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Title: A connected set of genes associated with programmed cell death implicated in controlling the hypersensitive response in maize

item OLUKOLU, B. - North Carolina State University
item NEGERI, A. - North Carolina State University
item DHAWAN, R. - North Carolina State University
item VENKATA, B. - Purdue University
item SHARMA, P. - Purdue University
item GARG, A. - Purdue University
item GACHOMO, E. - Purdue University
item MARLA, S. - Purdue University
item CHU, K. - Purdue University
item HASAN, A. - Purdue University
item JI, J. - Purdue University
item CHINTAMANANI, S. - Purdue University
item GREEN, J. - University Of Missouri
item Holland, Jim - Jim
item WISSER, R. - University Of Delaware
item SHYU, C.-R. - University Of Missouri
item JOHAL, G. - Purdue University
item Balint-Kurti, Peter

Submitted to: Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/21/2012
Publication Date: 2/1/2013
Citation: Olukolu, B., Negeri, A., Dhawan, R., Venkata, B.P., Sharma, P., Garg, A., Gachomo, E., Marla, S., Chu, K., Hasan, A., Ji, J., Chintamanani, S., Green, J., Holland, J.B., Wisser, R., Shyu, C., Johal, G., Balint Kurti, P.J. 2013. A connected set of genes associated with programmed cell death implicated in controlling the hypersensitive response in maize. Genetics. 193:609-620.

Interpretive Summary: It is difficult to identify genes involved in natural quantitative variation in the plant defense response and consequently very little is known about this subject. One of the main problems is that the defense response is extremely localized –often to just a few cells- and is therefore quite difficult to measure in a quantitative way. In this paper we use a genetic trick that we call MAGIC (Mutant –Assisted Gene Identification and Characterization) to amplify the defense response and make it much easier to measure. We use this MAGIC approach to measure the strength of the defense response in a high diversity panel of maize lines which have been genetically characterized to an unprecedented level. In this way we are able to identify very precisely 5 loci associated with natural variation in the defense response. Genes implicated in the control of programmed cell death occur at 4 of these loci.

Technical Abstract: Rp1-D21 is a maize auto-active resistance gene that confers a spontaneous hypersensitive response (HR). Depending on the genetic background in which it operates; variable levels of HR are observed. This offers a convenient system to identify alleles that modulate HR and genes involved in disease response. We report an association mapping strategy based on the MAGIC (Mutant Assisted Gene Identification and Characterization) approach to identify naturally occurring genetic variations associated with variation in HR in population of diverse maize lines. A collection of 232 diverse inbred lines of maize constituting a high-resolution association mapping panel were crossed to an Rp1-D21 heterozygous parent stock and the segregating F1 generation was evaluated for phenotypes associated with lesion severity for two years at two locations. Using a linear mixed model that controlled for spurious associations due to population structure, a genome-wide scan for associations with HR was conducted with 51,150 SNPs. Three of the five highly associated SNP markers identified were localized within exons and a promoter region of candidate genes (CGs). One of the two other associated SNP markers was localized 29 kb upstream of a CG (HSP70), a gene that lacked markers in our SNP marker panel, while the other was localized within a non-coding sequence flanked by a transposase gene. In each case, the CGs were predicted to play significant roles in the control of programmed cell death.