Comprehensive meta-analysis of QTL and gene expression studies identify candidate genes associated with Aspergillus flavus resistance in maize

Authors: BAISAKH, NIRANJAN - LSU Agcenter; DA SILVA, EDUARDO - LSU Agcenter; PRADHAN, ANJAN - LSU Agcenter; Rajasekaran, Kanniah - Rajah

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/26/2023
Publication Date: 7/18/2023
Citation: Baisakh, N., Da Silva, E.A., Pradhan, A.K., Rajasekaran, K. 2023. Comprehensive meta-analysis of QTL and gene expression studies identify candidate genes associated with Aspergillus flavus resistance in maize. Frontiers in Plant Science. 14:1214907. https://doi.org/10.3389/fpls.2023.1214907.
DOI: https://doi.org/10.3389/fpls.2023.1214907

Interpretive Summary: Aflatoxin (AF) is a potent carcinogen that is produced by Aspergillus flavus upon infection in food and feed crops, such as corn, cotton, and tree nuts. AF contamination compromises the food safety and marketability of the commodities. AF resistance is a complex trait, controlled by many genes, which makes conventional breeding of AF resistant commercial corn varieties difficult and slow. Several genes and associated molecular markers controlling AF resistance have been reported from multiple genetic mapping studies. But the genomic regions with low and inconsistent phenotypic variance create uncertainty for their use in marker-assisted selection to complement breeding. Meta analysis of published genes, on the other hand, can locate genes and reliable identification of linked markers for AF resistance. Using 276 of the 356 reported genomic regions controlling resistance to A. flavus infection and AF contamination, we identified 58 regions over all 10 maize chromosomes. Further comparative analysis of these genes with genes differentially expressed under other biotic and environmental stresses led to the identification of 14 high confidence genes that are expressed only under A. flavus infection. Assessment of molecular markers linked to these genes identified three markers that could discriminate 14 and eight cultivars with AF resistant and susceptible response, respectively. Our results from the comprehensive meta-analysis led to identification of genes and makers, which can be used to complement traditional breeding through marker-assisted selection, genetic engineering and/or gene editing to develop AF resistant maize varieties. This information will be useful to corn breeders and biotechnology companies.

Technical Abstract: Aflatoxin (AF) contamination, caused by Aspergillus flavus, compromises food safety and marketability of several commodities including maize, a major food and feed crop, worldwide. Multigenic control of AF resistance makes conventional introgression of resistance traits into high-yielding commercial maize varieties difficult and slow. Several QTLs and markers associated with AF resistance are reported from multiple biparental and genome-wide association mapping studies in maize. But QTLs with large confidence intervals (CI) explaining inconsistent phenotypic variance create uncertainty for their use in marker-assisted selection. Meta analysis of published QTLs can identify significant meta-QTLs (MQTLs) with narrower CI for reliable identification of genes and linked markers for AF resistance. Using 276 of the 356 reported QTLs controlling resistance to A. flavus infection and AF contamination, we identified 58 MQTLs over all 10 maize chromosomes with an average CI reduction of 66.5%. Nine MQTLs with CI <2.0 Mb and/or an average R2=0.1 were considered significant. Besides, meta-analysis of maize genes differentially expressed in response to biotic and abiotic stresses from RNA-seq and microarray experiments led to the identification of 591 genes putatively responding to only A. flavus infection, of which 43 were common to the genes in MQTL regions with significant differential gene expression (-1.0= Log2Fc =1.0; P=0.05). However, 30 out of 43 genes registered differential expression under various abiotic stresses on maize gene expression database, suggesting that 14 genes were uniquely expressed only under A. flavus infection. Assessment of 12 MQTLs-linked SSR markers identified three markers that could discriminate 14 and eight cultivars with resistant and susceptible response, respectively. Comprehensive meta-analysis of QTLs and DEGs could lead to identification of genes and makers for their potential application in marker-assisted breeding of A. flavus resistant maize varieties.