1
|
Wang L, Shi W, Aziz A, Wang X, Liu H, Shen W, Cui H, Dai Z. Mutating the arginine residue within the FRNK motif of telosma mosaic virus (TelMV) HC-Pro protein attenuates viral infection and confers effective protection against TelMV in passion fruit (Passiflora edulis). PEST MANAGEMENT SCIENCE 2024. [PMID: 38895838 DOI: 10.1002/ps.8252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/23/2024] [Accepted: 06/04/2024] [Indexed: 06/21/2024]
Abstract
BACKGROUND Telosma mosaic virus (TelMV, Potyvirus, Potyviridae) is an emerging viral pathogen that threatens passion fruit plantations worldwide. However, an efficient strategy for controlling such a virus is not yet available. Cross protection is a phenomenon in which pre-infection of a plant with one mild strain prevents or delays subsequent infection by the same or closely related virus. HC-Pro is the potyviral encoded multifunctional protein involved in several steps of viral infection, including multiplication, movement, transmission and RNA silencing suppression. In this study, we tested whether it is possible to generate attenuated viral strains capable of conferring protection against severe TelMV infection by manipulating the HC-Pro gene. RESULTS By introducing point mutation into the conserved motif FRNK of HC-Pro that is essential for RNA silencing suppression, we have successfully obtained three attenuated mutants of TelMV (R181K, R181D, and R181E, respectively). These attenuated TelMV mutants could systemically infect passion fruit plants without noticeable symptoms. Pre-inoculation of one of these attenuated mutants confers efficient protection against subsequent infection by severe TelMV strain. Moreover, we demonstrated that the HC-Pros harbored by the attenuated mutants exhibit reduced RNA silencing suppression activity in Nicotiana benthamiana leaves. CONCLUSION The attenuated TelMV mutants developed in this study that are suitable for cross protection offer a practical, powerful tool to fight against TelMV for sustainable passion fruit production. © 2024 Society of Chemical Industry.
Collapse
Affiliation(s)
- Linxi Wang
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Ministry of Education), School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Wei Shi
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Ministry of Education), School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Asma Aziz
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Ministry of Education), School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Xiaoqing Wang
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Ministry of Education), School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Haobin Liu
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Ministry of Education), School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Wentao Shen
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Hongguang Cui
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Ministry of Education), School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Zhaoji Dai
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Ministry of Education), School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| |
Collapse
|
2
|
Sun H, Li C, Li S, Ma J, Li S, Li X, Gao C, Yang R, Ma N, Yang J, Yang P, He X, Hu T. Identification and validation of stable reference genes for RT-qPCR analyses of Kobresia littledalei seedlings. BMC PLANT BIOLOGY 2024; 24:389. [PMID: 38730341 PMCID: PMC11088182 DOI: 10.1186/s12870-024-04924-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 03/18/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND Kobreisa littledalei, belonging to the Cyperaceae family is the first Kobresia species with a reference genome and the most dominant species in Qinghai-Tibet Plateau alpine meadows. It has several resistance genes which could be used to breed improved crop varieties. Reverse Transcription Quantitative Real-Time Polymerase Chain Reaction (RT-qPCR) is a popular and accurate gene expression analysis method. Its reliability depends on the expression levels of reference genes, which vary by species, tissues and environments. However, K.littledalei lacks a stable and normalized reference gene for RT-qPCR analysis. RESULTS The stability of 13 potential reference genes was tested and the stable reference genes were selected for RT-qPCR normalization for the expression analysis in the different tissues of K. littledalei under two abiotic stresses (salt and drought) and two hormonal treatments (abscisic acid (ABA) and gibberellin (GA)). Five algorithms were used to assess the stability of putative reference genes. The results showed a variation amongst the methods, and the same reference genes showed tissue expression differences under the same conditions. The stability of combining two reference genes was better than a single one. The expression levels of ACTIN were stable in leaves and stems under normal conditions, in leaves under drought stress and in roots under ABA treatment. The expression of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) expression was stable in the roots under the control conditions and salt stress and in stems exposed to drought stress. Expression levels of superoxide dismutase (SOD) were stable in stems of ABA-treated plants and in the roots under drought stress. Moreover, RPL6 expression was stable in the leaves and stems under salt stress and in the stems of the GA-treated plants. EF1-alpha expression was stable in leaves under ABA and GA treatments. The expression levels of 28 S were stable in the roots under GA treatment. In general, ACTIN and GAPDH could be employed as housekeeping genes for K. littledalei under different treatments. CONCLUSION This study identified the best RT-qPCR reference genes for different K. littledalei tissues under five experimental conditions. ACTIN and GAPDH genes can be employed as the ideal housekeeping genes for expression analysis under different conditions. This is the first study to investigate the stable reference genes for normalized gene expression analysis of K. littledalei under different conditions. The results could aid molecular biology and gene function research on Kobresia and other related species.
Collapse
Affiliation(s)
- Haoyang Sun
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Chunping Li
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Siyu Li
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Jiaxin Ma
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Shuo Li
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Xin Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Cai Gao
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Rongchen Yang
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Nan Ma
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Jing Yang
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Peizhi Yang
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Xueqing He
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China.
| | - Tianming Hu
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China.
| |
Collapse
|
3
|
Ni Y, Zhang Q, Li W, Cao L, Feng R, Zhao Z, Zhao X. Selection and validation of reference genes for normalization of gene expression in Floccularia luteovirens. Fungal Biol 2024; 128:1596-1606. [PMID: 38341265 DOI: 10.1016/j.funbio.2023.12.005] [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: 09/06/2023] [Revised: 12/09/2023] [Accepted: 12/18/2023] [Indexed: 02/12/2024]
Abstract
Floccularia luteovirens is one of the rare edible fungi with high nutritional value found on the Qinghai-Tibet Plateau. However, research at the molecular level on this species is currently constrained due to the lack of reliable reference genes for this species. Thirteen potential reference genes (ACT, GAPDH, EF-Tu, SAMDC, UBI, CLN1, β-TUB, γ-TUB, GTP, H3, UBC, UBC-E2, and GTPBP1) were chosen for the present study, and their expression under various abiotic conditions was investigated. Stability of gene expression was tested using GeNorm, NormFinder, BestKeeper, Delta-Ct, and RefFinder. The results showed that the most suitable reference genes for salt treatment were ACT and EF-Tu. Under drought stress, γ-TUB and UBC-E2 would be suitable for normalization. Under oxidative stress, the reference genes H3 and GAPDH worked well. Under heat stress, the reference genes EF-Tu and γ-TUB were suggested. Under extreme pH stress, UBC-E2 and H3 were appropriate reference genes. Under cadmium stress, the reference genes ACT and UBC-E2 functioned well. In different tissues, H3 and GTPBP1 were appropriate reference genes. The optimal internal reference genes when analyzing all samples were H3 and SAMDC. The expression level of HSP90 was studied to further validate the applicability of the genes identified in this study.
Collapse
Affiliation(s)
- Yanqing Ni
- College of Food and Biological Engineering, Chengdu University, Chengdu, 610106, Sichuan, China; Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610299, Sichuan, China.
| | - Qin Zhang
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610299, Sichuan, China; Chengdu National Agricultural Science and Technology Center, Chengdu, 610299, Sichuan, China.
| | - Wensheng Li
- College of Food and Biological Engineering, Chengdu University, Chengdu, 610106, Sichuan, China; Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610299, Sichuan, China.
| | - Luping Cao
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610299, Sichuan, China; College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, Gansu, China.
| | - Rencai Feng
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610299, Sichuan, China; Chengdu National Agricultural Science and Technology Center, Chengdu, 610299, Sichuan, China.
| | - Zhiqiang Zhao
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610299, Sichuan, China; Chengdu National Agricultural Science and Technology Center, Chengdu, 610299, Sichuan, China.
| | - Xu Zhao
- College of Food and Biological Engineering, Chengdu University, Chengdu, 610106, Sichuan, China; Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610299, Sichuan, China; Chengdu National Agricultural Science and Technology Center, Chengdu, 610299, Sichuan, China.
| |
Collapse
|
4
|
Cao L, Zhang Q, Miao R, Zhao X, Ni Y, Li W, Feng R, Yang D. Reference gene selection for quantitative real-time PCR analysis of Hymenopellis radicata under abiotic stress. Fungal Biol 2024; 128:1567-1577. [PMID: 38341262 DOI: 10.1016/j.funbio.2023.11.004] [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: 08/09/2023] [Revised: 11/14/2023] [Accepted: 11/20/2023] [Indexed: 02/12/2024]
Abstract
Hymenopellis radicata (H. radicata) is an edible fungus rich in protein and mineral elements, with high edible and medical value. And reference genes suitable for normalization of qRT-PCR data from this species have not been investigated. In this study, therefore, we selected 11 housekeeping genes common in biology. The expression levels of these housekeeping genes were measured in three different tissues and six different abiotic stress treatments in mycelium. They were evaluated for expression stability using online tools. The results showed that gene ACT could be stable expressed in all samples. The expressions of genes TUB and UBQ10 are the most stable under heat stress, ACT and EF are the most stable genes under salt stress, ACT and TUB are the most stable genes under oxidation stress, RPL6 and EF are the most stable genes under pH condition, ACT and RPB2 are the most stable genes under cadmium stress, and RPB2 and UBC are the most stable genes under drought condition. ACT and PP2A are the most stable genes at different tissue sites. This study is of great help to explore the gene expression pattern of H. radicata, and also provides reference for internal reference gene screening under other conditions.
Collapse
Affiliation(s)
- Luping Cao
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, Gansu, China
| | - Qin Zhang
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610299, Sichuan, China; Chengdu National Agricultural Science and Technology Center, Chengdu 610299, Sichuan, China
| | - Renyun Miao
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610299, Sichuan, China; Chengdu National Agricultural Science and Technology Center, Chengdu 610299, Sichuan, China
| | - Xu Zhao
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610299, Sichuan, China; Chengdu National Agricultural Science and Technology Center, Chengdu 610299, Sichuan, China.
| | - Yanqing Ni
- College of Food and Biological Engineering, Chengdu University, Chengdu 610106, Sichuan, China
| | - Wensheng Li
- College of Food and Biological Engineering, Chengdu University, Chengdu 610106, Sichuan, China
| | - Rencai Feng
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610299, Sichuan, China; Chengdu National Agricultural Science and Technology Center, Chengdu 610299, Sichuan, China
| | - Delong Yang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, Gansu, China.
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Ma F, Zhou H, Yang H, Huang D, Xing W, Wu B, Li H, Hu W, Song S, Xu Y. WRKY transcription factors in passion fruit analysis reveals key PeWRKYs involved in abiotic stress and flavonoid biosynthesis. Int J Biol Macromol 2024; 256:128063. [PMID: 37963507 DOI: 10.1016/j.ijbiomac.2023.128063] [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: 08/16/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 11/16/2023]
Abstract
WRKY transcription factors (TFs) are a superfamily of regulators involved in plant responses to pathogens and abiotic stress. Passion fruit is famous for its unique flavor and nutrient-rich juice, but its growth is limited by environmental factors and pathogens. In this study, 55 WRKY genes were identified from the Passiflora edulis genome. The structure and evolutionary characteristics of PeWRKYs were analyzed using a bioinformatics approach. PeWRKYs were classified into seven subgroups (I, IIa, IIb, IIc, IId, IIe, III) according to their homologs in Arabidopsis thaliana. Group IIa PeWRKY48 gene was highly up-regulated under cold stress by RNA expression analysis, and transgenic PeWRKY48 in yeast and Arabidopsis showed resistance exposure to cold, salt, and drought stress. Metabolome and transcriptome co-expression analysis of two different disease resistance genotypes of P. edulis identified PeWRKY30 as a key TF co-expressed with flavonoid accumulation in yellow fruit P. edulis, which may contribute to biotic or abiotic resistance. The qRT-PCR verified the expression of key genes in different tissues of P. edulis and in different species of Passiflora. This study provides a set of WRKY candidate genes that will facilitate the genetic improvement of disease and abiotic tolerance in passion fruit.
Collapse
Affiliation(s)
- Funing Ma
- Tropical Crops Genetic Resources Institute, CATAS, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, National Key Laboratory for Tropical Crop Breeding, Germplasm Repository of Passiflora, Haikou 571101, China; Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, CATAS, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Hongwu Zhou
- Yunnan Agricultural University, Yunnan 650201, China
| | - Huiting Yang
- Yunnan Agricultural University, Yunnan 650201, China
| | - Dongmei Huang
- Tropical Crops Genetic Resources Institute, CATAS, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, National Key Laboratory for Tropical Crop Breeding, Germplasm Repository of Passiflora, Haikou 571101, China; Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, CATAS, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Wenting Xing
- Tropical Crops Genetic Resources Institute, CATAS, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, National Key Laboratory for Tropical Crop Breeding, Germplasm Repository of Passiflora, Haikou 571101, China; Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, CATAS, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Bin Wu
- Tropical Crops Genetic Resources Institute, CATAS, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, National Key Laboratory for Tropical Crop Breeding, Germplasm Repository of Passiflora, Haikou 571101, China; Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, CATAS, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Hongli Li
- Tropical Crops Genetic Resources Institute, CATAS, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, National Key Laboratory for Tropical Crop Breeding, Germplasm Repository of Passiflora, Haikou 571101, China; Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, CATAS, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Wenbin Hu
- Tropical Crops Genetic Resources Institute, CATAS, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, National Key Laboratory for Tropical Crop Breeding, Germplasm Repository of Passiflora, Haikou 571101, China; Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, CATAS, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Shun Song
- Tropical Crops Genetic Resources Institute, CATAS, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, National Key Laboratory for Tropical Crop Breeding, Germplasm Repository of Passiflora, Haikou 571101, China; Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, CATAS, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China.
| | - Yi Xu
- Tropical Crops Genetic Resources Institute, CATAS, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, National Key Laboratory for Tropical Crop Breeding, Germplasm Repository of Passiflora, Haikou 571101, China; Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, CATAS, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China.
| |
Collapse
|
7
|
Chen M, Wang Z, Hao Z, Li H, Feng Q, Yang X, Han X, Zhao X. Screening and Validation of Appropriate Reference Genes for Real-Time Quantitative PCR under PEG, NaCl and ZnSO 4 Treatments in Broussonetia papyrifera. Int J Mol Sci 2023; 24:15087. [PMID: 37894768 PMCID: PMC10606616 DOI: 10.3390/ijms242015087] [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: 09/12/2023] [Revised: 10/04/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023] Open
Abstract
Real-time quantitative PCR (RT-qPCR) has a high sensitivity and strong specificity, and is widely used in the analysis of gene expression. Selecting appropriate internal reference genes is the key to accurately analyzing the expression changes of target genes by RT-qPCR. To find out the most suitable internal reference genes for studying the gene expression in Broussonetia papyrifera under abiotic stresses (including drought, salt, and ZnSO4 treatments), seven different tissues of B. papyrifera, as well as the roots, stems, and leaves of B. papyrifera under the abiotic stresses were used as test materials, and 15 candidate internal reference genes were screened based on the transcriptome data via RT-qPCR. Then, the expression stability of the candidate genes was comprehensively evaluated through the software geNorm (v3.5), NormFinder (v0.953), BestKeeper (v1.0), and RefFinder. The best internal reference genes and their combinations were screened out according to the analysis results. rRNA and Actin were the best reference genes under drought stress. Under salt stress, DOUB, HSP, NADH, and rRNA were the most stable reference genes. Under heavy metal stress, HSP and NADH were the most suitable reference genes. EIF3 and Actin were the most suitable internal reference genes in the different tissues of B. papyrifera. In addition, HSP, rRNA, NADH, and UBC were the most suitable internal reference genes for the abiotic stresses and the different tissues of B. papyrifera. The expression patterns of DREB and POD were analyzed by using the selected stable and unstable reference genes. This further verified the reliability of the screened internal reference genes. This study lays the foundation for the functional analysis and regulatory mechanism research of genes in B. papyrifera.
Collapse
Affiliation(s)
- Mengdi Chen
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; (M.C.)
| | - Zhengbo Wang
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; (M.C.)
| | - Ziyuan Hao
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; (M.C.)
| | - Hongying Li
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; (M.C.)
| | - Qi Feng
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; (M.C.)
| | - Xue Yang
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; (M.C.)
| | - Xiaojiao Han
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Xiping Zhao
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; (M.C.)
| |
Collapse
|
8
|
Wang H, Zhao J, Lai M, Zhang Y, Qiu W, Li Y, Tu H, Ling Q, Fu X. Differential gene expression analysis and physiological response characteristics of passion fruit ( Passiflora edulis) buds under high-temperature stress. PeerJ 2023; 11:e14839. [PMID: 36751639 PMCID: PMC9899434 DOI: 10.7717/peerj.14839] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 01/10/2023] [Indexed: 02/05/2023] Open
Abstract
High temperature in summer is an unfavorable factor for passion fruit (Passiflora edulis), which can lead to restricted growth, short flowering period, few flower buds, low fruit setting rate, severe fruit drop, and more deformed fruit. To explore the molecular physiology mechanism of passion fruit responding to high-temperature stress, we use 'Zhuangxiang Mibao', a hybrid passion fruit cultivar, as the test material. Several physiological indicators were measured and compared between high-temperature (average temperature 38 °C) and normal temperature (average temperature 25 °C) conditions, including photosynthesis, chlorophyll fluorescence parameters, peroxidase activity (POD), superoxide dismutase activity (SOD) and malondialdehyde content. We performed RNA-seq analysis combined with biochemistry experiment to investigate the gene and molecular pathways that respond to high-temperature stress. The results showed that some physiological indicators in the high-temperature group, including the net photosynthetic rate, stomatal conductance, intercellular CO2 concentration, transpiration rate, and the maximum chemical quantum yield of photosystemII (PSII), were significantly lower than those of the control group. Malondialdehyde content was substantially higher than the control group, while superoxide dismutase and superoxide dismutase activities decreased to different degrees. Transcriptome sequencing analysis showed that 140 genes were up-regulated and 75 genes were down-regulated under high-temperature stress. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation analysis of differentially expressed genes revealed many metabolic pathways related to high-temperature stress. Further investigation revealed that 30 genes might be related to high-temperature stress, such as chlorophyllide a oxygenase (CAO), glutathione (GSH), WRKY transcription factors (WRKY), and heat shock protein (HSP), which have also been reported in other species. The results of real-time fluorescence quantitative PCR and RNA-seq of randomly selected ten genes are consistent, which suggests that the transcriptome sequencing results were reliable. Our study provides a theoretical basis for the mechanism of passion fruit response to high-temperature stress. Also, it gives a theoretical basis for the subsequent breeding of new heat-resistant passion fruit varieties.
Collapse
Affiliation(s)
- Hongli Wang
- Qinzhou Branch of Guangxi Academy of Agricultural Sciences/Qinzhou Institute of Agricultural Sciences, Qinzhou, China
| | - Jiucheng Zhao
- Qinzhou Branch of Guangxi Academy of Agricultural Sciences/Qinzhou Institute of Agricultural Sciences, Qinzhou, China
| | - Miao Lai
- Qinzhou Branch of Guangxi Academy of Agricultural Sciences/Qinzhou Institute of Agricultural Sciences, Qinzhou, China
| | - Yingqing Zhang
- Qinzhou Branch of Guangxi Academy of Agricultural Sciences/Qinzhou Institute of Agricultural Sciences, Qinzhou, China
| | - Wenwu Qiu
- Institute of Horticulture, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Yanyan Li
- Qinzhou Branch of Guangxi Academy of Agricultural Sciences/Qinzhou Institute of Agricultural Sciences, Qinzhou, China
| | - Hailian Tu
- Qinzhou Branch of Guangxi Academy of Agricultural Sciences/Qinzhou Institute of Agricultural Sciences, Qinzhou, China
| | - Qichang Ling
- Qinzhou Branch of Guangxi Academy of Agricultural Sciences/Qinzhou Institute of Agricultural Sciences, Qinzhou, China
| | - Xinfeng Fu
- Qinzhou Branch of Guangxi Academy of Agricultural Sciences/Qinzhou Institute of Agricultural Sciences, Qinzhou, China
| |
Collapse
|
9
|
He F, Gui L, Zhang Y, Zhu B, Zhang X, Shen M, Wan F, Yang L, Xiao J. Validation of reference genes for gene expression analysis in fruit development of Vaccinium bracteatum Thunb. using quantitative real-time PCR. Sci Rep 2022; 12:16946. [PMID: 36210363 PMCID: PMC9548497 DOI: 10.1038/s41598-022-20864-7] [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: 06/15/2022] [Accepted: 09/20/2022] [Indexed: 12/29/2022] Open
Abstract
Vaccinium bracteatum Thunb. (VBT) is widely distributed in the mountainous areas in eastern and southern China. VBT leaves have great medical value and can be used to stain rice to produce "Wumifan". Its fruits also contain rich nutrients. However, there has been limited attention to exploring the molecular content of VBT. Previously, we performed RNA-seq on three typical VBT fruits that were at various stages of ripening, although a reliable reference gene was lost in validation.In this study, we selected ten candidate reference genes based on previous studies and transcriptomics analyses. Subsequently, these genes were evaluated using a combination of methods, including geNorm, NormFinder, and Bestkeeper, with a comprehensive ranking assessment. As a result, we found that the actin2, NADH, and ADK genes have high reliability for analysing the expression levels of genes involved in fruit development. Furthermore, the transcript levels of 15 DEGs from transcriptomic analysis were assessed using NADH as a reference gene, and RT-qPCR data were highly consistent with the transcriptomic data. These results provide reliable reference genes for further studying gene expression, which will be beneficial for comprehensively exploring VBT.
Collapse
Affiliation(s)
- Feng He
- grid.440646.40000 0004 1760 6105College of Life Sciences, Anhui Normal University, Wuhu, 241000 China
| | - Liangxian Gui
- grid.440646.40000 0004 1760 6105College of Life Sciences, Anhui Normal University, Wuhu, 241000 China
| | - Yan Zhang
- grid.440646.40000 0004 1760 6105College of Life Sciences, Anhui Normal University, Wuhu, 241000 China
| | - Bo Zhu
- grid.440646.40000 0004 1760 6105College of Life Sciences, Anhui Normal University, Wuhu, 241000 China
| | - Xiaoping Zhang
- grid.440646.40000 0004 1760 6105College of Life Sciences, Anhui Normal University, Wuhu, 241000 China
| | - Min Shen
- grid.440646.40000 0004 1760 6105College of Life Sciences, Anhui Normal University, Wuhu, 241000 China
| | - Fengying Wan
- grid.440646.40000 0004 1760 6105College of Life Sciences, Anhui Normal University, Wuhu, 241000 China
| | - Lu Yang
- grid.440646.40000 0004 1760 6105College of Life Sciences, Anhui Normal University, Wuhu, 241000 China
| | - Jiaxin Xiao
- grid.440646.40000 0004 1760 6105College of Life Sciences, Anhui Normal University, Wuhu, 241000 China
| |
Collapse
|