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Kaur N, Lozada DN, Bhatta M, Barchenger DW, Khokhar ES, Nourbakhsh SS, Sanogo S. Insights into the genetic architecture of Phytophthora capsici root rot resistance in chile pepper (Capsicum spp.) from multi-locus genome-wide association study. BMC PLANT BIOLOGY 2024; 24:416. [PMID: 38760676 PMCID: PMC11100198 DOI: 10.1186/s12870-024-05097-2] [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: 06/21/2023] [Accepted: 05/02/2024] [Indexed: 05/19/2024]
Abstract
BACKGROUND Phytophthora root rot, a major constraint in chile pepper production worldwide, is caused by the soil-borne oomycete, Phytophthora capsici. This study aimed to detect significant regions in the Capsicum genome linked to Phytophthora root rot resistance using a panel consisting of 157 Capsicum spp. genotypes. Multi-locus genome wide association study (GWAS) was conducted using single nucleotide polymorphism (SNP) markers derived from genotyping-by-sequencing (GBS). Individual plants were separately inoculated with P. capsici isolates, 'PWB-185', 'PWB-186', and '6347', at the 4-8 leaf stage and were scored for disease symptoms up to 14-days post-inoculation. Disease scores were used to calculate disease parameters including disease severity index percentage, percent of resistant plants, area under disease progress curve, and estimated marginal means for each genotype. RESULTS Most of the genotypes displayed root rot symptoms, whereas five accessions were completely resistant to all the isolates and displayed no symptoms of infection. A total of 55,117 SNP markers derived from GBS were used to perform multi-locus GWAS which identified 330 significant SNP markers associated with disease resistance. Of these, 56 SNP markers distributed across all the 12 chromosomes were common across the isolates, indicating association with more durable resistance. Candidate genes including nucleotide-binding site leucine-rich repeat (NBS-LRR), systemic acquired resistance (SAR8.2), and receptor-like kinase (RLKs), were identified within 0.5 Mb of the associated markers. CONCLUSIONS Results will be used to improve resistance to Phytophthora root rot in chile pepper by the development of Kompetitive allele-specific markers (KASP®) for marker validation, genomewide selection, and marker-assisted breeding.
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Affiliation(s)
- Navdeep Kaur
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
- Current address: Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Dennis N Lozada
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA.
- Chile Pepper Institute, New Mexico State University, Las Cruces, NM, 88003, USA.
| | | | | | - Ehtisham S Khokhar
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Seyed Shahabeddin Nourbakhsh
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
- Department of Extension Plant Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Soum Sanogo
- Department of Entomology, Plant Pathology and Weed Science, New Mexico State University, Las Cruces, NM, 88003, USA
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Mangal V, Lal MK, Tiwari RK, Altaf MA, Sood S, Gahlaut V, Bhatt A, Thakur AK, Kumar R, Bhardwaj V, Kumar V, Singh B, Singh R, Kumar D. A comprehensive and conceptual overview of omics-based approaches for enhancing the resilience of vegetable crops against abiotic stresses. PLANTA 2023; 257:80. [PMID: 36913037 DOI: 10.1007/s00425-023-04111-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
Abiotic stresses adversely affect the productivity and production of vegetable crops. The increasing number of crop genomes that have been sequenced or re-sequenced provides a set of computationally anticipated abiotic stress-related responsive genes on which further research may be focused. Knowledge of omics approaches and other advanced molecular tools have all been employed to understand the complex biology of these abiotic stresses. A vegetable can be defined as any component of a plant that is eaten for food. These plant parts may be celery stems, spinach leaves, radish roots, potato tubers, garlic bulbs, immature cauliflower flowers, cucumber fruits, and pea seeds. Abiotic stresses, such as deficient or excessive water, high temperature, cold, salinity, oxidative, heavy metals, and osmotic stress, are responsible for the adverse activity in plants and, ultimately major concern for decreasing yield in many vegetable crops. At the morphological level, altered leaf, shoot and root growth, altered life cycle duration and fewer or smaller organs can be observed. Likewise different physiological and biochemical/molecular processes are also affected in response to these abiotic stresses. In order to adapt and survive in a variety of stressful situations, plants have evolved physiological, biochemical, and molecular response mechanisms. A comprehensive understanding of the vegetable's response to different abiotic stresses and the identification of tolerant genotypes are essential to strengthening each vegetable's breeding program. The advances in genomics and next-generation sequencing have enabled the sequencing of many plant genomes over the last twenty years. A combination of modern genomics (MAS, GWAS, genomic selection, transgenic breeding, and gene editing), transcriptomics, and proteomics along with next-generation sequencing provides an array of new powerful approaches to the study of vegetable crops. This review examines the overall impact of major abiotic stresses on vegetables, adaptive mechanisms and functional genomic, transcriptomic, and proteomic processes used by researchers to minimize these challenges. The current status of genomics technologies for developing adaptable vegetable cultivars that will perform better in future climates is also examined.
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Affiliation(s)
- Vikas Mangal
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India.
| | - Milan Kumar Lal
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India.
| | - Rahul Kumar Tiwari
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India.
| | | | - Salej Sood
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Vijay Gahlaut
- CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
- Department of Biotechnology and University Center for Research and Development, Chandigarh University, Mohali, Punjab, India
| | | | - Ajay Kumar Thakur
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Ravinder Kumar
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Vinay Bhardwaj
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Vinod Kumar
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Brajesh Singh
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Rajender Singh
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Devendra Kumar
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
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Sharma D, Shree B, Kumar S, Kumar V, Sharma S, Sharma S. Stress induced production of plant secondary metabolites in vegetables: Functional approach for designing next generation super foods. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 192:252-272. [PMID: 36279745 DOI: 10.1016/j.plaphy.2022.09.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 07/17/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
Plant secondary metabolites are vital for human health leading to the gain the access to natural products. The quality of crops is the result of the interaction of different biotic and abiotic factors. Abiotic stresses during plant growth may reduce the crop performance and quality of the produce. However, abiotic stresses can result in numerous physiological, biochemical, and molecular responses in plants, aiming to deal with these conditions. Abiotic stresses are also elicitors of the biosynthesis of plant secondary metabolites in plants which possess plant defense mechanisms as well as human health benefits such as anti-inflammatory, antioxidative properties etc. Plants either synthesize new compounds or alter the concentration of bioactive compounds. Due to increasing attention towards the production of bioactive compounds, the understanding of crop responses to abiotic stresses in relation to the biosynthesis of bioactive compounds is critical. Plants alter their metabolism at the genetic level in response to different abiotic stresses resulting the changes in secondary metabolite production. Transcriptional factors regulate genes responsible for secondary metabolite biosynthesis in several plants under stress conditions. Understanding the signaling pathways involved in the secondary metabolite biosynthesis has become easy with the use of molecular biology. Therefore, aim of writing the review is to focus on secondary metabolite production in vegetable crops, their health benefits and transcription regulation under various abiotic stresses.
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Affiliation(s)
- Deepika Sharma
- MS Swaminathan School of Agriculture, Shoolini University of Biotechnology and Management Sciences, Solan, 173229, HP, India
| | - Bharti Shree
- Department of Agricultural Biotechnology, CSK HPKV, Palampur, 176062, HP, India
| | - Satish Kumar
- Dr. YS Parmar University of Horticulture and Forestry, Nauni, Solan, 173230, HP, India.
| | - Vikas Kumar
- Department of Food Science and Technology, Punjab Agricultural University, Ludhiana, Punjab, 141027, India
| | - Shweta Sharma
- MS Swaminathan School of Agriculture, Shoolini University of Biotechnology and Management Sciences, Solan, 173229, HP, India.
| | - Shivam Sharma
- Department of Vegetable Science, CSK HPKV, Palampur, 176062, HP, India
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Nieto-Garibay A, Barraza A, Caamal-Chan G, Murillo-Amador B, Troyo-Diéguez E, Burgoa-Cruz CA, Jaramillo-Limón JN, Loera-Muro A. Habanero pepper ( Capsicum chinense) adaptation to water-deficit stress in a protected agricultural system. FUNCTIONAL PLANT BIOLOGY : FPB 2022; 49:295-306. [PMID: 35130477 DOI: 10.1071/fp20394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Drought is one of the major factors limiting global crop yield. In Mexico, agriculture is expected to be severely affected by drought. The Capsicum genus has several crop species of agricultural importance. In this work, we analysed the Capsicum chinense plant physiological responses and differentially expressed genes under water stress mainly focused on the responses elicited following recovery through repetitive stress. Plants were cultivated in an experimental block. Each block consisted of plants under water deficit and a control group without deficit. Morphometric and functional parameters, and the expression of genes related to resistance to abiotic stresses were measured. Morphological differences were observed. Plants subjected to water deficit showed impaired growth. Nonetheless, in the physiological parameters, no differences were observed between treatments. We selected abiotic stress-related genes that include heat-shock proteins (HSPs), heat-shock factors (HSFs), transcription factors related to abiotic stress (MYB, ETR1 , and WRKY ), and those associated with biotic and abiotic stress responses (Jar1 and Lox2 ). HSF, HSP, MYB72, ETR1, Jar1, WRKYa , and Lox2 genes were involved in the response to water-deficit stress in C. chinense plants. In conclusion, our work may improve our understanding of the morphological, physiological, and molecular mechanisms underlying hydric stress response in C. chinense .
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Affiliation(s)
- Alejandra Nieto-Garibay
- Centro de Investigaciones Biológicas del Noroeste, SC, Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, C.P. 23096, La Paz, Baja California Sur, Mexico
| | - Aarón Barraza
- CONACYT-Centro de Investigaciones Biológicas del Noroeste, SC, Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, La Paz, Baja California Sur, C.P. 23096, Mexico
| | - Goretty Caamal-Chan
- CONACYT-Centro de Investigaciones Biológicas del Noroeste, SC, Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, La Paz, Baja California Sur, C.P. 23096, Mexico
| | - Bernardo Murillo-Amador
- Centro de Investigaciones Biológicas del Noroeste, SC, Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, C.P. 23096, La Paz, Baja California Sur, Mexico
| | - Enrique Troyo-Diéguez
- Centro de Investigaciones Biológicas del Noroeste, SC, Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, C.P. 23096, La Paz, Baja California Sur, Mexico
| | - Carlos Alexis Burgoa-Cruz
- Instituto Tecnológico de La Paz, Boulevard Forjadores de Baja California Sur 4720, 8 de Octubre 2da Secc, La Paz, Baja California Sur, C.P. 23080, Mexico
| | - Jhesy Nury Jaramillo-Limón
- Universidad de Occidente, Unidad los Mochis Boulevard Macario Gaxiola SN Col. Las Malvinas, C.P. 81216, Los Mochis, Sinaloa, Mexico
| | - Abraham Loera-Muro
- CONACYT-Centro de Investigaciones Biológicas del Noroeste, SC, Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, La Paz, Baja California Sur, C.P. 23096, Mexico
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Borràs D, Barchi L, Schulz K, Moglia A, Acquadro A, Kamranfar I, Balazadeh S, Lanteri S. Transcriptome-Based Identification and Functional Characterization of NAC Transcription Factors Responsive to Drought Stress in Capsicum annuum L. Front Genet 2021; 12:743902. [PMID: 34745217 PMCID: PMC8570119 DOI: 10.3389/fgene.2021.743902] [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: 07/19/2021] [Accepted: 09/28/2021] [Indexed: 11/13/2022] Open
Abstract
Capsicum annuum L. is one of the most cultivated Solanaceae species, and in the open field, water limitation leading to drought stress affects its fruit quality, fruit setting, fruit size and ultimately yield. We identified stage-specific and a common core set of differentially expressed genes, following RNA-seq transcriptome analyses of a breeding line subjected to acute drought stress followed by recovery (rewatering), at three stages of plant development. Among them, two NAC transcription factor (TF) genes, i.e., CaNAC072 and CaNAC104, were always upregulated after drought stress and downregulated after recovery. The two TF proteins were observed to be localized in the nucleus following their transient expression in Nicotiana benthamiana leaves. The expression of the two NACs was also induced by NaCl, polyethylene glycol (PEG) and abscisic acid (ABA) treatments, suggesting that CaNAC072 is an early, while CaNAC104 is a late abiotic stress-responsive gene. Virus-induced gene silencing (VIGS) of CaNAC104 did not affect the pepper plantlet’s tolerance to drought stress, while VIGS of CaNAC072 increased drought tolerance. Heterologous expression of CaNAC072 in Arabidopsis thaliana as well as in plants mutated for its homolog ANAC072 did not increase drought stress tolerance. This highlights a different role of the two NAC homologs in the two species. Here, we discuss the complex role of NACs as transcriptional switches in the response to drought stress in bell pepper.
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Affiliation(s)
- Dionis Borràs
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Turin, Italy
| | - Lorenzo Barchi
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Turin, Italy
| | - Karina Schulz
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Andrea Moglia
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Turin, Italy
| | - Alberto Acquadro
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Turin, Italy
| | - Iman Kamranfar
- Department Molecular Biology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Salma Balazadeh
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany.,Plant Sciences and Natural Products, Institute of Biology Leiden (IBL), Leiden University, Leiden, Netherlands
| | - Sergio Lanteri
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Turin, Italy
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6
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Transcriptomic analysis of a wild and a cultivated varieties of Capsicum annuum over fruit development and ripening. PLoS One 2021; 16:e0256319. [PMID: 34428253 PMCID: PMC8384167 DOI: 10.1371/journal.pone.0256319] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 08/03/2021] [Indexed: 12/13/2022] Open
Abstract
Chili pepper (Capsicum annuum) is one of the most important crops worldwide. Its fruits contain metabolites produced over the maturation process like capsaicinoids and carotenoids. This metabolic process produces internal changes in flavor, color, texture, and aroma in fruits to make them more attractive for seed dispersal organisms. The chiltepin (C. annuum L. var. glabriusculum) is a wild variety of the C. annuum L. species that is considered a source of genetic resources that could be used to improve the current chili crops. In this study, we performed a transcriptomic analysis on two fruit maturation stages: immature stage (green fruit) and mature stage (red fruit) of a wild and a cultivated pepper variety. We found 19,811 genes expressed, and 1,008 genes differentially expressed (DEGs) in at least one of the five contrast used; 730 DEGs were found only in one contrast, and most DEGs in all contrasts were downregulated. GO enrichment analysis showed that the majority of DEGs are related to stress responses. KEGG enrichment analysis detected differences in expression patterns in metabolic pathways related to phenylpropanoid biosynthesis, secondary metabolites, plant hormone signal transduction, carotenoid biosynthesis and sesquiterpenoid and triterpenoid biosynthesis. We selected 105 tomato fruit ripening-related genes, and found 53 pepper homologs differentially expressed related to shape, size, and secondary metabolite biosynthesis. According to the transcriptome analysis, the two peppers showed very similar gene expression patterns; differences in expression patterns of genes related to shape, size, ethylene and secondary metabolites biosynthesis suggest that changes produced by domestication of chilli pepper could be very specific to the expression of genes related to traits desired in commercial fruits.
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7
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Lee ON, Koo H, Yu JW, Park HY. Genotyping-by-Sequencing-Based Genome-Wide Association Studies of Fusarium Wilt Resistance in Radishes ( Raphanus sativus L.). Genes (Basel) 2021; 12:genes12060858. [PMID: 34205206 PMCID: PMC8228987 DOI: 10.3390/genes12060858] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/27/2021] [Accepted: 06/02/2021] [Indexed: 11/22/2022] Open
Abstract
Fusarium wilt (FW) is a fungal disease that causes severe yield losses in radish production. The most effective method to control the FW is the development and use of resistant varieties in cultivation. The identification of marker loci linked to FW resistance are expected to facilitate the breeding of disease-resistant radishes. In the present study, we applied an integrated framework of genome-wide association studies (GWAS) using genotyping-by-sequencing (GBS) to identify FW resistance loci among a panel of 225 radish accessions, including 58 elite breeding lines. Phenotyping was conducted by manual inoculation of seedlings with the FW pathogen, and scoring for the disease index was conducted three weeks after inoculation during two constitutive years. The GWAS analysis identified 44 single nucleotide polymorphisms (SNPs) and twenty putative candidate genes that were significantly associated with FW resistance. In addition, a total of four QTLs were identified from F2 population derived from a FW resistant line and a susceptible line, one of which was co-located with the SNPs on chromosome 7, detected in GWAS study. These markers will be valuable for molecular breeding programs and marker-assisted selection to develop FW resistant varieties of R. sativus.
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Affiliation(s)
- O New Lee
- College of Life Sciences, Sejong University, Seoul 05006, Korea;
| | - Hyunjin Koo
- Department of Agricultural Biotechnology and Research, Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea;
| | | | - Han Yong Park
- College of Life Sciences, Sejong University, Seoul 05006, Korea;
- Correspondence:
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Kim HM, Park SH, Ma SH, Park SY, Yun CH, Jang G, Joung YH. Promoted ABA Hydroxylation by Capsicum annuum CYP707As Overexpression Suppresses Pollen Maturation in Nicotiana tabacum. FRONTIERS IN PLANT SCIENCE 2020; 11:583767. [PMID: 33363553 PMCID: PMC7752897 DOI: 10.3389/fpls.2020.583767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 11/16/2020] [Indexed: 05/14/2023]
Abstract
Abscisic acid (ABA) is a key signaling molecule that mediates plant response to stress. Increasing evidence indicates that ABA also regulates many aspects of plant development, such as seed germination, leaf development, and ripening. ABA metabolism, including ABA biosynthesis and degradation, is an essential aspect of ABA response in plants. In this study, we identified four cytochrome P450 genes (CaCYP707A1, 2, 3, and 4) that mediate ABA hydroxylation, which is required for ABA degradation in Capsicum annuum. We observed that CaCYP707A-mediated ABA hydroxylation promotes ABA degradation, leading to low levels of ABA and a dehydration phenotype in 35S:CaCYP707A plants. Importantly, seed formation was strongly inhibited in 35S:CaCYP707A plants, and a cross-pollination test suggested that the defect in seed formation is caused by improper pollen development. Phenotypic analysis showed that pollen maturation is suppressed in 35S:CaCYP707A1 plants. Consequently, most 35S:CaCYP707A1 pollen grains degenerated, unlike non-transgenic (NT) pollen, which developed into mature pollen grains. Together our results indicate that CaCYP707A mediates ABA hydroxylation and thereby influences pollen development, helping to elucidate the mechanism underlying ABA-regulated pollen development.
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Kong X, Wei B, Gao Z, Zhou Y, Shi F, Zhou X, Zhou Q, Ji S. Changes in Membrane Lipid Composition and Function Accompanying Chilling Injury in Bell Peppers. PLANT & CELL PHYSIOLOGY 2018; 59:167-178. [PMID: 29136239 DOI: 10.1093/pcp/pcx171] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 11/06/2017] [Indexed: 05/22/2023]
Abstract
Bell peppers are vulnerable to low temperature (<7°C) and subject to chilling injury (CI). To elucidate the relationship between cell membrane lipid composition and CI, a membrane lipidomic approach was taken. In addition, we performed microstructural analysis and low-field nuclear magnetic resonance to better understand CI. We also monitored primary physiological metabolism parameters to explain lipidomics. Our study indicated that cellular structure damage was more serious at 4°C, mostly represented by damage to the plasmalemma and plastid degradation. Membrane lipidomic data analysis reveals monogalactosyldiacylglycerol, phosphatidylcholine, phosphatidylethanolamine and phosphatidic acid as crucial biomarkers during CI. Furthermore, the significant increase in proline, electrolyte leakage and phospholipase D in chilled fruits also proved that membrane lipid metabolism is involved in the response to low temperature stress. To our knowledge, this study is the first attempt to describe the CI mechanisms in bell peppers based on membrane lipidomics.
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Affiliation(s)
- Ximan Kong
- Post-harvest Biology and Storage of Fruits and Vegetables laboratory, Department of Food Science, Shenyang Agricultural University, 110866, China
| | - Baodong Wei
- Post-harvest Biology and Storage of Fruits and Vegetables laboratory, Department of Food Science, Shenyang Agricultural University, 110866, China
| | - Zhu Gao
- Post-harvest Biology and Storage of Fruits and Vegetables laboratory, Department of Food Science, Shenyang Agricultural University, 110866, China
| | - Ying Zhou
- College of Life Science, Sun Yat-sen University, 510275, China
| | - Fei Shi
- Post-harvest Biology and Storage of Fruits and Vegetables laboratory, Department of Food Science, Shenyang Agricultural University, 110866, China
| | - Xin Zhou
- Post-harvest Biology and Storage of Fruits and Vegetables laboratory, Department of Food Science, Shenyang Agricultural University, 110866, China
| | - Qian Zhou
- Post-harvest Biology and Storage of Fruits and Vegetables laboratory, Department of Food Science, Shenyang Agricultural University, 110866, China
| | - Shujuan Ji
- Post-harvest Biology and Storage of Fruits and Vegetables laboratory, Department of Food Science, Shenyang Agricultural University, 110866, China
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Fan M, Sun X, Xu N, Liao Z, Li Y, Wang J, Fan Y, Cui D, Li P, Miao Z. Integration of deep transcriptome and proteome analyses of salicylic acid regulation high temperature stress in Ulva prolifera. Sci Rep 2017; 7:11052. [PMID: 28887495 PMCID: PMC5591278 DOI: 10.1038/s41598-017-11449-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 08/21/2017] [Indexed: 01/17/2023] Open
Abstract
To investigate changes in transcript and relative protein levels in response to salicylic acid regulation of the thermotolerance in U. prolifera, complementary transcriptome and proteome analyses were performed with U. prolifera grown at 35 °C (UpHT) and with the addition of SA at high temperature (UpSHT). At mRNA level,12,296 differentially expressed genes (DEGs) were obtained from the comparison of UpSHT with UpHT. iTRAQ-labeling proteome analysis showed that a total of 4,449 proteins were identified and reliably quantified. At mRNA level, the up-regulated genes involved in antioxidant activity were thioredoxin,peroxiredoxin,FeSOD, glutathione peroxidase, partion catalase and MnSOD. The down-regulated genes were ascorbate peroxidase, glutathione S-transferase, catalase and MnSOD. In addition, the DEGs involved in plant signal transduction pathway (such as auxin response factors, BRI1 and JAZ) were down-regulated. At protein level, the up-regulated proteins involved in carbon fixation and the down-regulated protein mainly were polyubiquitin, ascorbate peroxidase. The expression of Ca2+-binding protein, heat shock protein and photosynthesis-related proteins, EDS1 were also significantly regulated both at mRNA and protein level. The results indicated that SA alleviated the high-temperature stimulus through partion antioxidant related proteins up-regulated, JA signal pathway enchanced, Ca2+-binding proteins, photosynthesis-related proteins significantly changed, antioxidant enzyme activities increased and photosynthesis index changed.
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Affiliation(s)
- Meihua Fan
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211, Zhejiang, China. .,Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316000, Zhejiang, China.
| | - Xue Sun
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Nianjun Xu
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211, Zhejiang, China.
| | - Zhi Liao
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316000, Zhejiang, China
| | - Yahe Li
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Jianxin Wang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316000, Zhejiang, China
| | - Yingping Fan
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316000, Zhejiang, China
| | - Dalian Cui
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316000, Zhejiang, China
| | - Peng Li
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316000, Zhejiang, China
| | - Zengliang Miao
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316000, Zhejiang, China
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Fugate KK, de Oliveira LS, Ferrareze JP, Bolton MD, Deckard EL, Finger FL. Jasmonic acid causes short- and long-term alterations to the transcriptome and the expression of defense genes in sugarbeet roots. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.plgene.2016.12.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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12
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Martínez-López LA, Ochoa-Alejo N, Martínez O. Dynamics of the chili pepper transcriptome during fruit development. BMC Genomics 2014; 15:143. [PMID: 24555715 PMCID: PMC3936869 DOI: 10.1186/1471-2164-15-143] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 02/18/2014] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The set of all mRNA molecules present in a cell constitute the transcriptome. The transcriptome varies depending on cell type as well as in response to internal and external stimuli during development. Here we present a study of the changes that occur in the transcriptome of chili pepper fruit during development and ripening. RESULTS RNA-Seq was used to obtain transcriptomes of whole Serrano-type chili pepper fruits (Capsicum annuum L.; 'Tampiqueño 74') collected at 10, 20, 40 and 60 days after anthesis (DAA). 15,550,468 Illumina MiSeq reads were assembled de novo into 34,066 chili genes. We classified the expression patterns of individual genes as well as genes grouped into Biological Process ontologies and Metabolic Pathway categories using statistical criteria. For the analyses of gene groups we added the weighted expression of individual genes. This method was effective in interpreting general patterns of expression changes and increased the statistical power of the analyses. We also estimated the variation in diversity and specialization of the transcriptome during chili pepper development. Approximately 17% of genes exhibited a significant change of expression in at least one of the intervals sampled. In contrast, significant differences in approximately 63% of the Biological Processes and 80% of the Metabolic Pathways studied were detected in at least one interval. Confirming previous reports, genes related to capsaicinoid and ascorbic acid biosynthesis were significantly upregulated at 20 DAA while those related to carotenoid biosynthesis were highly expressed in the last period of fruit maturation (40-60 DAA). Our RNA-Seq data was validated by examining the expression of nine genes involved in carotenoid biosynthesis by qRT-PCR. CONCLUSIONS In general, more profound changes in the chili fruit transcriptome were observed in the intervals between 10 to 20 and 40 to 60 DAA. The last interval, between 40 to 60 DAA, included 49% of all significant changes detected, and was characterized predominantly by a global decrease in gene expression. This period signals the end of maturation and the beginning of senescence of chili pepper fruit. The transcriptome at 60 DAA was the most specialized and least diverse of the four states sampled.
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Affiliation(s)
| | | | - Octavio Martínez
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), 36821 Irapuato, Guanajuato, México.
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