Location: Corn Host Plant Resistance Research
Title: Network analysis of maize RNA transport pathway genes associated with maize resistance to aflatoxin accumulation Authors
Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 8, 2014
Publication Date: April 28, 2014
Citation: Asters, M., Williams, W.P., Perkins, A., Mylroie, J.E., Windham, G.L., Shan, X. 2014. Relating significance and relations of differentially expressed genes in response to Aspergillus flavus infection in maize. Scientific Reports 4:4815. DOI:10.1038/srep04815. Interpretive Summary: Aflatoxin, which is produced by the fungus Aspergillus flavus, is highly toxic to humans, livestock, pets, and wildlife. Contamination of corn grain with aflatoxin is a major impediment to profitable corn production in the southern USA. Aflatoxin contamination poses a serious threat to food security in many of the developing countries where corn is a dietary staple. Growing corn hybrids or varieties with genetic resistance to A. flavus infection and subsequent accumulation of aflatoxin is generally considered a desirable means of reducing losses to aflatoxin contamination. Corn germplasm lines with genetic resistance to aflatoxin contamination have been developed and released by USDA-ARS at Mississippi State, Mississippi. In the current investigation, gene expression in response to A. flavus infection was compared in resistant and susceptible inbred lines. Molecular, computational, and statistical methods were used to identify genes associated with resistance to A. flavus infection and aflatoxin accumulation. Using these genes as molecular markers for resistance will enhance efforts to efficiently develop corn hybrids or varieties with resistance to aflatoxin contamination.
Technical Abstract: Aspergillus flavus is a pathogenic fungus producing alfatoxins that cause significant economic losses in maize production. This study analyzes the differences in expression levels of maize genes in response to A. flavus infection and aflatoxin accumulation. Identification of defense related genes and their interdependent relations is important for understanding the regulatory mechanisms of maize resistance and facilitating molecular maize breeding. We performed quantitative RT-PCR analysis on a total of 58 maize genes, among which 42 genes were newly selected from the RNA transport pathways for this study and 16 genes were tested in previous studies and found differentially expressed in response to A. flavus infection. Resistant maize inbred lines (Mp718, Mp719, and Mp04:104) and susceptible maize inbred lines (Va35, Mp04:85, and Mp04:89) were used in this study. Each maize inbred line was subjected to two treatments (inoculated and non-inoculated with A. flavus) with three replications under field conditions. Computational and statistical methods developed in programming language R were used for the preprocessing of the qRT-PCR data and the subsequent data analysis. Analysis of variance was used to identify significant genes among the contrasting groups. Twenty-three out of the 58 genes were differentially expressed with a significance level of p < 0.05 among different maize inbred lines. Seventeen out of the 58 genes were significant at p < 0.05 level between the resistant group and the susceptible group. Thirteen genes were significant in both tests. Correlation analysis by RNA transport pathways was performed using Pearson’s coefficients and Correlograms to reveal pairwise correlations between tested genes regardless of their significance levels. Among the highly correlated genes identified, expression of TC231674 (on chromosome 5, highly expressed in resistant maize inbred line Mp718) was positively correlated with the expression of BE050050 (close to the resistant SSR marker bnlg2291 on chromosome 4) and negatively correlated with the expression of AI664980 (on chromosome 1, highly expressed in susceptible maize inbred line Va35). The roles and relations among the RNA transport pathway genes and the pre-selected differentially expressed genes were revealed by using network analysis. Susceptibility related gene AI664980 was found adjacent to multiple RNA transport pathway genes and appeared to play a direct role in the nucleocytoplasmic trafficking activities. Whereas resistance related genes TC231674 and BE050050 appeared as isolates in the network graph and further analysis was required to reveal their associates in maize defense networks. A combination of molecular, computational, and statistical methods were used to identify significant maize genes and their relations associated with resistance to A. flavus infection and aflatoxin accumulation. Correlation and network analysis methods are powerful tools to provide new insights into the roles and positions of maize genes in maize defense networks.