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Zhang F, Long R, Ma Z, Xiao H, Xu X, Liu Z, Wei C, Wang Y, Peng Y, Yang X, Shi X, Cao S, Li M, Xu M, He F, Jiang X, Zhang T, Wang Z, Li X, Yu LX, Kang J, Zhang Z, Zhou Y, Yang Q. Evolutionary genomics of climatic adaptation and resilience to climate change in alfalfa. MOLECULAR PLANT 2024; 17:867-883. [PMID: 38678365 DOI: 10.1016/j.molp.2024.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 04/09/2024] [Accepted: 04/24/2024] [Indexed: 04/29/2024]
Abstract
Given the escalating impact of climate change on agriculture and food security, gaining insights into the evolutionary dynamics of climatic adaptation and uncovering climate-adapted variation can empower the breeding of climate-resilient crops to face future climate change. Alfalfa (Medicago sativa subsp. sativa), the queen of forages, shows remarkable adaptability across diverse global environments, making it an excellent model for investigating species responses to climate change. In this study, we performed population genomic analyses using genome resequencing data from 702 accessions of 24 Medicago species to unravel alfalfa's climatic adaptation and genetic susceptibility to future climate change. We found that interspecific genetic exchange has contributed to the gene pool of alfalfa, particularly enriching defense and stress-response genes. Intersubspecific introgression between M. sativa subsp. falcata (subsp. falcata) and alfalfa not only aids alfalfa's climatic adaptation but also introduces genetic burden. A total of 1671 genes were associated with climatic adaptation, and 5.7% of them were introgressions from subsp. falcata. By integrating climate-associated variants and climate data, we identified populations that are vulnerable to future climate change, particularly in higher latitudes of the Northern Hemisphere. These findings serve as a clarion call for targeted conservation initiatives and breeding efforts. We also identified pre-adaptive populations that demonstrate heightened resilience to climate fluctuations, illuminating a pathway for future breeding strategies. Collectively, this study enhances our understanding about the local adaptation mechanisms of alfalfa and facilitates the breeding of climate-resilient alfalfa cultivars, contributing to effective agricultural strategies for facing future climate change.
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Affiliation(s)
- Fan Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Ruicai Long
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhiyao Ma
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Hua Xiao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Xiaodong Xu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Zhongjie Liu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Chunxue Wei
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Yiwen Wang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Yanling Peng
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Xuanwen Yang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Xiaoya Shi
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Shuo Cao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Mingna Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ming Xu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fei He
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xueqian Jiang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tiejun Zhang
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China
| | - Zhen Wang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Xianran Li
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163, USA
| | - Long-Xi Yu
- U.S. Department of Agriculture-Agricultural Research Service, Plant Germplasm Introduction and Testing Research, Prosser, WA 99350, USA
| | - Junmei Kang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhiwu Zhang
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163, USA
| | - Yongfeng Zhou
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China; National Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Qingchuan Yang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Wang Y, Sun Y, Li Y, Shao H, Cheng X, Wang X, Yong B, Tao X. Genome-wide identification and expression profiles of the Phytophthora infestans responsive CYPome (cytochrome P450 complement) in Solanum tuberosum. Biosci Biotechnol Biochem 2024; 88:283-293. [PMID: 38115610 DOI: 10.1093/bbb/zbad180] [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: 09/15/2023] [Accepted: 12/18/2023] [Indexed: 12/21/2023]
Abstract
Cytochrome P450s represent one of the largest protein families across all domains of life. In plants, biotic stress can regulate the expression of some P450 genes. However, the CYPome (cytochrome P450 complement) in Solanum tuberosum and its response to Phytophthora infestans infection remains unrevealed. In this study, 488 P450 genes were identified from potato genome, which can be divided into 41 families and 57 subfamilies. Responding to the infection of P. infestans, 375 potato P450 genes were expressed in late blight resistant or susceptible cultivars. A total of 14 P450 genes were identified as resistant related candidates, and 81 P450 genes were identified as late blight responsive candidates. Several phytohormone biosynthesis, brassinosteroid biosynthesis, and phenylpropanoid biosynthesis involved P450 genes were differentially expressed during the potato-pathogen interactions. This study firstly reported the CYPome in S. tuberosum, and characterized the expression patterns of these P450 genes during the infection of P. infestans.
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Affiliation(s)
- Yajie Wang
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Yining Sun
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Yan Li
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Huanhuan Shao
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Xiaojie Cheng
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Xiaoyang Wang
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Bin Yong
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Xiang Tao
- College of Life Sciences, Sichuan Normal University, Chengdu, China
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Jan N, Wani UM, Wani MA, Qazi HA, John R. Comparative physiological, antioxidant and proteomic investigation reveal robust response to cold stress in Digitalis purpurea L. Mol Biol Rep 2023; 50:7319-7331. [PMID: 37439898 DOI: 10.1007/s11033-023-08635-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 06/26/2023] [Indexed: 07/14/2023]
Abstract
BACKGROUND OF THE STUDY Digitalis purpurea (L) is an important medicinal plant growing at Alpine region of Himalayas and withstands low temperatures and harsh climatic conditions existing at high altitude. It serves as an ideal plant system to decipher the tolerance to cold stress (CS) in plants from high altitudes. METHODS AND RESULTS To understand the complexity of plant response to CS, we performed a comparative physiological and biochemical study complemented with proteomics in one-month-old D. purpurea grown at 25 °C (control) and 4 °C (CS). We observed an enhanced accumulation of different osmo-protectants (glycine betaine, soluble sugar and proline) and higher transcription (mRNA levels) of various antioxidant enzymes with an increased antioxidant enzyme activity in D. purpurea when exposed to CS. Furthermore, higher concentrations of non-enzymatic antioxidants (flavonoids, phenolics) was also associated with the response to CS. Differential proteomic analysis revealed the role of various proteins primarily involved in redox reactions, protein stabilization, quinone and sterol metabolism involved in CS response in D. purpurea.. CONCLUSION Our results provide a framework for better understanding the physiological and molecular mechanism of CS response in D. purpurea at high altitudes.
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Affiliation(s)
- Nelofer Jan
- Department of Botany, University of Kashmir, Hazratbal, Srinagar, 190 006, Jammu and Kashmir, India
| | - Umer Majeed Wani
- Department of Botany, University of Kashmir, Hazratbal, Srinagar, 190 006, Jammu and Kashmir, India
| | - Mubashir Ahmad Wani
- Department of Botany, University of Kashmir, Hazratbal, Srinagar, 190 006, Jammu and Kashmir, India
| | - Hilal Ahmad Qazi
- Department of Botany, University of Kashmir, Hazratbal, Srinagar, 190 006, Jammu and Kashmir, India
| | - Riffat John
- Department of Botany, University of Kashmir, Hazratbal, Srinagar, 190 006, Jammu and Kashmir, India.
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Wang Z, Lu K, Liu X, Zhu Y, Liu C. Comparative Functional Genome Analysis Reveals the Habitat Adaptation and Biocontrol Characteristics of Plant Growth-Promoting Bacteria in NCBI Databases. Microbiol Spectr 2023; 11:e0500722. [PMID: 37098923 PMCID: PMC10269705 DOI: 10.1128/spectrum.05007-22] [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: 12/06/2022] [Accepted: 04/03/2023] [Indexed: 04/27/2023] Open
Abstract
Plant growth-promoting bacteria (PGPB) are a group of beneficial microorganisms that include 60 bacterial genera, such as Bacillus, Pseudomonas, and Burkholderia, which widely colonize plant leaves and soil, promote plant growth, and/or inhibit pathogen infection. However, the genetic factors underpinning adaptation of PGPB to plant leaves and soil remain poorly understood. In this study, we performed a comparative functional genome analysis approach to investigate the functional genes of 195 leaf-associated (LA) and 283 soil-associated (SA) PGPB strains and their roles in adapting to their environment, using 95 strains from other-associated (OA) environmental habitats with growth-promoting or antimicrobial functions as negative controls. Comparison analysis of the enrichment of nonredundant (NR) protein sequence databases showed that cytochrome P450, DNA repair, and motor chemotaxis genes were significantly enriched in LA PGPB strains related to environmental adaptation, while cell wall-degrading enzymes, TetR transcriptional regulatory factors, and sporulation-related genes were highly enriched in SA PGPB strains. Additionally, analysis of carbohydrate-active enzymes demonstrated that glycosyltransferases (GTs) and glycoside hydrolases (GHs) were abundant families in all PGPB strains, which is in favor of plant growth, and enriched in SA PGPB strains. Except for most Bacillus strains, SA PGPB genomes contained significantly more secondary metabolism clusters than LA PGPB. Most LA PGPB contained hormone biosynthesis genes, which may contribute to plant growth promotion, while SA PGPB harbored numerous carbohydrate and antibiotic metabolism genes. In summary, this study further deepens our understanding of the habitat adaptation and biocontrol characteristics of LA and SA PGPB strains. IMPORTANCE Plant growth-promoting bacteria (PGPB) are essential for the effectiveness of biocontrol agents in plant phyllosphere and rhizosphere. However, little is known about the ecological adaptation of PGPB to different habitats. In this study, comparative functional genome analysis of leaf-associated (LA), soil-associated (SA), and other-associated (OA) PGPB strains was performed. We found that genes related to the metabolism of hormones were enriched in LA PGPB. Carbohydrate and antibiotic metabolism genes were enriched in SA PGPB, which likely facilitated their adaptation to the plant growth environment. Our findings provide genetic insights on LA and SA PGPB strains' ecological adaptation and biocontrol characteristics.
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Affiliation(s)
- Zhen Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Kaiheng Lu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Xuan Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yuping Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Changhong Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
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Paul M, Tanskanen J, Jääskeläinen M, Chang W, Dalal A, Moshelion M, Schulman AH. Drought and recovery in barley: key gene networks and retrotransposon response. FRONTIERS IN PLANT SCIENCE 2023; 14:1193284. [PMID: 37377802 PMCID: PMC10291200 DOI: 10.3389/fpls.2023.1193284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/09/2023] [Indexed: 06/29/2023]
Abstract
Introduction During drought, plants close their stomata at a critical soil water content (SWC), together with making diverse physiological, developmental, and biochemical responses. Methods Using precision-phenotyping lysimeters, we imposed pre-flowering drought on four barley varieties (Arvo, Golden Promise, Hankkija 673, and Morex) and followed their physiological responses. For Golden Promise, we carried out RNA-seq on leaf transcripts before and during drought and during recovery, also examining retrotransposon BARE1expression. Transcriptional data were subjected to network analysis. Results The varieties differed by their critical SWC (ϴcrit), Hankkija 673 responding at the highest and Golden Promise at the lowest. Pathways connected to drought and salinity response were strongly upregulated during drought; pathways connected to growth and development were strongly downregulated. During recovery, growth and development pathways were upregulated; altogether, 117 networked genes involved in ubiquitin-mediated autophagy were downregulated. Discussion The differential response to SWC suggests adaptation to distinct rainfall patterns. We identified several strongly differentially expressed genes not earlier associated with drought response in barley. BARE1 transcription is strongly transcriptionally upregulated by drought and downregulated during recovery unequally between the investigated cultivars. The downregulation of networked autophagy genes suggests a role for autophagy in drought response; its importance to resilience should be further investigated.
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Affiliation(s)
- Maitry Paul
- HiLIFE Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Viikki Plant Science Centre (ViPS), University of Helsinki, Helsinki, Finland
| | - Jaakko Tanskanen
- HiLIFE Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Viikki Plant Science Centre (ViPS), University of Helsinki, Helsinki, Finland
- Production Systems, Natural Resources Institute Finland (LUKE), Helsinki, Finland
| | - Marko Jääskeläinen
- HiLIFE Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Viikki Plant Science Centre (ViPS), University of Helsinki, Helsinki, Finland
| | - Wei Chang
- HiLIFE Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Viikki Plant Science Centre (ViPS), University of Helsinki, Helsinki, Finland
| | - Ahan Dalal
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Menachem Moshelion
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Alan H. Schulman
- HiLIFE Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Viikki Plant Science Centre (ViPS), University of Helsinki, Helsinki, Finland
- Production Systems, Natural Resources Institute Finland (LUKE), Helsinki, Finland
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Wang N, Bai S, Bei F, Zhao N, Jia S, Jin T, Wang J, Wang H, Liu W. Resistance to ALS inhibitors conferred by non-target-site resistance mechanisms in Myosoton aquaticum L. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2022; 184:105067. [PMID: 35715029 DOI: 10.1016/j.pestbp.2022.105067] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 02/23/2022] [Accepted: 02/28/2022] [Indexed: 06/15/2023]
Abstract
Myosoton aquaticum L. is a competitive broadleaf weed commonly found in wheat fields in China and has become challenging due to its evolving herbicide resistance. In this study, one subpopulation, RF1 (derived from the tribenuron-methyl-resistant population HN10), with none of the known acetolactate synthase (ALS) resistance mutations was confirmed to exhibit resistance to tribenuron-methyl (SU), pyrithiobac‑sodium (PTB), florasulam (TP), flucarbazone-Na (SCT), and diflufenican (PDS). In vitro ALS activity assays showed that the total ALS activity of RF1 was lower than that of the susceptible (S) population. However, there was no difference in ALS gene expression induced by tribenuron-methyl between the two populations. The combination of the cytochrome P450 monooxygenase (P450) inhibitor malathion and tribenuron-methyl resulted in the RF1 population behaving like the S population. The rapid P450-mediated tribenuron-methyl metabolism in RF1 plants was also confirmed by liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis. In addition, approximately equal glutathione S-transferase (GST) activity was observed in RF1 and S plants of untreated and tribenuron-methyl treated groups. This study reported one M. aquaticum L. population without ALS resistance mutations exhibiting resistance to ALS inhibitors and the PDS inhibitor diflufenican, and the non-target-site resistance mechanism played a vital role in herbicide resistance.
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Affiliation(s)
- Nan Wang
- College of Plant Protection, Shandong Agricultural University, Tai'an 271018, Shandong, PR China
| | - Shuang Bai
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao 266000, PR China
| | - Feng Bei
- Tai'an Customs, Tai'an 271018, Shandong, PR China
| | - Ning Zhao
- School of Plant Protection, Anhui Agricultural University, Hefei 230036, PR China
| | - Sisi Jia
- Tai'an Customs, Tai'an 271018, Shandong, PR China
| | - Tao Jin
- Qingdao Kingagroot Chemical Compound Co., Ltd., Qingdao 266000, PR China
| | - Jinxin Wang
- College of Plant Protection, Shandong Agricultural University, Tai'an 271018, Shandong, PR China
| | - Hengzhi Wang
- College of Plant Protection, Shandong Agricultural University, Tai'an 271018, Shandong, PR China.
| | - Weitang Liu
- College of Plant Protection, Shandong Agricultural University, Tai'an 271018, Shandong, PR China.
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Zhang J, Chi Y, Zhang J. Analysis of CYP450 gene expression and function in white-rot fungus, Lenzites gibbosa, treated with Congo red. Biotech Histochem 2022; 97:519-535. [DOI: 10.1080/10520295.2022.2028307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Affiliation(s)
- Jian Zhang
- School of Forestry, Northeast Forestry University, Harbin, China
| | - YuJie Chi
- School of Forestry, Northeast Forestry University, Harbin, China
| | - Jun Zhang
- School of Forestry, Northeast Forestry University, Harbin, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
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Wang W, Tang W, Wang X, Liu W, Zhu F. Genes from Carboxypeptidase A, glutathione S-transferase, and cytochrome b families were found involved in lead transport in insect Musca domestica. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 230:113113. [PMID: 34968798 DOI: 10.1016/j.ecoenv.2021.113113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/10/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
Lead (Pb) is a typical toxic contamination source all over the world. In this research, larvae of the housefly (Musca domestica) were fed a Pb-contaminated diet at different Pb doses of 0, 20 and 5000 mg/kg. RNA sequencing was used to identify genes that were differentially expressed in relation to lead transport or detoxification. RNA interference (RNAi) was carried on 12 candidate genes. The results showed that three luminal pH regions of mid-gut were at pH values of 6.33, 3.10, and 7.80. With increasing Pb concentration, the pH of the middle mid-gut decreased by one unit. The expression levels of carboxypeptidase A (CPA1), glutathione S-transferase (GST), and cytochrome b (Cyt b) were linked to Pb treatments, particularly high Pb concentration of 5000 mg/kg. RNAi-mediated down expression of CPA1, GST2, and CYTb-c1 resulted in low Pb accumulation in the larvae of 5000 mg/kg Pb group. These proteins played key roles in Pb transport and detoxification in M. domestica larvae.
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Affiliation(s)
- Wanqiang Wang
- Hubei International Scientific and Technological Cooperation Base of Waste Conversion by Insects, Huazhong Agricultural University, Wuhan 430070, China.
| | - Wenzheng Tang
- Hubei International Scientific and Technological Cooperation Base of Waste Conversion by Insects, Huazhong Agricultural University, Wuhan 430070, China.
| | - Xiaoping Wang
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, Huazhong Agricultural University, Wuhan 430070, China.
| | - Wen Liu
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, Huazhong Agricultural University, Wuhan 430070, China.
| | - Fen Zhu
- Hubei International Scientific and Technological Cooperation Base of Waste Conversion by Insects, Huazhong Agricultural University, Wuhan 430070, China.
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Cross-Tolerance and Autoimmunity as Missing Links in Abiotic and Biotic Stress Responses in Plants: A Perspective toward Secondary Metabolic Engineering. Int J Mol Sci 2021; 22:ijms222111945. [PMID: 34769374 PMCID: PMC8584326 DOI: 10.3390/ijms222111945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/25/2021] [Accepted: 11/02/2021] [Indexed: 01/04/2023] Open
Abstract
Plants employ a diversified array of defense activities when they encounter stress. Continuous activation of defense pathways that were induced by mutation or altered expression of disease resistance genes and mRNA surveillance mechanisms develop abnormal phenotypes. These plants show continuous defense genes' expression, reduced growth, and also manifest tissue damage by apoptosis. These macroscopic abrasions appear even in the absence of the pathogen and can be attributed to a condition known as autoimmunity. The question is whether it is possible to develop an autoimmune mutant that does not fetch yield and growth penalty and provides enhanced protection against various biotic and abiotic stresses via secondary metabolic pathways' engineering. This review is a discussion about the common stress-fighting mechanisms, how the concept of cross-tolerance instigates propitious or protective autoimmunity, and how it can be achieved by engineering secondary metabolic pathways.
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Study of Triticum aestivum Resistome in Response to Wheat dwarf India Virus Infection. Life (Basel) 2021; 11:life11090955. [PMID: 34575104 PMCID: PMC8469153 DOI: 10.3390/life11090955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 02/07/2023] Open
Abstract
Susceptible and resistant germplasm respond differently to pathogenic attack, including virus infections. We compared the transcriptome changes between a resistant wheat cultivar, Sonalika, and a susceptible cultivar, WL711, to understand this process in wheat against wheat dwarf India virus (WDIV) infection. A total of 2760 and 1853 genes were differentially expressed in virus-infected and mock-inoculated Sonalika, respectively, compared to WL711. The overrepresentation of genes involved in signaling, hormone metabolism, enzymes, secondary metabolites, proteolysis, and transcription factors was documented, including the overexpression of multiple PR proteins. We hypothesize that the virus resistance in Sonalika is likely due to strong intracellular surveillance via the action of multiple PR proteins (PR1, RAR1, and RPM1) and ChiB. Other genes such as PIP1, LIP1, DnaJ, defensins, oxalate oxidase, ankyrin repeat protein, serine-threonine kinase, SR proteins, beta-1,3-glucanases, and O-methyltransferases had a significant differential expression and play roles in stress tolerance, may also be contributing towards the virus resistance in Sonalika. In addition, we identified putative genes with unknown functions, which are only expressed in response to WDIV infection in Sonalika. The role of these genes could be further validated and utilized in engineering resistance in wheat and other crops.
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M S A, Sridharan K, Puthur JT, Dhankher OP. Priming with Nanoscale Materials for Boosting Abiotic Stress Tolerance in Crop Plants. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:10017-10035. [PMID: 34459588 DOI: 10.1021/acs.jafc.1c03673] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Seed priming is a cost-effective, practical, environmental, and farmer-friendly method to improve seed germination that can potentially increase the growth and yield of plants. The priming process enhances various physiological and biochemical mechanisms of defense and empowers the seeds or seedlings to overcome different environmental stresses. However, under critical circumstances, plants are hindered from absorbing specific chemical priming reagents owing to their larger size, molecular structure, or lack of carriers. Therefore, nanoscale materials having exceptional physiochemical properties and a large surface/volume ratio are expected to be better absorbed by the seeds/seedlings as priming agents in comparison to bulk chemicals and can trigger enhanced molecular interactions at the cellular level. Further, the flexibility in altering the surface chemical properties of the nanomaterials can facilitate better interaction with the seeds/seedlings while inhibiting the wastage of priming agents. In this review, we have systematically discussed the potentiality of various nanostructured materials as priming agents in alleviating the adverse effects of various abiotic stresses, viz., drought, salinity, high temperature, cold temperature, and heavy metals, by studying the growth parameters and physiological and biochemical response of various crop plants subjected to these stress conditions. Also, we have highlighted the molecular mechanism and activation of genes involved in enabling abiotic stress tolerance in plants after being primed with nanostructured materials.
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Affiliation(s)
- Amritha M S
- Plant Physiology and Biochemistry Division, Department of Botany, University of Calicut, Thenhipalam, Kerala 673635, India
| | - Kishore Sridharan
- Department of Nanoscience and Technology, School of Physical Sciences, University of Calicut, Thenhipalam, Kerala 673635, India
| | - Jos T Puthur
- Plant Physiology and Biochemistry Division, Department of Botany, University of Calicut, Thenhipalam, Kerala 673635, India
| | - Om Parkash Dhankher
- Stockbridge School of Agriculture, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
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12
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Huang M, Xing H, Li Z, Li H, Wu L, Jiang Y. Identification and expression profile of the soil moisture and Ralstonia solanacearum response CYPome in ginger ( Zingiber officinale). PeerJ 2021; 9:e11755. [PMID: 34414026 PMCID: PMC8340902 DOI: 10.7717/peerj.11755] [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: 12/14/2020] [Accepted: 06/21/2021] [Indexed: 11/20/2022] Open
Abstract
Background Cytochrome P450s play crucial roles in various biosynthetic reactions. Ginger (Zingiber officinale), which is often threatened by Ralstonia solanacearum, is the most economically important crop in the family Zingiberaceae. Whether the cytochrome P450 complement (CYPome) significantly responds to this pathogen has remained unclear. Methods Transcriptomic responses to R. solanacearum and soil moisture were analyzed in ginger, and expression profiles of the CYPome were determined based on transcriptome data. Results A total of 821 P450 unigenes with ORFs ≥ 300 bp were identified. Forty percent soil moisture suppressed several key P450 unigenes involved in the biosynthesis of flavonoids, gingerols, and jasmonates, including unigenes encoding flavonoid 3'-hydroxylase, flavonoid 3',5'-hydroxylase, steroid 22-alpha-hydroxylase, cytochrome P450 family 724 subfamily B polypeptide 1, and allene oxide synthase. Conversely, the expression of P450 unigenes involved in gibberellin biosynthesis and abscisic acid catabolism, encoding ent-kaurene oxidase and abscisic acid 8'-hydroxylase, respectively, were promoted by 40% soil moisture. Under R. solanacearum infection, the expression of P450 unigenes involved in the biosynthesis of the above secondary metabolites were changed, but divergent expression patterns were observed under different soil moisture treatments. High moisture repressed expression of genes involved in flavonoid, brassinosteroid, gingerol, and jasmonate biosynthesis, but promoted expression of genes involved in GA anabolism and ABA catabolism. These results suggest possible mechanisms for how high moisture causes elevated susceptibility to R. solanacearum infection.
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Affiliation(s)
- Mengjun Huang
- College of Pharmaceutical Science and Chinese Medicine, Southwest University, Chongqing, Chongqing, China.,Research Institute for Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Haitao Xing
- Chongqing Key Laboratory of Economic Plant Biotechnology, Yongchuan, Chongqing, China
| | - Zhexin Li
- Research Institute for Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Honglei Li
- Research Institute for Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Lin Wu
- Chongqing Key Laboratory of Economic Plant Biotechnology, Yongchuan, Chongqing, China
| | - Yusong Jiang
- College of Pharmaceutical Science and Chinese Medicine, Southwest University, Chongqing, Chongqing, China.,Research Institute for Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
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Romero-Puertas MC, Terrón-Camero LC, Peláez-Vico MÁ, Molina-Moya E, Sandalio LM. An update on redox signals in plant responses to biotic and abiotic stress crosstalk: insights from cadmium and fungal pathogen interactions. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5857-5875. [PMID: 34111283 PMCID: PMC8355756 DOI: 10.1093/jxb/erab271] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 06/07/2021] [Indexed: 05/09/2023]
Abstract
Complex signalling pathways are involved in plant protection against single and combined stresses. Plants are able to coordinate genome-wide transcriptional reprogramming and display a unique programme of transcriptional responses to a combination of stresses that differs from the response to single stresses. However, a significant overlap between pathways and some defence genes in the form of shared and general stress-responsive genes appears to be commonly involved in responses to multiple biotic and abiotic stresses. Reactive oxygen and nitrogen species, as well as redox signals, are key molecules involved at the crossroads of the perception of different stress factors and the regulation of both specific and general plant responses to biotic and abiotic stresses. In this review, we focus on crosstalk between plant responses to biotic and abiotic stresses, in addition to possible plant protection against pathogens caused by previous abiotic stress. Bioinformatic analyses of transcriptome data from cadmium- and fungal pathogen-treated plants focusing on redox gene ontology categories were carried out to gain a better understanding of common plant responses to abiotic and biotic stresses. The role of reactive oxygen and nitrogen species in the complex network involved in plant responses to changes in their environment is also discussed.
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Affiliation(s)
- María C Romero-Puertas
- Department of Biochemistry and Molecular and Cellular Biology of Plants, Estacion Experimental del Zaidin (EEZ), Consejo Superior de Investigaciones Cientificas (CSIC), Apartado 419, 18080 Granada, Spain
- Correspondence:
| | - Laura C Terrón-Camero
- Department of Biochemistry and Molecular and Cellular Biology of Plants, Estacion Experimental del Zaidin (EEZ), Consejo Superior de Investigaciones Cientificas (CSIC), Apartado 419, 18080 Granada, Spain
- Bioinformatics Unit, Institute of Parasitology and Biomedicine “López-Neyra” (IPBLN-CSIC), Granada, Spain
| | - M Ángeles Peláez-Vico
- Department of Biochemistry and Molecular and Cellular Biology of Plants, Estacion Experimental del Zaidin (EEZ), Consejo Superior de Investigaciones Cientificas (CSIC), Apartado 419, 18080 Granada, Spain
| | - Eliana Molina-Moya
- Department of Biochemistry and Molecular and Cellular Biology of Plants, Estacion Experimental del Zaidin (EEZ), Consejo Superior de Investigaciones Cientificas (CSIC), Apartado 419, 18080 Granada, Spain
| | - Luisa M Sandalio
- Department of Biochemistry and Molecular and Cellular Biology of Plants, Estacion Experimental del Zaidin (EEZ), Consejo Superior de Investigaciones Cientificas (CSIC), Apartado 419, 18080 Granada, Spain
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Leitão ST, Santos C, Araújo SDS, Rubiales D, Vaz Patto MC. Shared and tailored common bean transcriptomic responses to combined fusarium wilt and water deficit. HORTICULTURE RESEARCH 2021; 8:149. [PMID: 34193847 PMCID: PMC8245569 DOI: 10.1038/s41438-021-00583-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 05/11/2021] [Accepted: 05/20/2021] [Indexed: 06/13/2023]
Abstract
Common bean (Phaseolus vulgaris L.), one of the most consumed food legumes worldwide, is threatened by two main constraints that are found frequently together in nature, water deficit (WD) and fusarium wilt (Fop). To understand the shared and unique responses of common bean to Fop and WD, we analyzed the transcriptomic changes and phenotypic responses in two accessions, one resistant and one susceptible to both stresses, exposed to single and combined stresses. Physiological responses (photosynthetic performance and pigments quantification) and disease progression were also assessed. The combined FopWD imposition negatively affected the photosynthetic performance and increased the susceptible accession disease symptoms. The susceptible accession revealed a higher level of transcriptional changes than the resistant one, and WD single stress triggered the highest transcriptional changes. While 89 differentially expressed genes were identified exclusively in combined stresses for the susceptible accession, 35 were identified in the resistant one. These genes belong mainly to "stress", "signaling", "cell wall", "hormone metabolism", and "secondary metabolism" functional categories. Among the up-regulated genes with higher expression in the resistant accession, the cysteine-rich secretory, antigen 5 and Pr-1 (CAP) superfamily protein, a ribulose bisphosphate carboxylase family protein, and a chitinase A seem promising targets for multiple stress breeding.
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Affiliation(s)
- Susana T Leitão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
| | - Carmen Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Susana de Sousa Araújo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Association BLC3 - Technology and Innovation Campus, Centre Bio R&D Unit, Lagares da Beira, Portugal
| | - Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, Córdoba, Spain
| | - Maria Carlota Vaz Patto
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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Krishnamurthy P, Vishal B, Bhal A, Kumar PP. WRKY9 transcription factor regulates cytochrome P450 genes CYP94B3 and CYP86B1, leading to increased root suberin and salt tolerance in Arabidopsis. PHYSIOLOGIA PLANTARUM 2021; 172:1673-1687. [PMID: 33619745 DOI: 10.1111/ppl.13371] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/08/2021] [Accepted: 02/12/2021] [Indexed: 05/27/2023]
Abstract
Salinity affects crop productivity worldwide and mangroves growing under high salinity exhibit adaptations such as enhanced root apoplastic barrier to survive under such conditions. We have identified two cytochrome P450 family genes, AoCYP94B3 and AoCYP86B1 from the mangrove tree Avicennia officinalis and characterized them using atcyp94b3 and atcyp86b1, which are mutants of their putative Arabidopsis orthologs and the corresponding complemented lines with A. officinalis genes. CYP94B3 and CYP86B1 transcripts were induced upon salt treatment in the roots of both A. officinalis and Arabidopsis. Both AoCYP94B3 and AoCYP86B1 were localized to the endoplasmic reticulum. Heterologous expression of 35S::AoCYP94B3 and 35S::AoCYP86B1 in their respective Arabidopsis mutants (atcyp94b3 and atcyp86b1) increased the salt tolerance of the transgenic seedlings by reducing the amount of Na+ accumulation in the shoots. Moreover, the reduced root suberin phenotype of atcyp94b3 was rescued in the 35S::AoCYP94B3;atcyp94b3 transgenic Arabidopsis seedlings. Gas-chromatography and mass spectrometry analyses showed that the amount of suberin monomers (C-16 ω-hydroxy acids, C-16 α, ω-dicarboxylic acids and C-20 eicosanol) were increased in the roots of 35S::AoCYP94B3;atcyp94b3 Arabidopsis seedlings. Using chromatin immunoprecipitation and electrophoretic mobility shift assays, we identified AtWRKY9 as the upstream regulator of AtCYP94B3 and AtCYP86B1 in Arabidopsis. In addition, atwrky9 showed suppressed expression of AtCYP94B3 and AtCYP86B1 transcripts, and reduced suberin in the roots. These results show that AtWRKY9 controls suberin deposition by regulating AtCYP94B3 and AtCYP86B1, leading to salt tolerance. Our data can be used for generating salt-tolerant crop plants in the future.
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Affiliation(s)
- Pannaga Krishnamurthy
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- NUS Environmental Research Institute (NERI), National University of Singapore, Singapore, Singapore
| | - Bhushan Vishal
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Amrit Bhal
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Prakash P Kumar
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- NUS Environmental Research Institute (NERI), National University of Singapore, Singapore, Singapore
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Aioub AAA, Zuo Y, Li Y, Qie X, Zhang X, Essmat N, Wu W, Hu Z. Transcriptome analysis of Plantago major as a phytoremediator to identify some genes related to cypermethrin detoxification. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:5101-5115. [PMID: 32954451 DOI: 10.1007/s11356-020-10774-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/08/2020] [Indexed: 06/11/2023]
Abstract
Cypermethrin (CYP) is a toxic manmade chemical compound belonging to pyrethroid insecticides contaminating the environment. Plantago major (PM) has numerous excellent advantages like high biomass yield and great stress tolerance, which make it able to increase the efficacy of phytoremediation. So far, no study has directly or indirectly made a transcriptome analysis (RNA-seq) of PM under CYP stress. The aim of this study is to identify the genes in PM related to CYP detoxification (10 μg mL-1) and compared with control. In this study, BGISEQ-500 high-throughput sequencing technology independently developed by BGI was used to sequence the transcriptome of P. major. Six libraries were constructed including (CK_1, CK_2, and CK_3) and (CYP_1, CYP_2, and CYP_3) were sequenced for transcripts involved in CYP detoxification. Our data showed that de novo assembly generated 138,806 unigenes with an average length of 1129 bp. Analyzing the annotation results of the KEGG database between the samples revealed 37,177 differentially expressed genes (DEGs), 18,062 down- and 19,115 upregulated under CYP treatment compared with control. A set of 107 genes of cytochrome P450 (Cyt P450), 43 genes of glutathione S-transferases (GST), 25 genes of glycosyltransferases (GTs), 113 genes from ABC transporters, 21 genes from multidrug and toxin efflux (MATE), 11 genes from oligopeptide transporter (OPT), and 3 genes of metallothioneins (MT) were upregulated notably. By using quantitative real-time PCR (qRT-PCR), the results of gene expression for 12 randomly selected DEGs were confirmed, showing the different patterns of response to CYP in PM tissues. Furthermore, the enzyme activity of Cyt P450 and GST in PM under CYP stress was significantly increased in roots and leaves than in control. This study introduces a clue to understand the metabolic pathways of plants used in phytoremediation by identifying the highly expressed genes related to phytoremediation which would be utilized to enhance pesticide detoxification and reduce pollution problem.
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Affiliation(s)
- Ahmed A A Aioub
- Institute of Pesticide Science, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Plant Protection Department, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt
| | - Yayun Zuo
- Institute of Pesticide Science, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Provincial Key Laboratory for Botanical Pesticide R & D of Shaanxi, Yangling, 712100, Shaanxi, China
| | - Yankai Li
- Institute of Pesticide Science, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Provincial Key Laboratory for Botanical Pesticide R & D of Shaanxi, Yangling, 712100, Shaanxi, China
| | - Xingtao Qie
- Institute of Pesticide Science, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Provincial Key Laboratory for Botanical Pesticide R & D of Shaanxi, Yangling, 712100, Shaanxi, China
| | - Xianxia Zhang
- Institute of Pesticide Science, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Provincial Key Laboratory for Botanical Pesticide R & D of Shaanxi, Yangling, 712100, Shaanxi, China
| | - Nariman Essmat
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Zagazig University, Zagazig, 44519, Egypt
| | - Wenjun Wu
- Provincial Key Laboratory for Botanical Pesticide R & D of Shaanxi, Yangling, 712100, Shaanxi, China
| | - Zhaonong Hu
- Institute of Pesticide Science, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China.
- Provincial Key Laboratory for Botanical Pesticide R & D of Shaanxi, Yangling, 712100, Shaanxi, China.
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Ministry of Agriculture, Yangling, 712100, Shaanxi, China.
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Yao L, Li Y, Ma C, Tong L, Du F, Xu M. Combined genome-wide association study and transcriptome analysis reveal candidate genes for resistance to Fusarium ear rot in maize. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:1535-1551. [PMID: 31961059 DOI: 10.1111/jipb.12911] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 01/15/2020] [Indexed: 05/24/2023]
Abstract
Fusarium ear rot, caused by Fusarium verticillioides, is a devastating fungal disease in maize that reduces yield and quality; moreover, F. verticillioides produces fumonisin mycotoxins, which pose serious threats to human and animal health. Here, we performed a genome-wide association study (GWAS) under three environmental conditions and identified 34 single-nucleotide polymorphisms (SNPs) that were significantly associated with Fusarium ear rot resistance. With reference to the maize B73 genome, 69 genes that overlapped with or were adjacent to the significant SNPs were identified as potential resistance genes to Fusarium ear rot. Comparing transcriptomes of the most resistant and most susceptible lines during the very early response to Fusarium ear rot, we detected many differentially expressed genes enriched for pathways related to plant immune responses, such as plant hormone signal transduction, phenylpropanoid biosynthesis, and cytochrome P450 metabolism. More than one-fourth of the potential resistance genes detected in the GWAS were differentially expressed in the transcriptome analysis, which allowed us to predict numbers of candidate genes for maize resistance to ear rot, including genes related to plant hormones, a MAP kinase, a PR5-like receptor kinase, and heat shock proteins. We propose that maize plants initiate early immune responses to Fusarium ear rot mainly by regulating the growth-defense balance and promoting biosynthesis of defense compounds.
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Affiliation(s)
- Lishan Yao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Yanmei Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Chuanyu Ma
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Lixiu Tong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Feili Du
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Mingliang Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
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Rastogi S, Satapathy S, Shah S, Mytrai, Prakash H. In silico identification of cytochrome P450s involved in Ocimum tenuiflorum subjected to four abiotic stresses. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Martin RC, Kronmiller BA, Dombrowski JE. Transcriptome analysis of responses in Brachypodium distachyon overexpressing the BdbZIP26 transcription factor. BMC PLANT BIOLOGY 2020; 20:174. [PMID: 32312226 PMCID: PMC7171782 DOI: 10.1186/s12870-020-02341-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 03/12/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Biotic and abiotic stresses are the major cause of reduced growth, persistence, and yield in agriculture. Over the past decade, RNA-Sequencing and the use of transgenics with altered expression of stress related genes have been utilized to gain a better understanding of the molecular mechanisms leading to salt tolerance in a variety of species. Identification of transcription factors that, when overexpressed in plants, improve multiple stress tolerance may be valuable for crop improvement, but sometimes overexpression leads to deleterious effects during normal plant growth. RESULTS Brachypodium constitutively expressing the BdbZIP26:GFP gene showed reduced stature compared to wild type plants (WT). RNA-Seq analysis comparing WT and bZIP26 transgenic plants revealed 7772 differentially expressed genes (DEGs). Of these DEGs, 987 of the DEGs were differentially expressed in all three transgenic lines. Many of these DEGs are similar to those often observed in response to abiotic and biotic stress, including signaling proteins such as kinases/phosphatases, calcium/calmodulin related proteins, oxidases/reductases, hormone production and signaling, transcription factors, as well as disease responsive proteins. Interestingly, there were many DEGs associated with protein turnover including ubiquitin-related proteins, F-Box and U-box related proteins, membrane proteins, and ribosomal synthesis proteins. Transgenic and control plants were exposed to salinity stress. Many of the DEGs between the WT and transgenic lines under control conditions were also found to be differentially expressed in WT in response to salinity stress. This suggests that the over-expression of the transcription factor is placing the plant in a state of stress, which may contribute to the plants diminished stature. CONCLUSION The constitutive expression of BdbZIP26:GFP had an overall negative effect on plant growth and resulted in stunted plants compared to WT plants under control conditions, and a similar response to WT plants under salt stress conditions. The results of gene expression analysis suggest that the transgenic plants are in a constant state of stress, and that they are trying to allocate resources to survive.
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Affiliation(s)
- Ruth C. Martin
- United States Department of Agriculture, Agricultural Research Service, National Forage Seed Production Research Center, 3450 SW Campus Way, Corvallis, OR 97331 USA
| | - Brent A. Kronmiller
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331 USA
| | - James E. Dombrowski
- United States Department of Agriculture, Agricultural Research Service, National Forage Seed Production Research Center, 3450 SW Campus Way, Corvallis, OR 97331 USA
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Wang M, Yuan J, Qin L, Shi W, Xia G, Liu S. TaCYP81D5, one member in a wheat cytochrome P450 gene cluster, confers salinity tolerance via reactive oxygen species scavenging. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:791-804. [PMID: 31472082 PMCID: PMC7004906 DOI: 10.1111/pbi.13247] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 08/16/2019] [Accepted: 08/27/2019] [Indexed: 05/03/2023]
Abstract
As one of the largest gene families in plants, the cytochrome P450 monooxygenase genes (CYPs) are involved in diverse biological processes including biotic and abiotic stress response. Moreover, P450 genes are prone to expanding due to gene tandem duplication during evolution, resulting in generations of novel alleles with the neo-function or enhanced function. Here, the bread wheat (Triticum aestivum) gene TaCYP81D5 was found to lie within a cluster of five tandemly arranged CYP81D genes, although only a single such gene (BdCYP81D1) was present in the equivalent genomic region of the wheat relative Brachypodium distachyon. The imposition of salinity stress could up-regulate TaCYP81D5, but the effect was abolished in plants treated with an inhibitor of reactive oxygen species synthesis. In SR3, a wheat cultivar with an elevated ROS content, the higher expression and the rapider response to salinity of TaCYP81D5 were related to the chromatin modification. Constitutively expressing TaCYP81D5 enhanced the salinity tolerance both at seedling and reproductive stages of wheat via accelerating ROS scavenging. Moreover, an important component of ROS signal transduction, Zat12, was proven crucial in this process. Though knockout of solely TaCYP81D5 showed no effect on salinity tolerance, knockdown of BdCYP81D1 or all TaCYP81D members in the cluster caused the sensitivity to salt stress. Our results provide the direct evidence that TaCYP81D5 confers salinity tolerance in bread wheat and this gene is prospective for crop improvement.
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Affiliation(s)
- Meng Wang
- State Key Laboratory of Soil and Sustainable AgricultureInstitute of Soil ScienceChinese Academy of SciencesNanjingChina
- Key Laboratory of Plant Development and Environmental Adaptation BiologyMinistry of EducationSchool of Life SciencesShandong UniversityQingdaoChina
| | - Jiarui Yuan
- Key Laboratory of Plant Development and Environmental Adaptation BiologyMinistry of EducationSchool of Life SciencesShandong UniversityQingdaoChina
| | - Lumin Qin
- Key Laboratory of Plant Development and Environmental Adaptation BiologyMinistry of EducationSchool of Life SciencesShandong UniversityQingdaoChina
| | - Weiming Shi
- State Key Laboratory of Soil and Sustainable AgricultureInstitute of Soil ScienceChinese Academy of SciencesNanjingChina
| | - Guangmin Xia
- Key Laboratory of Plant Development and Environmental Adaptation BiologyMinistry of EducationSchool of Life SciencesShandong UniversityQingdaoChina
| | - Shuwei Liu
- Key Laboratory of Plant Development and Environmental Adaptation BiologyMinistry of EducationSchool of Life SciencesShandong UniversityQingdaoChina
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Comparative Transcriptome Analysis of Two Cucumber Cultivars with Different Sensitivity to Cucumber Mosaic Virus Infection. Pathogens 2020; 9:pathogens9020145. [PMID: 32098056 PMCID: PMC7168641 DOI: 10.3390/pathogens9020145] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/17/2020] [Accepted: 02/19/2020] [Indexed: 12/15/2022] Open
Abstract
Cucumber mosaic virus (CMV), with extremely broad host range including both monocots and dicots around the world, belongs to most important viral crop threats. Either natural or genetically constructed sources of resistance are being intensively investigated; for this purpose, exhaustive knowledge of molecular virus-host interaction during compatible and incompatible infection is required. New technologies and computer-based “omics” on various levels contribute markedly to this topic. In this work, two cucumber cultivars with different response to CMV challenge were tested, i.e., sensitive cv. Vanda and resistant cv. Heliana. The transcriptomes were prepared from both cultivars at 18 days after CMV or mock inoculation. Subsequently, four independent comparative analyses of obtained data were performed, viz. mock- and CMV-inoculated samples within each cultivar, samples from mock-inoculated cultivars to each other and samples from virus-inoculated cultivars to each other. A detailed picture of CMV-influenced genes, as well as constitutive differences in cultivar-specific gene expression was obtained. The compatible CMV infection of cv. Vanda caused downregulation of genes involved in photosynthesis, and induction of genes connected with protein production and modification, as well as components of signaling pathways. CMV challenge caused practically no change in the transcription profile of the cv. Heliana. The main differences between constitutive transcription activity of the two cultivars relied in the expression of genes responsible for methylation, phosphorylation, cell wall organization and carbohydrate metabolism (prevailing in cv. Heliana), or chromosome condensation and glucan biosynthesis (prevailing in cv. Vanda). Involvement of several genes in the resistant cucumber phenotype was predicted; this can be after biological confirmation potentially applied in breeding programs for virus-resistant crops.
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Pérez-Palacios P, Funes-Pinter I, Agostini E, Talano MA, Ibáñez SG, Humphry M, Edwards K, Rodríguez-Llorente ID, Caviedes MA, Pajuelo E. Targeting Acr3 from Ensifer medicae to the plasma membrane or to the tonoplast of tobacco hairy roots allows arsenic extrusion or improved accumulation. Effect of acr3 expression on the root transcriptome. Metallomics 2019; 11:1864-1886. [PMID: 31588944 DOI: 10.1039/c9mt00191c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Transgenic tobacco hairy roots expressing the bacterial arsenite efflux pump Acr3 from Ensifer medicae were generated. The gene product was targeted either to the plasma membrane (ACR3 lines) or to the tonoplast by fusing the ACR3 protein to the tonoplast integral protein TIP1.1 (TIP-ACR3 lines). Roots expressing Acr3 at the tonoplast showed greater biomass than those expressing Acr3 at the plasma membrane. Furthermore, higher contents of malondialdehyde (MDA) and RNA degradation in ACR3 lines were indicative of higher oxidative stress. The determination of ROS-scavenging enzymes depicted the transient role of peroxidases in ROS detoxification, followed by the action of superoxide dismutase during both short- and medium-term exposure periods. Regarding As accumulation, ACR3 lines accumulated up to 20-30% less As, whereas TIP-ACR3 achieved a 2-fold increase in As accumulation in comparison to control hairy roots. Strategies that presumably induce As uptake, such as phosphate deprivation or dehydration followed by rehydration in the presence of As, fostered As accumulation up to 10 800 μg g-1. Finally, the effects of the heterologous expression of acr3 on the root transcriptome were assessed. Expression at the plasma membrane induced drastic changes in gene expression, with outstanding overexpression of genes related to electron transport, ATP synthesis and ATPases, suggesting that As efflux is the main detoxification mechanism in these lines. In addition, genes encoding heat shock proteins and those related to proline synthesis and drought tolerance were activated. On the other hand, TIP-ACR3 lines showed a similar gene expression profile to that of control roots, with overexpression of the glutathione and phytochelatin synthesis pathways, together with secondary metabolism pathways as the most important resistance mechanisms in TIP-ACR3, for which As allocation into the vacuole allowed better growth and stress management. Our results suggest that modulation of As accumulation can be achieved by subcellular targeting of Acr3: expression at the tonoplast enhances As accumulation in roots, whereas expression at the plasma membrane could promote As efflux. Thus, both approaches open the possibilities for developing safer crops when grown on As-polluted paddy soils, but expression at the tonoplast leads to better growth and less stressed roots, since the high energy cost of As efflux likely compromises growth in ACR3 lines.
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Affiliation(s)
- Patricia Pérez-Palacios
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, c/Profesor García González, 2, 41012-Sevilla, Spain. and Departamento de Biología Molecular, FCEFQyN, Universidad Nacional de Río Cuarto, Ruta Nacional 36 - Km. 601 - Río Cuarto, Córdoba, Argentina and Plant Biotechnology Division, British American Tobacco, Cambridge, CB4 0WA, UK
| | - Iván Funes-Pinter
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, c/Profesor García González, 2, 41012-Sevilla, Spain. and Facultad de Ciencias Agrarias, Universidad Nacional de Cuyo, Mendoza (CP 5507), Atte Brown 500, Chacras de Coria, Argentina
| | - Elizabeth Agostini
- Departamento de Biología Molecular, FCEFQyN, Universidad Nacional de Río Cuarto, Ruta Nacional 36 - Km. 601 - Río Cuarto, Córdoba, Argentina
| | - Melina A Talano
- Departamento de Biología Molecular, FCEFQyN, Universidad Nacional de Río Cuarto, Ruta Nacional 36 - Km. 601 - Río Cuarto, Córdoba, Argentina
| | - Sabrina G Ibáñez
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Matt Humphry
- British American Tobacco (Investments) Ltd, Cambridge, CB4 0WA, UK
| | - Kieron Edwards
- Plant Biotechnology Division, British American Tobacco, Cambridge, CB4 0WA, UK
| | - Ignacio D Rodríguez-Llorente
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, c/Profesor García González, 2, 41012-Sevilla, Spain.
| | - Miguel A Caviedes
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, c/Profesor García González, 2, 41012-Sevilla, Spain.
| | - Eloísa Pajuelo
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, c/Profesor García González, 2, 41012-Sevilla, Spain.
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Rubio MB, Martínez de Alba AE, Nicolás C, Monte E, Hermosa R. Early Root Transcriptomic Changes in Wheat Seedlings Colonized by Trichoderma harzianum Under Different Inorganic Nitrogen Supplies. Front Microbiol 2019; 10:2444. [PMID: 31749777 PMCID: PMC6842963 DOI: 10.3389/fmicb.2019.02444] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 10/10/2019] [Indexed: 12/02/2022] Open
Abstract
Wheat is one of the most important crops worldwide. The use of plant growth promoting microorganisms, such as those of the genus Trichoderma, constitutes an alternative to chemical fertilizers, since they are cheaper and are not detrimental to the environment. However, the interaction between Trichoderma and wheat plants has been scarcely studied, at least at a molecular level. In the present work, a microarray approach was used to study the early transcriptomic changes induced in wheat roots by Trichoderma harzianum, applied alone or in combination with different concentrations of calcium nitrate [Ca(NO3)2], which was last used as nitrogen (N) source. Our results show that T. harzianum causes larger transcriptomic changes than Ca(NO3)2 in wheat roots, and such changes are different when plants are challenged with Trichoderma alone or treated with a combination of T. harzianum and Ca(NO3)2. Overall, T. harzianum activates the expression of defense-related genes at early stages of the interaction with the roots, while this fungus reduces the expression of genes related to plant growth and development. Moreover, the current study in wheat roots, subjected to the different T. harzianum and Ca(NO3)2 combinations, reveals that the number of transcriptomic changes was higher when compared against those caused by the different Ca(NO3)2 concentrations than when it was compared against those caused by T. harzianum. N metabolism gene expression changes were in agreement with the levels of nitrate reductase activity measured in plants from Trichoderma plus Ca(NO3)2 conditions. Results were also concordant with plant phenotypes, which showed reduced growth at early interaction stages when inoculated with T. harzianum or with its combination with Ca(NO3)2 at the lowest dosage. These results were in a good agreement with the recognized role of Trichoderma as an inducer of plant defense.
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Affiliation(s)
- M Belén Rubio
- Department of Microbiology and Genetics, Spanish-Portuguese Institute for Agricultural Research (CIALE), University of Salamanca, Salamanca, Spain
| | - A Emilio Martínez de Alba
- Department of Microbiology and Genetics, Spanish-Portuguese Institute for Agricultural Research (CIALE), University of Salamanca, Salamanca, Spain
| | - Carlos Nicolás
- Department of Botany and Plant Pathology, Spanish-Portuguese Institute for Agricultural Research (CIALE), University of Salamanca, Salamanca, Spain
| | - Enrique Monte
- Department of Microbiology and Genetics, Spanish-Portuguese Institute for Agricultural Research (CIALE), University of Salamanca, Salamanca, Spain
| | - Rosa Hermosa
- Department of Microbiology and Genetics, Spanish-Portuguese Institute for Agricultural Research (CIALE), University of Salamanca, Salamanca, Spain
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Elucidating Drought Stress Tolerance in European Oaks Through Cross-Species Transcriptomics. G3-GENES GENOMES GENETICS 2019; 9:3181-3199. [PMID: 31395652 PMCID: PMC6778798 DOI: 10.1534/g3.119.400456] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The impact of climate change that comes with a dramatic increase of long periods of extreme summer drought associated with heat is a fundamental challenge for European forests. As a result, forests are expected to shift their distribution patterns toward north-east, which may lead to a dramatic loss in value of European forest land. Consequently, unraveling key processes that underlie drought stress tolerance is not only of great scientific but also of utmost economic importance for forests to withstand future heat and drought wave scenarios. To reveal drought stress-related molecular patterns we applied cross-species comparative transcriptomics of three major European oak species: the less tolerant deciduous pedunculate oak (Quercus robur), the deciduous but quite tolerant pubescent oak (Q. pubescens), and the very tolerant evergreen holm oak (Q. ilex). We found 415, 79, and 222 differentially expressed genes during drought stress in Q. robur, Q. pubescens, and Q. ilex, respectively, indicating species-specific response mechanisms. Further, by comparative orthologous gene family analysis, 517 orthologous genes could be characterized that may play an important role in drought stress adaptation on the genus level. New regulatory candidate pathways and genes in the context of drought stress response were identified, highlighting the importance of the antioxidant capacity, the mitochondrial respiration machinery, the lignification of the water transport system, and the suppression of drought-induced senescence - providing a valuable knowledge base that could be integrated in breeding programs in the face of climate change.
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Hussain A, Noman A, Khan MI, Zaynab M, Aqeel M, Anwar M, Ashraf MF, Liu Z, Raza A, Mahpara S, Bakhsh A, He S. Molecular regulation of pepper innate immunity and stress tolerance: An overview of WRKY TFs. Microb Pathog 2019; 135:103610. [DOI: 10.1016/j.micpath.2019.103610] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 04/22/2019] [Accepted: 06/21/2019] [Indexed: 01/20/2023]
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Hwang JE, Hwang SG, Jung IJ, Han SM, Ahn JW, Kim JB. Overexpression of rice F-box protein OsFBX322 confers increased sensitivity to gamma irradiation in Arabidopsis. Genet Mol Biol 2019; 43:e20180273. [PMID: 31479093 PMCID: PMC7251472 DOI: 10.1590/1678-4685-gmb-2018-0273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 03/25/2019] [Indexed: 11/30/2022] Open
Abstract
Ionizing radiation has a substantial effect on physiological and biochemical
processes in plants via induction of transcriptional changes and diverse genetic
alterations. Previous microarray analysis showed that rice
OsFBX322, which encodes a rice F-box protein, was
downregulated in response to three types of ionizing radiation: gamma
irradiation, ion beams, and cosmic rays. In order to characterize the
radiation-responsive genes in rice, OsFBX322 was selected for
further analysis. OsFBX322 expression patterns in response to
radiation were confirmed using quantitative RT-PCR. Transient expression of a
GFP-OsFBX322 fusion protein in tobacco leaf epidermis indicated that OsFBX322 is
localized to the nucleus. To determine the effect of OsFBX322
expression on radiation response, OsFBX322 was overexpressed in
Arabidopsis. Transgenic overexpression lines were more
sensitive to gamma irradiation than control plants. These results suggest that
OsFBX322 plays a negative role in the defense response to
radiation in plants. In addition, we obtained four co-expression genes of
OsFBX322 by specific co-expression networks using the
ARANCE. Quantitative RT-PCR showed that the four genes were also downregulated
after exposure to the three types of radiation. These results imply that the
co-expressed genes may serve as key regulators in the radiation response pathway
in plants.
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Affiliation(s)
- Jung Eun Hwang
- National Institute of Ecology, Research Center for Endangered Species, Division of Restoration Research, Yeongyang, Republic of Korea
| | - Sun-Goo Hwang
- Kangwon Natl University, Department of Applied Plant Sciences, Plant Genomics Lab, Chuncheon, Republic of Korea
| | - In Jung Jung
- Korea Atomic Energy Research Institute, Advanced Radiation Technology Institute, Jeongeup, Republic of Korea
| | - Sung Min Han
- Korea Atomic Energy Research Institute, Advanced Radiation Technology Institute, Jeongeup, Republic of Korea
| | - Joon-Woo Ahn
- Korea Atomic Energy Research Institute, Advanced Radiation Technology Institute, Jeongeup, Republic of Korea
| | - Jin-Baek Kim
- Korea Atomic Energy Research Institute, Advanced Radiation Technology Institute, Jeongeup, Republic of Korea
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Joshi R, Paul M, Kumar A, Pandey D. Role of calreticulin in biotic and abiotic stress signalling and tolerance mechanisms in plants. Gene 2019; 714:144004. [PMID: 31351124 DOI: 10.1016/j.gene.2019.144004] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 07/23/2019] [Accepted: 07/23/2019] [Indexed: 12/12/2022]
Abstract
Calreticulin (CRT) is calcium binding protein of endoplasmic reticulum (ER) which performs plethora of functions besides it's role as molecular chaperone. Among the three different isoforms of this protein, CRT3 is most closely related to primitive CRT gene of higher plants. Based on their distinct structural and functional organisation, the plant CRTs have been known to contain three different domains: N, P and the C domain. The domain organisation and various biochemical characterstics of plant and animal CRTs are common with the exception of some differences. In plant calreticulin, the important N-glycosylation site(s) are replaced by the glycan chain(s) and several consensus sequences for in vitro phosphorylation by protein kinase CK2 (casein kinase-2), are also present unlike the animal calreticulin. Biotic and abiotic stresses play a significant role in bringing down the crop production. The role of various phytohormones in defense against fungal pathogens is well documented. CRT3 has been reported to play important role in protecting the plants against fungal and bacterial pathogens and in maintaining plant innate immunity. There is remarkable crosstalk between CRT mediated signalling and biotic, abiotic stress, and phytohormone mediated signalling pathways The role of CRT mediated pathway in mitigating biotic and abiotic stress can be further explored in plants so as to strategically modify it for development of stress tolerant plants.
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Affiliation(s)
- Rini Joshi
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences & Humanities, G. B. Pant University of Ag.& Tech., Pantnagar 263145, Uttarakhand, India
| | - Meenu Paul
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences & Humanities, G. B. Pant University of Ag.& Tech., Pantnagar 263145, Uttarakhand, India
| | - Anil Kumar
- Rani Laxmi Bai Central Agriculture University, Jhansi, Uttar Pradesh 284003, India
| | - Dinesh Pandey
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences & Humanities, G. B. Pant University of Ag.& Tech., Pantnagar 263145, Uttarakhand, India.
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28
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Song Y, Yang X, Yang S, Wang J. Transcriptome sequencing and functional analysis of Sedum lineare Thunb. upon salt stress. Mol Genet Genomics 2019; 294:1441-1453. [DOI: 10.1007/s00438-019-01587-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 06/11/2019] [Indexed: 12/12/2022]
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29
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Liu X, Bi B, Xu X, Li B, Tian S, Wang J, Zhang H, Wang G, Han Y, McElroy JS. Rapid identification of a candidate nicosulfuron sensitivity gene (Nss) in maize (Zea mays L.) via combining bulked segregant analysis and RNA-seq. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1351-1361. [PMID: 30652203 DOI: 10.1007/s00122-019-03282-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 01/07/2019] [Indexed: 05/24/2023]
Abstract
A candidate nicosulfuron sensitivity gene Nss was identified by combining bulked segregant analysis and RNA-seq. Multiple mutations of this gene were discovered in nicosulfuron-sensitive maize compared with the tolerant. It has been demonstrated that variabilities exist in maize response to nicosulfuron. Two nicosulfuron-sensitive inbred lines (HB39, HB41) and two tolerant inbred lines (HB05, HB09) were identified via greenhouse and field trials. Genetic analysis indicated that the sensitivity to nicosulfuron in maize was controlled by a single, recessive gene. To precisely and rapidly map the nicosulfuron sensitivity gene (Nss), two independent F2 segregating populations, Population A (HB41 × HB09) and Population B (HB39 × HB05), were constructed. By applying bulked segregant RNA-Seq (BSR-Seq), the Nss gene was, respectively, mapped on the short arm of chromosome 5 (chr5: 1.1-15.3 Mb) and (chr5: 0.5-18.2 Mb) using two populations, with 14.2 Mb region in common. Further analysis revealed that there were 43 and 119 differentially expressed genes in the mapping intervals, with 18 genes in common. Gene annotation results showed that a cytochrome P450 gene (CYP81A9) appeared to be the candidate gene of Nss associated with nicosulfuron sensitivity in maize. Sequence analysis demonstrated that two common deletion mutations existed in the sensitive maize, which might lead to the nicosulfuron sensitivity in maize. The results will make valuable contributions to the understanding of molecular mechanism of herbicide sensitivity in maize.
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Affiliation(s)
- Xiaomin Liu
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, China
| | - Bo Bi
- Department of Crop, Soil and Environmental Science, Auburn University, Auburn, AL, 36849, USA
| | - Xian Xu
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, China
| | - Binghua Li
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, China
| | - Shengmin Tian
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, China
| | - Jianping Wang
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, China
| | - Hui Zhang
- Department of Crop, Soil and Environmental Science, Auburn University, Auburn, AL, 36849, USA
| | - Guiqi Wang
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, China.
| | - Yujun Han
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, China.
| | - J Scott McElroy
- Department of Crop, Soil and Environmental Science, Auburn University, Auburn, AL, 36849, USA.
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Park SC, Kim IR, Hwang JE, Kim JY, Jung YJ, Choi W, Lee Y, Jang MK, Lee JR. Functional Mechanisms Underlying the Antimicrobial Activity of the Oryza sativa Trx-like Protein. Int J Mol Sci 2019; 20:ijms20061413. [PMID: 30897830 PMCID: PMC6471494 DOI: 10.3390/ijms20061413] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/13/2019] [Accepted: 03/19/2019] [Indexed: 12/14/2022] Open
Abstract
Plants are constantly subjected to a variety of environmental stresses and have evolved regulatory responses to overcome unfavorable conditions that might reduce or adversely change a plant’s growth or development. Among these, the regulated production of reactive oxygen species (ROS) as a signaling molecule occurs during plant development and pathogen defense. This study demonstrates the possible antifungal activity of Oryza sativa Tetratricopeptide Domain-containing thioredoxin (OsTDX) protein against various fungal pathogens. The transcription of OsTDX was induced by various environmental stresses known to elicit the generation of ROS in plant cells. OsTDX protein showed potent antifungal activity, with minimum inhibitory concentrations (MICs) against yeast and filamentous fungi ranging between 1.56 and 6.25 and 50 and 100 µg/mL, respectively. The uptake of SYTOX-Green into fungal cells and efflux of calcein from artificial fungus-like liposomes suggest that its killing mechanism involves membrane permeabilization and damage. In addition, irregular blebs and holes apparent on the surfaces of OsTDX-treated fungal cells indicate the membranolytic action of this protein. Our results suggest that the OsTDX protein represents a potentially useful lead for the development of pathogen-resistant plants.
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Affiliation(s)
- Seong-Cheol Park
- Department of Polymer Science and Engineering, Sunchon National University, Suncheon 57922, Korea.
| | - Il Ryong Kim
- National Institute of Ecology, 1210 Geumgang-ro, Maseo-myeon, Seocheon-gun 33657, Korea.
- Division of Applied Life Science (BK21+ Program) and PMBBRC, Gyeongsang National University, Jinju 52828, Korea.
| | - Jung Eun Hwang
- National Institute of Ecology, 1210 Geumgang-ro, Maseo-myeon, Seocheon-gun 33657, Korea.
| | - Jin-Young Kim
- Department of Polymer Science and Engineering, Sunchon National University, Suncheon 57922, Korea.
| | - Young Jun Jung
- National Institute of Ecology, 1210 Geumgang-ro, Maseo-myeon, Seocheon-gun 33657, Korea.
| | - Wonkyun Choi
- National Institute of Ecology, 1210 Geumgang-ro, Maseo-myeon, Seocheon-gun 33657, Korea.
| | - Yongjae Lee
- Department of Nutrition and Food Science, Texas A&M University, College Station, TX 77843, USA.
| | - Mi-Kyeong Jang
- Department of Polymer Science and Engineering, Sunchon National University, Suncheon 57922, Korea.
- The Research Institute for Sanitation and Environment of Coastal Areas, Sunchon National University, Suncheon 57922, Korea.
| | - Jung Ro Lee
- National Institute of Ecology, 1210 Geumgang-ro, Maseo-myeon, Seocheon-gun 33657, Korea.
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Panozzo A, Dal Cortivo C, Ferrari M, Vicelli B, Varotto S, Vamerali T. Morphological Changes and Expressions of AOX1A, CYP81D8, and Putative PFP Genes in a Large Set of Commercial Maize Hybrids Under Extreme Waterlogging. FRONTIERS IN PLANT SCIENCE 2019; 10:62. [PMID: 30778365 PMCID: PMC6369177 DOI: 10.3389/fpls.2019.00062] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/16/2019] [Indexed: 05/24/2023]
Abstract
Waterlogging is a severe abiotic stressor causing significant growth impairment and yield losses in many crops. Maize is highly sensitive to the excess of water, and against the background of climate change there is an urgent need for deeper insights into the mechanisms of crop adaptation to waterlogging. In the present study, changes in maize morphology at the 4-5 leaf stage and the expression of three candidate genes for flooding tolerance in plants subjected to six continuous days of waterlogging were recorded in 19 commercial hybrids and in the inbred line B73, with the aim of investigating the current variability in cultivated hybrids and identifying useful morphological and molecular markers for screening tolerant genotypes. Here it was demonstrated that root parameters (length, area, biomass) were more impaired by waterlogging than shoot parameters (shoot height and biomass). Culm height generally increased in stressed plants (by up to +24% vs. controls), while shoot biomass was significantly reduced in only two hybrids. Root biomass was reduced in all the hybrids, by an average of 30%, and significantly in 7 hybrids, while root length and area were even more severely reduced, by 30-55% vs. controls, depending on the hybrid. The earlier appearance of aerial roots seemed to be associated with greater root injuries. In leaves, the transcript of the PFP enzyme (phosphofructokinase), which is involved in glycolytic reactions, was markedly up-regulated (up to double the values) in half the waterlogged hybrids, but down-regulated in the others. The transcript of CYP81D8 (ROS-related proteins) in waterlogged plants exhibited relevant increases or strong decreases in level, depending on the hybrid. The transcript of the AOX1A gene, coding for a mitochondrial respiratory electron transport chain-related protein, was markedly down-regulated in all the treated hybrids. Expression analysis of these genes under extreme waterlogging only partially correlate with the shoot and root growth impairments observed, and AOX1A seems to be the most informative of them.
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Lekklar C, Pongpanich M, Suriya-arunroj D, Chinpongpanich A, Tsai H, Comai L, Chadchawan S, Buaboocha T. Genome-wide association study for salinity tolerance at the flowering stage in a panel of rice accessions from Thailand. BMC Genomics 2019; 20:76. [PMID: 30669971 PMCID: PMC6343365 DOI: 10.1186/s12864-018-5317-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 11/27/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Salt stress, a major plant environmental stress, is a critical constraint for rice productivity. Dissecting the genetic loci controlling salt tolerance in rice for improving productivity, especially at the flowering stage, remains challenging. Here, we conducted a genome-wide association study (GWAS) of salt tolerance based on exome sequencing of the Thai rice accessions. RESULTS Photosynthetic parameters and cell membrane stability under salt stress at the flowering stage; and yield-related traits of 104 Thai rice (Oryza sativa L.) accessions belonging to the indica subspecies were evaluated. The rice accessions were subjected to exome sequencing, resulting in 112,565 single nucleotide polymorphisms (SNPs) called with a minor allele frequency of at least 5%. LD decay analysis of the panel indicates that the average LD for SNPs at 20 kb distance from each other was 0.34 (r2), which decayed to its half value (~ 0.17) at around 80 kb. By GWAS performed using mixed linear model, two hundred loci containing 448 SNPs on exons were identified based on the salt susceptibility index of the net photosynthetic rate at day 6 after salt stress; and the number of panicles, filled grains and unfilled grains per plant. One hundred and forty six genes, which accounted for 73% of the identified loci, co-localized with the previously reported salt quantitative trait loci (QTLs). The top four regions that contained a high number of significant SNPs were found on chromosome 8, 12, 1 and 2. While many are novel, their annotation is consistent with potential involvement in plant salt tolerance and in related agronomic traits. These significant SNPs greatly help narrow down the region within these QTLs where the likely underlying candidate genes can be identified. CONCLUSIONS Insight into the contribution of potential genes controlling salt tolerance from this GWAS provides further understanding of salt tolerance mechanisms of rice at the flowering stage, which can help improve yield productivity under salinity via gene cloning and genomic selection.
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Affiliation(s)
- Chakkree Lekklar
- Biological Sciences Program, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Center of Excellent in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Monnat Pongpanich
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Duangjai Suriya-arunroj
- Nakhon Ratchasima Rice Research Center, Rice Department, Ministry of Agriculture and Cooperatives, Nakhon Ratchasima, Thailand
| | - Aumnart Chinpongpanich
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Helen Tsai
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA USA
| | - Luca Comai
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA USA
| | - Supachitra Chadchawan
- Center of Excellent in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Teerapong Buaboocha
- Center of Excellent in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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Vemanna RS, Bakade R, Bharti P, Kumar MKP, Sreeman SM, Senthil-Kumar M, Makarla U. Cross-Talk Signaling in Rice During Combined Drought and Bacterial Blight Stress. FRONTIERS IN PLANT SCIENCE 2019; 10:193. [PMID: 30894866 PMCID: PMC6415615 DOI: 10.3389/fpls.2019.00193] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 02/05/2019] [Indexed: 05/22/2023]
Abstract
Due to climatic changes, rice crop is affected by moisture deficit stress and pathogens. Tissue water limitation besides reducing growth rates, also renders the crop susceptible to the infection by Xanthomonas oryzae pv. oryzae (Xoo) that causes bacterial leaf blight. Independently, both drought adaptation and Xoo resistance have been extensively studied. Though the cross-talk between drought and Xoo stress responses have been explored from individual stress studies, examining the combinatorial stress response is limited in rice. Recently published combined stress studies showed that under the combined stress, maintenance of carbon assimilation is hindered and such response is regulated by overlapping cellular mechanisms that are different from either of the individual stresses. Several receptors, MAP kinases, transcription factors, and ribosomal proteins, are predicted for playing a role in cellular homeostasis and protects cells from combined stress effects. Here we provide a critical analysis of these aspects using information from the recently published combined stress literature. This review is useful for researchers to comprehend combinatorial stress response of rice plants to drought and Xoo.
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Affiliation(s)
- Ramu S. Vemanna
- Department of Crop Physiology, University of Agriculture Sciences, Bengaluru, India
- Regional Center for Biotechnology, Faridabad, India
- *Correspondence: Ramu S. Vemanna, ;
| | - Rahul Bakade
- Department of Plant Pathology, University of Agriculture Sciences, Bengaluru, India
| | - Pooja Bharti
- Department of Crop Physiology, University of Agriculture Sciences, Bengaluru, India
| | - M. K. Prasanna Kumar
- Department of Plant Pathology, University of Agriculture Sciences, Bengaluru, India
| | | | | | - Udayakumar Makarla
- Department of Crop Physiology, University of Agriculture Sciences, Bengaluru, India
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Woldesemayat AA, Ntwasa M. Pathways and Network Based Analysis of Candidate Genes to Reveal Cross-Talk and Specificity in the Sorghum ( Sorghum bicolor (L.) Moench) Responses to Drought and It's Co-occurring Stresses. Front Genet 2018; 9:557. [PMID: 30515190 PMCID: PMC6255970 DOI: 10.3389/fgene.2018.00557] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 10/31/2018] [Indexed: 12/01/2022] Open
Abstract
Drought alone or in combination with other stresses forms the major crop production constraint worldwide. Sorghum, one of the most important cereal crops is affected by drought alone or in combination with co-occurring stresses; notwithstanding, sorghum has evolved adaptive responses to combined stresses. Furthermore, an impressive number of sorghum genes have been investigated for drought tolerance. However, the molecular mechanism underling drought response remains poorly understood. We employed a systems biology approach to elucidate regulatory and broad functional features of these genes. Their interaction network would provide insight into understanding the molecular mechanisms of drought tolerance and underpinning signal pathways. Functional analysis was undertaken to determine significantly enriched genesets for pathways involved in drought tolerance. Analysis of distinct pathway cross-talk network was performed and drought-specific subnetwork was extracted. Investigation of various data sources such as gene expression, regulatory pathways, sorghumCyc, sorghum protein-protein interaction (PPI) and Gene Ontology (GO) revealed 14 major drought stress related hub genes (DSRhub genes). Significantly enriched genesets have shown association with various biological processes underlying drought-related responses. Key metabolic pathways were significantly enriched in the drought-related genes. Systematic analysis of pathways cross-talk and gene interaction network revealed major cross-talk pathway modules associated with drought tolerance. Further investigation of the major DSRhub genes revealed distinct regulatory genes such as ZEP, NCED, AAO, and MCSU and CYP707A1. These were involved in the regulation of ABA biosynthesis and signal transduction. Other protein families, namely, aldehyde and alcohol dehydrogenases, mitogene activated protein kinases (MAPKs), and Ribulose-1,5-biphosphate carboxylase (RuBisCO) were shown to be involved in the drought-related responses. This shows a diversity of complex functional features in sorghum to respond to various abiotic stresses. Finally, we constructed a drought-specific subnetwork, characterized by unique candidate genes that were associated with DSRhub genes. According to our knowledge, this is the first in sorghum drought investigation that introduces pathway and network-based candidate gene approach for analysis of drought tolerance. We provide novel information about pathways cross-talk and signaling networks used in further systems level analysis for understanding the molecular mechanism behind drought tolerance and can, therefore, be adapted to other model and non-model crops.
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Affiliation(s)
- Adugna Abdi Woldesemayat
- Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Johannesburg, South Africa
| | - Monde Ntwasa
- Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Johannesburg, South Africa
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Characterization of squalene-induced PgCYP736B involved in salt tolerance by modulating key genes of abscisic acid biosynthesis. Int J Biol Macromol 2018; 121:796-805. [PMID: 30336242 DOI: 10.1016/j.ijbiomac.2018.10.058] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 10/02/2018] [Accepted: 10/14/2018] [Indexed: 11/22/2022]
Abstract
Cytochrome P450 genes as the one of the largest superfamily genes mediate a wide range of plant biochemical pathways. In this study, a full-length cytochrome P450 monooxygenase (CYP736B) cDNA was isolated and characterized from Panax ginseng. It was revealed that the deduced amino acid of PgCYP736B shares a high degree of sequence homology with CYP736A12 encoded by P. ginseng. Expression of PgCYP736B was differentially induced not only during a Pseudomonas syringae infection (7.7-fold) and wounding (47.3-fold) but also after exposure to salt (7.4-fold), cold (8.3-fold), and drought stress (3.24-fold). The gene transcription was highly affected by methyl jasmonate (476-fold) in the ginseng, suggesting that PgCYP736B was elicitor-responsive. Furthermore, we overexpressed the PgCYP736B gene in Arabidopsis and found that PgCYP736B is a transmembrane protein. Overexpression of PgCYP736B in Arabidopsis conferred enhanced resistance to salt stress via decreased H2O2 accumulation, increased carotenoid levels, and through abscisic acid biosynthesis gene expression. Our results suggest that the induction of ginsenoside biosynthetic pathway genes along with PgCYP736B by an exogenous supply of 10-100 μM of squalene most likely affects the metabolite profile of ginsenoside triterpenoid. Overall, our findings indicate that PgCYP736B protects ginseng from salt stress and may contribute to triterpenoid biosynthesis.
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Kim SW, Gupta R, Min CW, Lee SH, Cheon YE, Meng QF, Jang JW, Hong CE, Lee JY, Jo IH, Kim ST. Label-free quantitative proteomic analysis of Panax ginseng leaves upon exposure to heat stress. J Ginseng Res 2018; 43:143-153. [PMID: 30662303 PMCID: PMC6323179 DOI: 10.1016/j.jgr.2018.09.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/28/2018] [Accepted: 09/27/2018] [Indexed: 11/25/2022] Open
Abstract
Background Ginseng is one of the well-known medicinal plants, exhibiting diverse medicinal effects. Its roots possess anticancer and antiaging properties and are being used in the medical systems of East Asian countries. It is grown in low-light and low-temperature conditions, and its growth is strongly inhibited at temperatures above 25°C. However, the molecular responses of ginseng to heat stress are currently poorly understood, especially at the protein level. Methods We used a shotgun proteomics approach to investigate the effect of heat stress on ginseng leaves. We monitored their photosynthetic efficiency to confirm physiological responses to a high-temperature stress. Results The results showed a reduction in photosynthetic efficiency on heat treatment (35°C) starting at 48 h. Label-free quantitative proteome analysis led to the identification of 3,332 proteins, of which 847 were differentially modulated in response to heat stress. The MapMan analysis showed that the proteins with increased abundance were mainly associated with antioxidant and translation-regulating activities, whereas the proteins related to the receptor and structural-binding activities exhibited decreased abundance. Several other proteins including chaperones, G-proteins, calcium-signaling proteins, transcription factors, and transfer/carrier proteins were specifically downregulated. Conclusion These results increase our understanding of heat stress responses in the leaves of ginseng at the protein level, for the first time providing a resource for the scientific community.
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Affiliation(s)
- So Wun Kim
- Department of Plant Bioscience, Pusan National University, Miryang, Republic of Korea
| | - Ravi Gupta
- Department of Plant Bioscience, Pusan National University, Miryang, Republic of Korea
| | - Cheol Woo Min
- Department of Plant Bioscience, Pusan National University, Miryang, Republic of Korea
| | - Seo Hyun Lee
- Department of Plant Bioscience, Pusan National University, Miryang, Republic of Korea
| | - Ye Eun Cheon
- Department of Plant Bioscience, Pusan National University, Miryang, Republic of Korea
| | - Qing Feng Meng
- Department of Plant Bioscience, Pusan National University, Miryang, Republic of Korea
| | - Jeong Woo Jang
- Department of Plant Bioscience, Pusan National University, Miryang, Republic of Korea
| | - Chi Eun Hong
- Department of Herbal Crop Research, Rural Development Administration, Eumseong, Republic of Korea
| | - Ji Yoon Lee
- National Instrumentation Center for Environmental Management, Seoul National University, Seoul, Republic of Korea
| | - Ick Hyun Jo
- Department of Herbal Crop Research, Rural Development Administration, Eumseong, Republic of Korea
| | - Sun Tae Kim
- Department of Plant Bioscience, Pusan National University, Miryang, Republic of Korea
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Bai S, Liu W, Wang H, Zhao N, Jia S, Zou N, Guo W, Wang J. Enhanced Herbicide Metabolism and Metabolic Resistance Genes Identified in Tribenuron-Methyl Resistant Myosoton aquaticum L. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:9850-9857. [PMID: 30142979 DOI: 10.1021/acs.jafc.8b02740] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The evolved resistance of Myosoton aquaticum L. to acetolactate synthase (ALS) inhibitors is well established, but most research has focused on target-site resistance, while nontarget-site resistance remains neglected. Here, we investigated mechanisms of the latter. The pretreatment with the P450 inhibitor malathion significantly increased the sensitivity of resistant plants to tribenuron-methyl. The rapid P450-mediated tribenuron-methyl metabolism in resistant plants was confirmed by LC-MS/MS analysis. Besides, GST activity was higher among resistant than susceptible individuals. The next transcriptome analysis generated 544,102,236 clean reads from RNA sequencing libraries. De novo assembly yielded 102,529 unigenes with an average length of 866 bp, annotated across seven databases. Digital gene expression selected 25 differentially expressed genes, further validated with qRT-PCR. Three P450 genes, two GST genes, two glucosyltransferase genes, four ABC transporter genes, and four additional contigs were constitutively up-regulated in resistant individuals. Overall, our research confirmed that enhanced herbicide metabolism drives tribenuron-methyl resistance in M. aquaticum.
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Affiliation(s)
- Shuang Bai
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection , Shandong Agricultural University , Tai'an 271018 , Shandong , China
| | - Weitang Liu
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection , Shandong Agricultural University , Tai'an 271018 , Shandong , China
| | - Hengzhi Wang
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection , Shandong Agricultural University , Tai'an 271018 , Shandong , China
| | - Ning Zhao
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection , Shandong Agricultural University , Tai'an 271018 , Shandong , China
| | - Sisi Jia
- Taian Customs , Tai'an 271000 , Shandong , China
| | - Nan Zou
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection , Shandong Agricultural University , Tai'an 271018 , Shandong , China
| | - Wenlei Guo
- Plant Protection Research Institute , Guangdong Academy of Agricultural Sciences , Guangzhou 510640 , P.R. China
| | - Jinxin Wang
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection , Shandong Agricultural University , Tai'an 271018 , Shandong , China
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Kumar J, Gunapati S, Kianian SF, Singh SP. Comparative analysis of transcriptome in two wheat genotypes with contrasting levels of drought tolerance. PROTOPLASMA 2018; 255:1487-1504. [PMID: 29651660 DOI: 10.1007/s00709-018-1237-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 03/05/2018] [Indexed: 05/19/2023]
Abstract
Drought tolerance is a complex trait that is governed by multiple genes. The study presents differential transcriptome analysis between drought-tolerant (Triticum aestivum Cv. C306) and drought-sensitive (Triticum aestivum Cv. WL711) genotypes, using Affymetrix GeneChip® Wheat Genome Array. Both genotypes exhibited diverse global transcriptional responses under control and drought conditions. Pathway analysis suggested significant induction or repression of genes involved in secondary metabolism, nucleic acid synthesis, protein synthesis, and transport in C306, as compared to WL711. Significant up- and downregulation of transcripts for enzymes, hormone metabolism, and stress response pathways were observed in C306 under drought. The elevated expression of plasma membrane intrinsic protein 1 and downregulation of late embryogenesis abundant in the leaf tissues could play an important role in delayed wilting in C306. The other regulatory genes such as MT, FT, AP2, SKP1, ABA2, ARF6, WRKY6, AOS, and LOX2 are involved in defense response in C306 genotype. Additionally, transcripts with unknown functions were identified as differentially expressed, which could participate in drought responses.
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Affiliation(s)
- Jitendra Kumar
- National Agri-Food Biotechnology Institute, Mohali, India
- USDA-ARS Cereal Disease Laboratory, St. Paul, MN, USA
| | - Samatha Gunapati
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA
| | | | - Sudhir P Singh
- National Agri-Food Biotechnology Institute, Mohali, India.
- Center of Innovative and Applied Bioprocessing, Mohali, India.
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Xu Y, Huang B. Transcriptomic analysis reveals unique molecular factors for lipid hydrolysis, secondary cell-walls and oxidative protection associated with thermotolerance in perennial grass. BMC Genomics 2018; 19:70. [PMID: 29357827 PMCID: PMC5778672 DOI: 10.1186/s12864-018-4437-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 01/04/2018] [Indexed: 11/11/2022] Open
Abstract
Background Heat stress is the primary abiotic stress limiting growth of cool-season grass species. The objective of this study was to determine molecular factors and metabolic pathways associated with superior heat tolerance in thermal bentgrass (Agrostis scabra) by comparative analysis of transcriptomic profiles with its co-generic heat-sensitive species creeping bentgrass (A. stolonifera). Results Transcriptomic profiling by RNA-seq in both heat-sensitive A. stolonifera (cv. ‘Penncross’) and heat-tolerant A. scabra exposed to heat stress found 1393 (675 up- and 718 down-regulated) and 1508 (777 up- and 731 down-regulated) differentially-expressed genes, respectively. The superior heat tolerance in A. scabra was associated with more up-regulation of genes in oxidative protection, proline biosynthesis, lipid hydrolysis, hemicellulose and lignin biosynthesis, compared to heat-sensitive A. stolonifera. Several transcriptional factors (TFs), such as high mobility group B protein 7 (HMGB7), dehydration-responsive element-binding factor 1a (DREB1a), multiprotein-bridging factor 1c (MBF1c), CCCH-domain containing protein 47 (CCCH47), were also found to be up-regulated in A. scabra under heat stress. Conclusions The unique TFs and genes identified in thermal A. scabra could be potential candidate genes for genetic modification of cultivated grass species for improving heat tolerance, and the associated pathways could contribute to the transcriptional regulation for superior heat tolerance in bentgrass species. Electronic supplementary material The online version of this article (10.1186/s12864-018-4437-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yi Xu
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Bingru Huang
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, 08901, USA.
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Zhang L, Xu B, Wu T, Wen MX, Fan LX, Feng ZZ, Paoletti E. Transcriptomic analysis of Pak Choi under acute ozone exposure revealed regulatory mechanism against ozone stress. BMC PLANT BIOLOGY 2017; 17:236. [PMID: 29216819 PMCID: PMC5721698 DOI: 10.1186/s12870-017-1202-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 12/01/2017] [Indexed: 05/23/2023]
Abstract
BACKGROUND Ground-level ozone (O3) is one of the major air pollutants, which cause oxidative injury to plants. The physiological and biochemical mechanisms underlying the responses of plants to O3 stress have been well investigated. However, there are limited reports about the molecular basis of plant responses to O3. In this study, a comparative transcriptomic analysis of Pak Choi (Brassica campestris ssp. chinensis) exposed to different O3 concentrations was conducted for the first time. RESULTS Seedlings of Pak Choi with five leaves were exposed to non-filtered air (NF, 31 ppb) or elevated O3 (E-O3, 252 ppb) for 2 days (8 h per day, from 9:00-17:00). Compared with plants in the NF, a total of 675 differentially expressed genes (DEGs) were identified in plants under E-O3, including 219 DEGs with decreased expressions and 456 DEGs with increased expressions. Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that O3 stress invoked multiple cellular defense pathways to mitigate the impaired cellular integrity and metabolism, including 'glutathione metabolism', 'phenylpropanoid biosynthesis', 'sulfur metabolism', 'glucosinolate biosynthesis', 'cutin, suberine and wax biosynthesis' and others. Transcription factors potentially involved in this cellular regulation were also found, such as AP2-ERF, WRKY, JAZ, MYB etc. Based on the RNA-Seq data and previous studies, a working model was proposed integrating O3 caused reactive oxygen burst, oxidation-reduction regulation, jasmonic acid and downstream functional genes for the regulation of cellular homeostasis after acute O3 stress. CONCLUSION The present results provide a valuable insight into the molecular responses of Pak Choi to acute O3 stress and the specific DEGs revealed in this study could be used for further functional identification of key allelic genes determining the O3 sensitivity of Pak Choi.
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Affiliation(s)
- Lu Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Bin Xu
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Tao Wu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Mu-xuan Wen
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Lian-xue Fan
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Zhao-zhong Feng
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Elena Paoletti
- Institute of Sustainable Plant Protection, National Research Council, Florence, Italy
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Zhai N, Jia H, Liu D, Liu S, Ma M, Guo X, Li H. GhMAP3K65, a Cotton Raf-Like MAP3K Gene, Enhances Susceptibility to Pathogen Infection and Heat Stress by Negatively Modulating Growth and Development in Transgenic Nicotiana benthamiana. Int J Mol Sci 2017; 18:E2462. [PMID: 29160794 PMCID: PMC5713428 DOI: 10.3390/ijms18112462] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 11/17/2017] [Accepted: 11/17/2017] [Indexed: 11/21/2022] Open
Abstract
Mitogen-activated protein kinase kinase kinases (MAP3Ks), the top components of MAPK cascades, modulate many biological processes, such as growth, development and various environmental stresses. Nevertheless, the roles of MAP3Ks remain poorly understood in cotton. In this study, GhMAP3K65 was identified in cotton, and its transcription was inducible by pathogen infection, heat stress, and multiple signalling molecules. Silencing of GhMAP3K65 enhanced resistance to pathogen infection and heat stress in cotton. In contrast, overexpression of GhMAP3K65 enhanced susceptibility to pathogen infection and heat stress in transgenic Nicotiana benthamiana. The expression of defence-associated genes was activated in transgenic N. benthamiana plants after pathogen infection and heat stress, indicating that GhMAP3K65 positively regulates plant defence responses. Nevertheless, transgenic N. benthamiana plants impaired lignin biosynthesis and stomatal immunity in their leaves and repressed vitality of their root systems. In addition, the expression of lignin biosynthesis genes and lignin content were inhibited after pathogen infection and heat stress. Collectively, these results demonstrate that GhMAP3K65 enhances susceptibility to pathogen infection and heat stress by negatively modulating growth and development in transgenic N. benthamiana plants.
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Affiliation(s)
- Na Zhai
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China.
| | - Haihong Jia
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China.
| | - Dongdong Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China.
| | - Shuchang Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China.
| | - Manli Ma
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China.
| | - Xingqi Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China.
| | - Han Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China.
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Zhang JJ, Xu JY, Lu FF, Jin SF, Yang H. Detoxification of Atrazine by Low Molecular Weight Thiols in Alfalfa (Medicago sativa). Chem Res Toxicol 2017; 30:1835-1846. [DOI: 10.1021/acs.chemrestox.7b00166] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Jing Zhang
- Jiangsu
Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
- College
of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Jiang Yan Xu
- Jiangsu
Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Feng Fan Lu
- Jiangsu
Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - She Feng Jin
- Jiangsu
Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Hong Yang
- Jiangsu
Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
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Proteome characterization of copper stress responses in the roots of sorghum. Biometals 2017; 30:765-785. [PMID: 28936772 DOI: 10.1007/s10534-017-0045-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 08/18/2017] [Indexed: 10/18/2022]
Abstract
Copper (Cu) is a important micronutrient for plants, but it is extremely toxic to plants at high concentration and can inactivate and disturb protein structures. To explore the Cu stress-induced tolerance mechanism, the present study was conducted on the roots of sorghum seedlings exposed to 50 and 100 µM CuSO4 for 5 days. Accumulation of Cu increased in roots when the seedlings were treated with the highest concentration of Cu2+ ions (100 μM). Elevated Cu concentration provoked notable reduction of Fe, Zn, Ca, and Mn uptake in the roots of sorghum seedlings. In the proteome analysis, high-throughput two-dimensional polyacrylamide gel electrophoresis combined with MALDI-TOF-TOF MS was performed to explore the molecular responses of Cu-induced sorghum seedling roots. In two-dimensional silver-stained gels, 422 protein spots were identified in the 2-D gel whereas twenty-one protein spots (≥1.5-fold) were used to analyze mass spectrometry from Cu-induced sorghum roots. Among the 21 differentially expressed proteins, 10 proteins were increased, while 11 proteins were decreased due to the intake of Cu ions by roots of sorghum. Abundance of most of the identified proteins from the roots that function in stress response and metabolism was remarkably enhanced, while proteins involved in transcription and regulation were severely reduced. Taken together, these results imply insights into a potential molecular mechanism towards Cu stress in C4 plant, sorghum.
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Environmental stress is the major cause of transcriptomic and proteomic changes in GM and non-GM plants. Sci Rep 2017; 7:10624. [PMID: 28878216 PMCID: PMC5587699 DOI: 10.1038/s41598-017-09646-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 07/27/2017] [Indexed: 11/08/2022] Open
Abstract
The approval of genetically modified (GM) crops is preceded by years of intensive research to demonstrate safety to humans and environment. We recently showed that in vitro culture stress is the major factor influencing proteomic differences of GM vs. non-GM plants. This made us question the number of generations needed to erase such "memory". We also wondered about the relevance of alterations promoted by transgenesis as compared to environment-induced ones. Here we followed three rice lines (1-control, 1-transgenic and 1-negative segregant) throughout eight generations after transgenesis combining proteomics and transcriptomics, and further analyzed their response to salinity stress on the F6 generation. Our results show that: (a) differences promoted during genetic modification are mainly short-term physiological changes, attenuating throughout generations, and (b) environmental stress may cause far more proteomic/transcriptomic alterations than transgenesis. Based on our data, we question what is really relevant in risk assessment design for GM food crops.
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Ortiz D, Hu J, Salas Fernandez MG. Genetic architecture of photosynthesis in Sorghum bicolor under non-stress and cold stress conditions. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4545-4557. [PMID: 28981780 PMCID: PMC5853419 DOI: 10.1093/jxb/erx276] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 07/15/2017] [Indexed: 05/18/2023]
Abstract
Sorghum (Sorghum bicolor L. Moench) is a C4 species sensitive to the cold spring conditions that occur at northern latitudes, especially when coupled with excessive light, and that greatly affect the photosynthetic rate. The objective of this study was to discover genes/genomic regions that control the capacity to cope with excessive energy under low temperature conditions during the vegetative growth period. A genome-wide association study (GWAS) was conducted for seven photosynthetic gas exchange and chlorophyll fluorescence traits under three consecutive temperature treatments: control (28 °C/24 °C), cold (15 °C/15 °C), and recovery (28 °C/24 °C). Cold stress significantly reduced the rate of photosynthetic CO2 uptake of sorghum plants, and a total of 143 unique genomic regions were discovered associated with at least one trait in a particular treatment or with derived variables. Ten regions on chromosomes 3, 4, 6, 7, and 8 that harbor multiple significant markers in linkage disequilibrium (LD) were consistently identified in gas exchange and chlorophyll fluorescence traits. Several candidate genes within those intervals have predicted functions related to carotenoids, phytohormones, thioredoxin, components of PSI, and antioxidants. These regions represent the most promising results for future validation and with potential application for the improvement of crop productivity under cold stress.
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Affiliation(s)
- Diego Ortiz
- Department of Agronomy, Iowa State University, Ames, IA, USA
| | - Jieyun Hu
- Department of Agronomy, Iowa State University, Ames, IA, USA
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Matzrafi M, Shaar-Moshe L, Rubin B, Peleg Z. Unraveling the Transcriptional Basis of Temperature-Dependent Pinoxaden Resistance in Brachypodium hybridum. FRONTIERS IN PLANT SCIENCE 2017; 8:1064. [PMID: 28680434 PMCID: PMC5478685 DOI: 10.3389/fpls.2017.01064] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 06/02/2017] [Indexed: 05/26/2023]
Abstract
Climate change endangers food security and our ability to feed the ever-increasing human population. Weeds are the most important biotic stress, reducing crop-plant productivity worldwide. Chemical control, the main approach for weed management, can be strongly affected by temperature. Previously, we have shown that temperature-dependent non-target site (NTS) resistance of Brachypodium hybridum is due to enhanced detoxification of acetyl-CoA carboxylase inhibitors. Here, we explored the transcriptional basis of this phenomenon. Plants were characterized for the transcriptional response to herbicide application, high-temperature and their combination, in an attempt to uncover the genetic basis of temperature-dependent pinoxaden resistance. Even though most of the variance among treatments was due to pinoxaden application (61%), plants were able to survive pinoxaden application only when grown under high-temperatures. Biological pathways and expression patterns of members of specific gene families, previously shown to be involved in NTS metabolic resistance to different herbicides, were examined. Cytochrome P450, glucosyl transferase and glutathione-S-transferase genes were found to be up-regulated in response to pinoxaden application under both control and high-temperature conditions. However, biological pathways related to oxidation and glucose conjugation were found to be significantly enriched only under the combination of pinoxaden application and high-temperature. Analysis of reactive oxygen species (ROS) was conducted at several time points after treatment using a probe detecting H2O2/peroxides. Comparison of ROS accumulation among treatments revealed a significant reduction in ROS quantities 24 h after pinoxaden application only under high-temperature conditions. These results may indicate significant activity of enzymatic ROS scavengers that can be correlated with the activation of herbicide-resistance mechanisms. This study shows that up-regulation of genes related to metabolic resistance is not sufficient to explain temperature-dependent pinoxaden resistance. We suggest that elevated activity of enzymatic processes at high-temperature may induce rapid and efficient pinoxaden metabolism leading to temperature-dependent herbicide resistance.
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Affiliation(s)
| | | | | | - Zvi Peleg
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of JerusalemRehovot, Israel
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Yang Q, Shohag MJI, Feng Y, He Z, Yang X. Transcriptome Comparison Reveals the Adaptive Evolution of Two Contrasting Ecotypes of Zn/Cd Hyperaccumulator Sedum alfredii Hance. FRONTIERS IN PLANT SCIENCE 2017; 8:425. [PMID: 28439276 PMCID: PMC5383727 DOI: 10.3389/fpls.2017.00425] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 03/13/2017] [Indexed: 05/29/2023]
Abstract
Hyperaccumulating ecotype (HE) and non-hyperaccumulating ecotype (NHE) of Sedum alfredii Hance belong to the same species but exhibit contrasting characteristics regarding hyperaccumulation and hypertolerance to cadmium and zinc. The Illumina Hiseq 2500 platform was employed to sequence HE and NHE to study the genetic evolution of this contrasting trait. Greater than 90 million clean reads were obtained and 118,479/228,051 unigenes of HE/NHE were annotated based on seven existing databases. We identified 149,668/319,830 single nucleotide polymorphisms (SNPs) and 12,691/14,428 simple sequence repeats (SSRs) of HE/NHE. We used a branch-site model to identify 18 divergent orthologous genes and 57 conserved orthologous genes of S. alfredii Hance. The divergent orthologous genes were mainly involved in the transcription and translation processes, protein metabolism process, calcium (Ca2+) pathway, stress response process and signal transduction process. To the best of our knowledge, this is the first study to use RNA-seq to compare the genetic evolution of hyperaccumulating and non-hyperaccumulating plants from the same species. In addition, this study made the sole concrete for further studies on molecular markers and divergent orthologous genes to depict the evolution process and formation of the hyperaccumulation and hypertolerance traits in S. alfredii Hance.
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Affiliation(s)
- Qianying Yang
- Ministry of Education Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang UniversityHangzhou, China
| | - M. J. I. Shohag
- Ministry of Education Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang UniversityHangzhou, China
- Department of Agriculture, Bangabandhu Sheikh Mujibur Rahman Science and Technology UniversityGopalganj, Bangladesh
| | - Ying Feng
- Ministry of Education Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang UniversityHangzhou, China
| | - Zhenli He
- Institute of Food and Agricultural Sciences, Indian River Research and Education Center, University of FloridaFort Pierce, FL, USA
| | - Xiaoe Yang
- Ministry of Education Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang UniversityHangzhou, China
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Luo W, Zhang C, Zhang J, Jiang D, Guo W, Wan D. Transcriptome analysis of four poplars exposed to continuous salinity stress. BIOCHEM SYST ECOL 2017. [DOI: 10.1016/j.bse.2017.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Carvalho LC, Silva M, Coito JL, Rocheta MP, Amâncio S. Design of a Custom RT-qPCR Array for Assignment of Abiotic Stress Tolerance in Traditional Portuguese Grapevine Varieties. FRONTIERS IN PLANT SCIENCE 2017; 8:1835. [PMID: 29118776 PMCID: PMC5660995 DOI: 10.3389/fpls.2017.01835] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Accepted: 10/10/2017] [Indexed: 05/21/2023]
Abstract
Widespread agricultural losses attributed to drought, often combined with high temperatures, frequently occur in the field, namely in Mediterranean climate areas, where the existing scenarios for climate change indicate an increase in the frequency of heat waves and severe drought events in summer. Grapevine (Vitis vinifera L.) is the most cultivated fruit species in the world and the most valuable one and is a traditional Mediterranean species. Currently, viticulture must adjust to impending climate changes that are already pushing vine-growers toward the use of ancient and resilient varieties. Portugal is very rich in grapevine biodiversity, however, currently, 90% of the total producing area is planted with only 16 varieties. There is a pressing need to understand the existing genetic diversity and the physiological potential of the varieties/genotypes available to be able to respond to climate changes. With the above scenario in mind, an assembly of 65 differentially expresses genes (DEGs) previously identified as responsive to abiotic stresses in two well studied genotypes, 'Touriga Nacional' and 'Trincadeira,' was designed to scan the gene expression of leaf samples from 10 traditional Portuguese varieties growing in two regions with distinct environmental conditions. Forty-five of those DEGs proved to be associated to "abiotic stress" and were chosen to build a custom qPCR array to identify uncharacterized genotypes as sensitive or tolerant to abiotic stress. According to the experimental set-up behind the array design these DEGs can also be used as indicators of the main abiotic stress that the plant is subjected and responding to (drought, heat, or excess light).
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Tao X, Wang MX, Dai Y, Wang Y, Fan YF, Mao P, Ma XR. Identification and Expression Profile of CYPome in Perennial Ryegrass and Tall Fescue in Response to Temperature Stress. FRONTIERS IN PLANT SCIENCE 2017; 8:1519. [PMID: 29209335 PMCID: PMC5702011 DOI: 10.3389/fpls.2017.01519] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 08/18/2017] [Indexed: 05/03/2023]
Abstract
Plant cytochrome P450s are involved in a wide range of biosynthetic reactions that generate various biomolecules, including a variety of defensive compounds. Perennial ryegrass (Lolium perenne) and tall fescue (Festuca arundinacea) are two major species of turf and forage grasses that usually experience low temperature below -10°C and high temperature over 38°C around the world. In this study, we re-analyzed transcriptome of perennial ryegrass and tall fescue treated with heat and cold stress. Thus, we can evaluate P450 composition in these species and confirm whether P450 genes response to temperature stress. We identified 277 and 319 P450 transcripts with open reading frames larger than 300 bp, respectively. These P450 transcripts were mainly classed in the CYP71, 51, 94, 89, 72, and 734 families. In perennial ryegrass and tall fescue, a total of 66 and 62 P450 transcripts were up-regulated, and 65 and 117 transcripts were down-regulated when subjected to heat stress, respectively. When exposed to cold stress, 60 and 73 transcripts were up-regulated, and 59 and 77 transcripts were down-regulated in perennial ryegrass and tall fescue. Among these differentially expressed transcripts, 64 and 87 of them showed expression level changes that followed the same trend, and these temperature-responsive genes primarily belong to the CYP71, 72 and 99 families. Besides, heat and cold stress altered phenylalanine and brassinosteroid involved P450 transcripts in perennial ryegrass and tall fescue. P450 transcripts involved in the metabolism of these compounds showed a strong response to heat and/or cold stress, indicating that they likely play important roles in temperature acclimation in these two species. The CYPome provide a genetic base for the future functional studies, as well as genetic studies that may improve stress tolerance for perennial ryegrass and tall fescue to extreme temperature.
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Affiliation(s)
- Xiang Tao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Ming-Xiu Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- College of Life Sciences, Sichuan University, Chengdu, China
| | - Ya Dai
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Yan-Fen Fan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ping Mao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Xin-Rong Ma
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- *Correspondence: Xin-Rong Ma
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