title: A connected set of genes associated with programmed cell death implicated in controlling the hypersensitive response in maize.
abstract: Rp1-D21 is a maize auto-active resistance gene conferring a spontaneous hypersensitive response (HR) of variable severity depending on genetic background. We report an association mapping strategy based on the Mutant Assisted Gene Identification and Characterization approach to identify naturally occurring allelic variants associated with phenotypic variation in HR. Each member of a collection of 231 diverse inbred lines of maize constituting a high-resolution association mapping panel were crossed to a parental stock heterozygous for Rp1-D21, and the segregating F(1) generation testcrosses were evaluated for phenotypes associated with lesion severity for 2 years at two locations. A genome-wide scan for associations with HR was conducted with 47,445 SNPs using a linear mixed model that controlled for spurious associations due to population structure. Since the ability to identify candidate genes and the resolution of association mapping are highly influenced by linkage disequilibrium (LD), we examined the extent of genome-wide LD. On average, marker pairs separated by >10 kbp had an r(2) value of <0.1. Genomic regions surrounding SNPs significantly associated with HR traits were locally saturated with additional SNP markers to establish local LD structure and precisely identify candidate genes. Six significantly associated SNPs at five loci were detected. At each locus, the associated SNP was located within or immediately adjacent to candidate causative genes predicted to play significant roles in the control of programmed cell death and especially in ubiquitin pathway-related processes.
authors.affiliation: Department of Plant Pathology, North Carolina State University, Raleigh, NC 27695-7616, USA.
authors.forename: Bode A
authors.initials: BA
authors.lastname: Olukolu
authors.forename: Adisu
authors.initials: A
authors.lastname: Negeri
authors.forename: Rahul
authors.initials: R
authors.lastname: Dhawan
authors.forename: Bala P
authors.initials: BP
authors.lastname: Venkata
authors.forename: Pankaj
authors.initials: P
authors.lastname: Sharma
authors.forename: Anshu
authors.initials: A
authors.lastname: Garg
authors.forename: Emma
authors.initials: E
authors.lastname: Gachomo
authors.forename: Sandeep
authors.initials: S
authors.lastname: Marla
authors.forename: Kevin
authors.initials: K
authors.lastname: Chu
authors.forename: Anna
authors.initials: A
authors.lastname: Hasan
authors.forename: Jiabing
authors.initials: J
authors.lastname: Ji
authors.forename: Satya
authors.initials: S
authors.lastname: Chintamanani
authors.forename: Jason
authors.initials: J
authors.lastname: Green
authors.forename: Chi-Ren
authors.initials: CR
authors.lastname: Shyu
authors.forename: Randall
authors.initials: R
authors.lastname: Wisser
authors.forename: James
authors.initials: J
authors.lastname: Holland
authors.forename: Guri
authors.initials: G
authors.lastname: Johal
authors.forename: Peter
authors.initials: P
authors.lastname: Balint-Kurti
mesh_terms: D000483:Alleles; D017209:Apoptosis / Q000235:genetics*; D003433:Crosses, Genetic; D060467:Disease Resistance / Q000235:genetics*; D017343:Genes, Plant; D005819:Genetic Markers; D014644:Genetic Variation; D055106:Genome-Wide Association Study; D016014:Linear Models; D015810:Linkage Disequilibrium; D010641:Phenotype; D020161:Physical Chromosome Mapping; D020641:Polymorphism, Single Nucleotide; D003313:Zea mays / Q000235:genetics* / Q000502:physiology
chemical_list: D005819:Genetic Markers