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

Niranjan Baisakh; Eduardo A Da Silva; Anjan K Pradhan; Kanniah Rajasekaran

doi:10.3389/fpls.2023.1214907

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

Front Plant Sci. 2023 Jul 18:14:1214907. doi: 10.3389/fpls.2023.1214907. eCollection 2023.

Authors

Niranjan Baisakh¹, Eduardo A Da Silva^{1

2}, Anjan K Pradhan¹, Kanniah Rajasekaran³

Affiliations

¹ School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States.
² Department of Agriculture, Federal University of Lavras, Lavras, Brazil.
³ 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.

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.

Keywords: Meta-QTL; RNA-seq; aflatoxin; co-expression network; genomic region; maize; marker; microarray.

Grants and funding

This study was funded by a grant from the USDA-ARS NACA #58-6054-0-010.