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Zhang K, Wang X, Chen X, Zhang R, Guo J, Wang Q, Li D, Shao L, Shi X, Han J, Liu Z, Xia Y, Zhang J. Establishment of a Homologous Silencing System with Intact-Plant Infiltration and Minimized Operation for Studying Gene Function in Herbaceous Peonies. Int J Mol Sci 2024; 25:4412. [PMID: 38673996 PMCID: PMC11050706 DOI: 10.3390/ijms25084412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/04/2024] [Accepted: 04/13/2024] [Indexed: 04/28/2024] Open
Abstract
Gene function verification is a crucial step in studying the molecular mechanisms regulating various plant life activities. However, a stable and efficient homologous genetic transgenic system for herbaceous peonies has not been established. In this study, using virus-induced gene silencing technology (VIGS), a highly efficient homologous transient verification system with distinctive advantages was proposed, which not only achieves true "intact-plant" infiltration but also minimizes the operation. One-year-old roots of the representative species, Paeonia lactiflora Pall., were used as the materials; prechilling (4 °C) treatment for 3-5 weeks was applied as a critical precondition for P. lactiflora to acquire a certain chilling accumulation. A dormancy-related gene named HOMEOBOX PROTEIN 31 (PlHB31), believed to negatively regulate bud endodormancy release (BER), was chosen as the target gene in this study. GFP fluorescence was detected in directly infiltrated and newly developed roots and buds; the transgenic plantlets exhibited remarkably earlier budbreak, and PlHB31 was significantly downregulated in silenced plantlets. This study established a homologous transient silencing system featuring intact-plant infiltration and minimized manipulation for gene function research, and also offers technical support and serves as a theoretical basis for gene function discovery in numerous other geophytes.
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Affiliation(s)
- Kaijing Zhang
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, Institute of Landscape Architecture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (K.Z.); (X.W.); (X.C.); (R.Z.); (J.G.); (Q.W.); (D.L.); (L.S.); (J.H.); (Y.X.)
| | - Xiaobin Wang
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, Institute of Landscape Architecture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (K.Z.); (X.W.); (X.C.); (R.Z.); (J.G.); (Q.W.); (D.L.); (L.S.); (J.H.); (Y.X.)
| | - Xiaoxuan Chen
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, Institute of Landscape Architecture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (K.Z.); (X.W.); (X.C.); (R.Z.); (J.G.); (Q.W.); (D.L.); (L.S.); (J.H.); (Y.X.)
| | - Runlong Zhang
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, Institute of Landscape Architecture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (K.Z.); (X.W.); (X.C.); (R.Z.); (J.G.); (Q.W.); (D.L.); (L.S.); (J.H.); (Y.X.)
| | - Junhong Guo
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, Institute of Landscape Architecture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (K.Z.); (X.W.); (X.C.); (R.Z.); (J.G.); (Q.W.); (D.L.); (L.S.); (J.H.); (Y.X.)
| | - Qiyao Wang
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, Institute of Landscape Architecture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (K.Z.); (X.W.); (X.C.); (R.Z.); (J.G.); (Q.W.); (D.L.); (L.S.); (J.H.); (Y.X.)
| | - Danqing Li
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, Institute of Landscape Architecture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (K.Z.); (X.W.); (X.C.); (R.Z.); (J.G.); (Q.W.); (D.L.); (L.S.); (J.H.); (Y.X.)
| | - Lingmei Shao
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, Institute of Landscape Architecture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (K.Z.); (X.W.); (X.C.); (R.Z.); (J.G.); (Q.W.); (D.L.); (L.S.); (J.H.); (Y.X.)
| | - Xiaohua Shi
- Zhejiang Institute of Landscape Plants and Flowers, Hangzhou 311251, China;
| | - Jingtong Han
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, Institute of Landscape Architecture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (K.Z.); (X.W.); (X.C.); (R.Z.); (J.G.); (Q.W.); (D.L.); (L.S.); (J.H.); (Y.X.)
| | - Zhiyang Liu
- Harbin Academy of Agricultural Sciences, Harbin 150029, China;
| | - Yiping Xia
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, Institute of Landscape Architecture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (K.Z.); (X.W.); (X.C.); (R.Z.); (J.G.); (Q.W.); (D.L.); (L.S.); (J.H.); (Y.X.)
| | - Jiaping Zhang
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, Institute of Landscape Architecture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (K.Z.); (X.W.); (X.C.); (R.Z.); (J.G.); (Q.W.); (D.L.); (L.S.); (J.H.); (Y.X.)
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Kong H, Hou M, Ma B, Xie Z, Wang J, Zhu X. Calcium-dependent protein kinase GhCDPK4 plays a role in drought and abscisic acid stress responses. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 332:111704. [PMID: 37037298 DOI: 10.1016/j.plantsci.2023.111704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 04/02/2023] [Accepted: 04/05/2023] [Indexed: 05/27/2023]
Abstract
Drought is an important factor limiting the yield and quality of cotton. In the present study, the gene encoding the cotton calcium-dependent protein kinase GhCDPK4 was identified and characterized in the transcriptome of cotton under PEG-induced drought stress. In RT-qPCR experiments, GhCDPK4 expression was found to be up-regulated under drought and abscisic acid (ABA) stress. Under drought conditions, heterologous overexpression of GhCDPK4 in tobacco showed a better phenotypic status, higher antioxidant enzyme activity, and lower relative electrolyte leakage (REL) and malondialdehyde (MDA) content. Meanwhile, ghcdpk4-silenced cotton plants, which were extremely sensitive to drought, exhibited higher levels of O2-,H2O2, and MDA contents compared to the control. Meanwhile, silenced lines showed impaired stomatal closure under drought stress, resulting in increased water loss from transpiration in silenced lines. GhCDPK4 expression was induced by ABA, and there are five ABA-responsive elements in its promoter. and C2-DOMAIN ABA-RELATED 4(CAR4, Gh_D09G1653) were found to interact and be co-expressed in the GhCDPK4 interaction network. Therefore, GhCDPK4 may reduce the extent of water loss and oxidative damage in cotton under drought by positively regulating ABA-controlled stomatal closure and reactive oxygen species (ROS) scavenging systems. This study demonstrates the great potential of GhCDPK4 in improving drought resistance in crops.
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Affiliation(s)
- Hui Kong
- Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-basin System Ecology, College of Life Science, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Mengjuan Hou
- Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-basin System Ecology, College of Life Science, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Bin Ma
- Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-basin System Ecology, College of Life Science, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Zhaosong Xie
- Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-basin System Ecology, College of Life Science, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Jiameng Wang
- Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-basin System Ecology, College of Life Science, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Xinxia Zhu
- Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-basin System Ecology, College of Life Science, Shihezi University, Shihezi, Xinjiang 832003, China.
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Zhang YS, Xu Y, Xing WT, Wu B, Huang DM, Ma FN, Zhan RL, Sun PG, Xu YY, Song S. Identification of the passion fruit ( Passiflora edulis Sims) MYB family in fruit development and abiotic stress, and functional analysis of PeMYB87 in abiotic stresses. FRONTIERS IN PLANT SCIENCE 2023; 14:1124351. [PMID: 37215287 PMCID: PMC10196401 DOI: 10.3389/fpls.2023.1124351] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/21/2023] [Indexed: 05/24/2023]
Abstract
Environmental stresses are ubiquitous in agricultural cultivation, and they affect the healthy growth and development of edible tissues in passion fruit. The study of resistance mechanisms is important in understanding the adaptation and resistance of plants to environmental stresses. In this work, two differently resistant passion fruit varieties were selected, using the expression characteristics of the transcription factor MYB, to explore the resistance mechanism of the MYB gene under various environmental stresses. A total of 174 MYB family members were identified using high-quality passion fruit genomes: 98 2R-MYB, 5 3R-MYB, and 71 1R-MYB (MYB-relate). Their family information was systematically analyzed, including subcellular localization, physicochemical properties, phylogeny at the genomic level, promoter function, encoded proteins, and reciprocal regulation. In this study, bioinformatics and transcriptome sequencing were used to identify members of the PeMYB genes in passion fruit whole-genome data, and biological techniques, such as qPCR, gene clone, and transient transformation of yeast, were used to determine the function of the passion fruit MYB genes in abiotic stress tolerance. Transcriptomic data were obtained for differential expression characteristics of two resistant and susceptible varieties, three expression patterns during pulp development, and four induced expression patterns under abiotic stress conditions. We further focused on the resistance mechanism of PeMYB87 in environmental stress, and we selected 10 representative PeMYB genes for quantitative expression verification. Most of the genes were differentially induced by four abiotic stresses, among which PeMYB87 responded significantly to high-temperature-induced expression and overexpression of the PeMYB87 gene in the yeast system. The transgenic PeMYB87 in yeast showed different degrees of stress resistance under exposure to cold, high temperatures, drought, and salt stresses. These findings lay the foundation for further analysis of the biological functions of PeMYBs involved in stress resistance in passion fruit.
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Affiliation(s)
- Yan-shu Zhang
- National Key Laboratory for Tropical Crop Breeding, Haikou Experimental Station, Tropical Crops Genetic Resources Institute, CATAS/ Germplasm Repository of Passiflora, Haikou, Hainan, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
- College of Landscape and Horticulture, Southwest Forestry University, Kunming, Yunnan, China
| | - Yi Xu
- National Key Laboratory for Tropical Crop Breeding, Haikou Experimental Station, Tropical Crops Genetic Resources Institute, CATAS/ Germplasm Repository of Passiflora, Haikou, Hainan, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
| | - Wen-ting Xing
- National Key Laboratory for Tropical Crop Breeding, Haikou Experimental Station, Tropical Crops Genetic Resources Institute, CATAS/ Germplasm Repository of Passiflora, Haikou, Hainan, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
| | - Bin Wu
- National Key Laboratory for Tropical Crop Breeding, Haikou Experimental Station, Tropical Crops Genetic Resources Institute, CATAS/ Germplasm Repository of Passiflora, Haikou, Hainan, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
| | - Dong-mei Huang
- National Key Laboratory for Tropical Crop Breeding, Haikou Experimental Station, Tropical Crops Genetic Resources Institute, CATAS/ Germplasm Repository of Passiflora, Haikou, Hainan, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
| | - Fu-ning Ma
- National Key Laboratory for Tropical Crop Breeding, Haikou Experimental Station, Tropical Crops Genetic Resources Institute, CATAS/ Germplasm Repository of Passiflora, Haikou, Hainan, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
| | - Ru-lin Zhan
- National Key Laboratory for Tropical Crop Breeding, Haikou Experimental Station, Tropical Crops Genetic Resources Institute, CATAS/ Germplasm Repository of Passiflora, Haikou, Hainan, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
| | - Pei-guang Sun
- National Key Laboratory for Tropical Crop Breeding, Haikou Experimental Station, Tropical Crops Genetic Resources Institute, CATAS/ Germplasm Repository of Passiflora, Haikou, Hainan, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
| | - Yong-yan Xu
- College of Landscape and Horticulture, Southwest Forestry University, Kunming, Yunnan, China
| | - Shun Song
- National Key Laboratory for Tropical Crop Breeding, Haikou Experimental Station, Tropical Crops Genetic Resources Institute, CATAS/ Germplasm Repository of Passiflora, Haikou, Hainan, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
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Liu H, Du B, Ma X, Wang Y, Cheng N, Zhang Y. Overexpression of major latex protein 423 (NtMLP423) enhances the chilling stress tolerance in Nicotiana tabacum. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 329:111604. [PMID: 36709884 DOI: 10.1016/j.plantsci.2023.111604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/19/2023] [Accepted: 01/21/2023] [Indexed: 06/18/2023]
Abstract
Chilling stress impedes plant growth and hinders crop development and productivity. In this study, we identified the major latex protein (MLP) in tobacco (NtMLP423) and examined its roles in chilling resistance. NtMLP423 expression was considerably upregulated in response to chilling stress. NtMLP423 function was assessed and compared in plants with overexpression and antisense characteristics. Under chilling stress, plants with overexpression characteristics grew better than wild-type and antisense plants. NtMLP423 overexpression reduced membrane lipid damage, increased antioxidant enzyme activity, and reduced reactive oxygen species (ROS) accumulation under chilling stress. Here, we screened for the first time the upstream transcription factor NtMYB108, which regulates NtMLP423 expression under chilling stress. The NtMYB108 transcription factor directly binds to the NtMLP423 promoter and improves NtMLP423 resistance to chilling stress. Subjecting NtMYB018 to virus-induced gene silencing reduced chilling stress tolerance. Overall, NtMLP423 overexpression enhances chilling stress tolerance, while its suppression has the opposite effect.
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Affiliation(s)
- Heng Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, PR China; Linyi University, Linyi 276005, Shandong, PR China
| | - Bingyang Du
- State Key Laboratories of Agrobiotechnology, Department of Pomology, College of Horticulture, China Agricultural University, Beijing 100193, PR China
| | - Xiaocen Ma
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, PR China
| | - Yong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, PR China
| | - Nini Cheng
- Linyi University, Linyi 276005, Shandong, PR China.
| | - Yuanhu Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, PR China.
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Establishment of a Virus-Induced Gene-Silencing (VIGS) System in Tea Plant and Its Use in the Functional Analysis of CsTCS1. Int J Mol Sci 2022; 24:ijms24010392. [PMID: 36613837 PMCID: PMC9820744 DOI: 10.3390/ijms24010392] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 12/09/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
Tea (Camellia sinensis [L.] O. Kuntze) is an important global economic crop and is considered to enhance health. However, the functions of many genes in tea plants are unknown. Virus-induced gene silencing (VIGS) mediated by tobacco rattle virus (TRV) is an effective tool for the analysis of gene functions, although this method has rarely been reported in tea plants. In this study, we established an effective VIGS-mediated gene knockout technology to understand the functional identification of large-scale genomic sequences in tea plants. The results showed that the VIGS system was verified by detecting the virus and using a real-time quantitative reverse transcription PCR (qRT-PCR) analysis. The reporter gene CsPOR1 (protochlorophyllide oxidoreductase) was silenced using the vacuum infiltration method, and typical photobleaching and albino symptoms were observed in newly sprouted leaves at the whole plant level of tea after infection for 12 d and 25 d. After optimization, the VIGS system was successfully used to silence the tea plant CsTCS1 (caffeine synthase) gene. The results showed that the relative caffeine content was reduced 6.26-fold compared with the control, and the level of expression of CsPOR1 decreased by approximately 3.12-fold in plants in which CsPOR1 was silenced. These results demonstrate that VIGS can be quickly and efficiently used to analyze the function of genes in tea plants. The successful establishment of VIGS could eliminate the need for tissue culture by providing an effective method to study gene function in tea plants and accelerate the process of functional genome research in tea.
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Wu Y, Lv S, Zhao Y, Chang C, Hong W, Jiang J. SlHSP17.7 Ameliorates Chilling Stress-Induced Damage by Regulating Phosphatidylglycerol Metabolism and Calcium Signal in Tomato Plants. PLANTS (BASEL, SWITZERLAND) 2022; 11:1865. [PMID: 35890502 PMCID: PMC9324031 DOI: 10.3390/plants11141865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/08/2022] [Accepted: 07/13/2022] [Indexed: 11/16/2022]
Abstract
Tomatoes (Solanum lycopersicum L.) are sensitive to chilling temperatures between 0 °C and 12 °C owing to their tropical origin. SlHSP17.7, a cytoplasmic heat shock protein, interacts with cation/calcium exchanger 1-like (SlCCX1-like) protein and promotes chilling tolerance in tomato fruits (Zhang, et al., Plant Sci., 2020, 298, 1-12). The overexpression of SlHSP17.7 can also promote cold tolerance in tomato plants, but its specific mechanism remains unclear. In this study, we show that the overexpression of SlHSP17.7 in tomato plants enhances chilling tolerance with better activity of photosystem II (PSII). Metabolic analyses revealed that SlHSP17.7 improved membrane fluidity by raising the levels of polyunsaturated fatty acids. Transcriptome analyses showed that SlHSP17.7 activated Ca2+ signaling and induced the expression of C-repeat binding factor (CBF) genes, which in turn inhibited the production of reactive oxygen species (ROS). The gene coexpression network analysis showed that SlHSP17.7 is coexpressed with SlMED26b. SlMED26b silencing significantly lowered OE-HSP17.7 plants' chilling tolerance. Thus, SlHSP17.7 modulates tolerance to chilling via both membrane fluidity and Ca2+-mediated CBF pathway in tomato plants.
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Affiliation(s)
- Yuanyuan Wu
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Institute of Vegetable Science, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China
| | - Shuwen Lv
- Institute of Vegetable Science, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China
| | - Yaran Zhao
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Chenliang Chang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Wei Hong
- Shenyang Institute of Technology, Shenyang 113122, China
| | - Jing Jiang
- Key Laboratory of Protected Horticulture of Education Ministry, Shenyang 110866, China
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Hill MJ, Penning BW, McCann MC, Carpita NC. COMPILE: a GWAS computational pipeline for gene discovery in complex genomes. BMC PLANT BIOLOGY 2022; 22:315. [PMID: 35778686 PMCID: PMC9250234 DOI: 10.1186/s12870-022-03668-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Genome-Wide Association Studies (GWAS) are used to identify genes and alleles that contribute to quantitative traits in large and genetically diverse populations. However, traits with complex genetic architectures create an enormous computational load for discovery of candidate genes with acceptable statistical certainty. We developed a streamlined computational pipeline for GWAS (COMPILE) to accelerate identification and annotation of candidate maize genes associated with a quantitative trait, and then matches maize genes to their closest rice and Arabidopsis homologs by sequence similarity. RESULTS COMPILE executed GWAS using a Mixed Linear Model that incorporated, without compression, recent advancements in population structure control, then linked significant Quantitative Trait Loci (QTL) to candidate genes and RNA regulatory elements contained in any genome. COMPILE was validated using published data to identify QTL associated with the traits of α-tocopherol biosynthesis and flowering time, and identified published candidate genes as well as additional genes and non-coding RNAs. We then applied COMPILE to 274 genotypes of the maize Goodman Association Panel to identify candidate loci contributing to resistance of maize stems to penetration by larvae of the European Corn Borer (Ostrinia nubilalis). Candidate genes included those that encode a gene of unknown function, WRKY and MYB-like transcriptional factors, receptor-kinase signaling, riboflavin synthesis, nucleotide-sugar interconversion, and prolyl hydroxylation. Expression of the gene of unknown function has been associated with pathogen stress in maize and in rice homologs closest in sequence identity. CONCLUSIONS The relative speed of data analysis using COMPILE allowed comparison of population size and compression. Limitations in population size and diversity are major constraints for a trait and are not overcome by increasing marker density. COMPILE is customizable and is readily adaptable for application to species with robust genomic and proteome databases.
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Affiliation(s)
- Matthew J Hill
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, 47907, USA
- Present address: Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA, 02142, USA
- Present address: Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Bryan W Penning
- USDA-ARS Corn, Soybean and Wheat Quality Research Unit, Wooster, OH, 44691, USA
| | - Maureen C McCann
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907, USA
- Present address: Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Nicholas C Carpita
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, 47907, USA.
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907, USA.
- Present address: Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA.
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Wang M, Hao J, Chen X, Zhang X. SlMYB102 expression enhances low-temperature stress resistance in tomato plants. PeerJ 2020; 8:e10059. [PMID: 33083130 PMCID: PMC7547593 DOI: 10.7717/peerj.10059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 09/07/2020] [Indexed: 01/05/2023] Open
Abstract
Herein, we identified the tomato SlMYB102 gene as a MYB family transcription factor of the R2R3-MYB subfamily. We additionally determined that the SlMYB102 promoter region contains photoresponsive, abiotic stress-responsive, and hormone-responsive regulatory elements, and we detected higher SlMYB102 expression in the reproductive organs of tomato than that in vegetative organs, with the expression being highest in ripe fruits and in roots. SlMYB102 expression was also shown to be cold-inducible. The protein encoded by SlMYB102 localized to the nucleus wherein it was found to mediate the transcriptional activation of target genes through its C-terminal domain. Overexpression of SlMYB102 in tomato plants conferred enhanced tolerance to cold stress. Under such cold stress conditions, we found that proline levels in the leaves of SlMYB102 overexpressing transgenic plants were higher than those in WT plants. In addition, S1MYB102 overexpression was associated with the enhanced expression of cold response genes including SlCBF1, SlCBF3, SlDREB1, SlDEB2, and SlICE1. We also found that the overexpression of SlMYB102 further enhanced the cold-induced upregulation of SlP5CS and SlAPX2. Taken together, these results suggest that SlMYB102 may be involved in the C-repeat binding transcription factor (CBF) and proline synthesis pathways, thereby improving tomato plant cold resistance.
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Affiliation(s)
- Meiling Wang
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Juan Hao
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Xiuhua Chen
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Xichun Zhang
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
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Wang M, Hao J, Chen X, Zhang X. SlMYB102 expression enhances low-temperature stress resistance in tomato plants. PeerJ 2020; 8:e10059. [PMID: 33083130 DOI: 10.7717/peerj.10059/supp-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 09/07/2020] [Indexed: 05/27/2023] Open
Abstract
Herein, we identified the tomato SlMYB102 gene as a MYB family transcription factor of the R2R3-MYB subfamily. We additionally determined that the SlMYB102 promoter region contains photoresponsive, abiotic stress-responsive, and hormone-responsive regulatory elements, and we detected higher SlMYB102 expression in the reproductive organs of tomato than that in vegetative organs, with the expression being highest in ripe fruits and in roots. SlMYB102 expression was also shown to be cold-inducible. The protein encoded by SlMYB102 localized to the nucleus wherein it was found to mediate the transcriptional activation of target genes through its C-terminal domain. Overexpression of SlMYB102 in tomato plants conferred enhanced tolerance to cold stress. Under such cold stress conditions, we found that proline levels in the leaves of SlMYB102 overexpressing transgenic plants were higher than those in WT plants. In addition, S1MYB102 overexpression was associated with the enhanced expression of cold response genes including SlCBF1, SlCBF3, SlDREB1, SlDEB2, and SlICE1. We also found that the overexpression of SlMYB102 further enhanced the cold-induced upregulation of SlP5CS and SlAPX2. Taken together, these results suggest that SlMYB102 may be involved in the C-repeat binding transcription factor (CBF) and proline synthesis pathways, thereby improving tomato plant cold resistance.
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Affiliation(s)
- Meiling Wang
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Juan Hao
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Xiuhua Chen
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Xichun Zhang
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
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