Identification of candidate resistance genes of cotton against Aspergillus flavus infection using a comparative transcriptomics approach

Authors: MEHANATHAN, M - Louisiana State University Agcenter; BEDRE, R - Louisiana State University Agcenter; MANGU, VENKATA - Louisiana State University Agcenter; Rajasekaran, Kanniah - Rajah; Bhatnagar, Deepak; BAISAKH, N - Louisiana State University Agcenter

Submitted to: Physiology and Molecular Biology of Plants
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/15/2018
Publication Date: 3/22/2018
Citation: Mehanathan, M., Bedre, R., Mangu, V., Rajasekaran, K., Bhatnagar, D., Baisakh, N. 2018. Identification of candidate resistance genes of cotton against Aspergillus flavus infection using a comparative transcriptomics approach. Physiology and Molecular Biology of Plants. 24(3):513–519. https://doi.org/10.1007/s12298-018-0522-7.
DOI: https://doi.org/10.1007/s12298-018-0522-7

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. Our previous studies (PLoS 2014) on global gene expression analysis in cottonseed in response to infection by aflatoxigenic and non-aflatoxigenic strains of A. flavus indicated several potential genes involved in the host plant - fungal interaction. We have further identified that these A. flavus-responsive genes are conserved among susceptible crops including cotton, peanut and maize using comparative mapping approaches. Of the 732 putative resistant genes studied, 26 were common among all the three crops. Further studies should highlight their roles in physiological and molecular response to the fungus. In addition, this study paves the way for the functional validation of 26 resistance-associated genes toward development of cotton with resistance to Aspergillus flavus infection.

Technical Abstract: Nine hundred twenty two differentially expressed transcripts of cotton in non-inoculated pericarp (NIP) and seed (NIS), pericarp (NTP) and seed (NTS) of cotton inoculated with atoxigenic strain (AF13), and pericarp (TP) and seed (TS) inoculated with toxigenic strain (AF36) of Aspergillus flavus were queried against the A. flavus-induced transcripts of peanut and maize using an in-house Perl script (e-value of 1e-5, = 80% sequence identity and = 80% alignment length) to identify resistance-associated genes in cotton. Comparison of putative resistance genes identified between cotton-maize and cotton-peanut showed that 693 and 13 genes were unique in both cases, respectively, and 26 genes were common among all three genomes. Chromosomal localization of 732 putative resistance genes revealed an uneven distribution of 726 genes on 13 cotton chromosomes whereas 6 genes could not be mapped. Functional annotation showed enrichment of genes with binding activity and catalytic activity among the putative resistance genes. Biologically, the stress-responsive genes were predicted to be associated with defense response to various biotic factors such as fungus and bacterium. A higher proportion of these proteins were localized on membrane, followed by extracellular matrix and nucleus. Future studies will concentrate on the functional validation of 26 resistance-associated genes toward development of cotton with resistance to Aspergillus flavus infection.