genes on 19 chromosomes of M. sinensis. Also, evolutionary analysis showed that M. sinensis HD-Zip gene family members had more collinearity with monocotyledons and less with dicotyledons. The gene structure analysis showed that there were 93.5% of proteins with motif 1 and motif 4, while motif 10 was only found in group IV. Based on the cis-elements analysis, it appeared that most of the genes were related to plant growth and development, various hormones, and abiotic stress. Furthermore, qRT-PCR analysis showed that Misin06G303300.1 was significantly expressed in seed germination and Misin05G030000.1 and Misin06G303300.1 were highly expressed under chromium, salt, and drought stress. Results in this study will provide a basis for further exploring the potential role of HD-Zip genes in stress responses and genetic improvement of M. sinensis seed germination.
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HD-Zip III Gene Family: Identification and Expression Profiles during Leaf Vein Development in Soybean. PLANTS 2022; 11:plants11131728. [PMID: 35807680 PMCID: PMC9269512 DOI: 10.3390/plants11131728] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/16/2022] [Accepted: 06/24/2022] [Indexed: 12/14/2022]
Abstract
Leaf veins constitute the transport network for water and photosynthetic assimilates in vascular plants. The class III homeodomain-leucine zipper (HD-Zip III) gene family is central to the regulation of vascular development. In this research, we performed an overall analysis of the HD-Zip III genes in soybean (Glycine max L. Merr.). Our analysis included the phylogeny, conservation domains and cis-elements in the promoters of these genes. We used the quantitative reverse transcription-polymerase chain reaction to characterize the expression patterns of HD-Zip III genes in leaf vein development and analyze the effects of exogenous hormone treatments. In this study, twelve HD-Zip III genes were identified from the soybean genome and named. All soybean HD-Zip III proteins contained four highly conserved domains. GmHB15-L-1 transcripts showed steadily increasing accumulation during all stages of leaf vein development and were highly expressed in cambium cells. GmREV-L-1 and GmHB14-L-2 had nearly identical expression patterns in soybean leaf vein tissues. GmREV-L-1 and GmHB14-L-2 transcripts remained at stable high levels at all xylem developmental stages. GmREV-L-1 and GmHB14-L-2 were expressed at high levels in the vascular cambium and xylem cells. Overall, GmHB15-L-1 may be an essential regulator that is responsible for the formation or maintenance of soybean vein cambial cells. GmREV-L-1 and GmHB14-L-2 were correlated with xylem differentiation in soybean leaf veins. This study will pave the way for identifying the molecular mechanism of leaf vein development.
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12
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Qiu X, Wang G, Abou-Elwafa SF, Fu J, Liu Z, Zhang P, Xie X, Ku L, Ma Y, Guan X, Wei L. Genome-wide identification of HD-ZIP transcription factors in maize and their regulatory roles in promoting drought tolerance. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:425-437. [PMID: 35400885 PMCID: PMC8943141 DOI: 10.1007/s12298-022-01147-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/11/2022] [Accepted: 02/11/2022] [Indexed: 05/31/2023]
Abstract
Drought is the main limiting factor of maize productivity, therefore improving drought tolerance in maize has potential practical importance. Cloning and functional verification of drought-tolerant genes is of great importance to understand molecular mechanisms under drought stress. Here, we employed a bioinformatic pipeline to identify 42 ZmHDZ drought responsive genes using previously reported maize transcriptomic datasets. The coding sequences, exon-intron structure and domain organization of all the 42 genes were identified. Phylogenetic analysis revealed evolutionary conservation of members of the ZmHDZ genes in maize. Several regulatory elements associated with drought tolerance were identified in the promoter regions of ZmHDZ genes, indicating the implication of these genes in plant response to drought stress. 42 ZmHDZ genes were distributed unevenly on 10 chromosomes, and 24 pairs of gene duplications were the segmental duplication. The expression of several ZmHDZ genes was upregulated under drought stress, and ZmHDZ9 overexpressing transgenic plants exhibited higher SOD and POD activities and higher accumulation of soluble proteins under drought stress which resulted in enhanced developed phenotype and improved resistance. The present study provides evidence for the evolutionary conservation of HD-ZIP transcription factors homologs in maize. The results further provide a comprehensive insight into the roles of ZmHDZ genes in regulating drought stress tolerance in maize.
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Affiliation(s)
- Xiao Qiu
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002 China
| | - GuoRui Wang
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002 China
| | | | - Jiaxu Fu
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002 China
| | - Zhixue Liu
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002 China
| | - PengYu Zhang
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002 China
| | - Xiaowen Xie
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002 China
| | - Lixia Ku
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002 China
| | - Ying Ma
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002 China
| | - XiaoKang Guan
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002 China
| | - Li Wei
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002 China
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13
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Li T, Pan W, Yuan Y, Liu Y, Li Y, Wu X, Wang F, Cui L. Identification, Characterization, and Expression Profile Analysis of the mTERF Gene Family and Its Role in the Response to Abiotic Stress in Barley ( Hordeum vulgare L.). FRONTIERS IN PLANT SCIENCE 2021; 12:684619. [PMID: 34335653 PMCID: PMC8319850 DOI: 10.3389/fpls.2021.684619] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/23/2021] [Indexed: 05/17/2023]
Abstract
Plant mitochondrial transcription termination factor (mTERF) family regulates organellar gene expression (OGE) and is functionally characterized in diverse species. However, limited data are available about its functions in the agriculturally important cereal barley (Hordeum vulgare L.). In this study, we identified 60 mTERFs in the barley genome (HvmTERFs) through a comprehensive search against the most updated barley reference genome, Morex V2. Then, phylogenetic analysis categorized these genes into nine subfamilies, with approximately half of the HvmTERFs belonging to subfamily IX. Members within the same subfamily generally possessed conserved motif composition and exon-intron structure. Both segmental and tandem duplication contributed to the expansion of HvmTERFs, and the duplicated gene pairs were subjected to strong purifying selection. Expression analysis suggested that many HvmTERFs may play important roles in barley development (e.g., seedlings, leaves, and developing inflorescences) and abiotic stresses (e.g., cold, salt, and metal ion), and HvmTERF21 and HvmTERF23 were significant induced by various abiotic stresses and/or phytohormone treatment. Finally, the nucleotide diversity was decreased by only 4.5% for HvmTERFs during the process of barley domestication. Collectively, this is the first report to characterize HvmTERFs, which will not only provide important insights into further evolutionary studies but also contribute to a better understanding of the potential functions of HvmTERFs and ultimately will be useful in future gene functional studies.
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Affiliation(s)
- Tingting Li
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Wenqiu Pan
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
| | - Yiyuan Yuan
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Ying Liu
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Yihan Li
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Xiaoyu Wu
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Fei Wang
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Licao Cui
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
- *Correspondence: Licao Cui
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14
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Jiang W, Geng Y, Liu Y, Chen S, Cao S, Li W, Chen H, Ma D, Yin J. Genome-wide identification and characterization of SRO gene family in wheat: Molecular evolution and expression profiles during different stresses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 154:590-611. [PMID: 32912491 DOI: 10.1016/j.plaphy.2020.07.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 06/27/2020] [Accepted: 07/02/2020] [Indexed: 06/11/2023]
Abstract
SRO (SIMILAR TO RCD ONE), a type of plant-specific small protein family, play important roles in plant growth and development, as well as in response to biotic/abiotic stresses. Although characterization of SROs have been performed in model plants, little is known about their function in wheat, especially under stress conditions. In this study, 30 SRO genes were identified from the wheat genome (TaSRO). They were phylogenetically separated into two groups with distinct structures. The cis-regulatory elements in the promoter region of TaSROs were analyzed and numerous elements functionally associated with stress responding and hormones were interpreted, implying the reason for induction expression patterns of TaSROs during abiotic and biotic stresses in wheat. Whole-genome replication events in the SRO gene family of wheat and seven other species (Arabidopsis thaliana, rice, maize, barley, soybean, upland cotton, and cucumber) were analyzed, resulting in 1, 12, 9, 23, 6, 5, and 3 of gene pairs, respectively. The tissue-specific expression pattern profiling revealed that most TaSROs are highly expressed in one or more tissues and may play an important role in wheat growth and development. In addition, qRT-PCR results further confirmed that these TaSRO genes are involved in wheat stress response. In summary, our study laid a theoretical basis for molecular function deciphering of TaSROs, especially in plant hormones and biotic/abiotic stress responses.
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Affiliation(s)
- Wenqiang Jiang
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Forewarning and Management of Agricultural and Forestry Pests, Hubei Engineering Technology Center/College of Agriculture, Yangtze University, Jingzhou, 434000, Hubei, China; Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China
| | - Yuepan Geng
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, 210014, Jiangsu, China
| | - Yike Liu
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Shuhui Chen
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Forewarning and Management of Agricultural and Forestry Pests, Hubei Engineering Technology Center/College of Agriculture, Yangtze University, Jingzhou, 434000, Hubei, China
| | - Shulin Cao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China
| | - Wei Li
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China
| | - Huaigu Chen
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China
| | - Dongfang Ma
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Forewarning and Management of Agricultural and Forestry Pests, Hubei Engineering Technology Center/College of Agriculture, Yangtze University, Jingzhou, 434000, Hubei, China.
| | - Junliang Yin
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Forewarning and Management of Agricultural and Forestry Pests, Hubei Engineering Technology Center/College of Agriculture, Yangtze University, Jingzhou, 434000, Hubei, China; Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China.
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15
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Genome-wide identification and expression analysis of the superoxide dismutase (SOD) gene family in Salvia miltiorrhiza. Gene 2020; 742:144603. [PMID: 32198126 DOI: 10.1016/j.gene.2020.144603] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 03/12/2020] [Accepted: 03/16/2020] [Indexed: 12/19/2022]
Abstract
Adverse environmental conditions, such as salinity, cold, drought, heavy metals, and pathogens affect the yield and quality of Salvia miltiorrhiza, a well-known medicinal plant used for the treatment of cardiovascular and cerebrovascular diseases. Superoxide dismutase (SOD), a key enzyme of antioxidant system in plants, plays a vital role in protecting plants against various biotic and abiotic stresses via scavenging the reactive oxygen species produced by organisms. However, little is known about the SOD gene family in S. miltiorrhiza. In this study, eight SOD genes, including three Cu/Zn-SODs, two Fe-SODs and three Mn-SODs, were identified in the S. miltiorrhiza genome. Their gene structures, promoters, protein features, phylogenetic relationships, and expression profiles were comprehensively investigated. Gene structure analysis implied that most SmSODs have different introns/exons distrbution patterns. Many cis-elements related to different stress responses or plant hormones were found in the promoter of each SmSOD. Expression profile analysis indicated that SmSODs exhibited diverse responses to cold, salt, drought, heavy metal, and plant hormones. Additionally, 31 types of TFs regulating SmSODs were predicted and analyzed. These findings provided valuable information for further researches on the functions and applications of SmSODs in S. miltiorrhiza growth and adaptation to stress.
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