Genomic responses to multiple infections and to environmental factors
The genomic responses to the factors tested in WP1 and WP2 and their interactions will be studied using gene expression analysis with microarrays. Comparison across microarray experiments has proven extremely useful in honeybee genomics to understand the genomics of social regulations and pathology. A new honeybee oligonucleotide microarray that contains about twice as many genes as the first generation array is currently in use in the BEE DOC consortium. It contains about 13,440 different genes, based on gene predictions and annotation from the honeybee genome sequencing project and has already been validated.
The BEE DOC microarrays will test bees with sublethal exposure to pathogens and/or pesticides, limiting the number of doses and ages, and the costs involved. Pesticide doses tested will be close to lethal dose 10% (LD10) and follow the already published Varroa parasitism microarray study conducted by P5. We will compare bees with and without the different infections and pesticides to create a "top" list of genes showing the most consistent differences in expression by a cross-validated class prediction with GeneSpring (Agilent, Foster City, CA,).
After generating lists of differentially expressed genes, we will explore their functions and roles in biological processes. Specific gene expression patterns in response to one or few specific stressors may become useful for diagnostics (WP 5). Once the set of genes is identified, it will be validated through qRT-PCR expression quantification. Tested worker bees will be provided by WP1 and WP2. At least 3 replicate arrays per setting will be realized and we will take advantage of multiple comparisons by using a standard loop design. A master student will participate in the framework of WG 3, for training and educational purposes, at INRA (P5).