A Genome-Wide Association Study of the Maize Hypersensitive Defense Response Identifies Genes That Cluster in Related Pathways

Abstract

Much remains unknown of molecular events controlling the plant hypersensitive defense response (HR), a rapid localized cell death that limits pathogen spread and is mediated by resistance (R-) genes. Genetic control of the HR is hard to quantify due to its microscopic and rapid nature. Natural modifiers of the ectopic HR phenotype induced by an aberrant auto-active R-gene ( Rp1-D21), were mapped in a population of 3,381 recombinant inbred lines from the maize nested association mapping population. Joint linkage analysis was conducted to identify 32 additive but no epistatic quantitative trait loci (QTL) using a linkage map based on more than 7000 single nucleotide polymorphisms (SNPs). Genome-wide association (GWA) analysis of 26.5 million SNPs was conducted after adjusting for background QTL. GWA identified associated SNPs that colocalized with 44 candidate genes. Thirty-six of these genes colocalized within 23 of the 32 QTL identified by joint linkage analysis. The candidate genes included genes predicted to be in involved programmed cell death, defense response, ubiquitination, redox homeostasis, autophagy, calcium signalling, lignin biosynthesis and cell wall modification. Twelve of the candidate genes showed significant differential expression between isogenic lines differing for the presence of Rp1-D21. Low but significant correlations between HR-related traits and several previously-measured disease resistance traits suggested that the genetic control of these traits was substantially, though not entirely, independent. This study provides the first system-wide analysis of natural variation that modulates the HR response in plants.

Author Summary

The hypersensitive pathogen defense response (HR) in plants typically consists of a rapid, localized cell death around the point of attempted pathogen penetration. It is found in all plant species and is associated with high levels of resistance to a wide range of pathogens and pests including bacteria, fungi, viruses, nematodes, parasitic plants and insects. Little is known about the control of HR after initiation, largely because it is so rapid and localized and therefore difficult to quantify. Here we use a mutant maize gene conferring an exaggerated HR to quantify HR levels in a set of 3,381 mapping lines characterised at 26.5 million loci to identify genes associated with naturally-occurring variation in HR. Many of these genes seem to be involved in a set of connected regulatory pathways including protein degradation, control of programmed cell death, recycling of cellular components and regulation of oxidative stress. We have also shown that several of these genes show high levels of expression induction during HR. The study provides the first comprehensive list of natural variants in maize genes that modulate HR and cluster within reported pathways underlying molecular events during HR.