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Title: A genome-wide association study of the maize hypersensitive defense response identifies genes that cluster in related pathways

Author
item OLUKOLU, BODE - North Carolina State University
item WANG, GUAN-FENG - North Carolina State University
item VONTIMITTA, VIJAY - Purdue University
item VENKATA, BALA - Purdue University
item MARLA, SANDEEP - Purdue University
item JI, JIABING - Purdue University
item GACHOMO, EMMA - Purdue University
item CHU, KEVIN - Purdue University
item NEGERI, ADISU - North Carolina State University
item BENSON, JACQUELINE - Cornell University
item NELSON, REBECCA - Cornell University
item Bradbury, Peter
item NIELSEN, DAHLIA - North Carolina State University
item Holland, Jim - Jim
item Balint-Kurti, Peter
item JOHAL, GURMUKH - Purdue University

Submitted to: PLoS Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/27/2014
Publication Date: 8/28/2014
Citation: Olukolu, B., Wang, G., Vontimitta, V., Venkata, B.P., Marla, S., Ji, J., Gachomo, E., Chu, K., Negeri, A., Benson, J., Nelson, R., Bradbury, P., Nielsen, D., Holland, J.B., Balint Kurti, P.J., Johal, G. 2014. A genome-wide association study of the maize hypersensitive defense response identifies genes that cluster in related pathways. PLoS Genetics. 10(8): e1004562. doi: 10.1371/journal.pgen.1004562.

Interpretive Summary: A common plant defense response called the hypersensitive response (HR) typically consists of a rapid, localized cell death around the point of attempted pathogen penetration. Surprisingly little is known about how HR is controlled after it is initiated. In this paper we use a mutant gene conferring an exaggerated HR to identify locations in the genome associated with naturally-occuring variation in the HR phenotype. We identified 44 associated genes, many of which are predicted to be involved in a set of connected biochemical pathways including protein degradation, control of programed cell death, recycling of cellular components and regulation of oxidative stress. This study provides our most comprehensive understanding of the pathways that modulate HR in plants.

Technical Abstract: Much remains unknown of molecular events controling the plant hypersensitive response (HR), a rapid localized cell death that limits pathogen spread and is mediated by resistance (R-) genes. 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 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 non-overlapping QTL identifed by joint linkage analysis. The candidate genes included five genes predicted to be involved in redox homeostasis pathways, two in lignin biosynthesis, two in calcium signalling, and at least 20 genes with predicted involvement in control of programed cell death, autophagy, and/or ubiqutin-mediated protein degradation pathways. Four of the remaining genes have been implicated in some part of the defense response. Twelve of the candidate genes showed significant differential expression between isogenic lines differing for the presence of Rp1-D21. The study provides a first comprehensive understanding of the pathways that modulate HR in plants.