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Wang Q, Wu J, Di G, Zhao Q, Gao C, Zhang D, Wang J, Shen Z, Han W. Identification of Cold Tolerance Transcriptional Regulatory Genes in Seedlings of Medicago sativa L. and Medicago falcata L. Int J Mol Sci 2024; 25:10345. [PMID: 39408674 PMCID: PMC11476818 DOI: 10.3390/ijms251910345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2024] [Revised: 09/19/2024] [Accepted: 09/23/2024] [Indexed: 10/20/2024] Open
Abstract
Alfalfa species Medicago sativa L. (MS) and Medicago falcata L. (MF), globally prominent perennial leguminous forages, hold substantial economic value. However, our comprehension of the molecular mechanisms governing their resistance to cold stress remains limited. To address this knowledge gap, we scrutinized and compared MS and MF cold-stress responses at the molecular level following 24 h and 120 h low-temperature exposure (4 °C). Our study revealed that MF had superior physiological resilience to cold stress compared with MS, and its morphology was healthier under cold stress, and its malondialdehyde content and superoxide dismutase activity increased, first, and then decreased, while the soluble sugar content continued to accumulate. Transcriptome analysis showed that after 120 h of exposure, there were different gene-expression patterns between MS and MF, including 1274 and 2983 genes that were continuously up-regulated, respectively, and a total of 923 genes were included, including star cold-resistant genes such as ICE1 and SIP1. Gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed numerous inter-species differences in sustained cold-stress responses. Notably, MS-exclusive genes included a single transcription factor (TF) gene and several genes associated with a single DNA repair-related pathway, whereas MF-exclusive genes comprised nine TF genes and genes associated with 14 pathways. Both species exhibited high-level expression of genes encoding TFs belonging to AP2-EREBP, ARR-B, and bHLH TF families, indicating their potential roles in sustaining cold resistance in alfalfa-related species. These findings provide insights into the molecular mechanisms governing cold-stress responses in MS and MF, which could inform breeding programs aimed at enhancing cold-stress resistance in alfalfa cultivars.
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Affiliation(s)
- Qi Wang
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (Q.W.); (J.W.); (C.G.); (D.Z.); (J.W.); (Z.S.)
- College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
| | - Jianzhong Wu
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (Q.W.); (J.W.); (C.G.); (D.Z.); (J.W.); (Z.S.)
| | - Guili Di
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China;
| | - Qian Zhao
- Cultivation and Farming Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China;
| | - Chao Gao
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (Q.W.); (J.W.); (C.G.); (D.Z.); (J.W.); (Z.S.)
| | - Dongmei Zhang
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (Q.W.); (J.W.); (C.G.); (D.Z.); (J.W.); (Z.S.)
| | - Jianli Wang
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (Q.W.); (J.W.); (C.G.); (D.Z.); (J.W.); (Z.S.)
| | - Zhongbao Shen
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (Q.W.); (J.W.); (C.G.); (D.Z.); (J.W.); (Z.S.)
| | - Weibo Han
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (Q.W.); (J.W.); (C.G.); (D.Z.); (J.W.); (Z.S.)
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Hui W, Wu H, Zheng H, Wang K, Yang T, Fan J, Wu J, Wang J, Al Mutairi AA, Yang H, Yang C, Cui B, Loake GJ, Gong W. Genome-wide characterization of RR gene family members in Zanthoxylum armatum and the subsequent functional characterization of the C-type RR. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 214:108943. [PMID: 39032447 DOI: 10.1016/j.plaphy.2024.108943] [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: 12/27/2023] [Revised: 07/10/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024]
Abstract
Response Regulators (RRs) are crucial regulators in plant development and stress responses, comprising A-type, B-type, C-type, and pseudo-RR subfamilies. However, previous studies have often focused on specific subfamilies, which restricts our understanding of the complete RR gene family. In this study, we conducted a comprehensive analysis of 63 RR members from Zanthoxylum armatum, using phylogenetic relationships, motif composition, cis-acting elements, gene duplication and collinearity analyses. Segmental repeats among ZaRR genes enhanced the various environmental adaptabilities of Z. armatum, and the B-type ZaRR exhibited significant collinearity with the RRs in P. trichocarpa and C. sinensis. Cis-element analysis indicated ZaRRs play a significant role in abiotic stress and phytohormone pathways, particularly in light, drought, cold, abscisic acid (ABA) and salicylic acid (SA) responses. Abundant Ethylene Response Factor (ERF) and reproduction-associated binding sites in ZaRR promoters suggested their roles in stress and reproductive processes. A-type ZaRRs were implicated in plant vegetative and reproductive growth, whereas B-type ZaRRs contributed to both growth and stress responses. C-type ZaRRs were associated with plant reproductive growth, whereas pseudo-RRs may function in plant stress responses, such as water logging, cold, and response to ethylene (ETH), SA, and jasmonic acid (JA). Ectopic expression of ZaRR24, a C-type RR, inhibits growth, induces early flowering, and shortens fruit length in Arabidopsis. ZaRR24 overexpression also affected the expression of A- and B-type RRs, as well as floral meristem and organ identity genes. These findings establish a solid and comprehensive foundation for RR gene research in Z. armatum, and provide a platform for investigating signal transduction in other woody plants.
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Affiliation(s)
- Wenkai Hui
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Han Wu
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hao Zheng
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Kai Wang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ting Yang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiangtao Fan
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiaojiao Wu
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jingyan Wang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Ahmed A Al Mutairi
- Biology Department, College of Science, Jouf University, Sakaka, 41412, Saudi Arabia
| | - Hua Yang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chunlin Yang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Beimi Cui
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK.
| | - Gary J Loake
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK.
| | - Wei Gong
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China.
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Bian S, Shao D, Zhao Q, Li Q, Ren Y. Transcriptome-Based Screening of Candidate Low-Temperature-Associated Genes and Analysis of the BocARR-B Transcription Factor Gene Family in Kohlrabi ( Brassica oleracea L. var. caulorapa L.). Int J Mol Sci 2024; 25:9261. [PMID: 39273211 PMCID: PMC11394831 DOI: 10.3390/ijms25179261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Revised: 08/21/2024] [Accepted: 08/22/2024] [Indexed: 09/15/2024] Open
Abstract
Low temperature is a significant abiotic stress factor that not only impacts plant growth, development, yield, and quality but also constrains the geographical distribution of numerous wild plants. Kohlrabi (Brassica oleracea L. var. caulorapa L.) belongs to the Brassicaceae family and has a short growing period. In this study, a total of 196,642 unigenes were obtained from kohlrabi seedlings at low temperatures; of these, 52,836 unigenes were identified as differentially expressed genes. Transcription factor family members ARR-B, C3H, B3-ARF, etc. that had a high correlation with biochemical indicators related to low temperature were identified. A total of nineteen BocARR-B genes (named BocARR-B1-BocARR-B19) were obtained, and these genes were distributed unevenly across seven chromosomes. Nineteen BocARR-B genes searched four conserved motifs and were divided into three groups. The relative expression level analysis of 19 BocARR-B genes of kohlrabi showed obvious specificity in different tissues. This study lays a foundation and provides new insight to explain the low-temperature resistance mechanism and response pathways of kohlrabi. It also provides a theoretical basis for the functional analysis of 19 BocARR-B transcription factor gene family members.
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Affiliation(s)
- Shuanling Bian
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China
| | - Dengkui Shao
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China
- Laboratory of Research and Utilization of Germplasm Resources in Qinghai-Tibet Plateau, Qinghai University, Xining 810016, China
- Key Laboratory of Germplasm Resources Protection and Genetic Improvement of the Qinghai-Tibet Plateau in Ministry of Agriculture and Rural, Xining 810016, China
| | - Qingsheng Zhao
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Quanhui Li
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China
- Laboratory of Research and Utilization of Germplasm Resources in Qinghai-Tibet Plateau, Qinghai University, Xining 810016, China
- Key Laboratory of Germplasm Resources Protection and Genetic Improvement of the Qinghai-Tibet Plateau in Ministry of Agriculture and Rural, Xining 810016, China
| | - Yanjing Ren
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China
- Laboratory of Research and Utilization of Germplasm Resources in Qinghai-Tibet Plateau, Qinghai University, Xining 810016, China
- Key Laboratory of Germplasm Resources Protection and Genetic Improvement of the Qinghai-Tibet Plateau in Ministry of Agriculture and Rural, Xining 810016, China
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Hernández-Muñoz A, Agreda-Laguna KA, Ramírez-Bernabé IE, Oltehua-López O, Arteaga-Vázquez MA, Leon P. Marchantia polymorpha GOLDEN2-LIKE transcriptional factor; a central regulator of chloroplast and plant vegetative development. THE NEW PHYTOLOGIST 2024; 243:1406-1423. [PMID: 38922903 DOI: 10.1111/nph.19916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024]
Abstract
The GOLDEN2-LIKE (GLK) transcription factors act as a central regulatory node involved in both developmental processes and environmental responses. Marchantia polymorpha, a basal terrestrial plant with strategic evolutionary position, contains a single GLK representative that possesses an additional domain compared to spermatophytes. We analyzed the role of MpGLK in chloroplast biogenesis and development by altering its levels, preforming transcriptomic profiling and conducting chromatin immunoprecipitation. Decreased MpGLK levels impair chloroplast differentiation and disrupt the expression of photosynthesis-associated nuclear genes, while overexpressing MpGLK leads to ectopic chloroplast biogenesis. This demonstrates the MpGLK functions as a bona fide GLK protein, likely representing an ancestral GLK architecture. Altering MpGLK levels directly regulates the expression of genes involved in Chl synthesis and degradation, similar to processes observed in eudicots, and causes various developmental defects in Marchantia, including the formation of dorsal structures such as air pores and gemma cups. MpGLK, also directly activates MpMAX2 gene expression, regulating the timing of gemma cup development. Our study shows that MpGLK functions as a master regulator, potentially coupling chloroplast development with vegetative reproduction. This illustrates the complex regulatory networks governing chloroplast function and plant development communication and highlight the evolutionary conservation of GLK-mediated regulatory processes across plant species.
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Affiliation(s)
- Arihel Hernández-Muñoz
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, 62210, Mexico
| | - Kenny Alejandra Agreda-Laguna
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, 62210, Mexico
| | - Ignacio E Ramírez-Bernabé
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, 62210, Mexico
| | - Omar Oltehua-López
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, 62210, Mexico
| | - Mario A Arteaga-Vázquez
- Instituto de Biotecnología y Ecología Aplicada, Universidad Veracruzana, Avenida de las Culturas Veracruzanas 101, Col. Emiliano Zapata, Xalapa, Veracruz, 91090, Mexico
| | - Patricia Leon
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, 62210, Mexico
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Wang X, Wei C, Huang H, Kang J, Long R, Chen L, Li M, Yang Q. The GARP family transcription factor MtHHO3 negatively regulates salt tolerance in Medicago truncatula. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 209:108542. [PMID: 38531119 DOI: 10.1016/j.plaphy.2024.108542] [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: 08/25/2023] [Revised: 01/31/2024] [Accepted: 03/16/2024] [Indexed: 03/28/2024]
Abstract
High salinity is one of the detrimental environmental factors restricting plant growth and crop production throughout the world. This study demonstrated that the GARP family transcription factor MtHHO3 is involved in response to salt stress and abscisic acid (ABA) signaling in Medicago truncatula. The transcription of MtHHO3 was repressed by salt, osmotic stress, and ABA treatment. The seed germination assay showed that, overexpression of MtHHO3 in Arabidopsis thaliana caused hypersensitivity to salt and osmotic stress, but increased resistance to ABA inhibition. Overexpression of MtHHO3 in M. truncatula resulted in decreased tolerance of salinity, while loss-of-function mutants mthho3-1 and mthho3-2 were more resistant to salt stress compared with wild-type plants. qRT-PCR analyses showed that MtHHO3 downregulated the expression of genes in stress and ABA responsive pathways. We further demonstrated that MtHHO3 repressed the transcription of the pathogenesis-related gene MtPR2 by binding to its promoter. Overall, these results indicate that MtHHO3 negatively regulates salt stress response in plants and deepen our understanding of the role of the GARP subfamily transcription factors in modulating salt stress and ABA signaling.
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Affiliation(s)
- Xue Wang
- Institute of Animal Science, The Chinese Academy of Agricultural Sciences, Beijing, 10019, China.
| | - Chunxue Wei
- Institute of Animal Science, The Chinese Academy of Agricultural Sciences, Beijing, 10019, China
| | - Hongmei Huang
- Institute of Animal Science, The Chinese Academy of Agricultural Sciences, Beijing, 10019, China
| | - Junmei Kang
- Institute of Animal Science, The Chinese Academy of Agricultural Sciences, Beijing, 10019, China
| | - Ruicai Long
- Institute of Animal Science, The Chinese Academy of Agricultural Sciences, Beijing, 10019, China
| | - Lin Chen
- Institute of Animal Science, The Chinese Academy of Agricultural Sciences, Beijing, 10019, China
| | - Mingna Li
- Institute of Animal Science, The Chinese Academy of Agricultural Sciences, Beijing, 10019, China
| | - Qingchuan Yang
- Institute of Animal Science, The Chinese Academy of Agricultural Sciences, Beijing, 10019, China.
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Hu J, Chen Q, Idrees A, Bi W, Lai Z, Sun Y. Structural and Functional Analysis of the MADS-Box Genes Reveals Their Functions in Cold Stress Responses and Flower Development in Tea Plant ( Camellia sinensis). PLANTS (BASEL, SWITZERLAND) 2023; 12:2929. [PMID: 37631141 PMCID: PMC10458798 DOI: 10.3390/plants12162929] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/01/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023]
Abstract
MADS-box genes comprise a large family of transcription factors that play crucial roles in all aspects of plant growth and development. However, no detailed information on the evolutionary relationship and functional characterization of MADS-box genes is currently available for some representative lineages, such as the Camellia plant. In this study, 136 MADS-box genes were detected from a reference genome of the tea plant (Camellia sinensis) by employing a 569 bp HMM (Hidden Markov Model) developed using nucleotide sequencing including 73 type I and 63 type II genes. An additional twenty-seven genes were identified, with five MIKC-type genes. Truncated and/or inaccurate gene models were manually verified and curated to improve their functional characterization. Subsequently, phylogenetic relationships, chromosome locations, conserved motifs, gene structures, and gene expression profiles were systematically investigated. Tea plant MIKC genes were divided into all 14 major eudicot subfamilies, and no gene was found in Mβ. The expansion of MADS-box genes in the tea plant was mainly contributed by WGD/fragment and tandem duplications. The expression profiles of tea plant MADS-box genes in different tissues and seasons were analyzed, revealing widespread evolutionary conservation and genetic redundancy. The expression profiles linked to cold stress treatments suggested the wide involvement of MADS-box genes from the tea plant in response to low temperatures. Moreover, a floral 'ABCE' model was proposed in the tea plant and proved to be both conserved and ancient. Our analyses offer a detailed overview of MADS-box genes in the tea plant, allowing us to hypothesize the potential functions of unknown genes and providing a foundation for further functional characterizations.
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Affiliation(s)
- Juan Hu
- Key Laboratory of Tea Science in Fujian Province, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.H.); (W.B.)
| | - Qianqian Chen
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Atif Idrees
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Scientific Observing and Experimental Station of Crop Pest in Guiyang, Ministry of Agriculture and Rural Affairs, Institute of Entomology, Guizhou University, Guiyang 550025, China;
| | - Wanjun Bi
- Key Laboratory of Tea Science in Fujian Province, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.H.); (W.B.)
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yun Sun
- Key Laboratory of Tea Science in Fujian Province, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.H.); (W.B.)
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Hua YP, Wu PJ, Zhang TY, Song HL, Zhang YF, Chen JF, Yue CP, Huang JY, Sun T, Zhou T. Genome-Scale Investigation of GARP Family Genes Reveals Their Pivotal Roles in Nutrient Stress Resistance in Allotetraploid Rapeseed. Int J Mol Sci 2022; 23:ijms232214484. [PMID: 36430962 PMCID: PMC9698747 DOI: 10.3390/ijms232214484] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/14/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022] Open
Abstract
The GARP genes are plant-specific transcription factors (TFs) and play key roles in regulating plant development and abiotic stress resistance. However, few systematic analyses of GARPs have been reported in allotetraploid rapeseed (Brassica napus L.) yet. In the present study, a total of 146 BnaGARP members were identified from the rapeseed genome based on the sequence signature. The BnaGARP TFs were divided into five subfamilies: ARR, GLK, NIGT1/HRS1/HHO, KAN, and PHL subfamilies, and the members within the same subfamilies shared similar exon-intron structures and conserved motif configuration. Analyses of the Ka/Ks ratios indicated that the GARP family principally underwent purifying selection. Several cis-acting regulatory elements, essential for plant growth and diverse biotic and abiotic stresses, were identified in the promoter regions of BnaGARPs. Further, 29 putative miRNAs were identified to be targeting BnaGARPs. Differential expression of BnaGARPs under low nitrate, ammonium toxicity, limited phosphate, deficient boron, salt stress, and cadmium toxicity conditions indicated their potential involvement in diverse nutrient stress responses. Notably, BnaA9.HHO1 and BnaA1.HHO5 were simultaneously transcriptionally responsive to these nutrient stresses in both hoots and roots, which indicated that BnaA9.HHO1 and BnaA1.HHO5 might play a core role in regulating rapeseed resistance to nutrient stresses. Therefore, this study would enrich our understanding of molecular characteristics of the rapeseed GARPs and will provide valuable candidate genes for further in-depth study of the GARP-mediated nutrient stress resistance in rapeseed.
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Affiliation(s)
- Ying-Peng Hua
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Peng-Jia Wu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Tian-Yu Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Hai-Li Song
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yi-Fan Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Jun-Fan Chen
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Cai-Peng Yue
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Jin-Yong Huang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Tao Sun
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- Correspondence: (T.S.); (T.Z.); Tel.: +86-187-0271-0749 (T.Z.)
| | - Ting Zhou
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- Correspondence: (T.S.); (T.Z.); Tel.: +86-187-0271-0749 (T.Z.)
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Wang F, Zhang B, Wen D, Liu R, Yao X, Chen Z, Mu R, Pei H, Liu M, Song B, Lu L. Chromosome-scale genome assembly of Camellia sinensis combined with multi-omics provides insights into its responses to infestation with green leafhoppers. FRONTIERS IN PLANT SCIENCE 2022; 13:1004387. [PMID: 36212364 PMCID: PMC9539759 DOI: 10.3389/fpls.2022.1004387] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 08/25/2022] [Indexed: 06/16/2023]
Abstract
The tea plant (Camellia sinensis) is an important economic crop, which is becoming increasingly popular worldwide, and is now planted in more than 50 countries. Tea green leafhopper is one of the major pests in tea plantations, which can significantly reduce the yield and quality of tea during the growth of plant. In this study, we report a genome assembly for DuyunMaojian tea plants using a combination of Oxford Nanopore Technology PromethION™ with high-throughput chromosome conformation capture technology and used multi-omics to study how the tea plant responds to infestation with tea green leafhoppers. The final genome was 3.08 Gb. A total of 2.97 Gb of the genome was mapped to 15 pseudo-chromosomes, and 2.79 Gb of them could confirm the order and direction. The contig N50, scaffold N50 and GC content were 723.7 kb, 207.72 Mb and 38.54%, respectively. There were 2.67 Gb (86.77%) repetitive sequences, 34,896 protein-coding genes, 104 miRNAs, 261 rRNA, 669 tRNA, and 6,502 pseudogenes. A comparative genomics analysis showed that DuyunMaojian was the most closely related to Shuchazao and Yunkang 10, followed by DASZ and tea-oil tree. The multi-omics results indicated that phenylpropanoid biosynthesis, α-linolenic acid metabolism, flavonoid biosynthesis and 50 differentially expressed genes, particularly peroxidase, played important roles in response to infestation with tea green leafhoppers (Empoasca vitis Göthe). This study on the tea tree is highly significant for its role in illustrating the evolution of its genome and discovering how the tea plant responds to infestation with tea green leafhoppers will contribute to a theoretical foundation to breed tea plants resistant to insects that will ultimately result in an increase in the yield and quality of tea.
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Affiliation(s)
- Fen Wang
- The Department of Life Science and Agriculture, Qiannan Normal College for Nationalities, Duyun, China
- The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guiyang, China
| | - Baohui Zhang
- The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guiyang, China
- Horticulture Institute (Guizhou Horticultural Engineering Technology Research Center), Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Di Wen
- The Department of Life Science and Agriculture, Qiannan Normal College for Nationalities, Duyun, China
| | - Rong Liu
- The Department of Life Science and Agriculture, Qiannan Normal College for Nationalities, Duyun, China
| | - Xinzhuan Yao
- The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guiyang, China
- College of Tea Science, Guizhou University, Guiyang, China
| | - Zhi Chen
- The Department of Life Science and Agriculture, Qiannan Normal College for Nationalities, Duyun, China
| | - Ren Mu
- The Department of Life Science and Agriculture, Qiannan Normal College for Nationalities, Duyun, China
| | - Huimin Pei
- The Department of Life Science and Agriculture, Qiannan Normal College for Nationalities, Duyun, China
| | - Min Liu
- Biomarker Technologies Corporation, Beijing, China
| | - Baoxing Song
- The Department of Life Science and Agriculture, Qiannan Normal College for Nationalities, Duyun, China
- Peking University Institute of Advanced Agricultural Sciences, Weifang, China
| | - Litang Lu
- The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guiyang, China
- College of Tea Science, Guizhou University, Guiyang, China
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