First application of a high density microarray for Sunflower: Methodological aspects of the design and statistical analysis in the study of the tolerance to Sclerotinia sclerotiorum

DI RIENZO J.; PELUFFO L.; PRINICIPI D.; FERNANDEZ P.; LIA V.V.; EHRENBOLGER F.; CONESA A.; GARCIA F. ; BLESA D.; DOPAZO J.; PANIEGO N.; HEINZ R.A.

Córdoba

Congreso; 2do. Congreso Argentino de Bioinformática y Biología Computacional; 2011

Asociación Argentina de Bioinformática y Biología Computacional

In order to conduct gene expression profiling analysis in response to biotic and abiotic stresses insunflower, the CICVyA-INTA-Castelar, Argentina, and the Principe Felipe Research Center, Valencia, Spain, developed a high-density microarray for sunflower (Helianthus annuus) including approximately 42K unigenes. These studies were accomplished by a network of laboratorios representing argentine public, government and private sectors. We present the methodological aspects of the first application of microarray technology to study the response of sunflower to the infection caused by to the necrotrophic fungal Sclerotinia sclerotiorum.Materials and methodsThe genomic response of sunflower to S. sclerotiorum infection was evaluated through a tri-factorial experiment including two lines of sunflower: a tolerant (RHA801) and a susceptible (HA89); two inoculation treatments: fungal spore suspension or water spray; and two times after inoculation (DAI): 2 and 4 days. Considering the constraints imposed by the structure of the chip and the operacional limitations for the hybridization step, we proposed a hybridization strategy based on an incomplete block design in which the three replicates of f the experiment was allocated using an appropriate confounding plan. The pre-processing as well as the statistical modeling was performed using R software under the fgStatistics interface.ResultsThe model, including all interaction and random effects describing the plot structure of the design could be estimated for all genes. Seventy three genes were identified to be involved in the response to S.sclerotiorum. Eleven of them were directly related to the response to the infection regardless of the sunflower line or the time course, 62 were differentially expressed depending on the line and or the time course. The number of genes with genotype effect was larger than that with DAI effect. All these genes are currently being subjected to further expression analysis.ConclusionsThis first report of the use of the sunflower chip introduce important discuss on the rationality venid the hybridization design, the statistical modeling approach and the general analysis strategy.