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Title: Genome-wide transcriptome analysis of cotton (Gossypium hirsutum L.) identifies candidate gene signatures in response to aflatoxin producing fungus Aspergillus flavus

Author
item BEDRE, RENESH - Louisiana State University Agcenter
item Rajasekaran, Kanniah - Rajah
item MANGU, VENKATA - Louisiana State University Agcenter
item SANCHEZ TIMM, LUIS - Louisiana State University Agcenter
item Bhatnagar, Deepak
item BAISAKH, NIRANJAN - Louisiana State University Agcenter

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/24/2015
Publication Date: 9/14/2015
Citation: Bedre, R., Rajasekaran, K., Mangu, V.R., Sanchez Timm, L.E., Bhatnagar, D., Baisakh, N. 2015. Genome-wide transcriptome analysis of cotton (Gossypium hirsutum L.) identifies candidate gene signatures in response to aflatoxin producing fungus Aspergillus flavus. PLoS One. 10(9):e0138025. https://doi.org/10.1371/journal.pone.0138025.
DOI: https://doi.org/10.1371/journal.pone.0138025

Interpretive Summary: Aspergillus flavus is the primary causal agent of aflatoxin contamination of cottonseed resulting in a significant economic loss and a threat to food security. Improvement of commercial varieties of cotton, either by conventional breeding or by genetic engineering, for resistance to the fungus depends on our understanding of molecular regulation during host-pathogen interaction. As a defense mechanism, several hundreds of genes are turned on when the fungus invades the host cotton plant. How these genes are regulated in different plant tissues of diverse genotypes of cotton under different environmental conditions is not well known. Previously we identified a set of differentially-expressed cotton genes induced soon after Aspergillus infection of cotton bolls and seed. In this study, we expanded our research by conducting a throughput genome wide sequencing (Illumina) to investigate differentially expressed genes in response to infection by toxigenic and atoxigenic strains of A. flavus in boll pericarp and cottonseed. This global gene expression analysis in response to fungal invasion in cotton will serve as an important source for identifying biomarkers for breeding, potential candidate genes for transgenic manipulation and should be helpful in understanding complex plant-fungal interaction for future research.

Technical Abstract: Aflatoxins are toxic metabolites and potent carcinogen produced from asexual fungi Aspergillus flavus and A. parasiticus. Aflatoxins can contaminate cottonseed under conducive preharvest and postharvest conditions. U.S. federal regulations restrict the use of aflatoxin contaminated cottonseed at >20 ppb for animal feed. Several strategies have been proposed for controlling aflatoxin contamination and great success has been achieved by application of an atoxigenic strain of A. flavus cotton, peanut and maize growing fields. Development of cotton cultivars through genetic engineering for resistance to A. flavus and/or aflatoxin biosynthesis, is the most-effective strategy for controlling aflatoxin contamination in cotton. In this study, a high throughput single end Illumina sequencing technology was used to investigate differentially expressed genes (DEGs) in response to A. flavus infection (toxigenic and atoxigenic strains), on cotton (Gossypium hirsutum L.) pericarp and seed. The genes involved in antifungal response, oxidative burst, transcription factors defense signaling pathways and stress response were highly differentially expressed in pericarp and seed tissue in response to A. flavus infection. The principle component analysis (PCA) distinguished the responses in pericarp and seed tissue in response to infections by toxigenic and atoxigenic strains of A. flavus. The cell-wall modifying genes and genes involved in production of antimicrobial substances were more active in pericarp as compared to seed tissue. Phytohormone analysis revealed the antagonistic relationship between jasmonic acid (JA)-ethylene (ET) pathway, and salicylic acid (SA) pathway; JA-ET was activated and SA was deactivated in response to A. flavus infection. The genes involved in auxin and cytokinin (CK) signaling were also induced. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed the different defense related pathways enriched in both pericarp and seed tissue under A. flavus infection. However, most of the genes involved in defense response in cotton were highly induced in pericarp than in seed tissue. This global gene expression analysis in response to fungal invasion in cotton will serve as source for identifying biomarkers for breeding, potential candidate genes for transgenic manipulation and should be helpful in understanding complex plant-fungal interaction for future research.