Genome‐Wide Association Study of Resistance to Ear Rot byFusarium verticillioidesin a Tropical Field Maize and Popcorn Core Collection

Abstract

Fusarium ear rot [caused by Fusarium verticillioides (Sacc.) Nirenberg] is one of the most prevalent diseases of maize (Zea mays L.) worldwide, and has one of the greatest negative economic impacts on this cereal crop globally. Fusarium ear rot is a highly complex trait, under polygenic control with minor effects per gene and moderate heritability, and is strongly influenced by environmental conditions. The aim of this study was to identify genomic regions, including putative candidate genes, associated with resistance to Fusarium ear rot and the starburst pattern caused by F. verticillioides under artificial inoculation. We conducted a genome‐wide association study using phenotypic data from three environments on a panel of 183 inbred lines and a set of 267,525 single‐nucleotide polymorphism (SNPs) generated using genotyping by sequencing. Fourteen SNPs were significantly associated with Fusarium ear rot and two for starburst, some of which were colocalized to previously reported quantitative trait loci regions, and some of which were novel. Four genes linked to the associated SNPs encode defense‐related proteins, including gibberellin 2‐oxidase4, a glucosyltransferase, a Ras‐related protein RHN1, and phosphoribosylanthranilate transferase (PAT). Each of these SNPs explains a considerable proportion of the phenotypic variance, ranging from 15 to 25%. Once these SNPs are validated, they will be useful for marker‐assisted selection and for a better understanding of maize resistance to Fusarium ear rots.

A genome‐wide association study for partial resistance to southern corn rust in tropical maize

“…The research was conducted at the State University of Maringá (UEM), Maringá City, Paraná, Brazil. The association mapping panel consisted of 164 tropical inbred lines of maize (74 popcorn and 90 field corn lines), a subset from the UEM maize seed bank collection of inbred lines evaluated in 2014 (Coan et al, ), including inbred lines representing the main hybrids used by Brazilian farmers and companies involved in maize breeding programmes in Brazil. These are listed in Tables S1 and S2.…”

“…Genomic DNA was extracted from a bulk of five random seedlings of each 164 inbred lines using the CTAB method described by Helentjaris () and modified by the USDA‐ARS Corn Host Plant Resistance Research Unit, Starkville MS (Coan et al, ). DNA samples were sent to the Institute of Genomic Diversity at Cornell University for genotyping‐by‐sequencing (GBS).…”

“…DNA samples were sent to the Institute of Genomic Diversity at Cornell University for genotyping‐by‐sequencing (GBS). GBS was performed as described by Elshire et al () and Coan et al () for maize. Briefly, DNA was digested with the ApeKI methylation‐sensitive restriction enzyme ligated to adapters and then combined into pools of 96 samples and amplified with primers compatible with the adapter sequences.…”

“…GWAS generally have better mapping resolution than biparental mapping and have become more widely available to plant researchers (Gao, Kathryn Turner, Chao, Kolmer, & Anderson, ). In maize, GWAS have been used successfully to study agronomic traits (Farfan et al, ; Tian et al, ), quality traits (Owens et al, ; Suwarno, Pixley, Palacios‐Rojas, Kaeppler, & Babu, ), pest resistance (Samayoa, Malvar, Olukolu, Holland, & Butrón, ) and disease resistance (Coan et al, ; Gowda et al, ; Zila et al, ).…”

Genome-wide association analysis for fumonisin content in maize kernels

“…In this context, genome-wide association study (GWAS) using inbred line panels appears as an effective alternative to this step-by-step approach for detection of genes involved in resistance to maize kernel contamination with fumonisin. GWAS has been extensively used for detecting associations between molecular markers and resistance to FER or to seedling infection [19][20][21][22][23][24][25][26]. Novel maize loci significantly associated with improved resistance to FER were identified, each locus explaining a small proportion of phenotypic variability.…”