1
|
Gandham P, Rajasekaran K, Sickler C, Mohan H, Gilbert M, Baisakh N. MicroRNA (miRNA) profiling of maize genotypes with differential response to Aspergillus flavus implies zma-miR156-squamosa promoter binding protein (SBP) and zma-miR398/zma-miR394-F -box combinations involved in resistance mechanisms. STRESS BIOLOGY 2024; 4:26. [PMID: 38727957 PMCID: PMC11087424 DOI: 10.1007/s44154-024-00158-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 03/05/2024] [Indexed: 05/13/2024]
Abstract
Maize (Zea mays), a major food crop worldwide, is susceptible to infection by the saprophytic fungus Aspergillus flavus that can produce the carcinogenic metabolite aflatoxin (AF) especially under climate change induced abiotic stressors that favor mold growth. Several studies have used "-omics" approaches to identify genetic elements with potential roles in AF resistance, but there is a lack of research identifying the involvement of small RNAs such as microRNAs (miRNAs) in maize-A. flavus interaction. In this study, we compared the miRNA profiles of three maize lines (resistant TZAR102, moderately resistant MI82, and susceptible Va35) at 8 h, 3 d, and 7 d after A. flavus infection to investigate possible regulatory antifungal role of miRNAs. A total of 316 miRNAs (275 known and 41 putative novel) belonging to 115 miRNA families were identified in response to the fungal infection across all three maize lines. Eighty-two unique miRNAs were significantly differentially expressed with 39 miRNAs exhibiting temporal differential regulation irrespective of the maize genotype, which targeted 544 genes (mRNAs) involved in diverse molecular functions. The two most notable biological processes involved in plant immunity, namely cellular responses to oxidative stress (GO:00345990) and reactive oxygen species (GO:0034614) were significantly enriched in the resistant line TZAR102. Coexpression network analysis identified 34 hubs of miRNA-mRNA pairs where nine hubs had a node in the module connected to their target gene with potentially important roles in resistance/susceptible response of maize to A. flavus. The miRNA hubs in resistance modules (TZAR102 and MI82) were mostly connected to transcription factors and protein kinases. Specifically, the module of miRNA zma-miR156b-nb - squamosa promoter binding protein (SBP), zma-miR398a-3p - SKIP5, and zma-miR394a-5p - F-box protein 6 combinations in the resistance-associated modules were considered important candidates for future functional studies.
Collapse
Affiliation(s)
- Prasad Gandham
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA
| | - Kanniah Rajasekaran
- Food and Feed Safety Research Unit, Southern Regional Research Center, USDA-ARS, New Orleans, LA, 70726, USA.
| | - Christine Sickler
- Food and Feed Safety Research Unit, Southern Regional Research Center, USDA-ARS, New Orleans, LA, 70726, USA
| | - Harikrishnan Mohan
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA
| | - Matthew Gilbert
- Food and Feed Safety Research Unit, Southern Regional Research Center, USDA-ARS, New Orleans, LA, 70726, USA
| | - Niranjan Baisakh
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA.
| |
Collapse
|
2
|
Nji QN, Babalola OO, Mwanza M. Soil Aspergillus Species, Pathogenicity and Control Perspectives. J Fungi (Basel) 2023; 9:766. [PMID: 37504754 PMCID: PMC10381279 DOI: 10.3390/jof9070766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/05/2023] [Accepted: 07/18/2023] [Indexed: 07/29/2023] Open
Abstract
Five Aspergillus sections have members that are established agricultural pests and producers of different metabolites, threatening global food safety. Most of these pathogenic Aspergillus species have been isolated from almost all major biomes. The soil remains the primary habitat for most of these cryptic fungi. This review explored some of the ecological attributes that have contributed immensely to the success of the pathogenicity of some members of the genus Aspergillus over time. Hence, the virulence factors of the genus Aspergillus, their ecology and others were reviewed. Furthermore, some biological control techniques were recommended. Pathogenic effects of Aspergillus species are entirely accidental; therefore, the virulence evolution prediction model in such species becomes a challenge, unlike their obligate parasite counterparts. In all, differences in virulence among organisms involved both conserved and species-specific genetic factors. If the impacts of climate change continue, new cryptic Aspergillus species will emerge and mycotoxin contamination risks will increase in all ecosystems, as these species can metabolically adjust to nutritional and biophysical challenges. As most of their gene clusters are silent, fungi continue to be a source of underexplored bioactive compounds. The World Soil Charter recognizes the relevance of soil biodiversity in supporting healthy soil functions. The question of how a balance may be struck between supporting healthy soil biodiversity and the control of toxic fungi species in the field to ensure food security is therefore pertinent. Numerous advanced strategies and biocontrol methods so far remain the most environmentally sustainable solution to the control of toxigenic fungi in the field.
Collapse
Affiliation(s)
- Queenta Ngum Nji
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
| | - Mulunda Mwanza
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
- Department of Animal Health, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
| |
Collapse
|
3
|
Baisakh N, Da Silva EA, Pradhan AK, Rajasekaran K. Comprehensive meta-analysis of QTL and gene expression studies identify candidate genes associated with Aspergillus flavus resistance in maize. FRONTIERS IN PLANT SCIENCE 2023; 14:1214907. [PMID: 37534296 PMCID: PMC10392829 DOI: 10.3389/fpls.2023.1214907] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 06/26/2023] [Indexed: 08/04/2023]
Abstract
Aflatoxin (AF) contamination, caused by Aspergillus flavus, compromises the food safety and marketability of commodities, such as maize, cotton, peanuts, and tree nuts. Multigenic inheritance of AF resistance impedes conventional introgression of resistance traits into high-yielding commercial maize varieties. Several AF resistance-associated quantitative trait loci (QTLs) and markers have been reported from multiple biparental mapping and genome-wide association studies (GWAS) in maize. However, QTLs with large confidence intervals (CI) explaining inconsistent phenotypic variance limit their use in marker-assisted selection. Meta-analysis of published QTLs can identify significant meta-QTLs (MQTLs) with a narrower CI for reliable identification of genes and linked markers for AF resistance. Using 276 out of 356 reported QTLs controlling resistance to A. flavus infection and AF contamination in maize, we identified 58 MQTLs on all 10 chromosomes with a 66.5% reduction in the average CI. Similarly, a meta-analysis of maize genes differentially expressed in response to (a)biotic stresses from the to-date published literature identified 591 genes putatively responding to only A. flavus infection, of which 14 were significantly differentially expressed (-1.0 ≤ Log2Fc ≥ 1.0; p ≤ 0.05). Eight MQTLs were validated by their colocalization with 14 A. flavus resistance-associated SNPs identified from GWAS in maize. A total of 15 genes were physically close between the MQTL intervals and SNPs. Assessment of 12 MQTL-linked SSR markers identified three markers that could discriminate 14 and eight cultivars with resistance and susceptible responses, respectively. A comprehensive meta-analysis of QTLs and differentially expressed genes led to the identification of genes and makers for their potential application in marker-assisted breeding of A. flavus-resistant maize varieties.
Collapse
Affiliation(s)
- Niranjan Baisakh
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Eduardo A. Da Silva
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
- Department of Agriculture, Federal University of Lavras, Lavras, Brazil
| | - Anjan K. Pradhan
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Kanniah Rajasekaran
- Food and Feed Safety Research Unit, Southern Regional Research Center, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), New Orleans, LA, United States
| |
Collapse
|
4
|
Mehari TG, Hou Y, Xu Y, Umer MJ, Shiraku ML, Wang Y, Wang H, Peng R, Wei Y, Cai X, Zhou Z, Liu F. Overexpression of cotton GhNAC072 gene enhances drought and salt stress tolerance in transgenic Arabidopsis. BMC Genomics 2022; 23:648. [PMID: 36096725 PMCID: PMC9469605 DOI: 10.1186/s12864-022-08876-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 06/06/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Crops face several environmental stresses (biotic and abiotic), thus resulting in severe yield losses. Around the globe abiotic stresses are the main contributors of plant damages, primarily drought and salinity. Many genes and transcription factors are involved in abiotic and biotic stress responses. NAC TF (Transcription Factors) improves tolerance to stresses by controlling the physiological and enzyme activities of crops. RESULTS In current research, GhNAC072 a highly upregulated TF in RNA-Seq was identified as a hub gene in the co-expression network analysis (WGCNA). This gene was transformed to Arabidopsis thaliana to confirm its potential role in drought and salt stress tolerance. Significant variations were observed in the morpho-physiological traits with high relative leaf water contents, chlorophyll contents, higher germination and longer root lengths of the overexpressed lines and low excised leaf loss and ion leakage as compared to the wildtype plants. Besides, overexpressed lines have higher amounts of antioxidants and low oxidant enzyme activities than the wildtype during the period of stress exposure. CONCLUSIONS In summary, the above analysis showed that GhNAC072 might be the true candidate involved in boosting tolerance mechanisms under drought and salinity stress.
Collapse
Affiliation(s)
- Teame Gereziher Mehari
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Anyang, China.,School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China
| | - Yuqing Hou
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yanchao Xu
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Muhammad Jawad Umer
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Margaret Linyerera Shiraku
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yuhong Wang
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Heng Wang
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Renhai Peng
- Anyang Institute of Technology, Anyang, Henan, China
| | - Yangyang Wei
- Anyang Institute of Technology, Anyang, Henan, China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Anyang, China.
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Anyang, China.
| | - Fang Liu
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Anyang, China. .,School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China.
| |
Collapse
|
5
|
Bedre R, Avila C, Mandadi K. HTSQualC is a flexible and one-step quality control software for high-throughput sequencing data analysis. Sci Rep 2021; 11:18725. [PMID: 34548573 PMCID: PMC8455540 DOI: 10.1038/s41598-021-98124-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 09/03/2021] [Indexed: 11/24/2022] Open
Abstract
Use of high-throughput sequencing (HTS) has become indispensable in life science research. Raw HTS data contains several sequencing artifacts, and as a first step it is imperative to remove the artifacts for reliable downstream bioinformatics analysis. Although there are multiple stand-alone tools available that can perform the various quality control steps separately, availability of an integrated tool that can allow one-step, automated quality control analysis of HTS datasets will significantly enhance handling large number of samples parallelly. Here, we developed HTSQualC, a stand-alone, flexible, and easy-to-use software for one-step quality control analysis of raw HTS data. HTSQualC can evaluate HTS data quality and perform filtering and trimming analysis in a single run. We evaluated the performance of HTSQualC for conducting batch analysis of HTS datasets with 322 samples with an average ~ 1 M (paired end) sequence reads per sample. HTSQualC accomplished the QC analysis in ~ 3 h in distributed mode and ~ 31 h in shared mode, thus underscoring its utility and robust performance. In addition to command-line execution, we integrated HTSQualC into the free, open-source, CyVerse cyberinfrastructure resource as a GUI interface, for wider access to experimental biologists who have limited computational resources and/or programming abilities.
Collapse
Affiliation(s)
- Renesh Bedre
- Texas A&M AgriLife Research and Extension Center, Texas A&M University, Weslaco, TX, USA
| | - Carlos Avila
- Department of Horticultural Science, Texas A&M University, College Station, TX, USA
| | - Kranthi Mandadi
- Texas A&M AgriLife Research and Extension Center, Texas A&M University, Weslaco, TX, USA. .,Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA.
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
Brachypodium Phenylalanine Ammonia Lyase (PAL) Promotes Antiviral Defenses against Panicum mosaic virus and Its Satellites. mBio 2021; 12:mBio.03518-20. [PMID: 33593968 PMCID: PMC8545123 DOI: 10.1128/mbio.03518-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Brachypodium distachyon has recently emerged as a premier model plant for monocot biology, akin to Arabidopsis thaliana We previously reported genome-wide transcriptomic and alternative splicing changes occurring in Brachypodium during compatible infections with Panicum mosaic virus (PMV) and its satellite virus (SPMV). Here, we dissected the role of Brachypodium phenylalanine ammonia lyase 1 (PAL1), a key enzyme for phenylpropanoid and salicylic acid (SA) biosynthesis and the induction of plant defenses. Targeted metabolomics profiling of PMV-infected and PMV- plus SPMV-infected (PMV/SPMV) Brachypodium plants revealed enhanced levels of multiple defense-related hormones and metabolites such as cinnamic acid, SA, and fatty acids and lignin precursors during disease progression. The virus-induced accumulation of SA and lignin was significantly suppressed upon knockdown of B. distachyon PAL1 (BdPAL1) using RNA interference (RNAi). The compromised SA accumulation in PMV/SPMV-infected BdPAL1 RNAi plants correlated with weaker induction of multiple SA-related defense gene markers (pathogenesis related 1 [PR-1], PR-3, PR-5, and WRKY75) and enhanced susceptibility to PMV/SPMV compared to that of wild-type (WT) plants. Furthermore, exogenous application of SA alleviated the PMV/SPMV necrotic disease phenotypes and delayed plant death caused by single and mixed infections. Together, our results support an antiviral role for BdPAL1 during compatible host-virus interaction, perhaps as a last resort attempt to rescue the infected plant.IMPORTANCE Although the role of plant defense mechanisms against viruses are relatively well studied in dicots and in incompatible plant-microbe interactions, studies of their roles in compatible interactions and in grasses are lagging behind. In this study, we leveraged the emerging grass model Brachypodium and genetic resources to dissect Panicum mosaic virus (PMV)- and its satellite virus (SPMV)-compatible grass-virus interactions. We found a significant role for PAL1 in the production of salicylic acid (SA) in response to PMV/SPMV infections and that SA is an essential component of the defense response preventing the plant from succumbing to viral infection. Our results suggest a convergent role for the SA defense pathway in both compatible and incompatible plant-virus interactions and underscore the utility of Brachypodium for grass-virus biology.
Collapse
|
8
|
Musungu B, Bhatnagar D, Quiniou S, Brown RL, Payne GA, O’Brian G, Fakhoury AM, Geisler M. Use of Dual RNA-seq for Systems Biology Analysis of Zea mays and Aspergillus flavus Interaction. Front Microbiol 2020; 11:853. [PMID: 32582038 PMCID: PMC7285840 DOI: 10.3389/fmicb.2020.00853] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 04/09/2020] [Indexed: 11/18/2022] Open
Abstract
The interaction between Aspergillus flavus and Zea mays is complex, and the identification of plant genes and pathways conferring resistance to the fungus has been challenging. Therefore, the authors undertook a systems biology approach involving dual RNA-seq to determine the simultaneous response from the host and the pathogen. What was dramatically highlighted in the analysis is the uniformity in the development patterns of gene expression of the host and the pathogen during infection. This led to the development of a "stage of infection index" that was subsequently used to categorize the samples before down-stream system biology analysis. Additionally, we were able to ascertain that key maize genes in pathways such as the jasmonate, ethylene and ROS pathways, were up-regulated in the study. The stage of infection index used for the transcriptomic analysis revealed that A. flavus produces a relatively limited number of transcripts during the early stages (0 to 12 h) of infection. At later stages, in A. flavus, transcripts and pathways involved in endosomal transport, aflatoxin production, and carbohydrate metabolism were up-regulated. Multiple WRKY genes targeting the activation of the resistance pathways (i.e., jasmonate, phenylpropanoid, and ethylene) were detected using causal inference analysis. This analysis also revealed, for the first time, the activation of Z. mays resistance genes influencing the expression of specific A. flavus genes. Our results show that A. flavus seems to be reacting to a hostile environment resulting from the activation of resistance pathways in Z. mays. This study revealed the dynamic nature of the interaction between the two organisms.
Collapse
Affiliation(s)
- Bryan Musungu
- Department of Plant Biology, Southern Illinois University, Carbondale, IL, United States
| | - Deepak Bhatnagar
- Southern Regional Research Center, USDA-ARS, New Orleans, LA, United States
| | - Sylvie Quiniou
- Warm Water Aquaculture Research Unit, USDA-ARS, Stoneville, MS, United States
| | - Robert L. Brown
- Southern Regional Research Center, USDA-ARS, New Orleans, LA, United States
| | - Gary A. Payne
- Department of Plant Pathology, North Carolina State University, Raleigh, NC, United States
| | - Greg O’Brian
- Department of Plant Pathology, North Carolina State University, Raleigh, NC, United States
| | - Ahmad M. Fakhoury
- Department of Plant Soil and Agriculture Systems, Southern Illinois University, Carbondale, IL, United States
| | - Matt Geisler
- Department of Plant Biology, Southern Illinois University, Carbondale, IL, United States
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Awika HO, Marconi TG, Bedre R, Mandadi KK, Avila CA. Minor alleles are associated with white rust ( Albugo occidentalis) susceptibility in spinach ( Spinacia oleracea). HORTICULTURE RESEARCH 2019; 6:129. [PMID: 31814982 PMCID: PMC6885047 DOI: 10.1038/s41438-019-0214-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 10/29/2019] [Accepted: 11/03/2019] [Indexed: 05/05/2023]
Abstract
Minor alleles (MA) have been associated with disease incidence in human studies, enabling the identification of diagnostic risk factors for various diseases. However, allelic mapping has rarely been performed in plant systems. The goal of this study was to determine whether a difference in MA prevalence is a strong enough risk factor to indicate a likely significant difference in disease resistance against white rust (WR; Albugo occidentalis) in spinach (Spinacia oleracea). We used WR disease severity ratings (WR-DSRs) in a diversity panel of 267 spinach accessions to define resistant- and susceptibility-associated groups within the distribution scores and then tested the single-nucleotide polymorphism (SNP) variants to interrogate the MA prevalence in the most susceptible (MS) vs. most resistant (MR) individuals using permutation-based allelic association tests. A total of 448 minor alleles associated with WR severity were identified in the comparison between the 25% MS and the 25% MR accessions, while the MA were generally similar between the two halves of the interquartile range. The minor alleles in the MS group were distributed across all six chromosomes and made up ~71% of the markers that were also strongly associated with WR in parallel performed genome-wide association study. These results indicate that susceptibility may be highly determined by the disproportionate overrepresentation of minor alleles, which could be used to select for resistant plants. Furthermore, by focusing on the distribution tails, allelic mapping could be used to identify plant markers associated with quantitative traits on the most informative segments of the phenotypic distribution.
Collapse
Affiliation(s)
- Henry O. Awika
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX 78596 USA
| | - Thiago G. Marconi
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX 78596 USA
| | - Renesh Bedre
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX 78596 USA
| | - Kranthi K. Mandadi
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX 78596 USA
- Department of Plant Pathology and Microbiology, College Station, TX 77843 USA
| | - Carlos A. Avila
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX 78596 USA
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843 USA
| |
Collapse
|
11
|
Bedre R, Mandadi K. GenFam: A web application and database for gene family-based classification and functional enrichment analysis. PLANT DIRECT 2019; 3:e00191. [PMID: 31844835 PMCID: PMC6892992 DOI: 10.1002/pld3.191] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/11/2019] [Accepted: 11/13/2019] [Indexed: 05/25/2023]
Abstract
Genome-scale studies using high-throughput sequencing (HTS) technologies generate substantial lists of differentially expressed genes under different experimental conditions. These gene lists need to be further mined to narrow down biologically relevant genes and associated functions in order to guide downstream functional genetic analyses. A popular approach is to determine statistically overrepresented genes in a user-defined list through enrichment analysis tools, which rely on functional annotations of genes based on Gene Ontology (GO) terms. Here, we propose a new computational approach, GenFam, which allows annotation, classification, and enrichment of genes based on their gene family, thus simplifying identification of candidate gene families and associated genes that may be relevant to the query. GenFam and its integrated database comprises of three hundred and eighty-four unique gene families and supports gene family analyses for sixty plant genomes. Four comparative case studies with plant species belonging to different clades and families were performed using GenFam which demonstrated its robustness and comprehensiveness over preexisting functional enrichment tools. To make it readily accessible for plant biologists, GenFam is available as a web-based application where users can input gene IDs and export enrichment results in both tabular and graphical formats. Users can also customize analysis parameters by choosing from the various statistical enrichment tests and multiple testing correction methods. Additionally, the web-based application, source code, and database are freely available to use and download. Website: http://mandadilab.webfactional.com/home/. Source code and database: http://mandadilab.webfactional.com/home/dload/.
Collapse
Affiliation(s)
- Renesh Bedre
- Texas A&M AgriLife Research & Extension CenterWeslacoTXUSA
| | - Kranthi Mandadi
- Texas A&M AgriLife Research & Extension CenterWeslacoTXUSA
- Department of Plant Pathology & MicrobiologyTexas A&M UniversityCollege StationTXUSA
| |
Collapse
|
12
|
Awika HO, Bedre R, Yeom J, Marconi TG, Enciso J, Mandadi KK, Jung J, Avila CA. Developing Growth-Associated Molecular Markers Via High-Throughput Phenotyping in Spinach. THE PLANT GENOME 2019; 12:1-19. [PMID: 33016585 DOI: 10.3835/plantgenome2019.03.0027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/22/2019] [Indexed: 06/11/2023]
Abstract
High-throughput imaging and genomic information can be combined to optimize marker development. Genome-wide association studies identified loci associated with plant growth traits. We identified candidate genes associated with plant growth and development. Despite advances in sequencing for genotyping, the lack of rapid, accurate, and reproducible phenotyping platforms has hampered efforts to use genetic analysis to predict traits of interest. Therefore, the use of high-throughput systems to phenotype traits related to crop growth, yield, quality, and resistance to biotic and abiotic stresses has become a major asset for breeding. Here, we assessed the efficacy of unmanned aircraft system (UAS)-based high-throughput phenotyping to obtain data for molecular marker development for spinach (Spinacia oleracea L.) improvement. We used a UAS equipped with a red-green-blue sensor to capture raw images of 284 spinach accessions throughout the crop cycle. Processed images generated orthomosaic and digital surface models for estimating canopy cover, canopy volume, and excess greenness index models. In addition, we manually recorded the number of days to bolting. Genome-wide association studies against a single-nucleotide polymorphism (SNP) panel obtained by ddRADseq identified 99 SNPs significantly associated with growth parameters. Some of these SNPs are in transcription factor and stress-response genes with possible roles in plant growth and development. The results underscore the utility of combining aerial imaging and genomic data analysis to optimize marker development. This study lays the foundation for the use of UAS-based high-throughput phenotyping for the molecular breeding of spinach.
Collapse
Affiliation(s)
- Henry O Awika
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, 78596
| | - Renesh Bedre
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, 78596
| | - Junho Yeom
- Research Institute for Automotive Diagnosis Technology of Multi-scale Organic and Inorganic Structure, Kyungpook National Univ., Korea, 37224
- School of Engineering and Computing Sciences, Texas A&M-Corpus Christi, Corpus Christi, TX, 78412
| | - Thiago G Marconi
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, 78596
| | - Juan Enciso
- Biological and Agricultural Engineering Dep., Texas A&M Univ., College Station, TX, 77843
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, 78596
| | - Kranthi K Mandadi
- Dep. of Plant Pathology and Microbiology, Texas A&M Univ., College Station, TX, 77843
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, 78596
| | - Jinha Jung
- School of Engineering and Computing Sciences, Texas A&M-Corpus Christi, Corpus Christi, TX, 78412
| | - Carlos A Avila
- Dep. of Horticultural Sciences, Texas A&M Univ., College Station, TX, 77843
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, 78596
| |
Collapse
|
13
|
Bedre R, Irigoyen S, Schaker PDC, Monteiro-Vitorello CB, Da Silva JA, Mandadi KK. Genome-wide alternative splicing landscapes modulated by biotrophic sugarcane smut pathogen. Sci Rep 2019; 9:8876. [PMID: 31222001 PMCID: PMC6586842 DOI: 10.1038/s41598-019-45184-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/22/2019] [Indexed: 12/24/2022] Open
Abstract
Alternative splicing (AS) promotes transcriptome and proteome diversity during growth, development, and stress responses in eukaryotes. Genome-wide studies of AS in sugarcane (Saccharum spp.) are lacking, mainly due to the absence of a high-quality sequenced reference genome, sugarcane's large, complex genome, and the variable chromosome numbers and polyploidy of sugarcane cultivars. Here, we analyzed changes in the sugarcane isoform-level transcriptome and AS landscape during infection with the smut fungus (Sporisorium scitamineum) using a hybrid approach involving Sorghum bicolor reference-based and Trinity de novo mapping tools. In total, this analysis detected 16,039 and 15,379 transcripts (≥2 FPKM) at 5 and 200 days after infection, respectively. A conservative estimate of isoform-level expression suggested that approximately 5,000 (14%) sugarcane genes undergo AS. Differential expression analysis of the alternatively spliced genes in healthy and smut-infected sugarcane revealed 896 AS events modulated at different stages of infection. Gene family and gene ontology functional enrichment analysis of the differentially spliced genes revealed overrepresentation of functional categories related to the cell wall, defense, and redox homeostasis pathways. Our study provides novel insight into the AS landscape of sugarcane during smut disease interactions.
Collapse
Affiliation(s)
- Renesh Bedre
- Texas A&M AgriLife Research & Extension Center, Texas A&M University, Weslaco, TX, USA
| | - Sonia Irigoyen
- Texas A&M AgriLife Research & Extension Center, Texas A&M University, Weslaco, TX, USA
| | - Patricia D C Schaker
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura "Luiz de Queiroz," Piracicaba, São Paulo, Brazil
- Universidade Tecnológica Federal do Paraná, Toledo, Paraná, Brazil
| | - Claudia B Monteiro-Vitorello
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura "Luiz de Queiroz," Piracicaba, São Paulo, Brazil
| | - Jorge A Da Silva
- Texas A&M AgriLife Research & Extension Center, Texas A&M University, Weslaco, TX, USA
- Department of Soil & Crop Sciences, Texas A&M University, College Station, TX, USA
| | - Kranthi K Mandadi
- Texas A&M AgriLife Research & Extension Center, Texas A&M University, Weslaco, TX, USA.
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX, USA.
| |
Collapse
|
14
|
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.
Collapse
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.
| |
Collapse
|
15
|
Mehanathan M, Bedre R, Mangu V, Rajasekaran K, Bhatnagar D, Baisakh N. Identification of candidate resistance genes of cotton against Aspergillus flavus infection using a comparative transcriptomics approach. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:513-519. [PMID: 29692558 PMCID: PMC5911267 DOI: 10.1007/s12298-018-0522-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 01/23/2018] [Accepted: 02/15/2018] [Indexed: 06/08/2023]
Abstract
A comparative transcriptome analysis was performed using the genes significantly differentially expressed in cotton, corn and peanut in response to aflatoxin producing fungus Aspergillus flavus with an objective of identifying candidate resistance genes in cotton. Two-way analyses identified 732 unique genes to be differentially regulated by the fungus with only 26 genes common across all three crops that were considered candidate A. flavus resistance genes with an assumption that these genes have specific roles in conferring the resistance trait. Genes of membrane cellular component involved in DNA binding with involvement in defense responses were highly represented among the differentially expressed unique genes. Most (six) of these genes coded for 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily proteins. Genes encoding helix loop helix protein, alcohol dehydrogenase and UDP glycosylation transferase which were upregulated in response to both atoxigenic and toxigenic strains of A. flavus, could be potential resistance candidate genes for downstream functional manipulation to confer resistance.
Collapse
Affiliation(s)
- Muthamilarasan Mehanathan
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA USA
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Renesh Bedre
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA USA
- Department of Plant Pathology and Microbiology, Texas A&M AgriLife Research, Weslaco, TX USA
| | - Venkata Mangu
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA USA
- Department of Biochemistry, University of Pennsylvania, Philadelphia, PA USA
| | | | - Deepak Bhatnagar
- Southern Regional Research Center, USDA-ARS, New Orleans, LA USA
| | - Niranjan Baisakh
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA USA
| |
Collapse
|
16
|
Rajasekaran K, Sayler RJ, Sickler CM, Majumdar R, Jaynes JM, Cary JW. Control of Aspergillus flavus growth and aflatoxin production in transgenic maize kernels expressing a tachyplesin-derived synthetic peptide, AGM182. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 270:150-156. [PMID: 29576068 DOI: 10.1016/j.plantsci.2018.02.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 01/28/2018] [Accepted: 02/07/2018] [Indexed: 06/08/2023]
Abstract
Aspergillus flavus is an opportunistic, saprophytic fungus that infects maize and other fatty acid-rich food and feed crops and produces toxic and carcinogenic secondary metabolites known as aflatoxins. Contamination of maize with aflatoxin poses a serious threat to human health in addition to reducing the crop value leading to a substantial economic loss. Here we report designing a tachyplesin1-derived synthetic peptide AGM182 and testing its antifungal activity both in vitro and in planta. In vitro studies showed a five-fold increase in antifungal activity of AGM182 (vs. tachyplesin1) against A. flavus. Transgenic maize plants expressing AGM182 under maize Ubiquitin-1 promoter were produced through Agrobacterium-mediated transformation. PCR products confirmed integration of the AGM182 gene, while RT-PCR of maize RNA confirmed the presence of AGM182 transcripts. Maize kernel screening assay using a highly aflatoxigenic A. flavus strain (AF70) showed up to 72% reduction in fungal growth in the transgenic AGM182 seeds compared to isogenic negative control seeds. Reduced fungal growth in the AGM182 transgenic seeds resulted in a significant reduction in aflatoxin levels (76-98%). The results presented here show the power of computational and synthetic biology to rationally design and synthesize an antimicrobial peptide against A. flavus that is effective in reducing fungal growth and aflatoxin contamination in an economically important food and feed crop such as maize.
Collapse
Affiliation(s)
- Kanniah Rajasekaran
- Food and Feed Safety Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA 70124, United States.
| | - Ronald J Sayler
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR 72701, United States
| | - Christine M Sickler
- Food and Feed Safety Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA 70124, United States
| | - Rajtilak Majumdar
- Food and Feed Safety Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA 70124, United States
| | - Jesse M Jaynes
- College of Agriculture, Environment and Nutrition Sciences, Tuskegee University, Tuskegee, AL 36088, United States
| | - Jeffrey W Cary
- Food and Feed Safety Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA 70124, United States
| |
Collapse
|
17
|
Bhatnagar D, Rajasekaran K, Gilbert M, Cary J, Magan N. Advances in molecular and genomic research to safeguard food and feed supply from aflatoxin contamination. WORLD MYCOTOXIN J 2018. [DOI: 10.3920/wmj2017.2283] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Worldwide recognition that aflatoxin contamination of agricultural commodities by the fungus Aspergillus flavus is a global problem has significantly benefitted from global collaboration for understanding the contaminating fungus, as well as for developing and implementing solutions against the contamination. The effort to address this serious food and feed safety issue has led to a detailed understanding of the taxonomy, ecology, physiology, genomics and evolution of A. flavus, as well as strategies to reduce or control pre-harvest aflatoxin contamination, including (1) biological control, using atoxigenic aspergilli, (2) proteomic and genomic analyses for identifying resistance factors in maize as potential breeding markers to enable development of resistant maize lines, and (3) enhancing host-resistance by bioengineering of susceptible crops, such as cotton, maize, peanut and tree nuts. A post-harvest measure to prevent the occurrence of aflatoxin contamination in storage is also an important component for reducing exposure of populations worldwide to aflatoxins in food and feed supplies. The effect of environmental changes on aflatoxin contamination levels has recently become an important aspect for study to anticipate future contamination levels. The ability of A. flavus to produce dozens of secondary metabolites, in addition to aflatoxins, has created a new avenue of research for understanding the role these metabolites play in the survival and biodiversity of this fungus. The understanding of A. flavus, the aflatoxin contamination problem, and control measures to prevent the contamination has become a unique example for an integrated approach to safeguard global food and feed safety.
Collapse
Affiliation(s)
- D. Bhatnagar
- US Department of Agriculture, Agricultural Research Service, 1100 Robert E. Lee Boulevard, New Orleans, LA 70124, USA
| | - K. Rajasekaran
- US Department of Agriculture, Agricultural Research Service, 1100 Robert E. Lee Boulevard, New Orleans, LA 70124, USA
| | - M. Gilbert
- US Department of Agriculture, Agricultural Research Service, 1100 Robert E. Lee Boulevard, New Orleans, LA 70124, USA
| | - J.W. Cary
- US Department of Agriculture, Agricultural Research Service, 1100 Robert E. Lee Boulevard, New Orleans, LA 70124, USA
| | - N. Magan
- Applied Mycology Group, Cranfield University, MK45 4DT, Cranfield, United Kingdom
| |
Collapse
|
18
|
Lu X, Wang X, Chen X, Shu N, Wang J, Wang D, Wang S, Fan W, Guo L, Guo X, Ye W. Single-base resolution methylomes of upland cotton (Gossypium hirsutum L.) reveal epigenome modifications in response to drought stress. BMC Genomics 2017; 18:297. [PMID: 28407801 PMCID: PMC5390369 DOI: 10.1186/s12864-017-3681-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 04/05/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA methylation, with a cryptic role in genome stability, gene transcription and expression, is involved in the drought response process in plants, but the complex regulatory mechanism is still largely unknown. RESULTS Here, we performed whole-genome bisulfite sequencing (WGBS) and identified long non-coding RNAs on cotton leaves under drought stress and re-watering treatments. We obtained 31,223 and 30,997 differentially methylated regions (representing 2.48% of the genome) after drought stress and re-watering treatments, respectively. Our data also showed that three sequence contexts, including mCpG, mCHG, mCHH, all presented a hyper-methylation pattern under drought stress and were nearly restored to normal levels after the re-watering treatment. Among all the methylation variations, asymmetric CHH methylation was the most consistent with external environments, suggesting that methylation/demethylation in a CHH context may constitute a novel epigenetic modification in response to drought stress. Combined with the targets of long non-coding RNAs, we found that long non-coding RNAs may mediate variations in methylation patterns by splicing into microRNAs. Furthermore, the many hormone-related genes with methylation variations suggested that plant hormones might be a potential mechanism in the drought response. CONCLUSIONS Future crop-improvement strategies may benefit by taking into account not only the DNA genetic variations in cotton varieties but also the epigenetic modifications of the genome.
Collapse
Affiliation(s)
- Xuke Lu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Key Laboratory for Cotton Genetic Improvement, Anyang, 455000, Henan, China.,College of Agronomy, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Xiaoge Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Key Laboratory for Cotton Genetic Improvement, Anyang, 455000, Henan, China
| | - Xiugui Chen
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Key Laboratory for Cotton Genetic Improvement, Anyang, 455000, Henan, China
| | - Na Shu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Key Laboratory for Cotton Genetic Improvement, Anyang, 455000, Henan, China
| | - Junjuan Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Key Laboratory for Cotton Genetic Improvement, Anyang, 455000, Henan, China
| | - Delong Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Key Laboratory for Cotton Genetic Improvement, Anyang, 455000, Henan, China
| | - Shuai Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Key Laboratory for Cotton Genetic Improvement, Anyang, 455000, Henan, China
| | - Weili Fan
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Key Laboratory for Cotton Genetic Improvement, Anyang, 455000, Henan, China
| | - Lixue Guo
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Key Laboratory for Cotton Genetic Improvement, Anyang, 455000, Henan, China
| | - Xiaoning Guo
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Key Laboratory for Cotton Genetic Improvement, Anyang, 455000, Henan, China
| | - Wuwei Ye
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Key Laboratory for Cotton Genetic Improvement, Anyang, 455000, Henan, China.
| |
Collapse
|
19
|
Dhakal R, Chai C, Karan R, Windham GL, Williams WP, Subudhi PK. Expression Profiling Coupled with In-silico Mapping Identifies Candidate Genes for Reducing Aflatoxin Accumulation in Maize. FRONTIERS IN PLANT SCIENCE 2017; 8:503. [PMID: 28428796 PMCID: PMC5382453 DOI: 10.3389/fpls.2017.00503] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Accepted: 03/22/2017] [Indexed: 05/31/2023]
Abstract
Aflatoxin, produced by Aspergillus flavus, is hazardous to health of humans and livestock. The lack of information about large effect QTL for resistance to aflatoxin accumulation is a major obstacle to employ marker-assisted selection for maize improvement. The understanding of resistance mechanisms of the host plant and the associated genes is necessary for improving resistance to A. flavus infection. A suppression subtraction hybridization (SSH) cDNA library was made using the developing kernels of Mp715 (resistant inbred) and B73 (susceptible inbred) and 480 randomly selected cDNA clones were sequenced to identify differentially expressed genes (DEGs) in response to A. flavus infection and map these clones onto the corn genome by in-silico mapping. A total of 267 unigenes were identified and majority of genes were related to metabolism, stress response, and disease resistance. Based on the reverse northern hybridization experiment, 26 DEGs were selected for semi-quantitative RT-PCR analysis in seven inbreds with variable resistance to aflatoxin accumulation at two time points after A. flavus inoculation. Most of these genes were highly expressed in resistant inbreds. Quantitative RT-PCR analysis validated upregulation of PR-4, DEAD-box RNA helicase, and leucine rich repeat family protein in resistant inbreds. Fifty-six unigenes, which were placed on linkage map through in-silico mapping, overlapped the QTL regions for resistance to aflatoxin accumulation identified in a mapping population derived from the cross between B73 and Mp715. Since majority of these mapped genes were related to disease resistance, stress response, and metabolism, these should be ideal candidates to investigate host pathogen interaction and to reduce aflatoxin accumulation in maize.
Collapse
Affiliation(s)
- Ramesh Dhakal
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural CenterBaton Rouge, LA, USA
| | - Chenglin Chai
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural CenterBaton Rouge, LA, USA
| | - Ratna Karan
- Department of Agronomy, University of FloridaGainesville, FL, USA
| | - Gary L. Windham
- USDA-ARS Corn Host Plant Resistance Research UnitMississippi State, MS, USA
| | | | - Prasanta K. Subudhi
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural CenterBaton Rouge, LA, USA
| |
Collapse
|
20
|
Guerre P. Worldwide Mycotoxins Exposure in Pig and Poultry Feed Formulations. Toxins (Basel) 2016; 8:E350. [PMID: 27886128 PMCID: PMC5198545 DOI: 10.3390/toxins8120350] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 11/15/2016] [Accepted: 11/17/2016] [Indexed: 02/07/2023] Open
Abstract
The purpose of this review is to present information about raw materials that can be used in pig and poultry diets and the factors responsible for variations in their mycotoxin contents. The levels of mycotoxins in pig and poultry feeds are calculated based on mycotoxin contamination levels of the raw materials with different diet formulations, to highlight the important role the stage of production and the raw materials used can have on mycotoxins levels in diets. Our analysis focuses on mycotoxins for which maximum tolerated levels or regulatory guidelines exist, and for which sufficient contamination data are available. Raw materials used in feed formulation vary considerably depending on the species of animal, and the stage of production. Mycotoxins are secondary fungal metabolites whose frequency and levels also vary considerably depending on the raw materials used and on the geographic location where they were produced. Although several reviews of existing data and of the literature on worldwide mycotoxin contamination of food and feed are available, the impact of the different raw materials used on feed formulation has not been widely studied.
Collapse
Affiliation(s)
- Philippe Guerre
- Sciences Biologiques et Fonctionnelles, Université de Toulouse, ENVT, Toulouse, F-31076, France.
| |
Collapse
|
21
|
Clevenger J, Marasigan K, Liakos V, Sobolev V, Vellidis G, Holbrook C, Ozias-Akins P. RNA Sequencing of Contaminated Seeds Reveals the State of the Seed Permissive for Pre-Harvest Aflatoxin Contamination and Points to a Potential Susceptibility Factor. Toxins (Basel) 2016; 8:E317. [PMID: 27827875 PMCID: PMC5127114 DOI: 10.3390/toxins8110317] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 10/26/2016] [Accepted: 10/28/2016] [Indexed: 11/24/2022] Open
Abstract
Pre-harvest aflatoxin contamination (PAC) is a major problem facing peanut production worldwide. Produced by the ubiquitous soil fungus, Aspergillus flavus, aflatoxin is the most naturally occurring known carcinogen. The interaction between fungus and host resulting in PAC is complex, and breeding for PAC resistance has been slow. It has been shown that aflatoxin production can be induced by applying drought stress as peanut seeds mature. We have implemented an automated rainout shelter that controls temperature and moisture in the root and peg zone to induce aflatoxin production. Using polymerase chain reaction (PCR) and high performance liquid chromatography (HPLC), seeds meeting the following conditions were selected: infected with Aspergillus flavus and contaminated with aflatoxin; and not contaminated with aflatoxin. RNA sequencing analysis revealed groups of genes that describe the transcriptional state of contaminated vs. uncontaminated seed. These data suggest that fatty acid biosynthesis and abscisic acid (ABA) signaling are altered in contaminated seeds and point to a potential susceptibility factor, ABR1, as a repressor of ABA signaling that may play a role in permitting PAC.
Collapse
Affiliation(s)
- Josh Clevenger
- Department of Horticulture and Institute of Plant Breeding, Genetics & Genomics, The University of Georgia, Tifton, GA 31793, USA.
| | - Kathleen Marasigan
- Department of Horticulture and Institute of Plant Breeding, Genetics & Genomics, The University of Georgia, Tifton, GA 31793, USA.
| | - Vasileios Liakos
- Department of Crop and Soil Sciences, The University of Georgia, Tifton, GA 31793, USA.
| | - Victor Sobolev
- USDA-ARS National Peanut Research Laboratory, Dawson, GA 39842, USA.
| | - George Vellidis
- Department of Crop and Soil Sciences, The University of Georgia, Tifton, GA 31793, USA.
| | - Corley Holbrook
- USDA-ARS, Crop Genetics and Breeding Res. Unit, Tifton, GA 31793, USA.
| | - Peggy Ozias-Akins
- Department of Horticulture and Institute of Plant Breeding, Genetics & Genomics, The University of Georgia, Tifton, GA 31793, USA.
| |
Collapse
|