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.

Maize Homologs of CCoAOMT and HCT, Two Key Enzymes in Lignin Biosynthesis, Form Complexes with the NLR Rp1 Protein to Modulate the Defense Response

“…From previous GWAS analysis, we identified two SNP loci that were highly associated with variation in the severity of HR induced by Rp1-D21 (Olukolu et al, 2014) and were adjacent to or within genes encoding enzymes, HCT and CCoAOMT, involved in lignin biosynthesis pathway. We have previously shown that two HCT homologs that are encoded by genes adjacent to the HR-associated SNP on chromosome 1 (HCT1806 and HCT4918) suppress Rp1-D21-induced HR through physical interaction, while other HCT homologs, encoded by genes distant from any associated SNPs, confer no or weak suppression (Wang et al, 2015c).…”

“…Suppress Rp1-D21-Induced HR in N. benthamiana From previous genome-wide associate study (GWAS) analysis in maize, we identified 44 SNPs associated with variation in Rp1-D21-induced HR (Olukolu et al, 2014) using the NAM population (McMullen et al, 2009). Furthermore, we demonstrated that two maize proteins homologous to HCT, termed HCT1806 and HCT4918, which were encoded by genes on chromosome 1, adjacent to the most highly associated SNP identified in the study, suppress Rp1-D21-induced HR via physical interaction (Wang et al, 2015c).…”

“…In our previous study using the NAM population (Olukolu et al, 2014), we identified a QTL allelic series at the CCoAOMT2 locus with different alleles from the 26 NAM parents conferring different strengths of effect on HR. Among these, the QTL alleles from the lines NC350 and M37W had among the strongest suppressive , and the same leaf was cleared by ethanol (right).…”

“…We used Rp1-D21 as a tool to investigate the genetic basis of the control of HR by crossing a line carrying it into several mapping populations to identify loci, pathways, and genes associated with modulation of the HR strength (Chintamanani et al, 2010;Chaikam et al, 2011;Olukolu et al, 2013Olukolu et al, , 2014. One of the populations used, called the nested association mapping (NAM) population, is an extremely large and powerful mapping population that allows the mapping of quantitative trait loci (QTL) with high precision (McMullen et al, 2009).…”

“…One of the populations used, called the nested association mapping (NAM) population, is an extremely large and powerful mapping population that allows the mapping of quantitative trait loci (QTL) with high precision (McMullen et al, 2009). Using the NAM population (Olukolu et al, 2014), we identified single nucleotide polymorphism (SNP) markers highly associated with variation in the HR phenotype at 44 loci. Because the markers were mapped with extremely high resolution, we were able to tentatively identify candidate genes at the associated loci, which might underlie variation in the HR phenotype.…”