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Li D, Li H, Feng H, Qi P, Wu Z. Unveiling kiwifruit TCP genes: evolution, functions, and expression insights. PLANT SIGNALING & BEHAVIOR 2024; 19:2338985. [PMID: 38597293 PMCID: PMC11008546 DOI: 10.1080/15592324.2024.2338985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 03/26/2024] [Indexed: 04/11/2024]
Abstract
The TEOSINTE-BRANCHED1/CYCLOIDEA/PROLEFERATING-CELL-FACTORS (TCP) gene family is a plant-specific transcriptional factor family involved in leaf morphogenesis and senescence, lateral branching, hormone crosstalk, and stress responses. To date, a systematic study on the identification and characterization of the TCP gene family in kiwifruit has not been reported. Additionally, the function of kiwifruit TCPs in regulating kiwifruit responses to the ethylene treatment and bacterial canker disease pathogen (Pseudomonas syringae pv. actinidiae, Psa) has not been investigated. Here, we identified 40 and 26 TCP genes in Actinidia chinensis (Ac) and A. eriantha (Ae) genomes, respectively. The synteny analysis of AcTCPs illustrated that whole-genome duplication accounted for the expansion of the TCP family in Ac. Phylogenetic, conserved domain, and selection pressure analysis indicated that TCP family genes in Ac and Ae had undergone different evolutionary patterns after whole-genome duplication (WGD) events, causing differences in TCP gene number and distribution. Our results also suggested that protein structure and cis-element architecture in promoter regions of TCP genes have driven the function divergence of duplicated gene pairs. Three and four AcTCP genes significantly affected kiwifruit responses to the ethylene treatment and Psa invasion, respectively. Our results provided insight into general characters, evolutionary patterns, and functional diversity of kiwifruit TCPs.
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Affiliation(s)
- Donglin Li
- College of Biology and Agriculture, Shaoguan University, Shaoguan, Guangdong, China
| | - Haibo Li
- College of Biology and Agriculture, Shaoguan University, Shaoguan, Guangdong, China
| | - Huimin Feng
- College of Biology and Agriculture, Shaoguan University, Shaoguan, Guangdong, China
| | - Ping Qi
- College of Biology and Agriculture, Shaoguan University, Shaoguan, Guangdong, China
| | - Zhicheng Wu
- College of Biology and Agriculture, Shaoguan University, Shaoguan, Guangdong, China
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Chong X, Liu Y, Li P, Wang Y, Zhou T, Chen H, Wang H. Heterologous Expression of Chrysanthemum TCP Transcription Factor CmTCP13 Enhances Salinity Tolerance in Arabidopsis. PLANTS (BASEL, SWITZERLAND) 2024; 13:2118. [PMID: 39124235 PMCID: PMC11313808 DOI: 10.3390/plants13152118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Revised: 07/25/2024] [Accepted: 07/25/2024] [Indexed: 08/12/2024]
Abstract
Plant-specific TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) proteins play critical roles in plant development and stress responses; however, their functions in chrysanthemum (Chrysanthemum morifolium) have not been well-studied. In this study, we isolated and characterized the chrysanthemum TCP transcription factor family gene CmTCP13, a homolog of AtTCP13. This gene encoded a protein harboring a conserved basic helix-loop-helix motif, and its expression was induced by salinity stress in chrysanthemum plants. Subcellular localization experiments showed that CmTCP13 localized in the nucleus. Sequence analysis revealed the presence of multiple stress- and hormone-responsive cis-elements in the promoter region of CmTCP13. The heterologous expression of CmTCP13 in Arabidopsis plants enhanced their tolerance to salinity stress. Under salinity stress, CmTCP13 transgenic plants exhibited enhanced germination, root length, seedling growth, and chlorophyll content and reduced relative electrical conductivity compared with those exhibited by wild-type (WT) plants. Moreover, the expression levels of stress-related genes, including AtSOS3, AtP5CS2, AtRD22, AtRD29A, and AtDREB2A, were upregulated in CmTCP13 transgenic plants than in WT plants under salt stress. Taken together, our results demonstrate that CmTCP13 is a critical regulator of salt stress tolerance in plants.
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Affiliation(s)
- Xinran Chong
- 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 210014, China
| | - Yanan Liu
- Institute of Jiangxi Oil-Tea Camellia, Jiujiang University, Jiujiang 332005, China
| | - Peiling Li
- College of Horticulture, Xinyang Agriculture and Forestry University, Xinyang 464000, 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 210014, China
| | - Ting Zhou
- 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 210014, China
| | - Hong Chen
- 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 210014, China
| | - Haibin Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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Dorant Y, Quillien V, Le Luyer J, Ky CL. Comparative transcriptomics identifies genes underlying growth performance of the Pacific black-lipped pearl oyster Pinctada margaritifera. BMC Genomics 2024; 25:717. [PMID: 39049022 PMCID: PMC11270918 DOI: 10.1186/s12864-024-10636-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND In bivalves, the rate at which organisms grow is a major functional trait underlying many aspects of their commercial production. Growth is a highly polygenic trait, which is typically regulated by many genes with small to moderate effects. Due to its complexity, growth variability in such shellfish remains poorly understood. In this study, we aimed to investigate differential gene expression among spat of the pearl oyster Pinctada margaritifera with distinct growth phenotypes. RESULTS We selected two groups of P. margaritifera spat belonging to the same F2 cohort based on their growth performance at 5.5 months old. Transcriptome profile analysis identified a total of 394 differentially expressed genes between these Fast-growing (F) and Slow-growing (S) phenotypes. According to functional enrichment analysis, S oysters overexpressed genes associated with stress-pathways and regulation of innate immune responses. In contrast, F oysters up-regulated genes associated with cytoskeleton activity, cell proliferation, and apoptosis. Analysis of genome polymorphism identified 16 single nucleotide polymorphisms (SNPs) significantly associated with the growth phenotypes. SNP effect categorization revealed one SNP identified for high effect and annotated for a stop codon gained mutation. Interestingly, this SNP is located within a gene annotated for scavenger receptor class F member 1 (SRF1), which is known to modulate apoptosis. Our analyses also revealed that all F oysters showed up-regulation for this gene and were homozygous for the stop-codon mutation. Conversely, S oysters had a heterozygous genotype and a reduced expression of this gene. CONCLUSIONS Altogether, our findings suggest that differences in growth among the same oyster cohort may be explained by contrasted metabolic allocation between regulatory pathways for growth and the immune system. This study provides a valuable contribution towards our understanding of the molecular components associated with growth performance in the pearl oyster P. margaritifera and bivalves in general.
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Affiliation(s)
- Y Dorant
- Ifremer, ILM, IRD, UPF, UMR 241 SECOPOL, Polynésie française, Taravao, Tahiti, France.
- IHPE, UMR 5244, Université de Montpellier, CNRS, Université de Perpignan Via Domitia, Ifremer, Montpellier, France.
| | - V Quillien
- Ifremer, ILM, IRD, UPF, UMR 241 SECOPOL, Polynésie française, Taravao, Tahiti, France
- Ifremer, Univ Brest, CNRS, IRD, UMR 6539, LEMAR, Plouzane, F-29280, France
| | - J Le Luyer
- Ifremer, ILM, IRD, UPF, UMR 241 SECOPOL, Polynésie française, Taravao, Tahiti, France
- Ifremer, Univ Brest, CNRS, IRD, UMR 6539, LEMAR, Plouzane, F-29280, France
| | - C L Ky
- Ifremer, ILM, IRD, UPF, UMR 241 SECOPOL, Polynésie française, Taravao, Tahiti, France
- IHPE, UMR 5244, Université de Montpellier, CNRS, Université de Perpignan Via Domitia, Ifremer, Montpellier, France
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Zhang J, Dong T, Zhu M, Du D, Liu R, Yu Q, Sun Y, Zhang Z. Transcriptome- and genome-wide systematic identification of expansin gene family and their expression in tuberous root development and stress responses in sweetpotato ( Ipomoea batatas). FRONTIERS IN PLANT SCIENCE 2024; 15:1412540. [PMID: 38966148 PMCID: PMC11223104 DOI: 10.3389/fpls.2024.1412540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 05/14/2024] [Indexed: 07/06/2024]
Abstract
Introduction Expansins (EXPs) are essential components of the plant cell wall that function as relaxation factors to directly promote turgor-driven expansion of the cell wall, thereby controlling plant growth and development and diverse environmental stress responses. EXPs genes have been identified and characterized in numerous plant species, but not in sweetpotato. Results and methods In the present study, a total of 59 EXP genes unevenly distributed across 14 of 15 chromosomes were identified in the sweetpotato genome, and segmental and tandem duplications were found to make a dominant contribution to the diversity of functions of the IbEXP family. Phylogenetic analysis showed that IbEXP members could be clustered into four subfamilies based on the EXPs from Arabidopsis and rice, and the regularity of protein motif, domain, and gene structures was consistent with this subfamily classification. Collinearity analysis between IbEXP genes and related homologous sequences in nine plants provided further phylogenetic insights into the EXP gene family. Cis-element analysis further revealed the potential roles of IbEXP genes in sweetpotato development and stress responses. RNA-seq and qRT-PCR analysis of eight selected IbEXPs genes provided evidence of their specificity in different tissues and showed that their transcripts were variously induced or suppressed under different hormone treatments (abscisic acid, salicylic acid, jasmonic acid, and 1-aminocyclopropane-1-carboxylic acid) and abiotic stresses (low and high temperature). Discussion These results provide a foundation for further comprehensive investigation of the functions of IbEXP genes and indicate that several members of this family have potential applications as regulators to control plant development and enhance stress resistance in plants.
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Affiliation(s)
- Jianling Zhang
- Laboratory of Plant Germplasm Resources Innovation and Utilization, School of Life Sciences, Liaocheng University, Liaocheng, Shandong, China
| | - Tingting Dong
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Mingku Zhu
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Dan Du
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Ranran Liu
- Laboratory of Plant Germplasm Resources Innovation and Utilization, School of Life Sciences, Liaocheng University, Liaocheng, Shandong, China
| | - Qianqian Yu
- Laboratory of Plant Germplasm Resources Innovation and Utilization, School of Life Sciences, Liaocheng University, Liaocheng, Shandong, China
| | - Yueying Sun
- Laboratory of Plant Germplasm Resources Innovation and Utilization, School of Life Sciences, Liaocheng University, Liaocheng, Shandong, China
| | - Zhihuan Zhang
- Institute of Biotechnology, Qingdao Academy of Agricultural Sciences, Qingdao, Shandong, China
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Gao Y, Regad F, Li Z, Pirrello J, Bouzayen M, Van Der Rest B. Class I TCP in fruit development: much more than growth. FRONTIERS IN PLANT SCIENCE 2024; 15:1411341. [PMID: 38863555 PMCID: PMC11165105 DOI: 10.3389/fpls.2024.1411341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/13/2024] [Indexed: 06/13/2024]
Abstract
Fruit development can be viewed as the succession of three main steps consisting of the fruit initiation, growth and ripening. These processes are orchestrated by different factors, notably the successful fertilization of flowers, the environmental conditions and the hormones whose action is coordinated by a large variety of transcription factors. Among the different transcription factor families, TEOSINTE BRANCHED 1, CYCLOIDEA, PROLIFERATING CELL FACTOR (TCP) family has received little attention in the frame of fruit biology despite its large effects on several developmental processes and its action as modulator of different hormonal pathways. In this respect, the comprehension of TCP functions in fruit development remains an incomplete puzzle that needs to be assembled. Building on the abundance of genomic and transcriptomic data, this review aims at collecting available TCP expression data to allow their integration in the light of the different functional genetic studies reported so far. This reveals that several Class I TCP genes, already known for their involvement in the cell proliferation and growth, display significant expression levels in developing fruit, although clear evidence supporting their functional significance in this process remains scarce. The extensive expression data compiled in our study provide convincing elements that shed light on the specific involvement of Class I TCP genes in fruit ripening, once these reproductive organs acquire their mature size. They also emphasize their putative role in the control of specific biological processes such as fruit metabolism and hormonal dialogue.
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Affiliation(s)
- Yushuo Gao
- Laboratoire de Recherche en Sciences Veígeítales - Génomique et Biotechnologie des Fruits, Universiteí de Toulouse, Centre national de la recherche scientifique (CNRS), Université Toulouse III - Paul Sabatier (UPS), Toulouse-Institut National Polytechnique (INP), Toulouse, France
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China
| | - Farid Regad
- Laboratoire de Recherche en Sciences Veígeítales - Génomique et Biotechnologie des Fruits, Universiteí de Toulouse, Centre national de la recherche scientifique (CNRS), Université Toulouse III - Paul Sabatier (UPS), Toulouse-Institut National Polytechnique (INP), Toulouse, France
| | - Zhengguo Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, China
| | - Julien Pirrello
- Laboratoire de Recherche en Sciences Veígeítales - Génomique et Biotechnologie des Fruits, Universiteí de Toulouse, Centre national de la recherche scientifique (CNRS), Université Toulouse III - Paul Sabatier (UPS), Toulouse-Institut National Polytechnique (INP), Toulouse, France
| | - Mondher Bouzayen
- Laboratoire de Recherche en Sciences Veígeítales - Génomique et Biotechnologie des Fruits, Universiteí de Toulouse, Centre national de la recherche scientifique (CNRS), Université Toulouse III - Paul Sabatier (UPS), Toulouse-Institut National Polytechnique (INP), Toulouse, France
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, China
| | - Benoît Van Der Rest
- Laboratoire de Recherche en Sciences Veígeítales - Génomique et Biotechnologie des Fruits, Universiteí de Toulouse, Centre national de la recherche scientifique (CNRS), Université Toulouse III - Paul Sabatier (UPS), Toulouse-Institut National Polytechnique (INP), Toulouse, France
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Qi T, Yang W, Hassan MJ, Liu J, Yang Y, Zhou Q, Li H, Peng Y. Genome-wide identification of Aux/IAA gene family in white clover (Trifolium repens L.) and functional verification of TrIAA18 under different abiotic stress. BMC PLANT BIOLOGY 2024; 24:346. [PMID: 38684940 PMCID: PMC11057079 DOI: 10.1186/s12870-024-05034-3] [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: 01/19/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024]
Abstract
BACKGROUND White clover (Trifolium repens L.) is an excellent leguminous cool-season forage with a high protein content and strong nitrogen-fixing ability. Despite these advantages, its growth and development are markedly sensitive to environmental factors. Indole-3-acetic acid (IAA) is the major growth hormone in plants, regulating plant growth, development, and response to adversity. Nevertheless, the specific regulatory functions of Aux/IAA genes in response to abiotic stresses in white clover remain largely unexplored. RESULTS In this study, we identified 47 Aux/IAA genes in the white clover genome, which were categorized into five groups based on phylogenetic analysis. The TrIAAs promoter region co-existed with different cis-regulatory elements involved in developmental and hormonal regulation, and stress responses, which may be closely related to their diverse regulatory roles. Collinearity analysis showed that the amplification of the TrIAA gene family was mainly carried out by segmental duplication. White clover Aux/IAA genes showed different expression patterns in different tissues and under different stress treatments. In addition, we performed a yeast two-hybrid analysis to investigate the interaction between white clover Aux/IAA and ARF proteins. Heterologous expression indicated that TrIAA18 could enhance stress tolerance in both yeast and transgenic Arabidopsis thaliana. CONCLUSION These findings provide new scientific insights into the molecular mechanisms of growth hormone signaling in white clover and its functional characteristics in response to environmental stress.
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Affiliation(s)
- Tiangang Qi
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Weiqiang Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Muhammad Jawad Hassan
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiefang Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yujiao Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qinyu Zhou
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hang Li
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yan Peng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
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Pan J, Ju Z, Ma X, Duan L, Jia Z. Genome-wide characterization of TCP family and their potential roles in abiotic stress resistance of oat ( Avena sativa L.). FRONTIERS IN PLANT SCIENCE 2024; 15:1382790. [PMID: 38654900 PMCID: PMC11036127 DOI: 10.3389/fpls.2024.1382790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 03/26/2024] [Indexed: 04/26/2024]
Abstract
The TCP gene family members play multiple functions in plant growth and development and were named after the first three family members found in this family, TB1 (TEOSINTE BRANCHED 1), CYCLOIDEA (CYC), and Proliferating Cell Factor 1/2 (PCF1/2). Nitrogen (N) is a crucial element for forage yield; however, over-application of N fertilizer can increase agricultural production costs and environmental stress. Therefore, the discovery of low N tolerance genes is essential for the genetic improvement of superior oat germplasm and ecological protection. Oat (Avena sativa L.), is one of the world's staple grass forages, but no genome-wide analysis of TCP genes and their roles in low-nitrogen stress has been performed. This study identified the oat TCP gene family members using bioinformatics techniques. It analyzed their phylogeny, gene structure analysis, and expression patterns. The results showed that the AsTCP gene family includes 49 members, and most of the AsTCP-encoded proteins are neutral or acidic proteins; the phylogenetic tree classified the AsTCP gene family members into three subfamilies, and each subfamily has different conserved structural domains and functions. In addition, multiple cis-acting elements were detected in the promoter of the AsTCP genes, which were associated with abiotic stress, light response, and hormone response. The 49 AsTCP genes identified from oat were unevenly distributed on 18 oat chromosomes. The results of real-time quantitative polymerase chain reaction (qRT-PCR) showed that the AsTCP genes had different expression levels in various tissues under low nitrogen stress, which indicated that these genes (such as AsTCP01, AsTCP03, AsTCP22, and AsTCP38) played multiple roles in the growth and development of oat. In conclusion, this study analyzed the AsTCP gene family and their potential functions in low nitrogen stress at the genome-wide level, which lays a foundation for further analysis of the functions of AsTCP genes in oat and provides a theoretical basis for the exploration of excellent stress tolerance genes in oat. This study provides an essential basis for future in-depth studies of the TCP gene family in other oat genera and reveals new research ideas to improve gene utilization.
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Affiliation(s)
| | | | | | | | - Zhifeng Jia
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, China
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Wu L, Li G, Li D, Dong C, Zhang X, Zhang L, Yang Z, Kong X, Xia C, Chen J, Liu X. Identification and functional analysis of a chromosome 2D fragment harboring TaFPF1 gene with the potential for yield improvement using a late heading wheat mutant. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:92. [PMID: 38568320 DOI: 10.1007/s00122-024-04593-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 03/05/2024] [Indexed: 04/05/2024]
Abstract
KEY MESSAGE A chromosome fragment influencing wheat heading and grain size was identified using mapping of m406 mutant. The study of TaFPF1 in this fragment provides more insights into wheat yield improvement. In recent years, wheat production has faced formidable challenges driven by rapid population growth and climate change, emphasizing the importance of improving specific agronomic traits such as heading date, spike length, and grain size. To identify potential genes for improving these traits, we screened a wheat EMS mutant library and identified a mutant, designated m406, which exhibited a significantly delayed heading date compared to the wild-type. Intriguingly, the mutant also displayed significantly longer spike and larger grain size. Genetic analysis revealed that a single recessive gene was responsible for the delayed heading. Surprisingly, a large 46.58 Mb deletion at the terminal region of chromosome arm 2DS in the mutant was identified through fine mapping and fluorescence in situ hybridization. Thus, the phenotypes of the mutant m406 are controlled by a group of linked genes. This deletion encompassed 917 annotated high-confidence genes, including the previously studied wheat genes Ppd1 and TaDA1, which could affect heading date and grain size. Multiple genes in this region probably contribute to the phenotypes of m406. We further investigated the function of TaFPF1 using gene editing. TaFPF1 knockout mutants showed delayed heading and increased grain size. Moreover, we identified the direct upstream gene of TaFPF1 and investigated its relationship with other important flowering genes. Our study not only identified more genes affecting heading and grain development within this deleted region but also highlighted the potential of combining these genes for improvement of wheat traits.
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Affiliation(s)
- Lifen Wu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Baoding, 071001, Hebei, China
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guangrong Li
- Center for Informational Biology, School of Life Science and Technology, University of Electronic and Technology of China, Chengdu, 611731, Sichuan, China
| | - Danping Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chunhao Dong
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xueying Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lichao Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zujun Yang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic and Technology of China, Chengdu, 611731, Sichuan, China
| | - Xiuying Kong
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chuan Xia
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Jingtang Chen
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Baoding, 071001, Hebei, China.
| | - Xu Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Baoding, 071001, Hebei, China.
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Shao Y, Mu D, Zhou Y, Liu X, Huang X, Wilson IW, Qi Y, Lu Y, Zhu L, Zhang Y, Qiu D, Tang Q. Genome-Wide Mining of CULLIN E3 Ubiquitin Ligase Genes from Uncaria rhynchophylla. PLANTS (BASEL, SWITZERLAND) 2024; 13:532. [PMID: 38498523 PMCID: PMC10891735 DOI: 10.3390/plants13040532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/10/2024] [Accepted: 02/13/2024] [Indexed: 03/20/2024]
Abstract
CULLIN (CUL) protein is a subtype of E3 ubiquitin ligase that is involved in a variety of biological processes and responses to stress in plants. In Uncaria rhynchophylla, the CUL gene family has not been identified and its role in plant development, stress response and secondary metabolite synthesis has not been studied. In this study, 12 UrCUL gene members all contained the typical N-terminal domain and C-terminal domain identified from the U. rhynchophylla genome and were classified into four subfamilies based on the phylogenetic relationship with CULs in Arabidopsis thaliana. They were unevenly distributed on eight chromosomes but had a similar structural composition in the same subfamily, indicating that they were relatively conserved and potentially had similar gene functions. An interspecific and intraspecific collinearity analysis showed that fragment duplication played an important role in the evolution of the CUL gene family. The analysis of the cis-acting elements suggests that the UrCULs may play an important role in various biological processes, including the abscisic acid (ABA) response. To investigate this hypothesis, we treated the roots of U. rhynchophylla tissue-cultured seedlings with ABA. The expression pattern analysis showed that all the UrCUL genes were widely expressed in roots with various expression patterns. The co-expression association analysis of the UrCULs and key enzyme genes in the terpenoid indole alkaloid (TIA) synthesis pathway revealed the complex expression patterns of 12 UrCUL genes and some key TIA enzyme genes, especially UrCUL1, UrCUL1-likeA, UrCUL2-likeA and UrCUL2-likeB, which might be involved in the biosynthesis of TIAs. The results showed that the UrCULs were involved in the response to ABA hormones, providing important information for elucidating the function of UrCULs in U. rhynchophylla. The mining of UrCULs in the whole genome of U. rhynchophylla provided new information for understanding the CUL gene and its function in plant secondary metabolites, growth and development.
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Affiliation(s)
- Yingying Shao
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China; (Y.S.); (D.M.); (Y.Z.); (X.L.); (Y.L.); (L.Z.); (Y.Z.)
| | - Detian Mu
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China; (Y.S.); (D.M.); (Y.Z.); (X.L.); (Y.L.); (L.Z.); (Y.Z.)
| | - Yu Zhou
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China; (Y.S.); (D.M.); (Y.Z.); (X.L.); (Y.L.); (L.Z.); (Y.Z.)
| | - Xinghui Liu
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China; (Y.S.); (D.M.); (Y.Z.); (X.L.); (Y.L.); (L.Z.); (Y.Z.)
| | - Xueshuang Huang
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, Hunan University of Medicine, Huaihua 410208, China;
| | - Iain W. Wilson
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
| | - Yuxin Qi
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, Hunan University of Medicine, Huaihua 410208, China;
| | - Ying Lu
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China; (Y.S.); (D.M.); (Y.Z.); (X.L.); (Y.L.); (L.Z.); (Y.Z.)
| | - Lina Zhu
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China; (Y.S.); (D.M.); (Y.Z.); (X.L.); (Y.L.); (L.Z.); (Y.Z.)
| | - Yao Zhang
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China; (Y.S.); (D.M.); (Y.Z.); (X.L.); (Y.L.); (L.Z.); (Y.Z.)
| | - Deyou Qiu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China;
| | - Qi Tang
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China; (Y.S.); (D.M.); (Y.Z.); (X.L.); (Y.L.); (L.Z.); (Y.Z.)
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10
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Hou Z, Liang J, Cai X, Lin J, Wang X, Liu R, Lu L, Chai G, An C, Chen S, Qin Y, Zheng P. PeHVA22 gene family in passion fruit ( Passiflora edulis): initial characterization and expression profiling diversity. FRONTIERS IN PLANT SCIENCE 2024; 14:1279001. [PMID: 38312363 PMCID: PMC10835403 DOI: 10.3389/fpls.2023.1279001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 12/28/2023] [Indexed: 02/06/2024]
Abstract
Passion fruit, an economically valuable fruit crop, is highly vulnerable to adverse climate conditions. The HVA22 genes, recognized as abscisic acid (ABA) and stress-inducible, play vital roles in stress response and growth regulation in diverse eukaryotic organisms. Here, six HVA22 genes were firstly identified in passion fruit genome and all predicted to be localized within the endoplasmic reticulum. Phylogenetic analyses showed that all PeHVA22s were divided into four subgroups. The gene structural features of PeHVA22 genes clustered in the same subgroup were relatively conserved, while the gene structure characteristics of PeHVA22s from different subgroups varied significantly. PeHVA22A and PeHVA22C closely clustered with barley HVA22 in Group II, were also induced by ABA and drought stress treatment, suggesting conserved roles similar to barley HVA22. Meanwhile, most PeHVA22s exhibited induced expression post-drought treatment but were suppressed under salt, low and high-temperature conditions, indicating a unique role in drought response. Additionally, PeHVA22s displayed tissue-specific expression patterns across diverse tissues, except for PeHVA22B which maybe a pseudogene. Notably, PeHVA22C, PeHVA22E, and PeHVA22F predominantly expressed in fruit, indicating their involvement in fruit development. Almost all PeHVA22s showed variable expression at different developmental stages of stamens or ovules, implying their roles in passion fruit's sexual reproduction. The intricate roles of PeHVA22s may result from diverse regulatory factors including transcription factors and CREs related to plant growth and development, hormone and stress responsiveness. These observations highlighted that PeHVA22s might play conserved roles in ABA response and drought stress tolerance, and also be participated in the regulation of passion fruit growth and floral development.
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Affiliation(s)
- Zhimin Hou
- College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jianxiang Liang
- College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xinkai Cai
- College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jingting Lin
- College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaomei Wang
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning Investigation Station of South Subtropical Fruit Trees, Ministry of Agriculture, Nanning, China
| | - Ruoyu Liu
- Pingtan Science and Technology Research Institute, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lin Lu
- College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Gaifeng Chai
- College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chang An
- College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shengzhen Chen
- College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuan Qin
- College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- Pingtan Science and Technology Research Institute, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ping Zheng
- College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- Pingtan Science and Technology Research Institute, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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11
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Zhan W, Cui L, Guo G, Zhang Y. Genome-wide identification and functional analysis of the TCP gene family in rye (Secale cereale L.). Gene X 2023; 854:147104. [PMID: 36509294 DOI: 10.1016/j.gene.2022.147104] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/20/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCP) proteins are plant-specific transcription factors that play significant roles in plant growth, development, and stress response. Rye is a high-value crop with strong resistance to adverse environments. However, the functions of TCP proteins in rye are rarely reported. Based on a genome-wide analysis, the present study identified 26 TCP genes (ScTCPs) in rye. Mapping showed an uneven distribution of the ScTCP genes on the seven rye chromosomes and detected three pairs of tandem duplication genes. Phylogenetic analysis divided these genes into PCF (Proliferrating Cell Factors), CIN (CINCINNATA), and CYC (CYCLOIDEA)/TB1 (Teosinte Branched1) classes, which showed the highest homology between rye and wheat genes. Analysis of miRNA targeting sites indicated that five ScTCP genes were identified as potential targets of miRNA319. Promoter cis-acting elements analysis indicated that ScTCPs were regulated by light signals. Further analysis of the gene expression patterns and functional annotations suggested the role of a few ScTCPs in grain development and stress response. In addition, two TB1 homologous genes (ScTCP9 and ScTCP10) were identified in the ScTCP family. Synteny analysis showed that TB1 orthologous gene pairs existed before the ancestral divergence. Finally, the yeast two-hybrid assay and luciferase complementation imaging assay proved that ScTCP9, localized in the nucleus, interacts with ScFT (Flowering locus T), indicating their role in regulating flowering time. Taken together, this comprehensive study of ScTCPs provides important information for further research on gene function and crop improvement.
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Affiliation(s)
- Weimin Zhan
- College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Lianhua Cui
- College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Guanghui Guo
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng 475004, China
| | - Yanpei Zhang
- College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China.
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12
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Liang J, Fang Y, An C, Yao Y, Wang X, Zhang W, Liu R, Wang L, Aslam M, Cheng Y, Qin Y, Zheng P. Genome-wide identification and expression analysis of the bHLH gene family in passion fruit (Passiflora edulis) and its response to abiotic stress. Int J Biol Macromol 2023; 225:389-403. [PMID: 36400210 DOI: 10.1016/j.ijbiomac.2022.11.076] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/23/2022] [Accepted: 11/01/2022] [Indexed: 11/17/2022]
Abstract
Passion fruit is a tropical fruit crop with significant agricultural, economic and ornamental values. The growth and development of passion fruit are greatly affected by climatic conditions. In plants, the basic helix-loop-helix (bHLH) gene family plays essential roles in the floral organ and fruit development, as well as stress response. However, the characteristics and functions of the bHLH genes of passion fruit remain unclear. Here, 138 passion fruit bHLH members were identified and classified into 20 subfamilies. The structural analysis illustrated that PebHLH proteins of the specific subfamily are relatively conserved. Collinearity analysis indicated that the expansion of the PebHLH gene family mainly took place by segmental duplication, and the structural diversity of duplicated genes might contribute to their functional diversity. PebHLHs, which potentially regulate different floral organ and fruit development, were further screened out, and many of these genes were differentially expressed under various stress treatments. The co-presence of different cis-regulatory elements involved in developmental regulation, hormone and stress responses in the promoter regions of PebHLHs might be closely related to their diverse regulatory roles. Overall, this study will be helpful for further functional investigation of PebHLHs and provides clues for improvement of the passion fruit breeding.
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Affiliation(s)
- Jianxiang Liang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yunying Fang
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chang An
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Yuanbin Yao
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaomei Wang
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning Investigation Station of South Subtropical Fruit Trees, Ministry of Agriculture, Nanning 530004, China
| | - Wenbin Zhang
- Xinluo Breeding Center for Excellent Germplasms, Longyan 361000, China
| | - Ruoyu Liu
- Pingtan Science and Technology Research Institute, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lulu Wang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Mohammad Aslam
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yan Cheng
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuan Qin
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China; Pingtan Science and Technology Research Institute, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Ping Zheng
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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13
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Transcriptional signatures of wheat inflorescence development. Sci Rep 2022; 12:17224. [PMID: 36241895 PMCID: PMC9568521 DOI: 10.1038/s41598-022-21571-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/28/2022] [Indexed: 01/06/2023] Open
Abstract
In order to maintain global food security, it will be necessary to increase yields of the cereal crops that provide most of the calories and protein for the world's population, which includes common wheat (Triticum aestivum L.). An important wheat yield component is the number of grain-holding spikelets which form on the spike during inflorescence development. Characterizing the gene regulatory networks controlling the timing and rate of inflorescence development will facilitate the selection of natural and induced gene variants that contribute to increased spikelet number and yield. In the current study, co-expression and gene regulatory networks were assembled from a temporal wheat spike transcriptome dataset, revealing the dynamic expression profiles associated with the progression from vegetative meristem to terminal spikelet formation. Consensus co-expression networks revealed enrichment of several transcription factor families at specific developmental stages including the sequential activation of different classes of MIKC-MADS box genes. This gene regulatory network highlighted interactions among a small number of regulatory hub genes active during terminal spikelet formation. Finally, the CLAVATA and WUSCHEL gene families were investigated, revealing potential roles for TtCLE13, TtWOX2, and TtWOX7 in wheat meristem development. The hypotheses generated from these datasets and networks further our understanding of wheat inflorescence development.
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14
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Rees H, Rusholme-Pilcher R, Bailey P, Colmer J, White B, Reynolds C, Ward SJ, Coombes B, Graham CA, de Barros Dantas LL, Dodd AN, Hall A. Circadian regulation of the transcriptome in a complex polyploid crop. PLoS Biol 2022; 20:e3001802. [PMID: 36227835 PMCID: PMC9560141 DOI: 10.1371/journal.pbio.3001802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/18/2022] [Indexed: 11/07/2022] Open
Abstract
The circadian clock is a finely balanced timekeeping mechanism that coordinates programmes of gene expression. It is currently unknown how the clock regulates expression of homoeologous genes in polyploids. Here, we generate a high-resolution time-course dataset to investigate the circadian balance between sets of 3 homoeologous genes (triads) from hexaploid bread wheat. We find a large proportion of circadian triads exhibit imbalanced rhythmic expression patterns, with no specific subgenome favoured. In wheat, period lengths of rhythmic transcripts are found to be longer and have a higher level of variance than in other plant species. Expression of transcripts associated with circadian controlled biological processes is largely conserved between wheat and Arabidopsis; however, striking differences are seen in agriculturally critical processes such as starch metabolism. Together, this work highlights the ongoing selection for balance versus diversification in circadian homoeologs and identifies clock-controlled pathways that might provide important targets for future wheat breeding.
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Affiliation(s)
- Hannah Rees
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | | | - Paul Bailey
- Royal Botanic Gardens Kew, Richmond, Surrey, United Kingdom
| | - Joshua Colmer
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Benjamen White
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Connor Reynolds
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | | | - Benedict Coombes
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Calum A. Graham
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | | | - Antony N. Dodd
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Anthony Hall
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
- * E-mail:
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15
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de Souza Moraes T, van Es SW, Hernández-Pinzón I, Kirschner GK, van der Wal F, da Silveira SR, Busscher-Lange J, Angenent GC, Moscou M, Immink RGH, van Esse GW. The TCP transcription factor HvTB2 heterodimerizes with VRS5 and controls spike architecture in barley. PLANT REPRODUCTION 2022; 35:205-220. [PMID: 35254529 PMCID: PMC9352630 DOI: 10.1007/s00497-022-00441-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
Understanding the molecular network, including protein-protein interactions, of VRS5 provide new routes towards the identification of other key regulators of plant architecture in barley. The TCP transcriptional regulator TEOSINTE BRANCHED 1 (TB1) is a key regulator of plant architecture. In barley, an important cereal crop, HvTB1 (also referred to as VULGARE SIX-ROWED spike (VRS) 5), inhibits the outgrowth of side shoots, or tillers, and grains. Despite its key role in barley development, there is limited knowledge on the molecular network that is utilized by VRS5. In this work, we performed protein-protein interaction studies of VRS5. Our analysis shows that VRS5 potentially interacts with a diverse set of proteins, including other class II TCP's, NF-Y TF, but also chromatin remodelers. Zooming in on the interaction capacity of VRS5 with other TCP TFs shows that VRS5 preferably interacts with other class II TCP TFs in the TB1 clade. Induced mutagenesis through CRISPR-Cas of one of the putative VRS5 interactors, HvTB2 (also referred to as COMPOSITUM 1 and BRANCHED AND INDETERMINATE SPIKELET 1), resulted in plants that have lost their characteristic unbranched spike architecture. More specifically, hvtb2 mutants exhibited branches arising at the main spike, suggesting that HvTB2 acts as inhibitor of branching. Our protein-protein interaction studies of VRS5 resulted in the identification of HvTB2 as putative interactor of VRS5, another key regulator of spike architecture in barley. The study presented here provides a first step to underpin the protein-protein interactome of VRS5 and to identify other, yet unknown, key regulators of barley plant architecture.
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Affiliation(s)
- Tatiana de Souza Moraes
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Laboratório de Biotecnologia Vegetal, Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, CEP 13416-000, Brazil
| | - Sam W van Es
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | | | - Gwendolyn K Kirschner
- Institute of Crop Functional Genomics, Rheinische Friedrich-Wilhelms-Universität, Bonn, Germany
| | - Froukje van der Wal
- Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Sylvia Rodrigues da Silveira
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Laboratório de Biotecnologia Vegetal, Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, CEP 13416-000, Brazil
| | - Jacqueline Busscher-Lange
- Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Gerco C Angenent
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Matthew Moscou
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Richard G H Immink
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands.
- Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands.
| | - G Wilma van Esse
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands.
- Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands.
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16
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Singh L, Dhillon GS, Kaur S, Dhaliwal SK, Kaur A, Malik P, Kumar A, Gill RK, Kaur S. Genome-wide Association Study for Yield and Yield-Related Traits in Diverse Blackgram Panel (Vigna mungo L. Hepper) Reveals Novel Putative Alleles for Future Breeding Programs. Front Genet 2022; 13:849016. [PMID: 35899191 PMCID: PMC9310006 DOI: 10.3389/fgene.2022.849016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 06/20/2022] [Indexed: 11/29/2022] Open
Abstract
Blackgram (Vigna mungo L. Hepper) is an important tropical and sub-tropical short-duration legume that is rich in dietary protein and micronutrients. Producing high-yielding blackgram varieties is hampered by insufficient genetic variability, absence of suitable ideotypes, low harvest index and susceptibility to biotic-abiotic stresses. Seed yield, a complex trait resulting from the expression and interaction of multiple genes, necessitates the evaluation of diverse germplasm for the identification of novel yield contributing traits. Henceforth, a panel of 100 blackgram genotypes was evaluated at two locations (Ludhiana and Gurdaspur) across two seasons (Spring 2019 and Spring 2020) for 14 different yield related traits. A wide range of variability, high broad-sense heritability and a high correlation of grain yield were observed for 12 out of 14 traits studied among all environments. Investigation of population structure in the panel using a set of 4,623 filtered SNPs led to identification of four sub-populations based on ad-hoc delta K and Cross entropy value. Using Farm CPU model and Mixed Linear Model algorithms, a total of 49 significant SNP associations representing 42 QTLs were identified. Allelic effects were found to be statistically significant at 37 out of 42 QTLs and 50 known candidate genes were identified in 24 of QTLs.
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Affiliation(s)
- Lovejit Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | | | - Sarabjit Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Sandeep Kaur Dhaliwal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Amandeep Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Palvi Malik
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Ashok Kumar
- Regional Research Station, Punjab Agricultural University, Gurdaspur, India
| | - Ranjit Kaur Gill
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Satinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
- *Correspondence: Satinder Kaur,
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17
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Qu Z, Wu Y, Hu D, Li T, Liang H, Ye F, Xue J, Xu S. Genome-Wide Association Analysis for Candidate Genes Contributing to Kernel-Related Traits in Maize. FRONTIERS IN PLANT SCIENCE 2022; 13:872292. [PMID: 35685022 PMCID: PMC9171146 DOI: 10.3389/fpls.2022.872292] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/06/2022] [Indexed: 06/01/2023]
Abstract
Maize grain size is the main factor determining grain yield. Dissecting the genetic basis of maize grain size may help reveal the regulatory mechanism of maize seed development and yield formation. In this study, two associated populations were used for genome-wide association analysis of kernel length, kernel width, kernel thickness, and hundred-kernel weight from multiple locations in AM122 and AM180, respectively. Then, genome-wide association mapping was performed based on the maize 6H90K SNP chip. A total of 139 loci were identified as associated with the four traits with p < 1 × 10-4 using two models (FarmCPU and MLM). The transcriptome data showed that 15 of them were expressed differentially in two maize-inbred lines KB182 (small kernel) and KB020 (big kernel) during kernel development. These candidate genes were enriched in regulating peroxidase activity, oxidoreductase, and leaf senescence. The molecular function was major in binding and catalytic activity. This study provided important reference information for exploring maize kernel development mechanisms and applying molecular markers in high-yield breeding.
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Affiliation(s)
- Zhibo Qu
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, China
- Maize Engineering Technology Research Centre, Yangling, China
| | - Ying Wu
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, China
- Maize Engineering Technology Research Centre, Yangling, China
| | - Die Hu
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, China
- Maize Engineering Technology Research Centre, Yangling, China
| | - Ting Li
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, China
- Maize Engineering Technology Research Centre, Yangling, China
| | - Hangyu Liang
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, China
- Maize Engineering Technology Research Centre, Yangling, China
| | - Fan Ye
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, China
- Maize Engineering Technology Research Centre, Yangling, China
| | - Jiquan Xue
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, China
- Maize Engineering Technology Research Centre, Yangling, China
| | - Shutu Xu
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, China
- Maize Engineering Technology Research Centre, Yangling, China
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Jin K, Wang Y, Zhuo R, Xu J, Lu Z, Fan H, Huang B, Qiao G. TCP Transcription Factors Involved in Shoot Development of Ma Bamboo ( Dendrocalamus latiflorus Munro). FRONTIERS IN PLANT SCIENCE 2022; 13:884443. [PMID: 35620688 PMCID: PMC9127963 DOI: 10.3389/fpls.2022.884443] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/08/2022] [Indexed: 05/10/2023]
Abstract
Ma bamboo (Dendrocalamus latiflorus Munro) is the most widely cultivated clumping bamboo in Southern China and is valuable for both consumption and wood production. The development of bamboo shoots involving the occurrence of lateral buds is unique, and it affects both shoot yield and the resulting timber. Plant-specific TCP transcription factors are involved in plant growth and development, particularly in lateral bud outgrowth and morphogenesis. However, the comprehensive information of the TCP genes in Ma bamboo remains poorly understood. In this study, 66 TCP transcription factors were identified in Ma bamboo at the genome-wide level. Members of the same subfamily had conservative gene structures and conserved motifs. The collinear analysis demonstrated that segmental duplication occurred widely in the TCP transcription factors of Ma bamboo, which mainly led to the expansion of a gene family. Cis-acting elements related to growth and development and stress response were found in the promoter regions of DlTCPs. Expression patterns revealed that DlTCPs have tissue expression specificity, which is usually highly expressed in shoots and leaves. Subcellular localization and transcriptional self-activation experiments demonstrated that the five candidate TCP proteins were typical self-activating nuclear-localized transcription factors. Additionally, the transcriptome analysis of the bamboo shoot buds at different developmental stages helped to clarify the underlying functions of the TCP members during the growth of bamboo shoots. DlTCP12-C, significantly downregulated as the bamboo shoots developed, was selected to further verify its molecular function in Arabidopsis. The DlTCP12-C overexpressing lines exhibited a marked reduction in the number of rosettes and branches compared with the wild type in Arabidopsis, suggesting that DlTCP12-C conservatively inhibits lateral bud outgrowth and branching in plants. This study provides useful insights into the evolutionary patterns and molecular functions of the TCP transcription factors in Ma bamboo and provides a valuable reference for further research on the regulatory mechanism of bamboo shoot development and lateral bud growth.
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Affiliation(s)
- Kangming Jin
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
- Forestry Faculty, Nanjing Forestry University, Nanjing, China
| | - Yujun Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Renying Zhuo
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Jing Xu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Zhuchou Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Huijin Fan
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Biyun Huang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Guirong Qiao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
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Genome-Wide Identification and Expression Analysis of LBD Transcription Factor Genes in Passion Fruit (Passiflora edulis). Int J Mol Sci 2022; 23:ijms23094700. [PMID: 35563091 PMCID: PMC9104060 DOI: 10.3390/ijms23094700] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 04/21/2022] [Accepted: 04/22/2022] [Indexed: 02/05/2023] Open
Abstract
The lateral organ boundary domain (LBD) gene is a plant-specific transcription factor that plays a crucial role in plant growth and development, including the development of lateral vegetative organs such as leaf and root development, as well as floral organs such as sepal, petal, and pollen development. Passion fruit is a tropical fruit with important agricultural, economic and ornamental value. However, there is no systematic research report available on the LBD gene family of passion fruit. In this study, a genome-wide analysis of passion fruit LBD genes identified 33 PeLBDs that were unevenly distributed across nine chromosomes. According to phylogenetic and gene structure analysis, PeLBDs were divided into two categories: Class I (27) and Class II (6). Homologous protein modeling results showed that the gene members of the two subfamilies were structurally and functionally similar. Cis-acting element and target gene prediction analysis suggested that PeLBDs might participate in various biological processes by regulating diverse target genes involved in growth and development, metabolism, hormones and stress response. Collinearity analysis indicated that the expansion of the PeLBD gene family likely took place mainly by segmental duplication, and some duplicated gene pairs such as PeLBD13/15 might show functional redundancy, while most duplicated gene pairs such as PeLBD8/12 showed different expression profiles indicating their functional diversification. After filtering low expressed genes, all Class Id PeLBDs were more highly expressed during pollen development. At the same, all Class Ic and many other PeLBDs were relatively highly expressed during ovule development, similar with their homologous LBD genes in Arabidopsis, indicating their potential regulatory roles in reproductive tissue development in passion fruit. PeLBDs that were highly expressed in floral tissues were also expressed at a higher level in tendrils with some differences, indicating the close relationships of tendrils to floral tissues. Some genes such as PeLBD23/25 might be simultaneously related to floral development and leaf early formation in passion fruit, while other PeLBDs showed a strong tissue-specific expression. For example, PeLBD17/27/29 were specifically expressed in floral tissues, while PeLBD11 were only highly expressed in fruit, suggesting their specific function in the development of certain tissues. A qRT-PCR was conducted to verify the expression levels of six PeLBDs in different tissues. Our analysis provides a basis for the functional analysis of LBD genes and new insights into their regulatory roles in floral and vegetative tissue development.
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Systematic Characterization of TCP Gene Family in Four Cotton Species Revealed That GhTCP62 Regulates Branching in Arabidopsis. BIOLOGY 2021; 10:biology10111104. [PMID: 34827097 PMCID: PMC8614845 DOI: 10.3390/biology10111104] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/21/2021] [Accepted: 10/25/2021] [Indexed: 01/14/2023]
Abstract
TEOSINTE-BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factors play an essential role in regulating various physiological and biochemical functions during plant growth. However, the function of TCP transcription factors in G. hirsutum has not yet been studied. In this study, we performed genome-wide identification and correlation analysis of the TCP transcription factor family in G. hirsutum. We identified 72 non-redundant GhTCP genes and divided them into seven subfamilies, based on phylogenetic analysis. Most GhTCP genes in the same subfamily displayed similar exon and intron structures and featured highly conserved motif structures in their subfamily. Additionally, the pattern of chromosomal distribution demonstrated that GhTCP genes were unevenly distributed on 24 out of 26 chromosomes, and that fragment replication was the main replication event of GhTCP genes. In TB1 sub-family genes, GhTCP62 was highly expressed in the axillary buds, suggesting that GhTCP62 significantly affected cotton branching. Additionally, subcellular localization results indicated that GhTCP62 is located in the nucleus and possesses typical transcription factor characteristics. The overexpression of GhTCP62 in Arabidopsis resulted in fewer rosette-leaf branches and cauline-leaf branches. Furthermore, the increased expression of HB21 and HB40 genes in Arabidopsis plants overexpressing GhTCP62 suggests that GhTCP62 may regulate branching by positively regulating HB21 and HB40.
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21
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Xu Y, Liu H, Gao Y, Xiong R, Wu M, Zhang K, Xiang Y. The TCP transcription factor PeTCP10 modulates salt tolerance in transgenic Arabidopsis. PLANT CELL REPORTS 2021; 40:1971-1987. [PMID: 34392380 DOI: 10.1007/s00299-021-02765-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
PeTCP10 can be induced by salt stresses and play important regulation roles in salt stresses response in transgenic Arabidopsis. Salt stress is one of the major adverse environmental factors that affect normal plant development and growth. PeTCP10, a Class I TCP member, was markedly expressed in moso bamboo mature leaf, root and stem under normal conditions and also induced by salt stress. Overexpressed PeTCP10 was found to enhance salt tolerance of transgenic Arabidopsis at the vegetative growth stage. It was also found capable to increase relative water content, while decreasing relative electrolyte leakage and Na+ accumulation of transgenic Arabidopsis versus wild-type (WT) plants at high-salt conditions. In addition, it improved antioxidant capacity of transgenic Arabidopsis plants by promoting catalase activity and enhanced their H2O2 tolerance. In contrast to WT plants, transcriptome analysis demonstrated that multiple genes related to abscisic acid, salt and H2O2 response were induced after NaCl treatment in transgenic plants. Meanwhile, overexpressed PeTCP10 improved the tolerance of abscisic acid. Moreover, luciferase reporter assay results showed that PeTCP10 is able to directly activate the expression of BT2 in transgenic plants. In contrary, the germination rates of transgenic plants were significantly lower than those of WT plants under high-NaCl conditions. Both primary root length and survival rate at the seedling stage are also found lower in transgenic plants than in WT plants. It is concluded that overexpressed PeTCP10 enhances salt stress tolerance of transgenic plants at the vegetative growth stage, and it also improves salt sensitiveness in both germination and seedling stages. These research results will contribute to further understand the functions of TCPs in abiotic stress response.
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Affiliation(s)
- Yuzeng Xu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Huanlong Liu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Yameng Gao
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Rui Xiong
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Min Wu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Kaimei Zhang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Yan Xiang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China.
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Li Y, An S, Cheng Q, Zong Y, Chen W, Guo W, Zhang L. Analysis of Evolution, Expression and Genetic Transformation of TCP Transcription Factors in Blueberry Reveal That VcTCP18 Negatively Regulates the Release of Flower Bud Dormancy. FRONTIERS IN PLANT SCIENCE 2021; 12:697609. [PMID: 34305986 PMCID: PMC8299413 DOI: 10.3389/fpls.2021.697609] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 06/15/2021] [Indexed: 05/23/2023]
Abstract
Plant-specific TEOSINTE BRANCHED 1, CYCLOIDEA, PROLIFERATING CELL FACTORS (TCP) transcription factors have versatile functions in plant growth, development and response to environmental stress. Despite blueberry's value as an important fruit crop, the TCP gene family has not been systematically studied in this plant. The current study identified blueberry TCP genes (VcTCPs) using genomic data from the tetraploid blueberry variety 'Draper'; a total of 62 genes were obtained. Using multiple sequence alignment, conserved motif, and gene structure analyses, family members were divided into two subfamilies, of which class II was further divided into two subclasses, CIN and TB1. Synteny analysis showed that genome-wide or segment-based replication played an important role in the expansion of the blueberry TCP gene family. The expression patterns of VcTCP genes during fruit development, flower bud dormancy release, hormone treatment, and tissue-specific expression were analyzed using RNA-seq and qRT-PCR. The results showed that the TB1 subclass members exhibited a certain level of expression in the shoot, leaf, and bud; these genes were not expressed during fruit development, but transcript levels decreased uniformly during the release of flower bud dormancy by low-temperature accumulation. The further transgenic experiments showed the overexpression of VcTCP18 in Arabidopsis significantly decreased the seed germination rate in contrast to the wild type. The bud dormancy phenomena as late-flowering, fewer rosettes and main branches were also observed in transgenic plants. Overall, this study provides the first insight into the evolution, expression, and function of VcTCP genes, including the discovery that VcTCP18 negatively regulated bud dormancy release in blueberry. The results will deepen our understanding of the function of TCPs in plant growth and development.
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Affiliation(s)
- Yongqiang Li
- Key Laboratory of Silviculture, Co-Innovation Center of Jiangxi Typical Trees Cultivation and Utilization, College of Forestry, Jiangxi Agricultural University, Nanchang, China
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, China
| | - Shuang An
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, China
| | - Qiangqiang Cheng
- Key Laboratory of Silviculture, Co-Innovation Center of Jiangxi Typical Trees Cultivation and Utilization, College of Forestry, Jiangxi Agricultural University, Nanchang, China
| | - Yu Zong
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, China
| | - Wenrong Chen
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, China
| | - Weidong Guo
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, China
| | - Lu Zhang
- Key Laboratory of Silviculture, Co-Innovation Center of Jiangxi Typical Trees Cultivation and Utilization, College of Forestry, Jiangxi Agricultural University, Nanchang, China
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Ma Y, Xu D, Yan X, Wu Z, Kayani SI, Shen Q, Fu X, Xie L, Hao X, Hassani D, Li L, Liu H, Pan Q, Lv Z, Liu P, Sun X, Tang K. Jasmonate- and abscisic acid-activated AaGSW1-AaTCP15/AaORA transcriptional cascade promotes artemisinin biosynthesis in Artemisia annua. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1412-1428. [PMID: 33539631 PMCID: PMC8313134 DOI: 10.1111/pbi.13561] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/24/2021] [Accepted: 01/28/2021] [Indexed: 05/12/2023]
Abstract
Artemisinin, a sesquiterpene lactone widely used in malaria treatment, was discovered in the medicinal plant Artemisia annua. The biosynthesis of artemisinin is efficiently regulated by jasmonate (JA) and abscisic acid (ABA) via regulatory factors. However, the mechanisms linking JA and ABA signalling with artemisinin biosynthesis through an associated regulatory network of downstream transcription factors (TFs) remain enigmatic. Here we report AaTCP15, a JA and ABA dual-responsive teosinte branched1/cycloidea/proliferating (TCP) TF, which is essential for JA and ABA-induced artemisinin biosynthesis by directly binding to and activating the promoters of DBR2 and ALDH1, two genes encoding enzymes for artemisinin biosynthesis. Furthermore, AaORA, another positive regulator of artemisinin biosynthesis responds to JA and ABA, interacts with and enhances the transactivation activity of AaTCP15 and simultaneously activates AaTCP15 transcripts. Hence, they form an AaORA-AaTCP15 module to synergistically activate DBR2, a crucial gene for artemisinin biosynthesis. More importantly, AaTCP15 expression is activated by the multiple reported JA and ABA-responsive TFs that promote artemisinin biosynthesis. Among them, AaGSW1 acts at the nexus of JA and ABA signalling to activate the artemisinin biosynthetic pathway and directly binds to and activates the AaTCP15 promoter apart from the AaORA promoter, which further facilitates formation of the AaGSW1-AaTCP15/AaORA regulatory module to integrate JA and ABA-mediated artemisinin biosynthesis. Our results establish a multilayer regulatory network of the AaGSW1-AaTCP15/AaORA module to regulate artemisinin biosynthesis through JA and ABA signalling, and provide an interesting avenue for future research exploring the special transcriptional regulation module of TCP genes associated with specialized metabolites in plants.
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Affiliation(s)
- Ya‐Nan Ma
- Joint International Research Laboratory of Metabolic and Developmental SciencesKey Laboratory of Urban Agriculture (South) Ministry of AgriculturePlant Biotechnology Research CenterFudan‐SJTU‐Nottingham Plant Biotechnology R&D CenterSchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Dong‐Bei Xu
- Joint International Research Laboratory of Metabolic and Developmental SciencesKey Laboratory of Urban Agriculture (South) Ministry of AgriculturePlant Biotechnology Research CenterFudan‐SJTU‐Nottingham Plant Biotechnology R&D CenterSchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
- Institute of Ecological AgricultureSichuan Agricultural UniversityChengduChina
| | - Xin Yan
- Joint International Research Laboratory of Metabolic and Developmental SciencesKey Laboratory of Urban Agriculture (South) Ministry of AgriculturePlant Biotechnology Research CenterFudan‐SJTU‐Nottingham Plant Biotechnology R&D CenterSchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Zhang‐Kuanyu Wu
- Joint International Research Laboratory of Metabolic and Developmental SciencesKey Laboratory of Urban Agriculture (South) Ministry of AgriculturePlant Biotechnology Research CenterFudan‐SJTU‐Nottingham Plant Biotechnology R&D CenterSchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Sadaf Ilyas Kayani
- Joint International Research Laboratory of Metabolic and Developmental SciencesKey Laboratory of Urban Agriculture (South) Ministry of AgriculturePlant Biotechnology Research CenterFudan‐SJTU‐Nottingham Plant Biotechnology R&D CenterSchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Qian Shen
- Joint International Research Laboratory of Metabolic and Developmental SciencesKey Laboratory of Urban Agriculture (South) Ministry of AgriculturePlant Biotechnology Research CenterFudan‐SJTU‐Nottingham Plant Biotechnology R&D CenterSchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Xue‐Qing Fu
- Joint International Research Laboratory of Metabolic and Developmental SciencesKey Laboratory of Urban Agriculture (South) Ministry of AgriculturePlant Biotechnology Research CenterFudan‐SJTU‐Nottingham Plant Biotechnology R&D CenterSchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Li‐Hui Xie
- Joint International Research Laboratory of Metabolic and Developmental SciencesKey Laboratory of Urban Agriculture (South) Ministry of AgriculturePlant Biotechnology Research CenterFudan‐SJTU‐Nottingham Plant Biotechnology R&D CenterSchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Xiao‐Long Hao
- Laboratory of Medicinal Plant BiotechnologyCollege of PharmacyZhejiang Chinese Medical UniversityHangzhouChina
| | - Danial Hassani
- Joint International Research Laboratory of Metabolic and Developmental SciencesKey Laboratory of Urban Agriculture (South) Ministry of AgriculturePlant Biotechnology Research CenterFudan‐SJTU‐Nottingham Plant Biotechnology R&D CenterSchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Ling Li
- Joint International Research Laboratory of Metabolic and Developmental SciencesKey Laboratory of Urban Agriculture (South) Ministry of AgriculturePlant Biotechnology Research CenterFudan‐SJTU‐Nottingham Plant Biotechnology R&D CenterSchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Hang Liu
- Joint International Research Laboratory of Metabolic and Developmental SciencesKey Laboratory of Urban Agriculture (South) Ministry of AgriculturePlant Biotechnology Research CenterFudan‐SJTU‐Nottingham Plant Biotechnology R&D CenterSchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Qi‐Fang Pan
- Joint International Research Laboratory of Metabolic and Developmental SciencesKey Laboratory of Urban Agriculture (South) Ministry of AgriculturePlant Biotechnology Research CenterFudan‐SJTU‐Nottingham Plant Biotechnology R&D CenterSchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Zong‐You Lv
- Joint International Research Laboratory of Metabolic and Developmental SciencesKey Laboratory of Urban Agriculture (South) Ministry of AgriculturePlant Biotechnology Research CenterFudan‐SJTU‐Nottingham Plant Biotechnology R&D CenterSchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Pin Liu
- Joint International Research Laboratory of Metabolic and Developmental SciencesKey Laboratory of Urban Agriculture (South) Ministry of AgriculturePlant Biotechnology Research CenterFudan‐SJTU‐Nottingham Plant Biotechnology R&D CenterSchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Xiao‐Fen Sun
- Joint International Research Laboratory of Metabolic and Developmental SciencesKey Laboratory of Urban Agriculture (South) Ministry of AgriculturePlant Biotechnology Research CenterFudan‐SJTU‐Nottingham Plant Biotechnology R&D CenterSchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Ke‐Xuan Tang
- Joint International Research Laboratory of Metabolic and Developmental SciencesKey Laboratory of Urban Agriculture (South) Ministry of AgriculturePlant Biotechnology Research CenterFudan‐SJTU‐Nottingham Plant Biotechnology R&D CenterSchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
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Wang J, Wang Z, Jia C, Miao H, Zhang J, Liu J, Xu B, Jin Z. Genome-Wide Identification and Transcript Analysis of TCP Gene Family in Banana (Musa acuminata L.). Biochem Genet 2021; 60:204-222. [PMID: 34156635 DOI: 10.1007/s10528-021-10100-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 06/09/2021] [Indexed: 11/28/2022]
Abstract
Plant-specific TEOSINTE-BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR1 (TCP) gene family has versatile functions in diverse aspects of plants. However, less research on banana TCPs was done comprehensively. Accordingly, 48 banana TCP genes were characterized on aspects of gene structure, conserved motifs, phylogenetic relationship, and expression patterns. Members of the MaTCP gene family were unevenly distributed among 11 chromosomes and purification selection was the driving force of the MaTCP gene family. Gene duplication analysis indicated that segmental duplication is the major contributor to family expansion. Promoter analysis showed that MaTCPs might be involved in banana growth, development, and abiotic stress responses. Further, the expression of 12 MaTCPs was analyzed by real-time quantitative RT-PCR, and the protein interaction analysis showed that MaPCF10 and MaPCF13 may have an important function in banana fruit development and ripening. These results lay the foundation for further study of the functions of TCP genes in banana.
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Affiliation(s)
- Jingyi Wang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China
| | - Zhuo Wang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China.,Hainan Key Laboratory for Protection and Utilization of Tropical Bioresource, Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China
| | - Caihong Jia
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China
| | - Hongxia Miao
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China.,Hainan Key Laboratory for Protection and Utilization of Tropical Bioresource, Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China
| | - Jianbin Zhang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China
| | - Juhua Liu
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China. .,Hainan Key Laboratory for Protection and Utilization of Tropical Bioresource, Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China.
| | - Biyu Xu
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China.
| | - Zhiqiang Jin
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China. .,Hainan Key Laboratory for Protection and Utilization of Tropical Bioresource, Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China.
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25
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Li Y, Song J, Zhu G, Hou Z, Wang L, Wu X, Fang Z, Liu Y, Gao C. Genome-wide identification and expression analysis of ADP-ribosylation factors associated with biotic and abiotic stress in wheat ( Triticum aestivum L.). PeerJ 2021; 9:e10963. [PMID: 33717696 PMCID: PMC7934654 DOI: 10.7717/peerj.10963] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/27/2021] [Indexed: 12/27/2022] Open
Abstract
The ARF gene family plays important roles in intracellular transport in eukaryotes and is involved in conferring tolerance to biotic and abiotic stresses in plants. To explore the role of these genes in the development of wheat (Triticum aestivum L.), 74 wheat ARF genes (TaARFs; including 18 alternate transcripts) were identified and clustered into seven sub-groups. Phylogenetic analysis revealed that TaARFA1 sub-group genes were strongly conserved. Numerous cis-elements functionally associated with the stress response and hormones were identified in the TaARFA1 sub-group, implying that these TaARFs are induced in response to abiotic and biotic stresses in wheat. According to available transcriptome data and qRT-PCR analysis, the TaARFA1 genes displayed tissue-specific expression patterns and were regulated by biotic stress (powdery mildew and stripe rust) and abiotic stress (cold, heat, ABA, drought and NaCl). Protein interaction network analysis further indicated that TaARFA1 proteins may interact with protein phosphatase 2C (PP2C), which is a key protein in the ABA signaling pathway. This comprehensive analysis will be useful for further functional characterization of TaARF genes and the development of high-quality wheat varieties.
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Affiliation(s)
- Yaqian Li
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, China
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innovation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, China
| | - Jinghan Song
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, China
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innovation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, China
| | - Guang Zhu
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, China
| | - Zehao Hou
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innovation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, China
| | - Lin Wang
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innovation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, China
| | - Xiaoxue Wu
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innovation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, China
| | - Zhengwu Fang
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innovation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, China
| | - Yike Liu
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, China
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innovation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, China
| | - Chunbao Gao
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, China
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innovation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, China
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Shang Y, Yuan L, Di Z, Jia Y, Zhang Z, Li S, Xing L, Qi Z, Wang X, Zhu J, Hua W, Wu X, Zhu M, Li G, Li C. A CYC/TB1-type TCP transcription factor controls spikelet meristem identity in barley. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:7118-7131. [PMID: 32915968 DOI: 10.1093/jxb/eraa416] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 09/09/2020] [Indexed: 05/08/2023]
Abstract
Barley possesses a branchless, spike-shaped inflorescence where determinate spikelets attach directly to the main axis, but the developmental mechanism of spikelet identity remains largely unknown. Here we report the functional analysis of the barley gene BRANCHED AND INDETERMINATE SPIKELET 1 (BDI1), which encodes a TCP transcription factor and plays a crucial role in determining barley inflorescence architecture and spikelet development. The bdi1 mutant exhibited indeterminate spikelet meristems that continued to grow and differentiate after producing a floret meristem; some spikelet meristems at the base of the spike formed two fully developed seeds or converted to branched spikelets, producing a branched inflorescence. Map-based cloning analysis showed that this mutant has a deletion of ~600 kb on chromosome 5H containing three putative genes. Expression analysis and virus-induced gene silencing confirmed that the causative gene, BDI1, encodes a CYC/TB1-type TCP transcription factor and is highly conserved in both wild and cultivated barley. Transcriptome and regulatory network analysis demonstrated that BDI1 may integrate regulation of gene transcription cell wall modification and known trehalose-6-phosphate homeostasis to control spikelet development. Together, our findings reveal that BDI1 represents a key regulator of inflorescence architecture and meristem determinacy in cereal crop plants.
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Affiliation(s)
- Yi Shang
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, China
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Lu Yuan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/ JCIC-MCP, Nanjing, Jiangsu, China
| | - Zhaocan Di
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/ JCIC-MCP, Nanjing, Jiangsu, China
| | - Yong Jia
- Western Barley Genetics Alliance, Murdoch University, Murdoch WA, Australia
| | - Zhenlan Zhang
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, China
| | - Sujuan Li
- Central Laboratory of Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Liping Xing
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/ JCIC-MCP, Nanjing, Jiangsu, China
| | - Zengjun Qi
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/ JCIC-MCP, Nanjing, Jiangsu, China
| | - Xiaoyun Wang
- Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Jinghuan Zhu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Wei Hua
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Xiaojian Wu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Minqiu Zhu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/ JCIC-MCP, Nanjing, Jiangsu, China
| | - Gang Li
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
- School of Agriculture, Food, and Wine, University of Adelaide, Waite campus, Urrbrae, South Australia, Australia
| | - Chengdao Li
- Western Barley Genetics Alliance, Murdoch University, Murdoch WA, Australia
- Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, Hubei, China
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Gao G, Kan J, Jiang C, Ahmar S, Zhang J, Yang P. Genome-wide diversity analysis of TCP transcription factors revealed cases of selection from wild to cultivated barley. Funct Integr Genomics 2020; 21:31-42. [PMID: 33169329 DOI: 10.1007/s10142-020-00759-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 10/15/2020] [Accepted: 11/03/2020] [Indexed: 11/28/2022]
Abstract
Plant-specific TEOSINTE BRANCHED 1/CYCLOIDEA/PROLIFERATING CELL FACTORS 1/2 (TCP) transcription factors have known roles in inflorescence architecture. In barley, there are two family members INTERMEDIUM-C (INT-c/HvTB1-1) and COMPOSITUM 1 (COM1/HvTCP24) which are involved in the manipulation of spike architecture, whereas the participation of TCP family genes in selection from wild (Hordeum vulgare subsp. spontaneum, Hs) to cultivated barley (Hordeum vulgare subsp. vulgare, Hv) remains poorly investigated. Here, by conducting a genome-wide survey for TCP-like sequences in publicly-released datasets, 22 HsTCP and 20 HvTCP genes encoded for mature proteins were identified and assigned into two classes (I and II) based on their functional domains and the phylogenetic analysis. Each counterpart of the orthologous gene in wild and cultivated barley usually represented a similarity on the transcriptional profile across the tissues. The diversity analysis of TCPs in 90 wild barley accessions and 137 landraces with geographically-referenced passport information revealed the detectable selection at three loci including INT-c/HvTB1-1, HvPCF2, and HvPCF8. Especially, the HvPCF8 haplotypes in cultivated barley were found correlating with their geographical collection sites. There was no difference observed in either transactivation activity in yeast or subcellular localization in Nicotiana benthamiana among these haplotypes. Nevertheless, the genome-wide diversity analysis of barley TCP genes in wild and cultivated populations provided insight for future functional characterization in plant development such as spike architecture.
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Affiliation(s)
- Guangqi Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jinhong Kan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Congcong Jiang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Sunny Ahmar
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jing Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ping Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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COMPOSITUM 1 contributes to the architectural simplification of barley inflorescence via meristem identity signals. Nat Commun 2020; 11:5138. [PMID: 33046693 PMCID: PMC7550572 DOI: 10.1038/s41467-020-18890-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 09/15/2020] [Indexed: 11/23/2022] Open
Abstract
Grasses have varying inflorescence shapes; however, little is known about the genetic mechanisms specifying such shapes among tribes. Here, we identify the grass-specific TCP transcription factor COMPOSITUM 1 (COM1) expressing in inflorescence meristematic boundaries of different grasses. COM1 specifies branch-inhibition in barley (Triticeae) versus branch-formation in non-Triticeae grasses. Analyses of cell size, cell walls and transcripts reveal barley COM1 regulates cell growth, thereby affecting cell wall properties and signaling specifically in meristematic boundaries to establish identity of adjacent meristems. COM1 acts upstream of the boundary gene Liguleless1 and confers meristem identity partially independent of the COM2 pathway. Furthermore, COM1 is subject to purifying natural selection, thereby contributing to specification of the spike inflorescence shape. This meristem identity pathway has conceptual implications for both inflorescence evolution and molecular breeding in Triticeae. Grasses have diverse inflorescence morphologies, but the underlying genetic mechanisms are unclear. Here, the authors report a TCP transcription factor COM1 affects cell growth through regulation of cell wall properties and promotes branch formation in non-Triticeae grasses but branch inhibition in barley (Triticeae).
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Liu H, Mullan D, Zhang C, Zhao S, Li X, Zhang A, Lu Z, Wang Y, Yan G. Major genomic regions responsible for wheat yield and its components as revealed by meta-QTL and genotype-phenotype association analyses. PLANTA 2020; 252:65. [PMID: 32970252 DOI: 10.1007/s00425-020-03466-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 09/12/2020] [Indexed: 12/17/2022]
Abstract
MAIN CONCLUSION Meta-QTL (MQTL) analysis was done for yield-related traits in wheat. Candidate genes were identified within the refined MQTL and further validated by genotype-phenotype association analysis. Extensive studies have been undertaken on quantitative trait locus/loci (QTL) for wheat yield and its component traits. This study conducted a meta-analysis of 381 QTL related to wheat yield under various environments, including irrigated, drought- and/or heat-stressed conditions. Markers flanking meta-QTL (MQTL) were mapped on the wheat reference genome for their physical positions. Putative candidate genes were examined for MQTL with a physical interval of less than 20 Mbp. A total of 86 MQTL were identified as responsible for yield, of which 34 were for irrigated environments, 39 for drought-stressed environments, 36 for heat-stressed environments, and 23 for both drought- and heat-stressed environments. The high-confidence genes within the physical positions of the MQTL flanking markers were screened in the reference genome RefSeq V1.0, which identified 210 putative candidate genes. The phenotypic data for 14 contrasting genotypes with either high or low yield performance-according to the Australian National Variety Trials-were associated with their genotypic data obtained through ddRAD sequencing, which validated 18 genes or gene clusters associated with MQTL that had important roles for wheat yield. The detected and refined MQTL and candidate genes will be useful for marker-assisted selection of high yield in wheat breeding.
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Affiliation(s)
- Hui Liu
- School of Plant Biology, Faculty of Science and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Daniel Mullan
- InterGrain Pty Ltd, 19 Ambitious Link, Bibra Lake, WA, 6163, Australia
| | - Chi Zhang
- Beijing Genomics Institute, Shenzhen, 518053, China
| | - Shancen Zhao
- Beijing Genomics Institute, Shenzhen, 518053, China
| | - Xin Li
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chicness Academy of Sciences, Beijing, 100101, China
| | - Aimin Zhang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chicness Academy of Sciences, Beijing, 100101, China
| | - Zhanyuan Lu
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, No. 22, Yuquan Qu Zhaojun Lu, Hohhot, Inner Mongolia Autonomous Region, China
| | - Yong Wang
- Wheat Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Guijun Yan
- School of Plant Biology, Faculty of Science and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia.
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Song B, Tang Z, Li X, Li J, Zhang M, Zhao K, Liu H, Zhang S, Wu J. Mining and evolution analysis of lateral organ boundaries domain (LBD) genes in Chinese white pear (Pyrus bretschneideri). BMC Genomics 2020; 21:644. [PMID: 32957912 PMCID: PMC7504654 DOI: 10.1186/s12864-020-06999-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 08/17/2020] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND The lateral organ boundaries domain (LBD) gene is a plant-specific transcription factor that plays a critical role in diverse biological processes. However, the evolution and functional divergence of the LBD gene family has not yet been characterized for the Chinese White Pear. RESULTS In our study, a total of 60 PbrLBDs were identified in the pear genome. The PbrLBD gene family was divided into two classes based on gene structure and phylogenetic analysis: class I (53) and class II (7). Cis-acting element analysis results suggested that PbrLBDs may participate in various biological processes, such as flavonoid biosynthetic and stress response. Synteny analysis results indicated that segmental duplication played a key role in the expansion of the PbrLBD gene family. The mean Ks and 4DTv values showed that the PbrLBD gene family had undergone only one recent whole-genome duplication event occurring at 30-45 MYA. Purifying selection was a primary force during the PbrLBD gene family evolution process. Transcriptome data analysis revealed that 10 PbrLBDs were expressed in all six examined tissues, and 73.33% of members in the PbrLBD gene family were expressed in pear sepal. qRT-PCR was conducted to verify the expression levels of 11 PbrLBDs in these six tissues. Specifically, PbrLBD20, PbrLBD35 and PbrLBD53 genes were down-regulated when anthocyanin concentrations were high, whereas PbrLBD33 was significantly up-regulated in pear when anthocyanin concentrations were high. Furthermore, PbrLBD20, one of the candidate genes related to anthocyanins was localized in the nucleus. CONCLUSIONS Our analysis provides valuable information for understanding the evolution of the PbrLBD gene family, and provides new insights into the regulation of pear pigment metabolism and lays a foundation for the future disclosure of the molecular mechanism of LBD gene regulating flavonoid metabolism.
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Affiliation(s)
- Bobo Song
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zikai Tang
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaolong Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jiaming Li
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mingyue Zhang
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kejiao Zhao
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hainan Liu
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shaoling Zhang
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jun Wu
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
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31
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Huang X, Wu C, Gong K, Chen Q, Gu Q, Qin H, Zhao C, Yu T, Yang L, Fu W, Wang Y, Qin Q, Liu S. Sox Gene Family Revealed Genetic Variations in Autotetraploid Carassius auratus. Front Genet 2020; 11:804. [PMID: 32849805 PMCID: PMC7399338 DOI: 10.3389/fgene.2020.00804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/06/2020] [Indexed: 11/29/2022] Open
Abstract
The Sox gene family encoded transcription factors that played key roles in developmental processes in vertebrates. To further understand the evolutionary fate of the Sox gene family in teleosts, the Sox genes were comprehensively characterized in fish of different ploidy levels, including blunt snout bream (2n = 48, Megalobrama amblycephala, BSB), goldfish (2n = 100, Carassius auratus red var., 2nRCC), and autotetraploid C. auratus (4n = 200, 4nRCC). The 4nRCC, which derived from the whole genome duplication (WGD) of 2nRCC, were obtained through the distant hybridization of 2nRCC (♀) × BSB (♂). Compared with the 26 Sox genes in zebrafish (2n = 50, Danio rerio), 26, 47, and 92 putative Sox genes were identified in the BSB, 2nRCC, and 4nRCC genomes, respectively, and classified into seven subfamilies (B1, B2, C, D, E, F, and K). Comparative analyses showed that 89.36% (42/47) of Sox genes were duplicated in 2nRCC compared with those in BSB, while 97.83% (90/92) of Sox genes were duplicated in 4nRCC compared with those in 2nRCC, meaning the Sox gene family had undergone an expansion in BSB, 2nRCC, and 4nRCC, respectively, following polyploidization events. In addition, potential gene loss, genetic variations, and paternal parent SNP locus insertion occurred during the polyploidization events. Our data provided new insights into the evolution of the Sox gene family in polyploid vertebrates after several rounds of WGD events.
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Affiliation(s)
- Xu Huang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Chang Wu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Kaijun Gong
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Qian Chen
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Qianhong Gu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Huan Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Chun Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Tingting Yu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Li Yang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Wen Fu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Yude Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Qinbo Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
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Seven M, Akdemir H. DOF, MYB and TCP transcription factors: Their possible roles on barley germination and seedling establishment. Gene Expr Patterns 2020; 37:119116. [PMID: 32603687 DOI: 10.1016/j.gep.2020.119116] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 05/03/2020] [Indexed: 12/28/2022]
Abstract
Seed germination is a multi-staged complex process during seed plant life cycle, and it is tightly regulated through a coordinated expression of diverse genes in diverse tissues. As regulatory molecules of gene expression, determination of transcription factors is crucial to understanding molecular basis and regulatory network of germination process and seedling establishment. However, limited data on the contributions of these transcription factors to the germination of crop barley (Hordeum vulgare L.) are available. Here, we investigated the expression profiles of selected transcription factors from different families (DOF, MYB and TCP) with qRT-PCR analysis in various tissues including coleoptiles, leaves and roots following the germination. Analysis of MYB and DOF gene expression profiles indicated that there were differing expressions in different aged tissues, HvMYB5 and HvDOF2 being the most outstanding one in the oldest tissue, 15-day-old root. On the other hand, investigated TCP genes were lowly expressed compared to selected MYB and DOF genes, except HvTCP3, where the highest expression was observed in 15-day-old root tissue. The obtained expression profiles illustrate the importance of potential regulatory roles of transcription factors in early developmental stages of barley germination and seedling establishment.
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Affiliation(s)
- Merve Seven
- Yeditepe University, Department of Genetics and Bioengineering, 34755, Istanbul, Turkey
| | - Hulya Akdemir
- Gebze Technical University, Faculty of Science, Department of Molecular Biology and Genetics, 41400, Kocaeli, Turkey.
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33
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He J, He X, Chang P, Jiang H, Gong D, Sun Q. Genome-wide identification and characterization of TCP family genes in Brassica juncea var. tumida. PeerJ 2020; 8:e9130. [PMID: 32461831 PMCID: PMC7231505 DOI: 10.7717/peerj.9130] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 04/14/2020] [Indexed: 01/28/2023] Open
Abstract
Background Teosinte branched1/Cycloidea/proliferating cell factors (TCPs) are plant-specific transcription factors widely involved in leaf development, flowering, shoot branching, the circadian rhythm, hormone signaling, and stress responses. However, the TCP function in Brassica juncea var. tumida, the tumorous stem mustard, has not yet been reported. This study identified and characterized the entire TCP family members in B. juncea var. tumida. Methods We identified 62 BjTCP genes from the B. juncea var. tumida genome and analyzed their phylogenetic relationship, gene structure, protein motifs, chromosome location, and expression profile in different tissues. Results Of the 62 BjTCP genes we identified in B. juncea var. tumida, containing 34 class I and 28 class II subfamily members, 61 were distributed on 18 chromosomes. Gene structure and conserved motif analysis showed that the same clade genes displayed a similar exon/intron gene structure and conserved motifs. Cis-acting element results showed that the same clade genes also had a similar cis-acting element; however, subtle differences implied a different regulatory pathway. The BjTCP18s members were low-expressed in Dayejie strains and the unswelling stage of Yonganxiaoye strains. Treatment with gibberellin (GA) and salicylic acid (SA) showed that GA and SA affect the expression levels of multiple TCP genes. Conclusion We performed the first genome-wide analysis of the TCP gene family of B. juncea var. tumida. Our results have provided valuable information for understanding the classification and functions of TCP genes in B. juncea var. tumida.
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Affiliation(s)
- Jing He
- Chongqing University of Posts and Telecommunications, College of Bioinformation, Chongqing Key Laboratory of Big Data for Bio Intelligence, ChongQing, China
| | - Xiaohong He
- Chongqing University of Posts and Telecommunications, College of Bioinformation, Chongqing Key Laboratory of Big Data for Bio Intelligence, ChongQing, China
| | - Pingan Chang
- Chongqing University of Posts and Telecommunications, College of Bioinformation, Chongqing Key Laboratory of Big Data for Bio Intelligence, ChongQing, China
| | - Huaizhong Jiang
- Chongqing University of Posts and Telecommunications, College of Bioinformation, Chongqing Key Laboratory of Big Data for Bio Intelligence, ChongQing, China
| | - Daping Gong
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Quan Sun
- Chongqing University of Posts and Telecommunications, College of Bioinformation, Chongqing Key Laboratory of Big Data for Bio Intelligence, ChongQing, China
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Lu Q, Guo F, Xu Q, Cang J. LncRNA improves cold resistance of winter wheat by interacting with miR398. FUNCTIONAL PLANT BIOLOGY : FPB 2020; 47:544-557. [PMID: 32345432 DOI: 10.1071/fp19267] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/21/2019] [Indexed: 05/26/2023]
Abstract
One of the important functions of long non-coding RNA (lncRNA) is to be competing endogenous RNAs (ceRNAs). As miR398 is reported to respond to different stressors, it is necessary to explore its relationship with lncRNA in the cold resistance mechanism of winter wheat. Tae-miR398-precursor sequence was isolated from the winter wheat (Triticum aestivum). RLM-RACE verified that tae-miR398 cleaved its target CSD1. Quantitative detection at 5°C, -10°C and -25°C showed that the expression of tae-miR398 decreased in response to low temperatures, whereas CSD1 showed an opposite expression pattern. LncR9A, lncR117 and lncR616 were predicted and verified to interact with miR398. tae-miR398 and three lncRNAs were transferred into Arabidopsis thaliana respectively. The lncR9A were transferred into Brachypodium distachyom. Transgenic plants were cultivated at -8°C and assessed for the expression of malondialdehyde, chlorophyll, superoxide dismutase and miR398-lncRNA-target mRNA. The results demonstrate that tae-miR398 regulates low temperature tolerance by downregulating its target, CSD1. lncRNA regulates the expression of CSD1 indirectly by competitively binding miR398, which, in turn, affects the resistance of Dn1 to cold. miR398-regulation triggers a regulatory loop that is critical to cold stress tolerance in wheat. Our findings offer an improved strategy to crop plants with enhanced stress tolerance.
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Affiliation(s)
- Qiuwei Lu
- College of Life Science, Northeast Agricultural University, Harbin 15000, Heilongjiang, China
| | - Fuye Guo
- College of Life Science, Northeast Agricultural University, Harbin 15000, Heilongjiang, China
| | - Qinghua Xu
- College of Life Science, Northeast Agricultural University, Harbin 15000, Heilongjiang, China; and Corresponding authors. ;
| | - Jing Cang
- College of Life Science, Northeast Agricultural University, Harbin 15000, Heilongjiang, China; and Corresponding authors. ;
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35
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Molecular characterization of teosinte branched1 gene governing branching architecture in cultivated maize and wild relatives. 3 Biotech 2020; 10:77. [PMID: 32058540 DOI: 10.1007/s13205-020-2052-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 01/03/2020] [Indexed: 10/25/2022] Open
Abstract
We sequenced the entire tb1 gene in six maize inbreds and its wild relatives (parviglumis, mexicana, perennis and luxurians) to characterize it at molecular level. Hopscotch and Tourist transposable elements were observed in the upstream of tb1 in all maize inbreds, while they were absent in wild relatives. In maize, tb1 consisted of 431-443 bp 5'UTR, 1101 bp coding sequence and 211-219 bp 3'UTR. In promoter region, mutations in the light response element in mexicana (~ 35 bp and ~ 55 bp upstream of TSS) and perennis (at ~ 35 bp upstream of TSS) were found. A 6 bp insertion at 420 bp downstream of the polyA signal site was present among teosinte accessions, while it was not observed in maize. A codominant marker flanking the 6 bp InDel was developed, and it differentiated the teosintes from maize. In Tb1 protein, alanine (12.7-14.6%) was the most abundant amino acid with tryptophan as the rarest (0.5-0.9%). The molecular weight of Tb1 protein was 38757.15 g/mol except 'Palomero Toluqueno' and HKI1128. R and TCP motifs in Tb1 protein were highly conserved across maize, teosinte and orthologues, while TCP domain differed for tb1 paralogue. Tb1 possessed important role in light-, auxin-, stress-response and meristem identity maintenance. Presence of molecular signal suggested its localization in mitochondria, nucleus and nucleolus. Parviglumis and mexicana shared closer relationship with maize than perennis and luxurians. A highly conserved 59-60 amino acids long bHLH region was observed across genotypes. Information generated here assumes significance in evolution of tb1 gene and breeding for enhancement of prolificacy in maize.
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Liu MM, Wang MM, Yang J, Wen J, Guo PC, Wu YW, Ke YZ, Li PF, Li JN, Du H. Evolutionary and Comparative Expression Analyses of TCP Transcription Factor Gene Family in Land Plants. Int J Mol Sci 2019; 20:E3591. [PMID: 31340456 PMCID: PMC6679135 DOI: 10.3390/ijms20143591] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/15/2019] [Accepted: 07/19/2019] [Indexed: 01/01/2023] Open
Abstract
The plant-specific Teosinte-branched 1/Cycloidea/Proliferating (TCP) transcription factor genes are involved in plants' development, hormonal pathways, and stress response but their evolutionary history is uncertain. The genome-wide analysis performed here for 47 plant species revealed 535 TCP candidates in terrestrial plants and none in aquatic plants, and that TCP family genes originated early in the history of land plants. Phylogenetic analysis divided the candidate genes into Classes I and II, and Class II was further divided into CYCLOIDEA (CYC) and CINCINNATA (CIN) clades; CYC is more recent and originated from CIN in angiosperms. Protein architecture, intron pattern, and sequence characteristics were conserved in each class or clade supporting this classification. The two classes significantly expanded through whole-genome duplication during evolution. Expression analysis revealed the conserved expression of TCP genes from lower to higher plants. The expression patterns of Class I and CIN genes in different stages of the same tissue revealed their function in plant development and their opposite effects in the same biological process. Interaction network analysis showed that TCP proteins tend to form protein complexes, and their interaction networks were conserved during evolution. These results contribute to further functional studies on TCP family genes.
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Affiliation(s)
- Ming-Ming Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Mang-Mang Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Jin Yang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Jing Wen
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Peng-Cheng Guo
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Yun-Wen Wu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Yun-Zhuo Ke
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Peng-Feng Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Jia-Na Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Hai Du
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China.
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Genome-Wide Analysis of TCP Family Genes in Zea mays L. Identified a Role for ZmTCP42 in Drought Tolerance. Int J Mol Sci 2019; 20:ijms20112762. [PMID: 31195663 PMCID: PMC6600213 DOI: 10.3390/ijms20112762] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/03/2019] [Accepted: 06/04/2019] [Indexed: 11/26/2022] Open
Abstract
The Teosinte-branched 1/Cycloidea/Proliferating (TCP) plant-specific transcription factors (TFs) have been demonstrated to play a fundamental role in plant development and organ patterning. However, it remains unknown whether or not the TCP gene family plays a role in conferring a tolerance to drought stress in maize, which is a major constraint to maize production. In this study, we identified 46 ZmTCP genes in the maize genome and systematically analyzed their phylogenetic relationships and synteny with rice, sorghum, and ArabidopsisTCP genes. Expression analysis of the 46 ZmTCP genes in different tissues and under drought conditions, suggests their involvement in maize response to drought stress. Importantly, genetic variations in ZmTCP32 and ZmTCP42 are significantly associated with drought tolerance at the seedling stage. RT-qPCR results suggest that ZmTCP32 and ZmTCP42 RNA levels are both induced by ABA, drought, and polyethylene glycol treatments. Based on the significant association between the genetic variation of ZmTCP42 and drought tolerance, and the inducible expression of ZmTCP42 by drought stress, we selected ZmTCP42, to investigate its function in drought response. We found that overexpression of ZmTCP42 in Arabidopsis led to a hypersensitivity to ABA in seed germination and enhanced drought tolerance, validating its function in drought tolerance. These results suggested that ZmTCP42 functions as an important TCP TF in maize, which plays a positive role in drought tolerance.
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Characteristics and Expression Analysis of FmTCP15 under Abiotic Stresses and Hormones and Interact with DELLA Protein in Fraxinus mandshurica Rupr. FORESTS 2019. [DOI: 10.3390/f10040343] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The TEOSINTE BRANCHED1, CYCLOIDEA, and PROLIFERATION CELL FACTOR (TCP) transcription factor is a plant-specific gene family and acts on multiple functional genes in controlling growth, development, stress response, and the circadian clock. In this study, a class I member of the TCP family from Fraxinus mandshurica Rupr. was isolated and named FmTCP15, which encoded a protein of 362 amino acids. Protein structures were analyzed and five ligand binding sites were predicted. The phylogenetic relationship showed that FmTCP15 was most closely related to Solanaceae and Plantaginaceae. FmTCP15 was localized in the nuclei of F. mandshurica protoplast cells and highly expressed in cotyledons. The expression pattern revealed the FmTCP15 response to multiple abiotic stresses and hormone signals. Downstream genes for transient overexpression of FmTCP15 in seedlings were also investigated. A yeast two-hybrid assay confirmed that FmTCP15 could interact with DELLA proteins. FmTCP15 participated in the GA-signaling pathway, responded to abiotic stresses and hormone signals, and regulated multiple genes in these biological processes. Our study revealed the potential value of FmTCP15 for understanding the molecular mechanisms of stress and hormone signal responses.
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