Genome wide association study identifies SNPs associated with northern corn leaf blight caused by Exserohilum turcicum in tropical maize germplasm (Zea mays L.)

Abstract

The Northern corn leaf blight (NCLB) caused by the fungus Exserohilum turcicum is one of the oldest and most important leaf diseases of corn, occurring widely in Brazil and in the main producing regions of the world. The pathogen causes the devastating leaf disease that results in considerable losses in corn yield. The objective of this research was to identify genomic regions or associated SNPs involved in resistance to NCLB in a panel of field corn, popcorn, and sweet corn inbred lines. A genome-wide association study was carried out with phenotypic data collected in two environments on a panel of 320 maize inbred lines. The experiments were conducted in a 20 x 16 alpha-lattice experimental design, with three replications. The severity of NCLB was evaluated 25 days after the end of flowering. A set of 350, 643 high-quality polymorphic SNPs obtained using genotyping by sequencing were used, 14 of which were associated with E. turcicum resistance. The variation explained by each SNP ranged from 0.5 to 5.7%. In the first growing season, five SNPs explained 16.2% of the phenotypic variance, while during the second growing season, nine SNPs explained 16.5% of the total phenotypic variance. The candidate gene models GRMZM2G042920, GRMZM2G041774 and GRMZM2G056564 were the most promising, given that they were previously identified playing an important role in the response of corn to defense, abiotic and biotic stress through signaling mechanisms.