1. A Connected Set of Genes Associated with Programmed Cell Death Implicated in Controlling the Hypersensitive Response in Maize
- Author
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Anna Hasan, Chi-Ren Shyu, Bala P. Venkata, Adisu Negeri, Rahul Dhawan, Jason M. Green, Sandeep R. Marla, Jiabing Ji, Bode A. Olukolu, Guri Johal, Anshu Garg, Peter J. Balint-Kurti, Satya Chintamanani, Pakaj Sharma, Kevin Chu, James B. Holland, Emma W. Gachomo, and Randall J. Wisser
- Subjects
Genetic Markers ,Candidate gene ,Linkage disequilibrium ,Genome-wide association study ,Locus (genetics) ,Single-nucleotide polymorphism ,Apoptosis ,Biology ,Investigations ,Genes, Plant ,Polymorphism, Single Nucleotide ,Zea mays ,Linkage Disequilibrium ,Genetics ,Association mapping ,Alleles ,Crosses, Genetic ,Genetic association ,Disease Resistance ,Genetic Variation ,Tag SNP ,Physical Chromosome Mapping ,Phenotype ,Linear Models ,Genome-Wide Association Study - 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 F1 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 r2 value of
- Published
- 2013