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Yu B, Liu N, Huang L, Luo H, Zhou X, Lei Y, Yan L, Wang X, Chen W, Kang Y, Ding Y, Jin G, Pandey MK, Janila P, Kishan Sudini H, Varshney RK, Jiang H, Liu S, Liao B. Identification and application of a candidate gene AhAftr1 for aflatoxin production resistance in peanut seed (Arachis hypogaea L.). J Adv Res 2024; 62:15-26. [PMID: 37739123 PMCID: PMC11331177 DOI: 10.1016/j.jare.2023.09.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 09/15/2023] [Accepted: 09/17/2023] [Indexed: 09/24/2023] Open
Abstract
INTRODUCTION Peanut is susceptible to infection of Aspergillus fungi and conducive to aflatoxin contamination, hence developing aflatoxin-resistant variety is highly meaningful. Identifying functional genes or loci conferring aflatoxin resistance and molecular diagnostic marker are crucial for peanut breeding. OBJECTIVES This work aims to (1) identify candidate gene for aflatoxin production resistance, (2) reveal the related resistance mechanism, and (3) develop diagnostic marker for resistance breeding program. METHODS Resistance to aflatoxin production in a recombined inbred line (RIL) population derived from a high-yielding variety Xuhua13 crossed with an aflatoxin-resistant genotype Zhonghua 6 was evaluated under artificial inoculation for three consecutive years. Both genetic linkage analysis and QTL-seq were conducted for QTL mapping. The candidate gene was further fine-mapped using a secondary segregation mapping population and validated by transgenic experiments. RNA-Seq analysis among resistant and susceptible RILs was used to reveal the resistance pathway for the candidate genes. RESULTS The major effect QTL qAFTRA07.1 for aflatoxin production resistance was mapped to a 1.98 Mbp interval. A gene, AhAftr1 (Arachis hypogaea Aflatoxin resistance 1), was detected structure variation (SV) in leucine rich repeat (LRR) domain of its production, and involved in disease resistance response through the effector-triggered immunity (ETI) pathway. Transgenic plants with overexpression of AhAftr1(ZH6) exhibited 57.3% aflatoxin reduction compared to that of AhAftr1(XH13). A molecular diagnostic marker AFTR.Del.A07 was developed based on the SV. Thirty-six lines, with aflatoxin content decrease by over 77.67% compared to the susceptible control Zhonghua12 (ZH12), were identified from a panel of peanut germplasm accessions and breeding lines through using AFTR.Del.A07. CONCLUSION Our findings would provide insights of aflatoxin production resistance mechanisms and laid meaningful foundation for further breeding programs.
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Affiliation(s)
- Bolun Yu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Nian Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Li Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Huaiyong Luo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Xiaojing Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Liying Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Xin Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Weigang Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Yanping Kang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Yingbin Ding
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Gaorui Jin
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Manish K Pandey
- International Crops Research Institute for the Semi-Aird Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Pasupuleti Janila
- International Crops Research Institute for the Semi-Aird Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Hari Kishan Sudini
- International Crops Research Institute for the Semi-Aird Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Rajeev K Varshney
- Centre for Crop and Food Innovation, State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Australia
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China.
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Sultana T, Malik K, Raja NI, Mashwani ZUR, Hameed A, Ullah R, Alqahtani AS, Sohail. Aflatoxins in Peanut ( Arachis hypogaea): Prevalence, Global Health Concern, and Management from an Innovative Nanotechnology Approach: A Mechanistic Repertoire and Future Direction. ACS OMEGA 2024; 9:25555-25574. [PMID: 38911815 PMCID: PMC11190918 DOI: 10.1021/acsomega.4c01316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 05/10/2024] [Accepted: 05/22/2024] [Indexed: 06/25/2024]
Abstract
Arachis hypogaea is the most significant oilseed nutritious legume crop in agricultural trade across the world. It is recognized as a valued crop for its contributions to nourishing food, as a cooking oil, and for meeting the protein needs of people who are unable to afford animal protein. Currently, its production, marketability, and consumption are hindered because of Aspergillus species infection that consequently contaminates the kernels with aflatoxins. Regarding health concerns, humans and animals are affected by acute and chronic aflatoxin toxicity and millions of people are at high risk of chronic levels. Most methods used to store peanuts are traditional and serve effectively for short-term storage. Now the question for long-term storage has been raised, and this promptly finds potential approaches to the issue. It is imperative to reduce the aflatoxin levels in peanuts to a permissible level by introducing detoxifying innovations. Most of the detoxification reports mention physical, chemical, and biological techniques. However, many current approaches are impractical because of time consumption, loss of nutritional quality, or weak detoxifying efficiency. Therefore, it is crucial to investigate practical, economical, and green methods to control Aspergillus flavus that address current global food security problems. Herein, a green and economically revolutionary way is a nanotechnology that has demonstrated its potential to connect farmers to markets, elevate international marketability, improve human and animal health conditions, and enhance food quality and safety by the management of fungal diseases. Due to the antimicrobial potential of nanoparticles, they act as nanofungicides and have an incredible role in the control of aflatoxins. Nanoparticles have ultrasmall sizes and therefore penetrate the fungal body and invade the pathogen machinery, leading to fungal cell death by ROS production, mutation in DNA, disruption of organelles, and membrane leakage. This is the first mechanistic overview that unveils a comprehensive insight into aflatoxin contamination in peanuts, its prevalence, health effects, and management in addition to nanotechnological interventions that serve as a triple defense approach to detoxify aflatoxins. The optimum use of nanofungicides ensures food safety and the development of goals, especially "zero hunger".
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Affiliation(s)
- Tahira Sultana
- Department
of Botany, PMAS, Arid Agriculture University
Rawalpindi, Rawalpindi 46000, Pakistan
| | - Khafsa Malik
- Department
of Botany, PMAS, Arid Agriculture University
Rawalpindi, Rawalpindi 46000, Pakistan
| | - Naveed Iqbal Raja
- Department
of Botany, PMAS, Arid Agriculture University
Rawalpindi, Rawalpindi 46000, Pakistan
| | - Zia-Ur-Rehman Mashwani
- Department
of Botany, PMAS, Arid Agriculture University
Rawalpindi, Rawalpindi 46000, Pakistan
| | - Asma Hameed
- Department
of Botany, PMAS, Arid Agriculture University
Rawalpindi, Rawalpindi 46000, Pakistan
| | - Riaz Ullah
- Medicinal
Aromatic and Poisonous Plants Research Center College of Pharmacy King Saud University, Riyadh 11451, Saudi Arabia
| | - Ali S. Alqahtani
- Medicinal
Aromatic and Poisonous Plants Research Center College of Pharmacy King Saud University, Riyadh 11451, Saudi Arabia
| | - Sohail
- College
of Bioscience and Biotechnology, Yangzhou
University, Yangzhou 225009, Jiangsu, China
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Zhang Y, Li J, Li W, Gao X, Xu X, Zhang C, Yu S, Dou Y, Luo W, Yu L. Transcriptome Analysis Reveals POD as an Important Indicator for Assessing Low-Temperature Tolerance in Maize Radicles during Germination. PLANTS (BASEL, SWITZERLAND) 2024; 13:1362. [PMID: 38794432 PMCID: PMC11125230 DOI: 10.3390/plants13101362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024]
Abstract
Low-temperature stress (TS) limits maize (Zea mays L.) seed germination and agricultural production. Exposure to TS during germination inhibits radicle growth, triggering seedling emergence disorders. Here, we aimed to analyse the changes in gene expression in the radicles of maize seeds under TS by comparing Demeiya1 (DMY1) and Zhengdan958 (ZD958) (the main Northeast China cultivars) and exposing them to two temperatures: 15 °C (control) and 5 °C (TS). TS markedly decreased radicle growth as well as fresh and dry weights while increasing proline and malondialdehyde contents in both test varieties. Under TS treatment, the expression levels of 5301 and 4894 genes were significantly different in the radicles of DMY1 and ZD958, respectively, and 3005 differentially expressed genes coexisted in the radicles of both varieties. The phenylpropanoid biosynthesis pathway was implicated within the response to TS in maize radicles, and peroxidase may be an important indicator for assessing low-temperature tolerance during maize germination. Peroxidase-encoding genes could be important candidate genes for promoting low-temperature resistance in maize germinating radicles. We believe that this study enhances the knowledge of mechanisms of response and adaptation of the maize seed germination process to TS and provides a theoretical basis for efficiently assessing maize seed low-temperature tolerance and improving maize adversity germination performance.
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Affiliation(s)
- Yifei Zhang
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (J.L.); (W.L.); (X.G.); (X.X.); (C.Z.); (S.Y.); (Y.D.); (W.L.)
- Heilongjiang Provincial Key Laboratory of Modern Agricultural Cultivation and Crop Germplasm Improvement, Daqing 163319, China
- Key Laboratory of Low-Carbon Green Agriculture in Northeastern China, Ministry of Agriculture and Rural Affairs, Daqing 163319, China
| | - Jiayu Li
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (J.L.); (W.L.); (X.G.); (X.X.); (C.Z.); (S.Y.); (Y.D.); (W.L.)
| | - Weiqing Li
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (J.L.); (W.L.); (X.G.); (X.X.); (C.Z.); (S.Y.); (Y.D.); (W.L.)
| | - Xinhan Gao
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (J.L.); (W.L.); (X.G.); (X.X.); (C.Z.); (S.Y.); (Y.D.); (W.L.)
| | - Xiangru Xu
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (J.L.); (W.L.); (X.G.); (X.X.); (C.Z.); (S.Y.); (Y.D.); (W.L.)
| | - Chunyu Zhang
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (J.L.); (W.L.); (X.G.); (X.X.); (C.Z.); (S.Y.); (Y.D.); (W.L.)
- Heilongjiang Provincial Key Laboratory of Modern Agricultural Cultivation and Crop Germplasm Improvement, Daqing 163319, China
- Key Laboratory of Low-Carbon Green Agriculture in Northeastern China, Ministry of Agriculture and Rural Affairs, Daqing 163319, China
| | - Song Yu
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (J.L.); (W.L.); (X.G.); (X.X.); (C.Z.); (S.Y.); (Y.D.); (W.L.)
- Heilongjiang Provincial Key Laboratory of Modern Agricultural Cultivation and Crop Germplasm Improvement, Daqing 163319, China
- Key Laboratory of Low-Carbon Green Agriculture in Northeastern China, Ministry of Agriculture and Rural Affairs, Daqing 163319, China
| | - Yi Dou
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (J.L.); (W.L.); (X.G.); (X.X.); (C.Z.); (S.Y.); (Y.D.); (W.L.)
| | - Wenqi Luo
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (J.L.); (W.L.); (X.G.); (X.X.); (C.Z.); (S.Y.); (Y.D.); (W.L.)
| | - Lihe Yu
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (J.L.); (W.L.); (X.G.); (X.X.); (C.Z.); (S.Y.); (Y.D.); (W.L.)
- Heilongjiang Provincial Key Laboratory of Modern Agricultural Cultivation and Crop Germplasm Improvement, Daqing 163319, China
- Key Laboratory of Low-Carbon Green Agriculture in Northeastern China, Ministry of Agriculture and Rural Affairs, Daqing 163319, China
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Cerav EN, Wu N, Akkaya MS. Transcriptome-Wide N6-Methyladenosine (m 6A) Methylation Analyses in a Compatible Wheat- Puccinia striiformis f. sp. tritici Interaction. PLANTS (BASEL, SWITZERLAND) 2024; 13:982. [PMID: 38611510 PMCID: PMC11013425 DOI: 10.3390/plants13070982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 03/21/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024]
Abstract
N6-methyladenosine (m6A) is a prevalent internal modification in eukaryotic mRNA, tRNA, miRNA, and long non-coding RNA. It is also known for its role in plant responses to biotic and abiotic stresses. However, a comprehensive m6A transcriptome-wide map for Puccinia striiformis f. sp. tritici (Pst) infections in wheat (Triticum aestivum) is currently unavailable. Our study is the first to profile m6A modifications in wheat infected with a virulent Pst race. Analysis of RNA-seq and MeRIP-seq data revealed that the majority of differentially expressed genes are up-regulated and hyper-methylated. Some of these genes are enriched in the plant-pathogen interaction pathway. Notably, genes related to photosynthesis showed significant down-regulation and hypo-methylation, suggesting a potential mechanism facilitating successful Pst invasion by impairing photosynthetic function. The crucial genes, epitomizing the core molecular constituents that fortify plants against pathogenic assaults, were detected with varying expression and methylation levels, together with a newly identified methylation motif. Additionally, m6A regulator genes were also influenced by m6A modification, and their expression patterns varied at different time points of post-inoculation, with lower expression at early stages of infection. This study provides insights into the role of m6A modification regulation in wheat's response to Pst infection, establishing a foundation for understanding the potential function of m6A RNA methylation in plant resistance or susceptibility to pathogens.
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Affiliation(s)
| | | | - Mahinur S. Akkaya
- School of Bioengineering, Dalian University of Technology, No. 2 Linggong Road, Dalian 116024, China; (E.N.C.); (N.W.)
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Kumar D, Kirti PB. The genus Arachis: an excellent resource for studies on differential gene expression for stress tolerance. FRONTIERS IN PLANT SCIENCE 2023; 14:1275854. [PMID: 38023864 PMCID: PMC10646159 DOI: 10.3389/fpls.2023.1275854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023]
Abstract
Peanut Arachis hypogaea is a segmental allotetraploid in the section Arachis of the genus Arachis along with the Section Rhizomataceae. Section Arachis has several diploid species along with Arachis hypogaea and A. monticola. The section Rhizomataceae comprises polyploid species. Several species in the genus are highly tolerant to biotic and abiotic stresses and provide excellent sets of genotypes for studies on differential gene expression. Though there were several studies in this direction, more studies are needed to identify more and more gene combinations. Next generation RNA-seq based differential gene expression study is a powerful tool to identify the genes and regulatory pathways involved in stress tolerance. Transcriptomic and proteomic study of peanut plants under biotic stresses reveals a number of differentially expressed genes such as R genes (NBS-LRR, LRR-RLK, protein kinases, MAP kinases), pathogenesis related proteins (PR1, PR2, PR5, PR10) and defense related genes (defensin, F-box, glutathione S-transferase) that are the most consistently expressed genes throughout the studies reported so far. In most of the studies on biotic stress induction, the differentially expressed genes involved in the process with enriched pathways showed plant-pathogen interactions, phenylpropanoid biosynthesis, defense and signal transduction. Differential gene expression studies in response to abiotic stresses, reported the most commonly expressed genes are transcription factors (MYB, WRKY, NAC, bZIP, bHLH, AP2/ERF), LEA proteins, chitinase, aquaporins, F-box, cytochrome p450 and ROS scavenging enzymes. These differentially expressed genes are in enriched pathways of transcription regulation, starch and sucrose metabolism, signal transduction and biosynthesis of unsaturated fatty acids. These identified differentially expressed genes provide a better understanding of the resistance/tolerance mechanism, and the genes for manipulating biotic and abiotic stress tolerance in peanut and other crop plants. There are a number of differentially expressed genes during biotic and abiotic stresses were successfully characterized in peanut or model plants (tobacco or Arabidopsis) by genetic manipulation to develop stress tolerance plants, which have been detailed out in this review and more concerted studies are needed to identify more and more gene/gene combinations.
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Affiliation(s)
- Dilip Kumar
- Department of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Pulugurtha Bharadwaja Kirti
- Agri Biotech Foundation, Professor Jayashankar Telangana State (PJTS) Agricultural University, Hyderabad, Telangana, India
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Jayaprakash A, Roy A, Thanmalagan RR, Arunachalam A, P T V L. Understanding the mechanism of pathogenicity through interactome studies between Arachis hypogaea L. and Aspergillus flavus. J Proteomics 2023; 287:104975. [PMID: 37482270 DOI: 10.1016/j.jprot.2023.104975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 06/28/2023] [Accepted: 07/15/2023] [Indexed: 07/25/2023]
Abstract
Aspergillus flavus (A. flavus) infects the peanut seeds during pre-and post-harvest stages, causing seed quality destruction for humans and livestock consumption. Even though many resistant varieties were developed, the molecular mechanism of defense interactions of peanut against A. flavus still needs further investigation. Hence, an interologous host-pathogen protein interaction (HPPI) network was constructed to understand the subcellular level interaction mechanism between peanut and A. flavus. Out of the top 10 hub proteins of both organisms, protein phosphatase 2C and cyclic nucleotide-binding/kinase domain-containing protein and different ribosomal proteins were identified as candidate proteins involved in defense. Functional annotation and subcellular localization based characterization of HPPI identified protein SGT1 homolog, calmodulin and Rac-like GTP-binding proteins to be involved in defense response against fungus. The relevance of HPPI in infectious conditions was assessed using two transcriptome data which identified the interplay of host kinase class R proteins, bHLH TFs and cell wall related proteins to impart resistance against pathogen infection. Further, the pathogenicity analysis identified glycogen phosphorylase and molecular chaperone and allergen Mod-E/Hsp90/Hsp1 as potential pathogen targets to enhance the host defense mechanism. Hence, the computationally predicted host-pathogen PPI network could provide valuable support for molecular biology experiments to understand the host-pathogen interaction. SIGNIFICANCE: Protein-protein interactions execute significant cellular interactions in an organism and are influenced majorly by stress conditions. Here we reported the host-pathogen protein-protein interaction between peanut and A. flavus, and a detailed network analysis based on function, subcellular localization, gene co-expression, and pathogenicity was performed. The network analysis identified key proteins such as host kinase class R proteins, calmodulin, SGT1 homolog, Rac-like GTP-binding proteins bHLH TFs and cell wall related to impart resistance against pathogen infection. We observed the interplay of defense related proteins and cell wall related proteins predominantly, which could be subjected to further studies. The network analysis described in this study could be applied to understand other host-pathogen systems generally.
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Affiliation(s)
- Aiswarya Jayaprakash
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, R. V. Nagar Kalapet, Pondicherry 605014, India
| | - Abhijeet Roy
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, R. V. Nagar Kalapet, Pondicherry 605014, India
| | - Raja Rajeswary Thanmalagan
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, R. V. Nagar Kalapet, Pondicherry 605014, India
| | - Annamalai Arunachalam
- Department of Food Science & Technology, School of Life Sciences, Pondicherry University, R. V. Nagar Kalapet, Pondicherry 605014, India
| | - Lakshmi P T V
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, R. V. Nagar Kalapet, Pondicherry 605014, India.
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Wang Y, Liu D, Yin H, Wang H, Cao C, Wang J, Zheng J, Liu J. Transcriptomic and Metabolomic Analyses of the Response of Resistant Peanut Seeds to Aspergillus flavus Infection. Toxins (Basel) 2023; 15:414. [PMID: 37505683 PMCID: PMC10467056 DOI: 10.3390/toxins15070414] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/16/2023] [Accepted: 06/22/2023] [Indexed: 07/29/2023] Open
Abstract
Peanut seeds are susceptible to Aspergillus flavus infection, which has a severe impact on the peanut industry and human health. However, the molecular mechanism underlying this defense remains poorly understood. The aim of this study was to analyze the changes in differentially expressed genes (DEGs) and differential metabolites during A. flavus infection between Zhonghua 6 and Yuanza 9102 by transcriptomic and metabolomic analysis. A total of 5768 DEGs were detected in the transcriptomic study. Further functional analysis showed that some DEGs were significantly enriched in pectinase catabolism, hydrogen peroxide decomposition and cell wall tissues of resistant varieties at the early stage of infection, while these genes were differentially enriched in the middle and late stages of infection in the nonresponsive variety Yuanza 9102. Some DEGs, such as those encoding transcription factors, disease course-related proteins, peroxidase (POD), chitinase and phenylalanine ammonialyase (PAL), were highly expressed in the infection stage. Metabolomic analysis yielded 349 differential metabolites. Resveratrol, cinnamic acid, coumaric acid, ferulic acid in phenylalanine metabolism and 13S-HPODE in the linolenic acid metabolism pathway play major and active roles in peanut resistance to A. flavus. Combined analysis of the differential metabolites and DEGs showed that they were mainly enriched in phenylpropane metabolism and the linolenic acid metabolism pathway. Transcriptomic and metabolomic analyses further confirmed that peanuts infected with A. flavus activates various defense mechanisms, and the response to A. flavus is more rapid in resistant materials. These results can be used to further elucidate the molecular mechanism of peanut resistance to A. flavus infection and provide directions for early detection of infection and for breeding peanut varieties resistant to aflatoxin contamination.
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Affiliation(s)
| | | | | | | | | | | | | | - Jihong Liu
- Institute of Agricultural Quality Standards and Testing Technology, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (Y.W.); (D.L.); (H.Y.); (H.W.); (C.C.); (J.W.); (J.Z.)
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Huang R, Li H, Gao C, Yu W, Zhang S. Advances in omics research on peanut response to biotic stresses. FRONTIERS IN PLANT SCIENCE 2023; 14:1101994. [PMID: 37284721 PMCID: PMC10239885 DOI: 10.3389/fpls.2023.1101994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 04/18/2023] [Indexed: 06/08/2023]
Abstract
Peanut growth, development, and eventual production are constrained by biotic and abiotic stresses resulting in serious economic losses. To understand the response and tolerance mechanism of peanut to biotic and abiotic stresses, high-throughput Omics approaches have been applied in peanut research. Integrated Omics approaches are essential for elucidating the temporal and spatial changes that occur in peanut facing different stresses. The integration of functional genomics with other Omics highlights the relationships between peanut genomes and phenotypes under specific stress conditions. In this review, we focus on research on peanut biotic stresses. Here we review the primary types of biotic stresses that threaten sustainable peanut production, the multi-Omics technologies for peanut research and breeding, and the recent advances in various peanut Omics under biotic stresses, including genomics, transcriptomics, proteomics, metabolomics, miRNAomics, epigenomics and phenomics, for identification of biotic stress-related genes, proteins, metabolites and their networks as well as the development of potential traits. We also discuss the challenges, opportunities, and future directions for peanut Omics under biotic stresses, aiming sustainable food production. The Omics knowledge is instrumental for improving peanut tolerance to cope with various biotic stresses and for meeting the food demands of the exponentially growing global population.
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Affiliation(s)
- Ruihua Huang
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, China
| | - Hongqing Li
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, China
| | - Caiji Gao
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, China
| | - Weichang Yu
- Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Liaoning Peanut Research Institute, Liaoning Academy of Agricultural Sciences, Fuxing, China
- China Good Crop Company (Shenzhen) Limited, Shenzhen, China
| | - Shengchun Zhang
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, China
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Puppala N, Nayak SN, Sanz-Saez A, Chen C, Devi MJ, Nivedita N, Bao Y, He G, Traore SM, Wright DA, Pandey MK, Sharma V. Sustaining yield and nutritional quality of peanuts in harsh environments: Physiological and molecular basis of drought and heat stress tolerance. Front Genet 2023; 14:1121462. [PMID: 36968584 PMCID: PMC10030941 DOI: 10.3389/fgene.2023.1121462] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 02/06/2023] [Indexed: 03/29/2023] Open
Abstract
Climate change is significantly impacting agricultural production worldwide. Peanuts provide food and nutritional security to millions of people across the globe because of its high nutritive values. Drought and heat stress alone or in combination cause substantial yield losses to peanut production. The stress, in addition, adversely impact nutritional quality. Peanuts exposed to drought stress at reproductive stage are prone to aflatoxin contamination, which imposes a restriction on use of peanuts as health food and also adversely impact peanut trade. A comprehensive understanding of the impact of drought and heat stress at physiological and molecular levels may accelerate the development of stress tolerant productive peanut cultivars adapted to a given production system. Significant progress has been achieved towards the characterization of germplasm for drought and heat stress tolerance, unlocking the physiological and molecular basis of stress tolerance, identifying significant marker-trait associations as well major QTLs and candidate genes associated with drought tolerance, which after validation may be deployed to initiate marker-assisted breeding for abiotic stress adaptation in peanut. The proof of concept about the use of transgenic technology to add value to peanuts has been demonstrated. Advances in phenomics and artificial intelligence to accelerate the timely and cost-effective collection of phenotyping data in large germplasm/breeding populations have also been discussed. Greater focus is needed to accelerate research on heat stress tolerance in peanut. A suits of technological innovations are now available in the breeders toolbox to enhance productivity and nutritional quality of peanuts in harsh environments. A holistic breeding approach that considers drought and heat-tolerant traits to simultaneously address both stresses could be a successful strategy to produce climate-resilient peanut genotypes with improved nutritional quality.
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Affiliation(s)
- Naveen Puppala
- Agricultural Science Center at Clovis, New Mexico State University, Las Cruces, NM, United States
- *Correspondence: Naveen Puppala,
| | - Spurthi N. Nayak
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - Alvaro Sanz-Saez
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, United States
| | - Charles Chen
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, United States
| | - Mura Jyostna Devi
- USDA-ARS Vegetable Crops Research, Madison, WI, United States
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, United States
| | - Nivedita Nivedita
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, United States
| | - Yin Bao
- Biosystems Engineering Department, Auburn University, Auburn, AL, United States
| | - Guohao He
- Department of Plant and Soil Sciences, Tuskegee University, Tuskegee, AL, United States
| | - Sy M. Traore
- Department of Plant and Soil Sciences, Tuskegee University, Tuskegee, AL, United States
| | - David A. Wright
- Department of Biotechnology, Iowa State University, Ames, IA, United States
| | - Manish K. Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India
| | - Vinay Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India
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10
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Cui M, Han S, Wang D, Haider MS, Guo J, Zhao Q, Du P, Sun Z, Qi F, Zheng Z, Huang B, Dong W, Li P, Zhang X. Gene Co-expression Network Analysis of the Comparative Transcriptome Identifies Hub Genes Associated With Resistance to Aspergillus flavus L. in Cultivated Peanut ( Arachis hypogaea L.). FRONTIERS IN PLANT SCIENCE 2022; 13:899177. [PMID: 35812950 PMCID: PMC9264616 DOI: 10.3389/fpls.2022.899177] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/06/2022] [Indexed: 06/08/2023]
Abstract
Cultivated peanut (Arachis hypogaea L.), a cosmopolitan oil crop, is susceptible to a variety of pathogens, especially Aspergillus flavus L., which not only vastly reduce the quality of peanut products but also seriously threaten food safety for the contamination of aflatoxin. However, the key genes related to resistance to Aspergillus flavus L. in peanuts remain unclear. This study identifies hub genes positively associated with resistance to A. flavus in two genotypes by comparative transcriptome and weighted gene co-expression network analysis (WGCNA) method. Compared with susceptible genotype (Zhonghua 12, S), the rapid response to A. flavus and quick preparation for the translation of resistance-related genes in the resistant genotype (J-11, R) may be the drivers of its high resistance. WGCNA analysis revealed that 18 genes encoding pathogenesis-related proteins (PR10), 1-aminocyclopropane-1-carboxylate oxidase (ACO1), MAPK kinase, serine/threonine kinase (STK), pattern recognition receptors (PRRs), cytochrome P450, SNARE protein SYP121, pectinesterase, phosphatidylinositol transfer protein, and pentatricopeptide repeat (PPR) protein play major and active roles in peanut resistance to A. flavus. Collectively, this study provides new insight into resistance to A. flavus by employing WGCNA, and the identification of hub resistance-responsive genes may contribute to the development of resistant cultivars by molecular-assisted breeding.
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Affiliation(s)
- Mengjie Cui
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
- The Shennong Laboratory, Henan Academy of Crops Molecular Breeding, Henan Academy of Agricultural Science, Zhengzhou, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou, China
- Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou, China
- National Centre for Plant Breeding, Xinxiang, China
| | - Suoyi Han
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
- The Shennong Laboratory, Henan Academy of Crops Molecular Breeding, Henan Academy of Agricultural Science, Zhengzhou, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou, China
- Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou, China
- National Centre for Plant Breeding, Xinxiang, China
| | - Du Wang
- Key Laboratory of Detection for Mycotoxins, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | | | - Junjia Guo
- The Shennong Laboratory, Henan Academy of Crops Molecular Breeding, Henan Academy of Agricultural Science, Zhengzhou, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou, China
- Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou, China
- National Centre for Plant Breeding, Xinxiang, China
| | - Qi Zhao
- The Shennong Laboratory, Henan Academy of Crops Molecular Breeding, Henan Academy of Agricultural Science, Zhengzhou, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou, China
- Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou, China
| | - Pei Du
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
- The Shennong Laboratory, Henan Academy of Crops Molecular Breeding, Henan Academy of Agricultural Science, Zhengzhou, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou, China
- Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou, China
- National Centre for Plant Breeding, Xinxiang, China
| | - Ziqi Sun
- The Shennong Laboratory, Henan Academy of Crops Molecular Breeding, Henan Academy of Agricultural Science, Zhengzhou, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou, China
- Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou, China
- National Centre for Plant Breeding, Xinxiang, China
| | - Feiyan Qi
- The Shennong Laboratory, Henan Academy of Crops Molecular Breeding, Henan Academy of Agricultural Science, Zhengzhou, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou, China
- Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou, China
- National Centre for Plant Breeding, Xinxiang, China
| | - Zheng Zheng
- The Shennong Laboratory, Henan Academy of Crops Molecular Breeding, Henan Academy of Agricultural Science, Zhengzhou, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou, China
- Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou, China
- National Centre for Plant Breeding, Xinxiang, China
| | - Bingyan Huang
- The Shennong Laboratory, Henan Academy of Crops Molecular Breeding, Henan Academy of Agricultural Science, Zhengzhou, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou, China
- Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou, China
- National Centre for Plant Breeding, Xinxiang, China
| | - Wenzhao Dong
- The Shennong Laboratory, Henan Academy of Crops Molecular Breeding, Henan Academy of Agricultural Science, Zhengzhou, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou, China
- Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou, China
- National Centre for Plant Breeding, Xinxiang, China
| | - Peiwu Li
- Key Laboratory of Detection for Mycotoxins, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Xinyou Zhang
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
- The Shennong Laboratory, Henan Academy of Crops Molecular Breeding, Henan Academy of Agricultural Science, Zhengzhou, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou, China
- Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou, China
- National Centre for Plant Breeding, Xinxiang, China
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11
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Liu P, Cai Y, Wang R, Li B, Weng Q. Effect of Ethylenediaminetetraacetic acid (EDTA) on perillaldehyde-mediated regulation of postharvest Aspergillus flavus growth on peanuts. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.112826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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12
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Transcriptome and Metabolome Analysis Unveil Anthocyanin Metabolism in Pink and Red Testa of Peanut ( Arachis hypogaea L.). Int J Genomics 2021; 2021:5883901. [PMID: 34395608 PMCID: PMC8363441 DOI: 10.1155/2021/5883901] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/25/2021] [Indexed: 01/25/2023] Open
Abstract
Peanut (Arachis hypogaea L.) is an important source of oil and food around the world, and the testa color affects its appearance and commercial value. However, few studies focused on the mechanism of pigment formation in peanut testa. In this study, cultivars Shanhua 15 with pink testa and Zhonghua 12 with red testa were used as materials to perform the combined analysis of transcriptome and metabolome. A total of 198 flavonoid metabolites were detected, among which petunidin 3-O-glucoside and cyanidin O-acetylhexoside in Zhonghua12 were 15.23 and 14.72 times higher than those of Shanhua 15 at the R7 stage, revealing the anthocyanins underlying the red testa. Transcriptome analysis showed that there were 6059 and 3153 differentially expressed genes between Shanhua 15 and Zhonghua 12 in different growth periods, respectively. These differentially expressed genes were significantly enriched in the flavonoid biosynthesis, biosynthesis of secondary metabolites, and metabolic pathways. Integrated analysis of transcriptome and metabolome indicated CHS gene (arahy.CM90T6), F3'H genes (arahy. 8F7PE4 and arahy. K8H9R8), and DFR genes (arahy. LDV9QN and arahy. X8EVF3) may be the key functional genes controlling the formation of pink and red testa in peanut. Transcription factors MYB (arahy.A2IWKV, arahy.US2SKM, arahy.SJGE27, arahy.H8DJRL, and arahy.PR7AYB), bHLH (arahy.26781N, arahy.HM1IVV, and arahy.MP3D3D), and WD40 (arahy.L6JJW9) in the biosynthetic pathway of anthocyanin were significantly upregulated in Zhonghua 12 which may be the key regulatory genes in testa pigment formation. This is a comprehensive analysis on flavonoid metabolites and related genes expression in peanut testa, providing reference for revealing the regulatory mechanism of pigment accumulation in peanut testa.
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13
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Jayaprakash A, Roy A, Thanmalagan RR, Arunachalam A, Ptv L. Immune response gene coexpression network analysis of Arachis hypogaea infected with Aspergillus flavus. Genomics 2021; 113:2977-2988. [PMID: 34153499 DOI: 10.1016/j.ygeno.2021.06.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 02/07/2021] [Accepted: 06/16/2021] [Indexed: 01/21/2023]
Abstract
Aspergillus flavus (A. flavus) infection and aflatoxin contamination is a major bottleneck for peanut cultivation and value chain industry. In this study, a transcriptomic network study was conducted by retrieving publically available RNA-seq datasets of resistant and susceptible peanut varieties infected by A. flavus separately to understand the peanut defense mechanism against A. flavus. The gene expression analysis revealed differentially expressed genes (DEGs) in response to the different levels of infection and coexpression network of DEGs deciphered hub genes involved in the immune process in resistant and susceptible varieties. The interplay of resistance conferring genes and cell wall related genes was observed through functional enrichment analysis in response to pathogen infection and identified few key genes such as Protein P21, R genes, Pattern Recognition Receptor genes, Pectinesterases, Laccase and Thaumatin-like protein 1b as candidate genes in imparting immune response against A. flavus.
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Affiliation(s)
- Aiswarya Jayaprakash
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, R. V. Nagar Kalapet, Pondicherry 605014, India
| | - Abhijeet Roy
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, R. V. Nagar Kalapet, Pondicherry 605014, India
| | - Raja Rajeswary Thanmalagan
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, R. V. Nagar Kalapet, Pondicherry 605014, India
| | - Annamalai Arunachalam
- Postgraduate and Research Department of Botany, Arignar Anna Government Arts College, Villupuram, Tamil Nadu 605602, India
| | - Lakshmi Ptv
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, R. V. Nagar Kalapet, Pondicherry 605014, India.
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14
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Soni P, Pandey AK, Nayak SN, Pandey MK, Tolani P, Pandey S, Sudini HK, Bajaj P, Fountain JC, Singam P, Guo B, Varshney RK. Global Transcriptome Profiling Identified Transcription Factors, Biological Process, and Associated Pathways for Pre-Harvest Aflatoxin Contamination in Groundnut. J Fungi (Basel) 2021; 7:413. [PMID: 34073230 PMCID: PMC8227191 DOI: 10.3390/jof7060413] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/20/2021] [Accepted: 05/23/2021] [Indexed: 11/24/2022] Open
Abstract
Pre-harvest aflatoxin contamination (PAC) in groundnut is a serious quality concern globally, and drought stress before harvest further exacerbate its intensity, leading to the deterioration of produce quality. Understanding the host-pathogen interaction and identifying the candidate genes responsible for resistance to PAC will provide insights into the defense mechanism of the groundnut. In this context, about 971.63 million reads have been generated from 16 RNA samples under controlled and Aspergillus flavus infected conditions, from one susceptible and seven resistant genotypes. The RNA-seq analysis identified 45,336 genome-wide transcripts under control and infected conditions. This study identified 57 transcription factor (TF) families with major contributions from 6570 genes coding for bHLH (719), MYB-related (479), NAC (437), FAR1 family protein (320), and a few other families. In the host (groundnut), defense-related genes such as senescence-associated proteins, resveratrol synthase, seed linoleate, pathogenesis-related proteins, peroxidases, glutathione-S-transferases, chalcone synthase, ABA-responsive gene, and chitinases were found to be differentially expressed among resistant genotypes as compared to susceptible genotypes. This study also indicated the vital role of ABA-responsive ABR17, which co-regulates the genes of ABA responsive elements during drought stress, while providing resistance against A. flavus infection. It belongs to the PR-10 class and is also present in several plant-pathogen interactions.
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Affiliation(s)
- Pooja Soni
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (P.S.); (M.K.P.); (P.T.); (S.P.); (P.B.)
- Department of Genetics, Osmania University, Hyderabad 500007, India;
| | - Arun K. Pandey
- College of Life Science, China Jiliang University (CJLU), Hangzhou 310018, China;
| | - Spurthi N. Nayak
- Department of Biotechnology, University of Agricultural Sciences, Dharwad 580005, India;
| | - Manish K. Pandey
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (P.S.); (M.K.P.); (P.T.); (S.P.); (P.B.)
| | - Priya Tolani
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (P.S.); (M.K.P.); (P.T.); (S.P.); (P.B.)
| | - Sarita Pandey
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (P.S.); (M.K.P.); (P.T.); (S.P.); (P.B.)
| | - Hari K. Sudini
- Theme-Integrated Crop Improvement, Research Program-Asia, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India;
| | - Prasad Bajaj
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (P.S.); (M.K.P.); (P.T.); (S.P.); (P.B.)
| | - Jake C. Fountain
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS 39762, USA;
| | - Prashant Singam
- Department of Genetics, Osmania University, Hyderabad 500007, India;
| | - Baozhu Guo
- Crop Genetics and Breeding Research Unit, USDA-ARS, Tifton, GA 31793, USA;
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (P.S.); (M.K.P.); (P.T.); (S.P.); (P.B.)
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
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15
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Xie H, Jallow A, Yue X, Wang X, Fu J, Mwakinyali SE, Zhang Q, Li P. Aspergillus flavus's Response to Antagonism Bacterial Stress Sheds Light on a Regulation and Metabolic Trade-Off Mechanism for Adversity Survival. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:4840-4848. [PMID: 33856211 DOI: 10.1021/acs.jafc.0c07665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Biocontrol to combat the menace of Aspergillus flavus has gained considerable attention. However, the molecular mechanisms of A. flavus 's response to antagonism biotic stress are poorly deciphered. Here, we discovered that A. flavus switches an adaptive metabolic reprogramming to ensure its adversity survival by multiomics analyses (including four omics platform). Antifungal "weapons" lipopeptides and antibacterial metabolites of imizoquin were identified. The central metabolism fluxes were significantly depleted but the expressions of most corresponding genes were considerably increased in A. flavus. Secondary metabolism that does not contribute to stress was markedly suppressed. In contrast, A. flavus antibacterial "weapon arsenal" was activated to occupy an ecological niche. Our results revealed that interlinked mitochondrial central metabolism and secondary metabolism are central to A. flavus antagonism biotic stress response. This discovery contributes to the targeted design of biocontrol agents and smart regularization of rhizosphere microbiome homeostasis to realize long-term fungi pathogen control and mitigation mycotoxin contamination.
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Affiliation(s)
- Huali Xie
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430061, People's Republic of China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430061, People's Republic of China
- Key Laboratory of Detection for Aflatoxins, Ministry of Agriculture, Wuhan 430061, People's Republic of China
- Laboratory of Risk Assessment for Oilseeds Products (Wuhan), Ministry of Agriculture, Wuhan 430061, People's Republic of China
| | - Abdoulie Jallow
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430061, People's Republic of China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430061, People's Republic of China
- Key Laboratory of Detection for Aflatoxins, Ministry of Agriculture, Wuhan 430061, People's Republic of China
- Laboratory of Risk Assessment for Oilseeds Products (Wuhan), Ministry of Agriculture, Wuhan 430061, People's Republic of China
| | - Xiaofeng Yue
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430061, People's Republic of China
- Key Laboratory of Detection for Aflatoxins, Ministry of Agriculture, Wuhan 430061, People's Republic of China
- Laboratory of Risk Assessment for Oilseeds Products (Wuhan), Ministry of Agriculture, Wuhan 430061, People's Republic of China
| | - Xiuping Wang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430061, People's Republic of China
- Key Laboratory of Detection for Aflatoxins, Ministry of Agriculture, Wuhan 430061, People's Republic of China
- Laboratory of Risk Assessment for Oilseeds Products (Wuhan), Ministry of Agriculture, Wuhan 430061, People's Republic of China
- Quality Inspection and Test Center for Oilseeds Products, Ministry of Agriculture, Wuhan 430061, People's Republic of China
| | - Jiayun Fu
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430061, People's Republic of China
- Key Laboratory of Detection for Aflatoxins, Ministry of Agriculture, Wuhan 430061, People's Republic of China
- Laboratory of Risk Assessment for Oilseeds Products (Wuhan), Ministry of Agriculture, Wuhan 430061, People's Republic of China
- Quality Inspection and Test Center for Oilseeds Products, Ministry of Agriculture, Wuhan 430061, People's Republic of China
| | - Silvano E Mwakinyali
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430061, People's Republic of China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430061, People's Republic of China
- Key Laboratory of Detection for Aflatoxins, Ministry of Agriculture, Wuhan 430061, People's Republic of China
| | - Qi Zhang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430061, People's Republic of China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430061, People's Republic of China
- Key Laboratory of Detection for Aflatoxins, Ministry of Agriculture, Wuhan 430061, People's Republic of China
- Laboratory of Risk Assessment for Oilseeds Products (Wuhan), Ministry of Agriculture, Wuhan 430061, People's Republic of China
- Quality Inspection and Test Center for Oilseeds Products, Ministry of Agriculture, Wuhan 430061, People's Republic of China
| | - Peiwu Li
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430061, People's Republic of China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430061, People's Republic of China
- Key Laboratory of Detection for Aflatoxins, Ministry of Agriculture, Wuhan 430061, People's Republic of China
- Laboratory of Risk Assessment for Oilseeds Products (Wuhan), Ministry of Agriculture, Wuhan 430061, People's Republic of China
- Quality Inspection and Test Center for Oilseeds Products, Ministry of Agriculture, Wuhan 430061, People's Republic of China
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16
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Sharma S, Choudhary B, Yadav S, Mishra A, Mishra VK, Chand R, Chen C, Pandey SP. Metabolite profiling identified pipecolic acid as an important component of peanut seed resistance against Aspergillus flavus infection. JOURNAL OF HAZARDOUS MATERIALS 2021; 404:124155. [PMID: 33049626 DOI: 10.1016/j.jhazmat.2020.124155] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 09/03/2020] [Accepted: 09/28/2020] [Indexed: 06/11/2023]
Abstract
In a previous study, we identified a halotolerant rhizobacterium belonging to the genus Klebsiella (MBE02) that protected peanut seeds from Aspergillus flavus infection. Here, we investigated the mechanisms underlying the effect of MBE02 against A. flavus via untargeted metabolite profiling of peanut seeds treated with MBE02, A. flavus, or MBE02+A. flavus. Thirty-five metabolites were differentially accumulated across the three treatments (compared to the control), and the levels of pipecolic acid (Pip) were reduced upon A. flavus treatment only. We validated the function of Pip against A. flavus using multiple resistant and susceptible peanut cultivars. Pip accumulation was strongly associated with the resistant genotypes that also accumulated several mRNAs of the ALD1-like gene in the Pip biosynthesis pathway. Furthermore, exogenous treatment of a susceptible peanut cultivar with Pip reduced A. flavus infection in the seeds. Our findings indicate that Pip is a key component of peanut resistance to A. flavus.
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Affiliation(s)
- Sandeep Sharma
- Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India.
| | - Babita Choudhary
- CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar, India.
| | - Sonam Yadav
- CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar, India.
| | - Avinash Mishra
- CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar, India.
| | - Vinod K Mishra
- Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India.
| | - Ramesh Chand
- Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India.
| | - Chen Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China.
| | - Shree P Pandey
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, Germany.
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17
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Transcriptome Analysis Identified Coordinated Control of Key Pathways Regulating Cellular Physiology and Metabolism upon Aspergillus flavus Infection Resulting in Reduced Aflatoxin Production in Groundnut. J Fungi (Basel) 2020; 6:jof6040370. [PMID: 33339393 PMCID: PMC7767264 DOI: 10.3390/jof6040370] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 12/14/2022] Open
Abstract
Aflatoxin-affected groundnut or peanut presents a major global health issue to both commercial and subsistence farming. Therefore, understanding the genetic and molecular mechanisms associated with resistance to aflatoxin production during host–pathogen interactions is crucial for breeding groundnut cultivars with minimal level of aflatoxin contamination. Here, we performed gene expression profiling to better understand the mechanisms involved in reduction and prevention of aflatoxin contamination resulting from Aspergillus flavus infection in groundnut seeds. RNA sequencing (RNA-Seq) of 16 samples from different time points during infection (24 h, 48 h, 72 h and the 7th day after inoculation) in U 4-7-5 (resistant) and JL 24 (susceptible) genotypes yielded 840.5 million raw reads with an average of 52.5 million reads per sample. A total of 1779 unique differentially expressed genes (DEGs) were identified. Furthermore, comprehensive analysis revealed several pathways, such as disease resistance, hormone biosynthetic signaling, flavonoid biosynthesis, reactive oxygen species (ROS) detoxifying, cell wall metabolism and catabolizing and seed germination. We also detected several highly upregulated transcription factors, such as ARF, DBB, MYB, NAC and C2H2 in the resistant genotype in comparison to the susceptible genotype after inoculation. Moreover, RNA-Seq analysis suggested the occurrence of coordinated control of key pathways controlling cellular physiology and metabolism upon A. flavus infection, resulting in reduced aflatoxin production.
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Yuan C, Li C, Lu X, Zhao X, Yan C, Wang J, Sun Q, Shan S. Comprehensive genomic characterization of NAC transcription factor family and their response to salt and drought stress in peanut. BMC PLANT BIOLOGY 2020; 20:454. [PMID: 33008287 PMCID: PMC7532626 DOI: 10.1186/s12870-020-02678-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 09/24/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND Peanut is one of the most important oil crop species worldwide. NAC transcription factor (TF) genes play important roles in the salt and drought stress responses of plants by activating or repressing target gene expression. However, little is known about NAC genes in peanut. RESULTS We performed a genome-wide characterization of NAC genes from the diploid wild peanut species Arachis duranensis and Arachis ipaensis, which included analyses of chromosomal locations, gene structures, conserved motifs, expression patterns, and cis-acting elements within their promoter regions. In total, 81 and 79 NAC genes were identified from A. duranensis and A. ipaensis genomes. Phylogenetic analysis of peanut NACs along with their Arabidopsis and rice counterparts categorized these proteins into 18 distinct subgroups. Fifty-one orthologous gene pairs were identified, and 46 orthologues were found to be highly syntenic on the chromosomes of both A. duranensis and A. ipaensis. Comparative RNA sequencing (RNA-seq)-based analysis revealed that the expression of 43 NAC genes was up- or downregulated under salt stress and under drought stress. Among these genes, the expression of 17 genes in cultivated peanut (Arachis hypogaea) was up- or downregulated under both stresses. Moreover, quantitative reverse transcription PCR (RT-qPCR)-based analysis revealed that the expression of most of the randomly selected NAC genes tended to be consistent with the comparative RNA-seq results. CONCLUSION Our results facilitated the functional characterization of peanut NAC genes, and the genes involved in salt and drought stress responses identified in this study could be potential genes for peanut improvement.
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Affiliation(s)
- Cuiling Yuan
- Shandong Peanut Research Institute, Qingdao, 266100, China
| | - Chunjuan Li
- Shandong Peanut Research Institute, Qingdao, 266100, China
| | - Xiaodong Lu
- Shandong Peanut Research Institute, Qingdao, 266100, China
| | - Xiaobo Zhao
- Shandong Peanut Research Institute, Qingdao, 266100, China
| | - Caixia Yan
- Shandong Peanut Research Institute, Qingdao, 266100, China
| | - Juan Wang
- Shandong Peanut Research Institute, Qingdao, 266100, China
| | - Quanxi Sun
- Shandong Peanut Research Institute, Qingdao, 266100, China.
| | - Shihua Shan
- Shandong Peanut Research Institute, Qingdao, 266100, China.
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Khan SA, Chen H, Deng Y, Chen Y, Zhang C, Cai T, Ali N, Mamadou G, Xie D, Guo B, Varshney RK, Zhuang W. High-density SNP map facilitates fine mapping of QTLs and candidate genes discovery for Aspergillus flavus resistance in peanut (Arachis hypogaea). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2239-2257. [PMID: 32285164 DOI: 10.1007/s00122-020-03594-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 04/01/2020] [Indexed: 06/11/2023]
Abstract
Two novel resistant QTLs mapped and candidate genes identified for Aspergillus flavus resistance in cultivated peanut using SLAF-seq. Aflatoxin contamination in peanuts caused by Aspergillus flavus is a serious food safety issue for human health around the world. Host plant resistance to fungal infection and reduction in aflatoxin are crucial for mitigating this problem. Identification of the resistance-linked markers can be used in marker-assisted breeding for varietal development. Here we report construction of two high-density genetic linkage maps with 1975 SNP loci and 5022 SNP loci, respectively. Two consistent quantitative trait loci (QTL) were identified as qRAF-3-1 and qRAF-14-1, which located on chromosomes A03 and B04, respectively. QTL qRAF-3-1 was mapped within 1.67 cM and had more than 19% phenotypic variance explained (PVE), while qRAF-14-1 was located within 1.34 cM with 5.15% PVE. While comparing with the reference genome, the mapped QTLs, qRAF-3-1 and qRAF-14-1, were located within a physical distance of 1.44 Megabase pair (Mbp) and 2.22 Mbp, harboring 67 and 137 genes, respectively. Among the identified candidate genes, six genes with the same function were found within both QTLs regions. In addition, putative disease resistance RPP13-like protein 1 (RPP13), lipoxygenase (Lox), WRKY transcription factor (WRKY) and cytochrome P450 71B34 genes were also identified. Using microarray analysis, genes responded to A. flavus infection included coding for RPP13, pentatricopeptide repeat-containing-like protein, and Lox which may be possible candidate genes for resistance to A. flavus. The QTLs and candidate genes will further facilitate marker development and validation of genes for deployment in the molecular breeding programs against A. flavus in peanuts.
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Affiliation(s)
- Shahid Ali Khan
- Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Hua Chen
- Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Ye Deng
- Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yuhua Chen
- Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Chong Zhang
- Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Tiecheng Cai
- Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Niaz Ali
- Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Gandeka Mamadou
- Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Dongyang Xie
- Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Baozhu Guo
- Crop Protection and Management Research Unit, USDA-ARS, Tifton, GA, 31793, USA
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, 502324, India
| | - Weijian Zhuang
- Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
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20
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Zhao C, Li T, Zhao Y, Zhang B, Li A, Zhao S, Hou L, Xia H, Fan S, Qiu J, Li P, Zhang Y, Guo B, Wang X. Integrated small RNA and mRNA expression profiles reveal miRNAs and their target genes in response to Aspergillus flavus growth in peanut seeds. BMC PLANT BIOLOGY 2020; 20:215. [PMID: 32404101 PMCID: PMC7222326 DOI: 10.1186/s12870-020-02426-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 04/30/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND MicroRNAs are important gene expression regulators in plants immune system. Aspergillus flavus is the most common causal agents of aflatoxin contamination in peanuts, but information on the function of miRNA in peanut-A. flavus interaction is lacking. In this study, the resistant cultivar (GT-C20) and susceptible cultivar (Tifrunner) were used to investigate regulatory roles of miRNAs in response to A. flavus growth. RESULTS A total of 30 miRNAs, 447 genes and 21 potential miRNA/mRNA pairs were differentially expressed significantly when treated with A. flavus. A total of 62 miRNAs, 451 genes and 44 potential miRNA/mRNA pairs exhibited differential expression profiles between two peanut varieties. Gene Ontology (GO) analysis showed that metabolic-process related GO terms were enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses further supported the GO results, in which many enriched pathways were related with biosynthesis and metabolism, such as biosynthesis of secondary metabolites and metabolic pathways. Correlation analysis of small RNA, transcriptome and degradome indicated that miR156/SPL pairs might regulate the accumulation of flavonoids in resistant and susceptible genotypes. The miR482/2118 family might regulate NBS-LRR gene which had the higher expression level in resistant genotype. These results provided useful information for further understanding the roles of miR156/157/SPL and miR482/2118/NBS-LRR pairs. CONCLUSIONS Integration analysis of the transcriptome, miRNAome and degradome of resistant and susceptible peanut varieties were performed in this study. The knowledge gained will help to understand the roles of miRNAs of peanut in response to A. flavus.
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Affiliation(s)
- Chuanzhi Zhao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
- College of Life Sciences, Shandong Normal University, Jinan, 250014 PR China
| | - Tingting Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
- Rizhao Experimental High School od Shandong, Rizhao, 276826 PR China
| | - Yuhan Zhao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
- College of Life Sciences, Shandong Normal University, Jinan, 250014 PR China
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC USA
| | - Aiqin Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
| | - Shuzhen Zhao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
| | - Lei Hou
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
| | - Han Xia
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
| | - Shoujin Fan
- College of Life Sciences, Shandong Normal University, Jinan, 250014 PR China
| | - Jingjing Qiu
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
- College of Life Sciences, Shandong Normal University, Jinan, 250014 PR China
| | - Pengcheng Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
| | - Ye Zhang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
| | - Baozhu Guo
- Crop Protection and Management Research Unit, USDA-Agricultural Research Service, Tifton, GA 31793 USA
- Department of Plant Pathology, University of Georgia, Tifton, GA USA
| | - Xingjun Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
- College of Life Sciences, Shandong Normal University, Jinan, 250014 PR China
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21
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Soni P, Gangurde SS, Ortega-Beltran A, Kumar R, Parmar S, Sudini HK, Lei Y, Ni X, Huai D, Fountain JC, Njoroge S, Mahuku G, Radhakrishnan T, Zhuang W, Guo B, Liao B, Singam P, Pandey MK, Bandyopadhyay R, Varshney RK. Functional Biology and Molecular Mechanisms of Host-Pathogen Interactions for Aflatoxin Contamination in Groundnut ( Arachis hypogaea L.) and Maize ( Zea mays L.). Front Microbiol 2020; 11:227. [PMID: 32194520 PMCID: PMC7063101 DOI: 10.3389/fmicb.2020.00227] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 01/30/2020] [Indexed: 12/26/2022] Open
Abstract
Aflatoxins are secondary metabolites produced by soilborne saprophytic fungus Aspergillus flavus and closely related species that infect several agricultural commodities including groundnut and maize. The consumption of contaminated commodities adversely affects the health of humans and livestock. Aflatoxin contamination also causes significant economic and financial losses to producers. Research efforts and significant progress have been made in the past three decades to understand the genetic behavior, molecular mechanisms, as well as the detailed biology of host-pathogen interactions. A range of omics approaches have facilitated better understanding of the resistance mechanisms and identified pathways involved during host-pathogen interactions. Most of such studies were however undertaken in groundnut and maize. Current efforts are geared toward harnessing knowledge on host-pathogen interactions and crop resistant factors that control aflatoxin contamination. This study provides a summary of the recent progress made in enhancing the understanding of the functional biology and molecular mechanisms associated with host-pathogen interactions during aflatoxin contamination in groundnut and maize.
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Affiliation(s)
- Pooja Soni
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Sunil S. Gangurde
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | | | - Rakesh Kumar
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Sejal Parmar
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Hari K. Sudini
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Yong Lei
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xinzhi Ni
- Crop Genetics and Breeding Research Unit, United States Department of Agriculture – Agriculture Research Service, Tifton, GA, United States
| | - Dongxin Huai
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Jake C. Fountain
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
| | - Samuel Njoroge
- International Crops Research Institute for the Semi-Arid Tropics, Lilongwe, Malawi
| | - George Mahuku
- International Institute of Tropical Agriculture, Dar es Salaam, Tanzania
| | | | - Weijian Zhuang
- Oil Crops Research Institute, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Baozhu Guo
- Crop Protection and Management Research Unit, United States Department of Agriculture – Agricultural Research Service, Tifton, GA, United States
| | - Boshou Liao
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Prashant Singam
- Department of Genetics, Osmania University, Hyderabad, India
| | - Manish K. Pandey
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | | | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
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22
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Ncube J, Maphosa M. Current state of knowledge on groundnut aflatoxins and their management from a plant breeding perspective: Lessons for Africa. SCIENTIFIC AFRICAN 2020. [DOI: 10.1016/j.sciaf.2020.e00264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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23
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Zhang H, Zhao X, Sun Q, Yan C, Wang J, Yuan C, Li C, Shan S, Liu F. Comparative Transcriptome Analysis Reveals Molecular Defensive Mechanism of Arachis hypogaea in Response to Salt Stress. Int J Genomics 2020; 2020:6524093. [PMID: 32190641 PMCID: PMC7063224 DOI: 10.1155/2020/6524093] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 05/25/2019] [Accepted: 01/21/2020] [Indexed: 01/01/2023] Open
Abstract
Abiotic stresses comprise all nonliving factors, such as soil salinity, drought, extreme temperatures, and metal toxicity, posing a serious threat to agriculture and affecting the plant production around the world. Peanut (Arachis hypogaea L.) is one of the most important crops for vegetable oil, proteins, minerals, and vitamins in the world. Therefore, it is of importance to understand the molecular mechanism of peanut against salt stress. Six transcriptome sequencing libraries including 24-hour salt treatments and control samples were constructed from the young leaves of peanut. A comprehensive analysis between two groups detected 3,425 differentially expressed genes (DEGs) including 2,013 upregulated genes and 1,412 downregulated genes. Of these DEGs, 141 transcription factors (TFs) mainly consisting of MYB, AP2/ERF, WRKY, bHLH, and HSF were identified in response to salinity stress. Further, GO categories of the DEGs highly related to regulation of cell growth, cell periphery, sustained external encapsulating structure, cell wall organization or biogenesis, antioxidant activity, and peroxidase activity were significantly enriched for upregulated DEGs. The function of downregulated DEGs was mainly enriched in regulation of metabolic processes, oxidoreductase activity, and catalytic activity. Fourteen DEGs with response to salt tolerance were validated by real-time PCR. Taken together, the identification of DEGs' response to salt tolerance of cultivated peanut will provide a solid foundation for improving salt-tolerant peanut genetic manipulation in the future.
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Affiliation(s)
- Hao Zhang
- State Key Laboratory of Crop Biology and College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, China
- Shandong Peanut Research Institute, Qingdao, Shandong 266000, China
| | - Xiaobo Zhao
- Shandong Peanut Research Institute, Qingdao, Shandong 266000, China
| | - Quanxi Sun
- Shandong Peanut Research Institute, Qingdao, Shandong 266000, China
| | - Caixia Yan
- Shandong Peanut Research Institute, Qingdao, Shandong 266000, China
| | - Juan Wang
- Shandong Peanut Research Institute, Qingdao, Shandong 266000, China
| | - Cuiling Yuan
- Shandong Peanut Research Institute, Qingdao, Shandong 266000, China
| | - Chunjuan Li
- Shandong Peanut Research Institute, Qingdao, Shandong 266000, China
| | - Shihua Shan
- Shandong Peanut Research Institute, Qingdao, Shandong 266000, China
| | - Fengzhen Liu
- State Key Laboratory of Crop Biology and College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, China
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Pfliegler WP, Pócsi I, Győri Z, Pusztahelyi T. The Aspergilli and Their Mycotoxins: Metabolic Interactions With Plants and the Soil Biota. Front Microbiol 2020; 10:2921. [PMID: 32117074 PMCID: PMC7029702 DOI: 10.3389/fmicb.2019.02921] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 12/04/2019] [Indexed: 01/06/2023] Open
Abstract
Species of the highly diverse fungal genus Aspergillus are well-known agricultural pests, and, most importantly, producers of various mycotoxins threatening food safety worldwide. Mycotoxins are studied predominantly from the perspectives of human and livestock health. Meanwhile, their roles are far less known in nature. However, to understand the factors behind mycotoxin production, the roles of the toxins of Aspergilli must be understood from a complex ecological perspective, taking mold-plant, mold-microbe, and mold-animal interactions into account. The Aspergilli may switch between saprophytic and pathogenic lifestyles, and the production of secondary metabolites, such as mycotoxins, may vary according to these fungal ways of life. Recent studies highlighted the complex ecological network of soil microbiotas determining the niches that Aspergilli can fill in. Interactions with the soil microbiota and soil macro-organisms determine the role of secondary metabolite production to a great extent. While, upon infection of plants, metabolic communication including fungal secondary metabolites like aflatoxins, gliotoxin, patulin, cyclopiazonic acid, and ochratoxin, influences the fate of both the invader and the host. In this review, the role of mycotoxin producing Aspergillus species and their interactions in the ecosystem are discussed. We intend to highlight the complexity of the roles of the main toxic secondary metabolites as well as their fate in natural environments and agriculture, a field that still has important knowledge gaps.
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Affiliation(s)
- Walter P. Pfliegler
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - István Pócsi
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - Zoltán Győri
- Institute of Nutrition, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - Tünde Pusztahelyi
- Central Laboratory of Agricultural and Food Products, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Debrecen, Hungary
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25
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Pandey MK, Kumar R, Pandey AK, Soni P, Gangurde SS, Sudini HK, Fountain JC, Liao B, Desmae H, Okori P, Chen X, Jiang H, Mendu V, Falalou H, Njoroge S, Mwololo J, Guo B, Zhuang W, Wang X, Liang X, Varshney RK. Mitigating Aflatoxin Contamination in Groundnut through A Combination of Genetic Resistance and Post-Harvest Management Practices. Toxins (Basel) 2019; 11:E315. [PMID: 31163657 PMCID: PMC6628460 DOI: 10.3390/toxins11060315] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/19/2019] [Accepted: 05/23/2019] [Indexed: 01/12/2023] Open
Abstract
Aflatoxin is considered a "hidden poison" due to its slow and adverse effect on various biological pathways in humans, particularly among children, in whom it leads to delayed development, stunted growth, liver damage, and liver cancer. Unfortunately, the unpredictable behavior of the fungus as well as climatic conditions pose serious challenges in precise phenotyping, genetic prediction and genetic improvement, leaving the complete onus of preventing aflatoxin contamination in crops on post-harvest management. Equipping popular crop varieties with genetic resistance to aflatoxin is key to effective lowering of infection in farmer's fields. A combination of genetic resistance for in vitro seed colonization (IVSC), pre-harvest aflatoxin contamination (PAC) and aflatoxin production together with pre- and post-harvest management may provide a sustainable solution to aflatoxin contamination. In this context, modern "omics" approaches, including next-generation genomics technologies, can provide improved and decisive information and genetic solutions. Preventing contamination will not only drastically boost the consumption and trade of the crops and products across nations/regions, but more importantly, stave off deleterious health problems among consumers across the globe.
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Affiliation(s)
- Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India.
| | - Rakesh Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India.
| | - Arun K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India.
| | - Pooja Soni
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India.
| | - Sunil S Gangurde
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India.
| | - Hari K Sudini
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India.
| | - Jake C Fountain
- Crop Protection and Management Research Unit, United State Department of Agriculture-Agricultural Research Service (USDA-ARS), Tifton, GA 31793, USA.
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA.
| | - Boshou Liao
- Oil Crops Research Institute (OCRI) of Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China.
| | - Haile Desmae
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Bamako BP 320, Mali.
| | - Patrick Okori
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Lilongwe PB 1096, Malawi.
| | - Xiaoping Chen
- Crops Research Institute (CRI) of Guangdong Academy of Agricultural Sciences (GAAS), Guangzhou 510640, China.
| | - Huifang Jiang
- Oil Crops Research Institute (OCRI) of Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China.
| | - Venugopal Mendu
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409, USA.
| | - Hamidou Falalou
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Niamey BP 12404, Niger.
| | - Samuel Njoroge
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Lilongwe PB 1096, Malawi.
| | - James Mwololo
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Lilongwe PB 1096, Malawi.
| | - Baozhu Guo
- Crop Protection and Management Research Unit, United State Department of Agriculture-Agricultural Research Service (USDA-ARS), Tifton, GA 31793, USA.
| | - Weijian Zhuang
- Institute of Oil Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Xingjun Wang
- Shandong Academy of Agricultural Sciences, Jinan 250108, China.
| | - Xuanqiang Liang
- Crops Research Institute (CRI) of Guangdong Academy of Agricultural Sciences (GAAS), Guangzhou 510640, China.
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India.
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26
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Yu B, Huai D, Huang L, Kang Y, Ren X, Chen Y, Zhou X, Luo H, Liu N, Chen W, Lei Y, Pandey MK, Sudini H, Varshney RK, Liao B, Jiang H. Identification of genomic regions and diagnostic markers for resistance to aflatoxin contamination in peanut (Arachis hypogaea L.). BMC Genet 2019; 20:32. [PMID: 30866805 PMCID: PMC6417274 DOI: 10.1186/s12863-019-0734-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 03/01/2019] [Indexed: 11/15/2022] Open
Abstract
Background Aflatoxin contamination caused by Aspergillus flavus is a major constraint to peanut industry worldwide due to its toxicological effects to human and animals. Developing peanut varieties with resistance to seed infection and/or aflatoxin accumulation is the most effective and economic strategy for reducing aflatoxin risk in food chain. Breeding for resistance to aflatoxin in peanut is a challenging task for breeders because the genetic basis is still poorly understood. To identify the quantitative trait loci (QTLs) for resistance to aflatoxin contamination in peanut, a recombinant inbred line (RIL) population was developed from crossing Zhonghua 10 (susceptible) with ICG 12625 (resistant). The percent seed infection index (PSII), the contents of aflatoxin B1 (AFB1) and aflatoxin B2 (AFB2) of RILs were evaluated by a laboratory kernel inoculation assay. Results Two QTLs were identified for PSII including one major QTL with 11.32–13.00% phenotypic variance explained (PVE). A total of 12 QTLs for aflatoxin accumulation were detected by unconditional analysis, and four of them (qAFB1A07 and qAFB1B06.1 for AFB1, qAFB2A07 and qAFB2B06 for AFB2) exhibited major and stable effects across multiple environments with 9.32–21.02% PVE. Furthermore, not only qAFB1A07 and qAFB2A07 were co-localized in the same genetic interval on LG A07, but qAFB1B06.1 was also co-localized with qAFB2B06 on LG B06. Conditional QTL mapping also confirmed that there was a strong interaction between resistance to AFB1 and AFB2 accumulation. Genotyping of RILs revealed that qAFB1A07 and qAFB1B06.1 interacted additively to improve the resistance to both AFB1 and AFB2 accumulation. Additionally, validation of the two markers was performed in diversified germplasm collection and four accessions with resistance to aflatoxin accumulation were identified. Conclusions Single major QTL for resistance to PSII and two important co-localized intervals associated with major QTLs for resistance to AFB1 and AFB2. Combination of these intervals could improve the resistance to aflatoxin accumulation in peanut. SSR markers linked to these intervals were identified and validated. The identified QTLs and associated markers exhibit potential to be applied in improvement of resistance to aflatoxin contamination. Electronic supplementary material The online version of this article (10.1186/s12863-019-0734-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bolun Yu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Dongxin Huai
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Li Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yanping Kang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaoping Ren
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yuning Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaojing Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Huaiyong Luo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Nian Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Weigang Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Manish K Pandey
- International Crops Research Institute of the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Hari Sudini
- International Crops Research Institute of the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rajeev K Varshney
- International Crops Research Institute of the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China.
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27
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Nayak SN, Agarwal G, Pandey MK, Sudini HK, Jayale AS, Purohit S, Desai A, Wan L, Guo B, Liao B, Varshney RK. Aspergillus flavus infection triggered immune responses and host-pathogen cross-talks in groundnut during in-vitro seed colonization. Sci Rep 2017; 7:9659. [PMID: 28851929 PMCID: PMC5574979 DOI: 10.1038/s41598-017-09260-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 07/19/2017] [Indexed: 11/25/2022] Open
Abstract
Aflatoxin contamination, caused by fungal pathogen Aspergillus flavus, is a major quality and health problem delimiting the trade and consumption of groundnut (Arachis hypogaea L.) worldwide. RNA-seq approach was deployed to understand the host-pathogen interaction by identifying differentially expressed genes (DEGs) for resistance to in-vitro seed colonization (IVSC) at four critical stages after inoculation in J 11 (resistant) and JL 24 (susceptible) genotypes of groundnut. About 1,344.04 million sequencing reads have been generated from sixteen libraries representing four stages in control and infected conditions. About 64% and 67% of quality filtered reads (1,148.09 million) were mapped onto A (A. duranensis) and B (A. ipaёnsis) subgenomes of groundnut respectively. About 101 million unaligned reads each from J 11 and JL 24 were used to map onto A. flavus genome. As a result, 4,445 DEGs including defense-related genes like senescence-associated proteins, resveratrol synthase, 9s-lipoxygenase, pathogenesis-related proteins were identified. In A. flavus, about 578 DEGs coding for growth and development of fungus, aflatoxin biosynthesis, binding, transport, and signaling were identified in compatible interaction. Besides identifying candidate genes for IVSC resistance in groundnut, the study identified the genes involved in host-pathogen cross-talks and markers that can be used in breeding resistant varieties.
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Affiliation(s)
- Spurthi N Nayak
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - Gaurav Agarwal
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Crop Protection and Management Research Unit, USDA-Agricultural Research Service, Tifton, GA, USA
- University of Georgia, Department of Plant Pathology, Tifton, GA, USA
| | - Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Hari K Sudini
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Ashwin S Jayale
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Shilp Purohit
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Aarthi Desai
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Liyun Wan
- Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Baozhu Guo
- Crop Protection and Management Research Unit, USDA-Agricultural Research Service, Tifton, GA, USA
| | - Boshou Liao
- Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
- The University of Western Australia, Crawley, WA, Australia.
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28
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Differential evolutionary patterns and expression levels between sex-specific and somatic tissue-specific genes in peanut. Sci Rep 2017; 7:9016. [PMID: 28827710 PMCID: PMC5566475 DOI: 10.1038/s41598-017-09905-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 08/01/2017] [Indexed: 11/08/2022] Open
Abstract
The patterns of evolution and expression of tissue-specific genes are poorly understood beyond sex-specific genes. Accordingly, we identified 3,191 tissue-specific genes and 38,745 common genes using 22 RNA-seq datasets from cultivated peanut. The expression levels of tissue-specific genes were significantly lower than those of common genes. Further, the expression levels of sex-specific genes were significantly higher than those of somatic tissue-specific genes. Among sex-specific genes, the expression levels of gynoecium-specific genes were significantly higher than those of androecium-specific genes. Function-specific genes were lacking among tissue-specific genes, and tissue-specific gene annotations overlapped among different tissues. Duplicate gene pairs were classified as homogeneous pairs expressed within the same tissue or heterogeneous pairs expressed in different tissues. Heterogeneous gene pairs evolved more rapidly than homogeneous gene pairs. In addition, somatic tissue-specific genes evolved faster than sex-specific genes. Molecular signatures of selection indicated that somatic tissue-specific genes have mainly experienced relaxed selection, while sex-specific genes have been under stronger selective constraint. Somatic tissue-specific genes had higher codon usage bias than sex-specific genes. These contrasting patterns between somatic tissue-specific and sex-specific genes provide new insights into the basic biology and evolution of peanut, an important crop.
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29
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Korani WA, Chu Y, Holbrook C, Clevenger J, Ozias-Akins P. Genotypic Regulation of Aflatoxin Accumulation but Not Aspergillus Fungal Growth upon Post-Harvest Infection of Peanut (Arachis hypogaea L.) Seeds. Toxins (Basel) 2017; 9:E218. [PMID: 28704974 PMCID: PMC5535165 DOI: 10.3390/toxins9070218] [Citation(s) in RCA: 10] [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: 05/04/2017] [Accepted: 07/07/2017] [Indexed: 11/18/2022] Open
Abstract
Aflatoxin contamination is a major economic and food safety concern for the peanut industry that largely could be mitigated by genetic resistance. To screen peanut for aflatoxin resistance, ten genotypes were infected with a green fluorescent protein (GFP)-expressing Aspergillus flavus strain. Percentages of fungal infected area and fungal GFP signal intensity were documented by visual ratings every 8 h for 72 h after inoculation. Significant genotypic differences in fungal growth rates were documented by repeated measures and area under the disease progress curve (AUDPC) analyses. SICIA (Seed Infection Coverage and Intensity Analyzer), an image processing software, was developed to digitize fungal GFP signals. Data from SICIA image analysis confirmed visual rating results validating its utility for quantifying fungal growth. Among the tested peanut genotypes, NC 3033 and GT-C20 supported the lowest and highest fungal growth on the surface of peanut seeds, respectively. Although differential fungal growth was observed on the surface of peanut seeds, total fungal growth in the seeds was not significantly different across genotypes based on a fluorometric GFP assay. Significant differences in aflatoxin B levels were detected across peanut genotypes. ICG 1471 had the lowest aflatoxin level whereas Florida-07 had the highest. Two-year aflatoxin tests under simulated late-season drought also showed that ICG 1471 had reduced aflatoxin production under pre-harvest field conditions. These results suggest that all peanut genotypes support A. flavus fungal growth yet differentially influence aflatoxin production.
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Affiliation(s)
- Walid Ahmed Korani
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Tifton, GA 31793, USA.
| | - Ye Chu
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Tifton, GA 31793, USA.
| | - Corley Holbrook
- The United States Department of Agriculture-Agricultural Research Service, Crop Genetics and Breeding Research Unit, Tifton, GA 31793, USA.
| | - Josh Clevenger
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Tifton, GA 31793, USA.
| | - Peggy Ozias-Akins
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Tifton, GA 31793, USA.
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30
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Identification of lipoxygenase (LOX) genes from legumes and their responses in wild type and cultivated peanut upon Aspergillus flavus infection. Sci Rep 2016; 6:35245. [PMID: 27731413 PMCID: PMC5059700 DOI: 10.1038/srep35245] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 09/27/2016] [Indexed: 12/11/2022] Open
Abstract
Lipoxygenase (LOX) genes are widely distributed in plants and play crucial roles in resistance to biotic and abiotic stress. Although they have been characterized in various plants, little is known about the evolution of legume LOX genes. In this study, we identified 122 full-length LOX genes in Arachis duranensis, Arachis ipaënsis, Cajanus cajan, Cicer arietinum, Glycine max, Lotus japonicus and Medicago truncatula. In total, 64 orthologous and 36 paralogous genes were identified. The full-length, polycystin-1, lipoxygenase, alpha-toxin (PLAT) and lipoxygenase domain sequences from orthologous and paralogous genes exhibited a signature of purifying selection. However, purifying selection influenced orthologues more than paralogues, indicating greater functional conservation of orthologues than paralogues. Neutrality and effective number of codons plot results showed that natural selection primarily shapes codon usage, except for C. arietinum, L. japonicas and M. truncatula LOX genes. GCG, ACG, UCG, CGG and CCG codons exhibited low relative synonymous codon usage (RSCU) values, while CCA, GGA, GCU, CUU and GUU had high RSCU values, indicating that the latter codons are strongly preferred. LOX expression patterns differed significantly between wild-type peanut and cultivated peanut infected with Aspergillus flavus, which could explain the divergent disease resistance of wild progenitor and cultivars.
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31
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Wan L, Li B, Pandey MK, Wu Y, Lei Y, Yan L, Dai X, Jiang H, Zhang J, Wei G, Varshney RK, Liao B. Transcriptome Analysis of a New Peanut Seed Coat Mutant for the Physiological Regulatory Mechanism Involved in Seed Coat Cracking and Pigmentation. FRONTIERS IN PLANT SCIENCE 2016; 7:1491. [PMID: 27790222 PMCID: PMC5063860 DOI: 10.3389/fpls.2016.01491] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 09/20/2016] [Indexed: 05/21/2023]
Abstract
Seed-coat cracking and undesirable color of seed coat highly affects external appearance and commercial value of peanuts (Arachis hypogaea L.). With an objective to find genetic solution to the above problems, a peanut mutant with cracking and brown colored seed coat (testa) was identified from an EMS treated mutant population and designated as "peanut seed coat crack and brown color mutant line (pscb)." The seed coat weight of the mutant was almost twice of the wild type, and the germination time was significantly shorter than wild type. Further, the mutant had lower level of lignin, anthocyanin, proanthocyanidin content, and highly increased level of melanin content as compared to wild type. Using RNA-Seq, we examined the seed coat transcriptome in three stages of seed development in the wild type and the pscb mutant. The RNA-Seq analysis revealed presence of highly differentially expressed phenylpropanoid and flavonoid pathway genes in all the three seed development stages, especially at 40 days after flowering (DAF40). Also, the expression of polyphenol oxidases and peroxidase were found to be activated significantly especially in the late seed developmental stage. The genome-wide comparative study of the expression profiles revealed 62 differentially expressed genes common across all the three stages. By analyzing the expression patterns and the sequences of the common differentially expressed genes of the three stages, three candidate genes namely c36498_g1 (CCoAOMT1), c40902_g2 (kinesin), and c33560_g1 (MYB3) were identified responsible for seed-coat cracking and brown color phenotype. Therefore, this study not only provided candidate genes but also provided greater insights and molecular genetic control of peanut seed-coat cracking and color variation. The information generated in this study will facilitate further identification of causal gene and diagnostic markers for breeding improved peanut varieties with smooth and desirable seed coat color.
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Affiliation(s)
- Liyun Wan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural SciencesWuhan, China
| | - Bei Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural SciencesWuhan, China
| | - Manish K. Pandey
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Yanshan Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural SciencesWuhan, China
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural SciencesWuhan, China
| | - Liying Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural SciencesWuhan, China
| | - Xiaofeng Dai
- Institute of Food Science and Technology of Chinese Academy of Agricultural SciencesBeijing, China
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural SciencesWuhan, China
| | - Juncheng Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural SciencesWuhan, China
| | - Guo Wei
- Institute of Food Science and Technology of Chinese Academy of Agricultural SciencesBeijing, China
| | - Rajeev K. Varshney
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
- School of Plant Biology and Institute of Agriculture, The University of Western AustraliaCrawley, WA, Australia
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural SciencesWuhan, China
- *Correspondence: Boshou Liao
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