Comparative Analysis of Multiple GWAS Results Identifies Metabolic Pathways Associated with Resistance to A. flavus Infection and Aflatoxin Accumulation in Maize

Abstract

Aflatoxins are carcinogenic secondary metabolites produced by several species of Aspergillus, including Aspergillus flavus, an important ear rot pathogen in maize. Most commercial corn hybrids are susceptible to infection by A. flavus, and aflatoxin contaminated grain causes economic damage to farmers. The creation of inbred lines resistant to Aspergillus fungal infection or the accumulation of aflatoxins would be aided by knowing the pertinent alleles and metabolites associated with resistance in corn lines. Multiple Quantitative Trait Loci (QTL) and association mapping studies have uncovered several dozen potential genes, but each with a small effect on resistance. Metabolic pathway analysis, using the Pathway Association Study Tool (PAST), was performed on aflatoxin accumulation resistance using data from four Genome-wide Association Studies (GWAS). The present research compares the outputs of these pathway analyses and seeks common metabolic mechanisms underlying each. Genes, pathways, metabolites, and mechanisms highlighted here can contribute to improving phenotypic selection of resistant lines via measurement of more specific and highly heritable resistance-related traits and genetic gain via marker assisted or genomic selection with multiple SNPs linked to resistance-related pathways.

Genome-wide association study and pathway analysis to decipher loci associated with Fusarium ear rot resistance in tropical maize germplasm

“…The GWAS output was run through the Pathway Analysis Study Tool (PAST) (Thrash et al 2020 ) on the MaizeGDB website ( https://www.maizegdb.org/past ), as described in Tang et al ( 2015 ) and Warburton et al ( 2022 ). The data used in PAST included the p-values (the significant SNP-trait association values); R 2 (proportion of the explained phenotypic variation), effect values along with the calculated LD values for D’ and R 2 , and the p-value between each SNP marker and its closest neighboring SNPs (Tang et al 2015 ; Warburton et al 2022 ). SNPs were then assigned to genes, and the functions of candidate genes were assessed by examining the pathways in which the encoded enzymes were involved (Warburton et al 2022 ).…”

“…In addition to identifying genomic regions and genes involved in disease resistance, GWASs also assist in identifying resistance pathways and associated genes. Metabolic pathway analysis focuses on the combined effects of many genes clustered together because of their shared biological functions (Tang et al 2015 ; Warburton et al 2022 ). This type of research complements the study of the most significant marker-trait associations in addition to giving clues on the genetic basis of specific traits (Tang et al 2015 ).…”

Food Safety Aspects of Breeding Maize to Multi-Resistance against the Major (Fusarium graminearum, F. verticillioides, Aspergillus flavus) and Minor Toxigenic Fungi (Fusarium spp.) as Well as to Toxin Accumulation, Trends, and Solutions—A Review

“…However, no aflatoxin mapping was made, such that forecasting of the aflatoxin content could not be concluded. Another paper [169] reported that most commercial hybrids are susceptible to A. flavus and aflatoxin contamination. Through a multiple QTL analysis, several dozen QTLs with small effect were identified.…”

Dissection of Common Rust Resistance in Tropical Maize Multiparent Populations through GWAS and Linkage Studies

“…Accumulating disease-resistant QTL can enhance plant resistance, underscoring the importance of identifying additional resistance QTL to further enhance maize resistance to common rust. [12][13][14][15][16][17][18].…”