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PLoS Genet. 2014 Aug 28;10(8):e1004562. doi: 10.1371/journal.pgen.1004562. eCollection 2014 Aug.

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

Author information

1
Department of Plant Pathology, NC State University, Raleigh, North Carolina, United States of America.
2
Department of Botany and Plant Pathology, Purdue University, Lilly Hall, West Lafayette, Indiana, United States of America.
3
Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America.
4
Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America.
5
Department of Biological Sciences, NC State University, Raleigh, North Carolina, United States of America.
6
USDA-ARS Plant Science Research Unit, Raleigh, North Carolina, United States of America; Department of Crop Science, NC State University, Raleigh, North Carolina, United States of America.
7
Department of Plant Pathology, NC State University, Raleigh, North Carolina, United States of America; USDA-ARS Plant Science Research Unit, Raleigh, North Carolina, United States of America.

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.

PMID:
25166276
PMCID:
PMC4148229
DOI:
10.1371/journal.pgen.1004562
[Indexed for MEDLINE]
Free PMC Article

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