title: 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.
authors.affiliation: Department of Plant Pathology, NC State University, Raleigh, North Carolina, United States of America.
authors.forename: Bode A
authors.initials: BA
authors.lastname: Olukolu
authors.affiliation: Department of Plant Pathology, NC State University, Raleigh, North Carolina, United States of America.
authors.forename: Guan-Feng
authors.initials: GF
authors.lastname: Wang
authors.affiliation: Department of Botany and Plant Pathology, Purdue University, Lilly Hall, West Lafayette, Indiana, United States of America.
authors.forename: Vijay
authors.initials: V
authors.lastname: Vontimitta
authors.affiliation: Department of Botany and Plant Pathology, Purdue University, Lilly Hall, West Lafayette, Indiana, United States of America.
authors.forename: Bala P
authors.initials: BP
authors.lastname: Venkata
authors.affiliation: Department of Botany and Plant Pathology, Purdue University, Lilly Hall, West Lafayette, Indiana, United States of America.
authors.forename: Sandeep
authors.initials: S
authors.lastname: Marla
authors.affiliation: Department of Botany and Plant Pathology, Purdue University, Lilly Hall, West Lafayette, Indiana, United States of America.
authors.forename: Jiabing
authors.initials: J
authors.lastname: Ji
authors.affiliation: Department of Botany and Plant Pathology, Purdue University, Lilly Hall, West Lafayette, Indiana, United States of America.
authors.forename: Emma
authors.initials: E
authors.lastname: Gachomo
authors.affiliation: Department of Botany and Plant Pathology, Purdue University, Lilly Hall, West Lafayette, Indiana, United States of America.
authors.forename: Kevin
authors.initials: K
authors.lastname: Chu
authors.affiliation: Department of Plant Pathology, NC State University, Raleigh, North Carolina, United States of America.
authors.forename: Adisu
authors.initials: A
authors.lastname: Negeri
authors.affiliation: Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America.
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Benson
authors.affiliation: Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America.
authors.forename: Rebecca
authors.initials: R
authors.lastname: Nelson
authors.affiliation: Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America.
authors.forename: Peter
authors.initials: P
authors.lastname: Bradbury
authors.affiliation: Department of Biological Sciences, NC State University, Raleigh, North Carolina, United States of America.
authors.forename: Dahlia
authors.initials: D
authors.lastname: Nielsen
authors.affiliation: 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.
authors.forename: James B
authors.initials: JB
authors.lastname: Holland
authors.affiliation: 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.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Balint-Kurti
authors.affiliation: Department of Botany and Plant Pathology, Purdue University, Lilly Hall, West Lafayette, Indiana, United States of America.
authors.forename: Gurmukh
authors.initials: G
authors.lastname: Johal
mesh_terms: D002874:Chromosome Mapping; D060467:Disease Resistance / Q000235:genetics*; D055106:Genome-Wide Association Study; D015810:Linkage Disequilibrium; D010935:Plant Diseases / Q000235:genetics; D010940:Plant Proteins / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci / Q000235:genetics*; D003313:Zea mays / Q000235:genetics*
chemical_list: D010940:Plant Proteins; C113020:ZmCip1 protein, Zea mays