Exploiting genomic tools for genetic dissection and improving the resistance to Fusarium stalk rot in tropical maize

Abstract

Abstract Fusarium stalk rot (FSR) is a global destructive disease in maize, the efficiency of phenotypic selection for improving FSR resistance was low. Novel genomic tools - genome-wide association study (GWAS) and genomic prediction (GP) - provide an opportunity for genetic dissection and improving FSR resistance. In this study, GWAS and GP analyses were performed on 562 tropical maize inbred lines consisting of two populations in four environments under artificial inoculation. In total, 15 SNPs significantly associated with FSR resistance were identified across two populations and the CombinedPOP consisting of all 562 inbred lines, with the P-values ranging from 1.99×10-7 to 8.27×10-13, and the phenotype variance explained (PVE) values ranging from 0.94 to 8.30%. The effects of the 15 favorable alleles ranged from -4.29 to -14.21%. One stable genomic region in the interval of 0.95 Mb from 250,089,724 bp to 251,044,933 bp on chromosome 1 was detected across all populations, and the PVE values of the detected SNPs ranged from 2.16 to 5.18%. Medium GP accuracy of FSR severity, 0.29 to 0.51, was observed in two cross-validation (CV) schemes. When incorporating genotype-by-environment interaction, GP accuracy was improved from 0.36 to 0.40 in the CV1 scheme, and from 0.42 to 0.55 in the CV2 scheme. Considering both the genome coverage and the total PVE of SNPs for selecting a subset of molecular markers further improved the GP accuracy. These findings extend the knowledge of exploiting genomic tools for genetic dissection and improving FSR resistance in tropical maize.