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Chen C, Wu Q, Yue J, Wang X, Wang C, Wei R, Li R, Jin G, Chen T, Chen P. A cyclic nucleotide-gated channel gene HcCNGC21 positively regulates salt and drought stress responses in kenaf (Hibiscus cannabinus L.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 345:112111. [PMID: 38734143 DOI: 10.1016/j.plantsci.2024.112111] [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: 12/29/2023] [Revised: 05/01/2024] [Accepted: 05/05/2024] [Indexed: 05/13/2024]
Abstract
Cyclic Nucleotide-Gated Channels (CNGCs) serve as Ca2+ permeable cation transport pathways, which are involved in the regulation of various biological functions such as plant cell ion selective permeability, growth and development, responses to biotic and abiotic stresses. At the present study, a total of 31 CNGC genes were identified and bioinformatically analyzed in kenaf. Among these genes, HcCNGC21 characterized to localize at the plasma membrane, with the highest expression levels in leaves, followed by roots. In addition, HcCNGC21 could be significantly induced under salt or drought stress. Virus-induced gene silencing (VIGS) of HcCNGC21 in kenaf caused notable growth inhibition under salt or drought stress, characterized by reductions in plant height, stem diameter, leaf area, root length, root surface area, and root tip number. Meanwhile, the activities of superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) were significantly decreased, accompanied by reduced levels of osmoregulatory substances and total chlorophyll content. However, ROS accumulation and Na+ content increased. The expression of stress-responsive genes, such as HcSOD, HcPOD, HcCAT, HcERF3, HcNAC29, HcP5CS, HcLTP, and HcNCED, was significantly downregulated in these silenced lines. However, under salt or drought stress, the physiological performance and expression of stress-related genes in transgenic Arabidopsis thaliana plants overexpressing HcCNGC21 were diametrically opposite to those of TRV2-HcCNGC21 kenaf line. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays revealed that HcCNGC21 interacts with HcAnnexin D1. These findings collectively underscore the positive role of HcCNGC21 in plant resistance to salt and drought stress.
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Affiliation(s)
- Canni Chen
- College of Agriculture, Guangxi University, Key Laboratory of Crop Genetic Breeding and Germplasm Innovation, Guangxi Key Laboratory of Agro-environment and Agric-products safety, Nanning 530004, China
| | - Qijing Wu
- College of Agriculture, Guangxi University, Key Laboratory of Crop Genetic Breeding and Germplasm Innovation, Guangxi Key Laboratory of Agro-environment and Agric-products safety, Nanning 530004, China
| | - Jiao Yue
- College of Agriculture, Guangxi University, Key Laboratory of Crop Genetic Breeding and Germplasm Innovation, Guangxi Key Laboratory of Agro-environment and Agric-products safety, Nanning 530004, China
| | - Xu Wang
- College of Agriculture, Guangxi University, Key Laboratory of Crop Genetic Breeding and Germplasm Innovation, Guangxi Key Laboratory of Agro-environment and Agric-products safety, Nanning 530004, China
| | - Caijin Wang
- College of Agriculture, Guangxi University, Key Laboratory of Crop Genetic Breeding and Germplasm Innovation, Guangxi Key Laboratory of Agro-environment and Agric-products safety, Nanning 530004, China
| | - Rujian Wei
- College of Agriculture, Guangxi University, Key Laboratory of Crop Genetic Breeding and Germplasm Innovation, Guangxi Key Laboratory of Agro-environment and Agric-products safety, Nanning 530004, China
| | - Ru Li
- College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Gang Jin
- Guangxi Subtropical Crops Research Institute, Nanning 530001, China
| | - Tao Chen
- Guangxi Subtropical Crops Research Institute, Nanning 530001, China
| | - Peng Chen
- College of Agriculture, Guangxi University, Key Laboratory of Crop Genetic Breeding and Germplasm Innovation, Guangxi Key Laboratory of Agro-environment and Agric-products safety, Nanning 530004, China.
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Yang CA, Hu SY, Ge J, Wang H, Wang Y, Gu C, Xue JY. Frequent polyploidization events in Hibiscus shaped its karyotype and species diversity. J Genet Genomics 2024:S1673-8527(24)00119-X. [PMID: 38801944 DOI: 10.1016/j.jgg.2024.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/21/2024] [Accepted: 05/22/2024] [Indexed: 05/29/2024]
Affiliation(s)
- Cheng-Ao Yang
- College of Horticulture, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Shuai-Ya Hu
- College of Horticulture, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Jing Ge
- College of Horticulture, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Haibin Wang
- College of Horticulture, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yue Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, Jiangsu 210014, China.
| | - Chunsun Gu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, Jiangsu 210014, China.
| | - Jia-Yu Xue
- College of Horticulture, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
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Shao L, Jin S, Chen J, Yang G, Fan R, Zhang Z, Deng Q, Han J, Ma X, Dong Z, Lu H, Hu W, Wang K, Hu L, Shen Z, Huang S, Zhao T, Guan X, Hu Y, Zhang T, Fang L. High-quality genomes of Bombax ceiba and Ceiba pentandra provide insights into the evolution of Malvaceae species and differences in their natural fiber development. PLANT COMMUNICATIONS 2024; 5:100832. [PMID: 38321741 PMCID: PMC11121743 DOI: 10.1016/j.xplc.2024.100832] [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: 08/07/2023] [Revised: 09/15/2023] [Accepted: 02/01/2024] [Indexed: 02/08/2024]
Abstract
Members of the Malvaceae family, including Corchorus spp., Gossypium spp., Bombax spp., and Ceiba spp., are important sources of natural fibers. In the past decade, the genomes of several Malvaceae species have been assembled; however, the evolutionary history of Malvaceae species and the differences in their fiber development remain to be clarified. Here, we report the genome assembly and annotation of two natural fiber plants from the Malvaceae, Bombax ceiba and Ceiba pentandra, whose assembled genome sizes are 783.56 Mb and 1575.47 Mb, respectively. Comparative analysis revealed that whole-genome duplication and Gypsy long terminal repeat retroelements have been the major causes of differences in chromosome number (2n = 14 to 2n = 96) and genome size (234 Mb to 2676 Mb) among Malvaceae species. We also used comparative genomic analyses to reconstruct the ancestral Malvaceae karyotype with 11 proto-chromosomes, providing new insights into the evolutionary trajectories of Malvaceae species. MYB-MIXTA-like 3 is relatively conserved among the Malvaceae and functions in fiber cell-fate determination in the epidermis. It appears to perform this function in any tissue where it is expressed, i.e. in fibers on the endocarp of B. ceiba and in ovule fibers of cotton. We identified a structural variation in a cellulose synthase gene and a higher copy number of cellulose synthase-like genes as possible causes of the finer, less spinnable, weaker fibers of B. ceiba. Our study provides two high-quality genomes of natural fiber plants and offers insights into the evolution of Malvaceae species and differences in their natural fiber formation and development through multi-omics analysis.
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Affiliation(s)
- Lei Shao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Shangkun Jin
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jinwen Chen
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Guangsui Yang
- Tropical Crop Germplasm Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Rui Fan
- Spices and Beverages Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China
| | - Zhiyuan Zhang
- Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Qian Deng
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jin Han
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xiaowei Ma
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zeyu Dong
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Hejun Lu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Wanying Hu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Kai Wang
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Lisong Hu
- Spices and Beverages Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China
| | - Zhen Shen
- Tropical Crop Germplasm Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Surong Huang
- Tropical Crop Germplasm Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Ting Zhao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Xueying Guan
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Yan Hu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Tianzhen Zhang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Lei Fang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China.
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Wang C, Deng L, Zhang Y, Zhao M, Liang M, Lee LC, Cristhian CO, Yang L, He T. Farmland phytoremediation in bibliometric analysis. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 351:119971. [PMID: 38169268 DOI: 10.1016/j.jenvman.2023.119971] [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: 08/13/2023] [Revised: 12/09/2023] [Accepted: 12/25/2023] [Indexed: 01/05/2024]
Abstract
Phytoremediation is an environmentally friendly, economical, and sustainable technique for restoring farmland. It can remove heavy metals and organic pollutants from the soil through the implementation of hyperaccumulator plants. In recent years, it has garnered significant interest from academic and industrial sectors. This article screened 368 research papers from the Web of Science core collection database related to farmland phytoremediation and conducted a bibliometric analysis of the domain based on CiteSpace. The paper intuitively demonstrates the most influential countries, the most productive institutions, the most contributing groups of authors, and the primary sources of farmland phytoremediation research domain. The findings additionally indicate that the research hotspots include: (1) mechanisms and principles of phytoremediation, (2) the improvement of restoration efficiency, (3) the economic, ecological, and sustainable development of phytoremediation. The exploration of plants with potential to accumulate heavy metals and produce large amounts of biomass is the research frontier within the field of farmland phytoremediation. Additionally, this bibliometric analysis can help scholars willing to work in this research field by concisely understanding the overall research field and frontiers. With the continuous improvement of phytoremediation and its combination with other remediation technologies, the future of farmland remediation will have a promising prospect.
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Affiliation(s)
- Chaoqun Wang
- School of Ecology and Environment, Ningxia University, Yinchuan, 750021, PR China.
| | - Lirong Deng
- College of Resources and Environment, Yangtze University, Wuhan, 430100, PR China.
| | - Yongxiang Zhang
- College of Resources and Environment, Yangtze University, Wuhan, 430100, PR China.
| | - Mingtao Zhao
- School of Ecology and Environment, Ningxia University, Yinchuan, 750021, PR China.
| | - Meiqi Liang
- School of Ecology and Environment, Ningxia University, Yinchuan, 750021, PR China.
| | - Lien-Chieh Lee
- School of Environmental Science and Engineering, Hubei Polytechnic University, Huangshi, 435003, PR China.
| | - Chicaiza-Ortiz Cristhian
- School of Environmental Science and Engineering, China-UK·Low-Carbon College, Shanghai Jiao Tong University, Shanghai, 200240, PR China; Biomass to Resources Group, Universidad Regional Amazónica IKIAM, Tena, Napo, 150150, Ecuador.
| | - Long Yang
- School of Ecology and Environment, Institute of Disaster Prevention, 065201, PR China.
| | - Tonghui He
- School of Ecology and Environment, Ningxia University, Yinchuan, 750021, PR China.
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Koo H, Lee GW, Ko SR, Go S, Kwon SY, Kim YM, Shin AY. Two long read-based genome assembly and annotation of polyploidy woody plants, Hibiscus syriacus L. using PacBio and Nanopore platforms. Sci Data 2023; 10:713. [PMID: 37853021 PMCID: PMC10584963 DOI: 10.1038/s41597-023-02631-z] [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: 06/16/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023] Open
Abstract
Improvements in long read DNA sequencing and related techniques facilitated the generation of complex eukaryotic genomes. Despite these advances, the quality of constructed plant reference genomes remains relatively poor due to the large size of genomes, high content of repetitive sequences, and wide variety of ploidy. Here, we developed the de novo sequencing and assembly of high polyploid plant genome, Hibiscus syriacus, a flowering plant species of the Malvaceae family, using the Oxford Nanopore Technologies and Pacific Biosciences Sequel sequencing platforms. We investigated an efficient combination of high-quality and high-molecular-weight DNA isolation procedure and suitable assembler to achieve optimal results using long read sequencing data. We found that abundant ultra-long reads allow for large and complex polyploid plant genome assemblies with great recovery of repetitive sequences and error correction even at relatively low depth Nanopore sequencing data and polishing compared to previous studies. Collectively, our combination provides cost effective methods to improve genome continuity and quality compared to the previously reported reference genome by accessing highly repetitive regions. The application of this combination may enable genetic research and breeding of polyploid crops, thus leading to improvements in crop production.
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Affiliation(s)
- Hyunjin Koo
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Gir-Won Lee
- SML Genetree Co. Ltd., Seoul, 05855, Republic of Korea
| | - Seo-Rin Ko
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Biosystems and Bioengineering Program, University of Science and Technology, Daejeon, 34113, Korea
| | - Sangjin Go
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Biosystems and Bioengineering Program, University of Science and Technology, Daejeon, 34113, Korea
| | - Suk-Yoon Kwon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Biosystems and Bioengineering Program, University of Science and Technology, Daejeon, 34113, Korea
| | - Yong-Min Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34141, Republic of Korea.
- Digital Biotech Innovation Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
| | - Ah-Young Shin
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34141, Republic of Korea.
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Koshimizu S, Masuda S, Shibata A, Ishii T, Shirasu K, Hoshino A, Arita M. Genome and transcriptome analyses reveal genes involved in the formation of fine ridges on petal epidermal cells in Hibiscus trionum. DNA Res 2023; 30:dsad019. [PMID: 37691489 PMCID: PMC10558197 DOI: 10.1093/dnares/dsad019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/11/2023] [Accepted: 09/07/2023] [Indexed: 09/12/2023] Open
Abstract
Hibiscus trionum, commonly known as the 'Flower of an Hour', is an easily cultivated plant in the Malvaceae family that is widespread in tropical and temperate regions, including drylands. The purple base part of its petal exhibits structural colour due to the fine ridges on the epidermal cell surface, and the molecular mechanism of ridge formation has been actively investigated. We performed genome sequencing of H. trionum using a long-read sequencing technology with transcriptome and pathway analyses to identify candidate genes for fine structure formation. The ortholog of AtSHINE1, which is involved in the biosynthesis of cuticular wax in Arabidopsis thaliana, was significantly overexpressed in the iridescent tissue. In addition, orthologs of AtCUS2 and AtCYP77A, which contribute to cutin synthesis, were also overexpressed. Our results provide important insights into the formation of fine ridges on epidermal cells in plants using H. trionum as a model.
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Affiliation(s)
- Shizuka Koshimizu
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima 411-8540, Japan
| | - Sachiko Masuda
- Center for Sustainable Resource Science, RIKEN, Yokohama 230-0045, Japan
| | - Arisa Shibata
- Center for Sustainable Resource Science, RIKEN, Yokohama 230-0045, Japan
| | - Takayoshi Ishii
- Arid Land Research Center, Tottori University, Tottori 680-001, Japan
| | - Ken Shirasu
- Center for Sustainable Resource Science, RIKEN, Yokohama 230-0045, Japan
| | - Atsushi Hoshino
- National Institute for Basic Biology, Okazaki 444-8585, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Okazaki 444-8585, Japan
| | - Masanori Arita
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima 411-8540, Japan
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Zhang H, Ding X, Wang H, Chen H, Dong W, Zhu J, Wang J, Peng S, Dai H, Mei W. Systematic evolution of bZIP transcription factors in Malvales and functional exploration of AsbZIP14 and AsbZIP41 in Aquilaria sinensis. FRONTIERS IN PLANT SCIENCE 2023; 14:1243323. [PMID: 37719219 PMCID: PMC10499555 DOI: 10.3389/fpls.2023.1243323] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 07/24/2023] [Indexed: 09/19/2023]
Abstract
Introduction Agarwood, the dark-brown resin produced by Aquilaria trees, has been widely used as incense, spice, perfume or traditional medicine and 2-(2-phenethyl) chromones (PECs) are the key markers responsible for agarwood formation. But the biosynthesis and regulatory mechanism of PECs were still not illuminated. The transcription factor of basic leucine zipper (bZIP) presented the pivotal regulatory roles in various secondary metabolites biosynthesis in plants, which might also contribute to regulate PECs biosynthesis. However, molecular evolution and function of bZIP are rarely reported in Malvales plants, especially in Aquilaria trees. Methods and results Here, 1,150 bZIPs were comprehensively identified from twelve Malvales and model species genomes and the evolutionary process were subsequently analyzed. Duplication types and collinearity indicated that bZIP is an ancient or conserved TF family and recent whole genome duplication drove its evolution. Interesting is that fewer bZIPs in A. sinensis than that species also experienced two genome duplication events in Malvales. 62 AsbZIPs were divided into 13 subfamilies and gene structures, conservative domains, motifs, cis-elements, and nearby genes of AsbZIPs were further characterized. Seven AsbZIPs in subfamily D were significantly regulated by ethylene and agarwood inducer. As the typical representation of subfamily D, AsbZIP14 and AsbZIP41 were localized in nuclear and potentially regulated PECs biosynthesis by activating or suppressing type III polyketide synthases (PKSs) genes expression via interaction with the AsPKS promoters. Discussion Our results provide a basis for molecular evolution of bZIP gene family in Malvales and facilitate the understanding the potential functions of AsbZIP in regulating 2-(2-phenethyl) chromone biosynthesis and agarwood formation.
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Affiliation(s)
- Hao Zhang
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xupo Ding
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Hao Wang
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Huiqin Chen
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Wenhua Dong
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jiahong Zhu
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jian Wang
- Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan, College of Forestry, Hainan University, Haikou, China
| | - Shiqing Peng
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Haofu Dai
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Wenli Mei
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
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8
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Wang R, Li W, He Q, Zhang H, Wang M, Zheng X, Liu Z, Wang Y, Du C, Du H, Xing L. The genome of okra ( Abelmoschus esculentus) provides insights into its genome evolution and high nutrient content. HORTICULTURE RESEARCH 2023; 10:uhad120. [PMID: 37554345 PMCID: PMC10405168 DOI: 10.1093/hr/uhad120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 05/26/2023] [Indexed: 08/10/2023]
Abstract
Okra (Abelmoschus esculentus) is an important vegetable crop with high nutritional value. However, the mechanism underlying its high nutrient content remains poorly understood. Here, we present a chromosome-scale genome of okra with a size of 1.19 Gb. Comparative genomics analysis revealed the phylogenetic status of A. esculentus, as well as whole-genome duplication (WGD) events that have occurred widely across the Malvaceae species. We found that okra has experienced three additional WGDs compared with the diploid cotton Gossypium raimondii, resulting in a large chromosome number (2n = 130). After three WGDs, okra has undergone extensive genomic deletions and retained substantial numbers of genes related to secondary metabolite biosynthesis and environmental adaptation, resulting in significant differences between okra and G. raimondii in the gene families related to cellulose synthesis. Combining transcriptomic and metabolomic analysis, we revealed the relationship between gene expression and metabolite content change across different okra developmental stages. Furthermore, the sinapic acid/S-lignin biosynthesis-related gene families have experienced remarkable expansion in okra, and the expression of key enzymes involved in the sinapic acid/S-lignin biosynthesis pathway vary greatly across developmental periods, which partially explains the differences in metabolite content across the different stages. Our study gains insights into the comprehensive evolutionary history of Malvaceae species and the genetic basis that underlies the nutrient content changes in okra, which will facilitate the functional study and genetic improvement of okra varieties.
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Affiliation(s)
- Ruyu Wang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
| | - Wei Li
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
- Hebei Basic Science Center for Biotic Interaction, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
| | - Qiang He
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
- Hebei Basic Science Center for Biotic Interaction, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
| | - Hongyu Zhang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
| | - Meijia Wang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
| | - Xinyuan Zheng
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
| | - Ze Liu
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
| | - Yu Wang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
| | - Cailian Du
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
| | - Huilong Du
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
- Hebei Basic Science Center for Biotic Interaction, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
| | - Longsheng Xing
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
- Hebei Basic Science Center for Biotic Interaction, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
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9
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Tang M, Li R, Chen P. Exogenous glutathione can alleviate chromium toxicity in kenaf by activating antioxidant system and regulating DNA methylation. CHEMOSPHERE 2023:139305. [PMID: 37364644 DOI: 10.1016/j.chemosphere.2023.139305] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 06/28/2023]
Abstract
Glutathione (GSH) participates in plant response to heavy metals (HMs) stress, however, the epigenetic regulating mechanisms of GSH in HMs detoxification remains unclear. In this study, to reveal the potential epigenetic regulating mechanisms, kenaf seedlings were treated with/without GSH under chromium (Cr) stress. A comprehensive physiological, genome-wide DNA methylation and gene functional analysis were performed. Results showed that external GSH obviously recovered Cr-induced growth inhibition, significantly decreased H2O2, O2.- and MDA accumulation, increased the activities of antioxidant enzymes (SOD, CAT, GR and APX) in kenaf exposed to Cr. In addition, the expression level of the main DNA methyltransferase (MET1, CMT3 and DRM1) and demethylase (ROS1, DEM, DML2, DML3 and DDM1) genes were investigated by qRT-PCR. The result indicated that Cr stress decreased DNA methyltransferase genes expression while increased demethylase genes expression; however, apply exogenous GSH led to the recovery trend. These indicating exogenous GSH alleviation Cr stress on kenaf seedlings by increasing DNA methylation level. At the same time, the MethylRAD-seq genome-wide DNA methylation analysis showed the DNA methylation level was significantly increased after GSH treatment compared with Cr treatment alone. The differentially methylated genes (DMGs) were uniquely enriched in DNA repair, flavin adenine dinucleotide binding and oxidoreductase activity. Furthermore, a ROS homeostasis-associated DMG, HcTrx, was selected for further functional analysis. Results showed that the knock-down of HcTrx kenaf seedlings displayed yellow-green phenotype and impaired antioxidant enzyme activity; in contrast, the overexpression lines of HcTrx improved chlorophyll levels and enhanced Cr tolerance in Arabidopsis. Taken together, our results illustrate the novel role of GSH-mediated Cr detoxification in kenaf by modulating the DNA methylation, and thus further affect the activation of antioxidant defense systems. The present characterized Cr tolerant gene resource could be further used for kenaf Cr tolerant breeding via genetic improvement.
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Affiliation(s)
- Meiqiong Tang
- Guangxi Key Laboratory of Agro-environment and Agric-products Safety, Key Laboratory of Crop Genetics Breeding and Germplasm Innovation, College of Agriculture, Guangxi University, Nanning, 530004, China; Guangxi Botanical Garden of Medicinal Plants, Guangxi Key Laboratory Resources Protection and Genetic Improvement, Nanning, China.
| | - Ru Li
- College of Life Science & Technology, Guangxi University, Nanning, China.
| | - Peng Chen
- Guangxi Key Laboratory of Agro-environment and Agric-products Safety, Key Laboratory of Crop Genetics Breeding and Germplasm Innovation, College of Agriculture, Guangxi University, Nanning, 530004, China.
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10
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Luo D, Lu H, Wang C, Mubeen S, Cao S, Yue J, Pan J, Wu X, Wu Q, Zhang H, Chen C, Rehman M, Li R, Chen P. Physiological and DNA methylation analysis provides epigenetic insights into kenaf cadmium tolerance heterosis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 331:111663. [PMID: 36841339 DOI: 10.1016/j.plantsci.2023.111663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 02/19/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Soil heavy metal pollution is one of the most challenging problems. Kenaf is an important natural fiber crop with strong heterosis and a higher tolerance to heavy metals. However, little is known about the molecular mechanisms of kenaf heavy metal tolerance, especially the mechanism of genomic DNA methylation regulating heterosis. In this study, kenaf cultivars CP085, CP089, and their hybrid F1 seedlings were subjected to 300 µM cadmium stress and found obvious heterosis of cadmium resistance in morphology and antioxidant enzyme activity of F1 hybrid seedlings. Through methylation-sensitive amplification polymorphism (MSAP) analysis, we highlighted that the total DNA methylation level under cadmium decreased by 16.9 % in F1 and increased by 14.0 % and 3.0 % in parents CP085 and CP089, respectively. The hypomethylation rate was highest (21.84 %), but hypermethylation was lowest (17.24 %) in F1 compared to parent cultivars. In particular, principal coordinates analysis (PCoA) indicates a significant epigenetic differentiation between F1 and its parents under cadmium. Furthermore, 21 differentially methylated DNA fragments (DMFs) were analyzed. Especially, the expression of NPF2.7, NADP-ME, NAC71, TPP-D, LRR-RLKs, and DHX51 genes were changed due to cadmium stress and related to cytosine methylation regulation. Finally, the knocked-down of the differentially methylated gene NPF2.7 by virus-induced gene silencing (VIGS) resulted in increased sensitivity of kenaf seedlings under cadmium stress. It is speculated that low DNA methylation levels can regulate gene expression that led to the heterosis of cadmium tolerance in kenaf.
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Affiliation(s)
- Dengjie Luo
- Guangxi Key Laboratory of Agro-environment and Agric-products safety, Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Hai Lu
- Guangxi Key Laboratory of Agro-environment and Agric-products safety, Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Caijin Wang
- Guangxi Key Laboratory of Agro-environment and Agric-products safety, Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Samavia Mubeen
- Guangxi Key Laboratory of Agro-environment and Agric-products safety, Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Shan Cao
- Guangxi Key Laboratory of Agro-environment and Agric-products safety, Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Jiao Yue
- Guangxi Key Laboratory of Agro-environment and Agric-products safety, Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Jiao Pan
- Guangxi Key Laboratory of Agro-environment and Agric-products safety, Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Xia Wu
- Guangxi Key Laboratory of Agro-environment and Agric-products safety, Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Qijing Wu
- Guangxi Key Laboratory of Agro-environment and Agric-products safety, Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Hui Zhang
- Guangxi Key Laboratory of Agro-environment and Agric-products safety, Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Canni Chen
- Guangxi Key Laboratory of Agro-environment and Agric-products safety, Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Muzammal Rehman
- Guangxi Key Laboratory of Agro-environment and Agric-products safety, Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Ru Li
- College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Peng Chen
- Guangxi Key Laboratory of Agro-environment and Agric-products safety, Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530004, China.
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11
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Mottiar Y, Smith RA, Karlen SD, Ralph J, Mansfield SD. Evolution of p-coumaroylated lignin in eudicots provides new tools for cell wall engineering. THE NEW PHYTOLOGIST 2023; 237:251-264. [PMID: 36196006 PMCID: PMC10099755 DOI: 10.1111/nph.18518] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
Ester-linked p-coumarate (pCA) is a hallmark feature of the secondary cell walls in commelinid monocot plants. It has been shown that pCA groups arise during lignin polymerisation from the participation of monolignol conjugates assembled by p-coumaroyl-CoA:monolignol transferase (PMT) enzymes, members of the BAHD superfamily of acyltransferases. Herein, we report that a eudicot species, kenaf (Hibiscus cannabinus), naturally contains p-coumaroylated lignin in the core tissues of the stems but not in the bast fibres. Moreover, we identified a novel acyltransferase, HcPMT, that shares <30% amino acid identity with known monocot PMT sequences. Recombinant HcPMT showed a preference in enzyme assays for p-coumaroyl-CoA and benzoyl-CoA as acyl donor substrates and sinapyl alcohol as an acyl acceptor. Heterologous expression of HcPMT in hybrid poplar trees led to the incorporation of pCA in lignin, but no improvement in the saccharification potential of the wood. This work illustrates the value in mining diverse plant taxa for new monolignol acyltransferases. Furthermore, the occurrence of pCA outside monocot lineages may represent another example of convergent evolution in lignin structure. This discovery expands textbook views on cell wall biochemistry and provides a new molecular tool for engineering the lignin of biomass feedstock plants.
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Affiliation(s)
- Yaseen Mottiar
- Department of Wood ScienceUniversity of British Columbia2424 Main MallVancouverBCV6T 1Z4Canada
- Department of Energy Great Lakes Bioenergy Research CenterUniversity of Wisconsin1552 University AvenueMadisonWI53726USA
| | - Rebecca A. Smith
- Department of Energy Great Lakes Bioenergy Research CenterUniversity of Wisconsin1552 University AvenueMadisonWI53726USA
- Department of BiochemistryUniversity of Wisconsin433 Babcock DriveMadisonWI53706USA
| | - Steven D. Karlen
- Department of Energy Great Lakes Bioenergy Research CenterUniversity of Wisconsin1552 University AvenueMadisonWI53726USA
- Department of BiochemistryUniversity of Wisconsin433 Babcock DriveMadisonWI53706USA
| | - John Ralph
- Department of Energy Great Lakes Bioenergy Research CenterUniversity of Wisconsin1552 University AvenueMadisonWI53726USA
- Department of BiochemistryUniversity of Wisconsin433 Babcock DriveMadisonWI53706USA
| | - Shawn D. Mansfield
- Department of Wood ScienceUniversity of British Columbia2424 Main MallVancouverBCV6T 1Z4Canada
- Department of Energy Great Lakes Bioenergy Research CenterUniversity of Wisconsin1552 University AvenueMadisonWI53726USA
- Department of BotanyUniversity of British Columbia6270 University BoulevardVancouverBCV6T 1Z4Canada
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12
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Chen M, She Z, Aslam M, Liu T, Wang Z, Qi J, Niu X. Genomic insights of the WRKY genes in kenaf ( Hibiscus cannabinus L.) reveal that HcWRKY44 improves the plant's tolerance to the salinity stress. FRONTIERS IN PLANT SCIENCE 2022; 13:984233. [PMID: 36061791 PMCID: PMC9433988 DOI: 10.3389/fpls.2022.984233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
The WRKY transcription factors (TFs) are among the most diverse TF families of plants. They are implicated in various processes related to plant growth and stress response. Kenaf (Hibiscus cannabinus L.), an important fiber crop, has many applications, including the phytoremediation of saline-alkaline soil. However, the roles of WRKY TFs in kenaf are rarely studied. In the present study, 46 kenaf WRKY genes were genome-widely identified and characterized by gene structure, phylogeny and expression pattern analysis. Furthermore, the HcWRKY44 gene was functionally characterized in Arabidopsis under salinity and drought stresses. HcWRKY44 is a nuclear-localized protein that is positively induced by salinity and drought, with roots showing maximum accumulation of its transcripts. Under NaCl and abscisic acid (ABA) stress conditions, plants overexpressing HcWRKY44 had higher germination rates, better root growth and increased survival than control plants; however, it did not improve the ability to withstand drought stress. Moreover, ABA signaling genes (ABI1, ABI2, and ABI5), ABA-responsive genes (ABF4, RD29B, COR15A, COR47, and RD22), stress-related genes (STZ, P5CS, and KIN1), and ionic homeostasis-related genes (SOS1, AHA1, AHA2, and HKT1) were positively induced in HcWRKY44 transgenic plants under NaCl treatment. These results suggest that HcWRKY44 improved plant's tolerance to salt stress but not osmotic stress through an ABA-mediated pathway. In summary, this study provides provided comprehensive information about HcWRKY genes and revealed that HcWRKY44 is involved in salinity tolerance and ABA signaling.
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Affiliation(s)
- Meixia Chen
- Industry and University Research Cooperation Demonstration Base in Fujian Province, College of Life Sciences, Ningde Normal University, Ningde, China
| | - Zeyuan She
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Mohammad Aslam
- College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ting Liu
- Industry and University Research Cooperation Demonstration Base in Fujian Province, College of Life Sciences, Ningde Normal University, Ningde, China
- College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zerong Wang
- Industry and University Research Cooperation Demonstration Base in Fujian Province, College of Life Sciences, Ningde Normal University, Ningde, China
- College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jianmin Qi
- College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaoping Niu
- College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
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13
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Jan M, Liu Z, Guo C, Zhou Y, Sun X. An Overview of Cotton Gland Development and Its Transcriptional Regulation. Int J Mol Sci 2022; 23:ijms23094892. [PMID: 35563290 PMCID: PMC9103798 DOI: 10.3390/ijms23094892] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 04/20/2022] [Accepted: 04/26/2022] [Indexed: 11/16/2022] Open
Abstract
Cotton refers to species in the genus Gossypium that bear spinnable seed coat fibers. A total of 50 species in the genus Gossypium have been described to date. Of these, only four species, viz. Gossypium, hirsutum, G. barbadense, G. arboretum, and G. herbaceum are cultivated; the rest are wild. The black dot-like structures on the surfaces of cotton organs or tissues, such as the leaves, stem, calyx, bracts, and boll surface, are called gossypol glands or pigment glands, which store terpenoid aldehydes, including gossypol. The cotton (Gossypium hirsutum) pigment gland is a distinctive structure that stores gossypol and its derivatives. It provides an ideal system for studying cell differentiation and organogenesis. However, only a few genes involved in the process of gland formation have been identified to date, and the molecular mechanisms underlying gland initiation remain unclear. The terpenoid aldehydes in the lysigenous glands of Gossypium species are important secondary phytoalexins (with gossypol being the most important) and one of the main defenses of plants against pests and diseases. Here, we review recent research on the development of gossypol glands in Gossypium species, the regulation of the terpenoid aldehyde biosynthesis pathway, discoveries from genetic engineering studies, and future research directions.
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Affiliation(s)
- Masood Jan
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China; (M.J.); (Z.L.); (C.G.); (Y.Z.)
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Zhixin Liu
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China; (M.J.); (Z.L.); (C.G.); (Y.Z.)
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Chenxi Guo
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China; (M.J.); (Z.L.); (C.G.); (Y.Z.)
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Yaping Zhou
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China; (M.J.); (Z.L.); (C.G.); (Y.Z.)
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Xuwu Sun
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China; (M.J.); (Z.L.); (C.G.); (Y.Z.)
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
- Correspondence:
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14
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Wang Z, Xue JY, Hu SY, Zhang F, Yu R, Chen D, Van de Peer Y, Jiang J, Song A, Ni L, Hua J, Lu Z, Yu C, Yin Y, Gu C. The genome of hibiscus hamabo reveals its adaptation to saline and waterlogged habitat. HORTICULTURE RESEARCH 2022; 9:uhac067. [PMID: 35480957 PMCID: PMC9039499 DOI: 10.1093/hr/uhac067] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
Hibiscus hamabo is a semi-mangrove species with strong tolerance to salt and waterlogging stress. However, the molecular basis and mechanisms that underlie this strong adaptability to harsh environments remain poorly understood. Here, we assembled a high-quality, chromosome-level genome of this semi-mangrove plant and analyzed its transcriptome under different stress treatments to reveal regulatory responses and mechanisms. Our analyses suggested that H. hamabo has undergone two recent successive polyploidy events, a whole-genome duplication followed by a whole-genome triplication, resulting in an unusually large gene number (107 309 genes). Comparison of the H. hamabo genome with that of its close relative Hibiscus cannabinus, which has not experienced a recent WGT, indicated that genes associated with high stress resistance have been preferentially preserved in the H. hamabo genome, suggesting an underlying association between polyploidy and stronger stress resistance. Transcriptomic data indicated that genes in the roots and leaves responded differently to stress. In roots, genes that regulate ion channels involved in biosynthetic and metabolic processes responded quickly to adjust the ion concentration and provide metabolic products to protect root cells, whereas no such rapid response was observed from genes in leaves. Using co-expression networks, potential stress resistance genes were identified for use in future functional investigations. The genome sequence, along with several transcriptome datasets, provide insights into genome evolution and the mechanism of salt and waterlogging tolerance in H. hamabo, suggesting the importance of polyploidization for environmental adaptation.
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Affiliation(s)
- Zhiquan Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Jia-Yu Xue
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuai-Ya Hu
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Fengjiao Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Ranran Yu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yves Van de Peer
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
- Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB-UGent Center for Plant Systems Biology, B-9052 Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
| | - Jiafu Jiang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Aiping Song
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Longjie Ni
- College of Forest Sciences, Nanjing Forestry University, Nanjing, 210037, China
| | - Jianfeng Hua
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Zhiguo Lu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Chaoguang Yu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Yunlong Yin
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Chunsun Gu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
- College of Forest Sciences, Nanjing Forestry University, Nanjing, 210037, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Utilization of Agricultural Germplasm, Nanjing, 210014, China
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15
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Tay Fernandez CG, Nestor BJ, Danilevicz MF, Gill M, Petereit J, Bayer PE, Finnegan PM, Batley J, Edwards D. Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species. Int J Mol Sci 2022; 23:2671. [PMID: 35269811 PMCID: PMC8910360 DOI: 10.3390/ijms23052671] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/21/2022] [Accepted: 02/21/2022] [Indexed: 02/01/2023] Open
Abstract
Pangenomes are a rich resource to examine the genomic variation observed within a species or genera, supporting population genetics studies, with applications for the improvement of crop traits. Major crop species such as maize (Zea mays), rice (Oryza sativa), Brassica (Brassica spp.), and soybean (Glycine max) have had pangenomes constructed and released, and this has led to the discovery of valuable genes associated with disease resistance and yield components. However, pangenome data are not available for many less prominent crop species that are currently under-utilised. Despite many under-utilised species being important food sources in regional populations, the scarcity of genomic data for these species hinders their improvement. Here, we assess several under-utilised crops and review the pangenome approaches that could be used to build resources for their improvement. Many of these under-utilised crops are cultivated in arid or semi-arid environments, suggesting that novel genes related to drought tolerance may be identified and used for introgression into related major crop species. In addition, we discuss how previously collected data could be used to enrich pangenome functional analysis in genome-wide association studies (GWAS) based on studies in major crops. Considering the technological advances in genome sequencing, pangenome references for under-utilised species are becoming more obtainable, offering the opportunity to identify novel genes related to agro-morphological traits in these species.
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Affiliation(s)
| | | | | | | | | | | | | | | | - David Edwards
- School of Biological Sciences, The University of Western Australia, Perth, WA 6009, Australia; (C.G.T.F.); (B.J.N.); (M.F.D.); (M.G.); (J.P.); (P.E.B.); (P.M.F.); (J.B.)
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16
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Yang Y, Liu X, Shi X, Ma J, Zeng X, Zhu Z, Li F, Zhou M, Guo X, Liu X. A High-Quality, Chromosome-Level Genome Provides Insights Into Determinate Flowering Time and Color of Cotton Rose ( Hibiscus mutabilis). FRONTIERS IN PLANT SCIENCE 2022; 13:818206. [PMID: 35251086 PMCID: PMC8896357 DOI: 10.3389/fpls.2022.818206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
Hibiscus mutabilis (cotton rose) is a deciduous shrub or small tree of the Malvaceae family. Here, we report a chromosome-scale assembly of the H. mutabilis genome based on a combination of single-molecule sequencing and Hi-C technology. We obtained an optimized assembly of 2.68 Gb with a scaffold N50 length of 54.7 Mb. An integrated strategy of homology-based, de novo, and transcriptome-based gene predictions identified 118,222 protein-coding genes. Repetitive DNA sequences made up 58.55% of the genome, and LTR retrotransposons were the most common repetitive sequence type, accounting for 53.15% of the genome. Through the use of Hi-C data, we constructed a chromosome-scale assembly in which Nanopore scaffolds were assembled into 46 pseudomolecule sequences. We identified important genes involved in anthocyanin biosynthesis and documented copy number variation in floral regulators. Phylogenetic analysis indicated that H. mutabilis was closely related to H. syriacus, from which it diverged approximately 15.3 million years ago. The availability of cotton rose genome data increases our understanding of the species' genetic evolution and will support further biological research and breeding in cotton rose, as well as other Malvaceae species.
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Affiliation(s)
| | | | | | - Jiao Ma
- Chengdu Botanical Garden, Chengdu, China
| | | | | | - Fangwen Li
- Chengdu Botanical Garden, Chengdu, China
| | - Mengyan Zhou
- Novogene Bioinformatics Institute, Beijing, China
| | - Xiaodan Guo
- Novogene Bioinformatics Institute, Beijing, China
| | - Xiaoli Liu
- Chengdu Botanical Garden, Chengdu, China
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17
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Zhang L, Ma X, Zhang X, Xu Y, Ibrahim AK, Yao J, Huang H, Chen S, Liao Z, Zhang Q, Niyitanga S, Yu J, Liu Y, Xu X, Wang J, Tao A, Xu J, Chen S, Yang X, He Q, Lin L, Fang P, Zhang L, Ming R, Qi J, Zhang L. Reference genomes of the two cultivated jute species. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2235-2248. [PMID: 34170619 PMCID: PMC8541789 DOI: 10.1111/pbi.13652] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/08/2021] [Accepted: 06/17/2021] [Indexed: 05/10/2023]
Abstract
Cultivated jute, which comprises the two species Corchorus capsularis and C. olitorius, is the second most important natural fibre source after cotton. Here we describe chromosome-level assemblies of the genomes of both cultivated species. The C. capsularis and C. olitorius assemblies are each comprised of seven pseudo-chromosomes, with the C. capsularis assembly consisting of 336 Mb with 25,874 genes and the C. olitorius assembly containing 361 Mb with 28 479 genes. Although the two Corchorus genomes exhibit collinearity, the genome of C. olitorius contains 25 Mb of additional sequences than that of C. capsularis with 13 putative inversions, which might give a hint to the difference of phenotypic variants between the two cultivated jute species. Analysis of gene expression in isolated fibre tissues reveals candidate genes involved in fibre development. Our analysis of the population structures of 242 cultivars from C. capsularis and 57 cultivars from C. olitorius by whole-genome resequencing resulted in post-domestication bottlenecks occurred ~2000 years ago in these species. We identified hundreds of putative significant marker-trait associations (MTAs) controlling fibre fineness, cellulose content and lignin content of fibre by integrating data from genome-wide association studies (GWAS) with data from analyses of selective sweeps due to natural and artificial selection in these two jute species. Among them, we further validated that CcCOBRA1 and CcC4H1 regulate fibre quality in transgenic plants via improving the biosynthesis of the secondary cell wall. Our results yielded important new resources for functional genomics research and genetic improvement in jute and allied fibre crops.
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Affiliation(s)
- Lilan Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Xiaokai Ma
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Xingtan Zhang
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Yi Xu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Aminu Kurawa Ibrahim
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Jiayu Yao
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Huaxing Huang
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Shuai Chen
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Zhenyang Liao
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Qing Zhang
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Sylvain Niyitanga
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Jiaxin Yu
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Yi Liu
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Xiuming Xu
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Jingjing Wang
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Aifen Tao
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Jiantang Xu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Siyuan Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Xin Yang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Qingyao He
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Lihui Lin
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Pingping Fang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Liemei Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
| | - Ray Ming
- Department of Plant Biologythe University of Illinois at Urbana‐ChampaignUrbanaILUSA
| | - Jianmin Qi
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Liwu Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
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18
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Wang Y, Li F, He Q, Bao Z, Zeng Z, An D, Zhang T, Yan L, Wang H, Zhu S, Liu T. Genomic analyses provide comprehensive insights into the domestication of bast fiber crop ramie (Boehmeria nivea). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:787-800. [PMID: 33993558 DOI: 10.1111/tpj.15346] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/30/2021] [Accepted: 05/10/2021] [Indexed: 05/27/2023]
Abstract
Ramie (Boehmeria nivea) is an economically important natural fiber-producing crop that has been cultivated for thousands of years in China; however, the evolution of this crop remains largely unknown. Here, we report a ramie domestication analysis based on genome assembly and resequencing of cultivated and wild accessions. Two chromosome-level genomes representing wild and cultivated ramie were assembled de novo. Numerous structural variations between two assemblies, together with the genetic variations from population resequencing, constituted a comprehensive genomic variation map for ramie. Domestication analysis identified 71 high-confidence selective sweeps comprising 320 predicted genes, and 29 genes from sweeps were associated with fiber growth in the expression. In addition, we identified seven genetic loci associated with the fiber yield trait in the segregated population derived from the crossing of two assembled accessions, and two of which showed an overlap with the selective sweeps. These findings indicated that bast fiber traits were focused on during the domestication history of ramie. This study sheds light on the domestication of ramie and provides a valuable resource for biological and breeding studies of this important crop.
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Affiliation(s)
- Yanzhou Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, Western Road of Xiajiahu, Changsha, 410205, China
| | - Fu Li
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, Western Road of Xiajiahu, Changsha, 410205, China
| | - Qiaoyun He
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, Western Road of Xiajiahu, Changsha, 410205, China
| | - Zhigui Bao
- Shanghai OE Biotech. Co., Ltd, No. 138, Road of Xinjun, Shanghai, 201100, China
| | - Zheng Zeng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, Western Road of Xiajiahu, Changsha, 410205, China
| | - Dong An
- Shanghai OE Biotech. Co., Ltd, No. 138, Road of Xinjun, Shanghai, 201100, China
| | - Ting Zhang
- Shanghai OE Biotech. Co., Ltd, No. 138, Road of Xinjun, Shanghai, 201100, China
| | - Li Yan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, Western Road of Xiajiahu, Changsha, 410205, China
| | - Hengyun Wang
- Shanghai OE Biotech. Co., Ltd, No. 138, Road of Xinjun, Shanghai, 201100, China
| | - Siyuan Zhu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, Western Road of Xiajiahu, Changsha, 410205, China
| | - Touming Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, Western Road of Xiajiahu, Changsha, 410205, China
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19
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Kim J, Han GD, Muthukathan G, Rodrogues R, Hyun DY, Kim SH, Yu JK, Park J, Yoo SC, Chung YS. What Traits Should Be Measured for Biomass in Kenaf? PLANTS 2021; 10:plants10071394. [PMID: 34371597 PMCID: PMC8309238 DOI: 10.3390/plants10071394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/01/2021] [Accepted: 07/03/2021] [Indexed: 11/30/2022]
Abstract
Kenaf (Hibiscus cannabinus L.) is widely used as an important industrial crop. It has the potential to act as a sustainable energy provider in the future, and contains beneficial compounds for medical and therapeutic use. However, there are no clear breeding strategies to increase its biomass or leaf volume. Thus, to attain an increase in these parameters, we examined potential key traits such as stem diameter, plant height, and number of nodes to determine the relationship among them. We hypothesized that it would be easier to reduce the amount of time and labor required for breeding if correlations among these parameters are identified. In this study, we found a strong positive correlation between height and number of nodes (Spearman’s Rho = 0.67, p < 0.001) and number of nodes and stem diameter (Spearman’s Rho = 0.65, p < 0.001), but a relatively low correlation (Spearman’s Rho = 0.34, p < 0.01) between height and stem diameter in the later stages of kenaf growth. We suggest that an efficient breeding strategy could be devised according to the breeding purpose, considering the correlations between various individual traits of kenaf.
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Affiliation(s)
- Jaeyoung Kim
- Department of Plant Resources and Environment, Jeju National University, Jeju 63243, Korea; (J.K.); (G.D.H.); (J.P.)
| | - Gyung Deok Han
- Department of Plant Resources and Environment, Jeju National University, Jeju 63243, Korea; (J.K.); (G.D.H.); (J.P.)
| | - Gopi Muthukathan
- ICAR-National Research Centre for Banana, Tiruchirappalli 620102, India;
| | - Renato Rodrogues
- Institute of Mathematics and Statistics, Federal University of Goias, Goiania 74001, Brazil;
| | - Do Yoon Hyun
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), RDA, Jeonju 54875, Korea; (D.Y.H.); (S.-H.K.)
| | - Seong-Hoon Kim
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), RDA, Jeonju 54875, Korea; (D.Y.H.); (S.-H.K.)
| | - Ju-Kyung Yu
- Seeds Research, Syngenta Crop Protection LLC, Research Triangle Park, NC 27709, USA;
| | - Jieun Park
- Department of Plant Resources and Environment, Jeju National University, Jeju 63243, Korea; (J.K.); (G.D.H.); (J.P.)
| | - Soo-Cheul Yoo
- Department of Plant Life and Environmental Science, Hankyong National University, Anseong-si 17579, Korea
- Correspondence: (S.-C.Y.); (Y.S.C.)
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju 63243, Korea; (J.K.); (G.D.H.); (J.P.)
- Correspondence: (S.-C.Y.); (Y.S.C.)
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20
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Huang G, Huang JQ, Chen XY, Zhu YX. Recent Advances and Future Perspectives in Cotton Research. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:437-462. [PMID: 33428477 DOI: 10.1146/annurev-arplant-080720-113241] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Cotton is not only the world's most important natural fiber crop, but it is also an ideal system in which to study genome evolution, polyploidization, and cell elongation. With the assembly of five different cotton genomes, a cotton-specific whole-genome duplication with an allopolyploidization process that combined the A- and D-genomes became evident. All existing A-genomes seemed to originate from the A0-genome as a common ancestor, and several transposable element bursts contributed to A-genome size expansion and speciation. The ethylene production pathway is shown to regulate fiber elongation. A tip-biased diffuse growth mode and several regulatory mechanisms, including plant hormones, transcription factors, and epigenetic modifications, are involved in fiber development. Finally, we describe the involvement of the gossypol biosynthetic pathway in the manipulation of herbivorous insects, the role of GoPGF in gland formation, and host-induced gene silencing for pest and disease control. These new genes, modules, and pathways will accelerate the genetic improvement of cotton.
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Affiliation(s)
- Gai Huang
- Institute for Advanced Studies, Wuhan University, Wuhan 430072, China;
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jin-Quan Huang
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xiao-Ya Chen
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yu-Xian Zhu
- Institute for Advanced Studies, Wuhan University, Wuhan 430072, China;
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21
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Li Z, Hu Y, Chang M, Kashif MH, Tang M, Luo D, Cao S, Lu H, Zhang W, Huang Z, Yue J, Chen P. 5-azacytidine pre-treatment alters DNA methylation levels and induces genes responsive to salt stress in kenaf (Hibiscus cannabinus L.). CHEMOSPHERE 2021; 271:129562. [PMID: 33453481 DOI: 10.1016/j.chemosphere.2021.129562] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/15/2020] [Accepted: 12/19/2020] [Indexed: 05/19/2023]
Abstract
Soil salinization is becoming a major threat to the sustainable development of global agriculture. Kenaf is an industrial fiber crop with high tolerance to salt stress and could be used for soil phytoremediation. However, the molecular mechanism of kenaf salt tolerance remains largely unknown. DNA methylation is an important epigenetic modifications phenomena and plays a key role in gene expression regulation under abiotic stress condition. In the present study, the kenaf seedlings were pre-treated or not with 50 μM 5-azacytidine (5-azaC, a DNA methylation inhibitor) and then subjected to different concentrations of NaCl. Results showed that the biomass and antioxidant activities (superoxide dismutase, peroxidase and catalase) of kenaf seedlings pre-treated with 5-azaC were significantly increased, while the contents of superoxide anion (O2-) and malondialdehyde (MDA) were decreased, indicating that 5-azaC pre-treatment could significantly alleviate salt stress injury. Furthermore, the methylation-sensitive amplified polymorphism (MSAP) analysis revealed that DNA methylation level of keanf seedlings pre-treated with 5-azaC significantly decreased. The expression of seven differentially methylated genes responsing to salt stress was significantly changed from real-time fluorescent quantitative (qRT-PCR) analysis. Finally, knocked-down of the l-ascorbate oxidase (L-AAO) gene by virus-induced gene silencing (VIGS) resulted in increased sensitivity of kenaf seedlings under salt stress. Overall, it was suggested that 5-azaC pre-treatment can significantly improve salt tolerance in kenaf by decreasing ROS content, raising anti-oxidant activities, and regulating DNA methylation and expression of stress-responsive genes.
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Affiliation(s)
- Zengqiang Li
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Yali Hu
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Mengmeng Chang
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Muhammad Haneef Kashif
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Meiqiong Tang
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Dengjie Luo
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Shan Cao
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Hai Lu
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Wenxian Zhang
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Zhen Huang
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Jiao Yue
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Peng Chen
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China.
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22
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Niyitanga S, Yang X, Guerriero G, Jin S, Qi J, Zhang L, Zhang L. Editorial: Applied Genetics of Natural Fiber Plants. Front Genet 2021; 12:647225. [PMID: 33927750 PMCID: PMC8078908 DOI: 10.3389/fgene.2021.647225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 03/19/2021] [Indexed: 11/28/2022] Open
Affiliation(s)
- Sylvain Niyitanga
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops/Fujian Key Laboratory for Crop Breeding by Design, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China.,Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China/Public Platform of Fujian for Germplasm Resources of Bast Fiber Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xin Yang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops/Fujian Key Laboratory for Crop Breeding by Design, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China.,Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China/Public Platform of Fujian for Germplasm Resources of Bast Fiber Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Gea Guerriero
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, Hautcharage, Luxembourg
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jianmin Qi
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops/Fujian Key Laboratory for Crop Breeding by Design, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liemei Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops/Fujian Key Laboratory for Crop Breeding by Design, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liwu Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops/Fujian Key Laboratory for Crop Breeding by Design, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China.,Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China/Public Platform of Fujian for Germplasm Resources of Bast Fiber Crops, Fujian Agriculture and Forestry University, Fuzhou, China
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23
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In silico identification of conserved miRNAs in the genome of fibre biogenesis crop Corchorus capsularis. Heliyon 2021; 7:e06705. [PMID: 33869875 PMCID: PMC8045047 DOI: 10.1016/j.heliyon.2021.e06705] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 02/02/2021] [Accepted: 03/31/2021] [Indexed: 11/24/2022] Open
Abstract
Corchorus capsularis, commonly known as jute occupies the leading position in the production of natural fibre alongside lower environmental threat. Small noncoding ~21 to 24 nucleotides long microRNAs play significant roles in regulating the gene expression as well as different functions in cellular growth and development. Here, the study adopted a comprehensive in silico approach to identify and characterize the conserved miRNAs in the genome of C. capsularis including functional annotation of specific gene targets. Expressed Sequence Tags (ESTs) based homology search of 3350 known miRNAs of dicotyledons were allowed against 763 non-redundant ESTs of jute genome, resulted in the prediction of 5 potential miRNA candidates belonging five different miRNA families (miR1536, miR9567-3p, miR4391, miR11300, and miR8689). The putative miRNAs were composed of 18 nucleotides having a range of -0.49 to -1.56 MFEI values and 55%–61% of (A + U) content in their pre-miRNAs. A total of 1052 gene targets of putative miRNAs were identified and their functions were extensively analyzed. Most of the gene targets were involved in plant growth, cell cycle regulation, organelle synthesis, developmental process and environmental responses. Five gene targets, namely, NAC Domain Containing Protein, WRKY DNA binding protein, 3-dehydroquinate synthase, S-adenosyl-L-Met–dependent methyl transferase and Vascular-related NAC-Domain were found to be involved in the lignin biosynthesis, phenylpropanoid pathways and secondary wall formation. The present study might accelerate the more miRNA discovery, strengthening the complete understanding of miRNAs association in the cellular basis of lignin biosynthesis towards the production of high standard jute products.
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24
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Hu L, Zhang H, Sun Y, Shen X, Amoo O, Wang Y, Fan C, Zhou Y. BnA10.RCO, a homeobox gene, positively regulates leaf lobe formation in Brassica napus L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:3333-3343. [PMID: 32816057 DOI: 10.1007/s00122-020-03672-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 08/13/2020] [Indexed: 06/11/2023]
Abstract
BnA10.RCO positively regulates the development of leaf lobes in Brassica napus, and cis-regulatory divergences cause the different allele effects. The functional importance of lobed leaves in rapeseed (Brassica napus L.) has been identified with potential advantages for high-density planting and hybrid production. Our previous studies indicated that the tandemly duplicated LMI1-like genes BnA10. RCO and BnA10.LMI1 are candidate genes of an incompletely dominant locus, which is responsible for the lobed-leaf shape in rapeseed. We provided strong evidence that BnA10.LMI1 positively regulates leaf lobe formation. Here, we show that BnA10.RCO is a nucleus-specific protein, encoding an HD-ZIP I transcription factor, which is responsible for the lobed-leaf shape in rapeseed. Sequence analysis of parental alleles revealed that no vital sequence variation was detected in the coding sequence of BnA10.RCO, whereas abundant variations were identified in the regulatory regions. Consistent with this finding, the expression level of BnRCO was substantially elevated in the lobed-leaved parent HY compared with its near-isogenic line. Moreover, the altered expression of BnA10.RCO in transgenic lines showed a positive connection with leaf complexity without a substantial change in BnLMI1 transcript level. Furthermore, CRISPR/Cas9-induced null mutations of BnA10.RCO in the lobed-leaved parent HY were sufficient to produce an unlobed leaf without alteration in BnLMI1 transcript level. Our results indicate that BnA10.RCO functions together with BnA10.LMI1 to positively determine the lobed-leaf development, providing a fundamental basis for crop improvement by targeting leaf shape in rapeseed.
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Affiliation(s)
- Limin Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hao Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yunxia Sun
- Shenyang Agricultural University, Shenyang, 110000, China
| | - Xiaoxiao Shen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Olalekan Amoo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuguang Wang
- Shenyang Agricultural University, Shenyang, 110000, China
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Yongming Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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