Transcriptome database as a resource for candidate gene analysis in Rhododendron simsii hybrids.

Eighty percent of the European production of pot azalea (R. simsii hybrids) occurs in Flanders (Belgium). Moreover, ILVO has an azalea breeding programme that would like to take advantage of genomics data for the study of several important traits such as broad mite resistance, flowering, flower colour and plant architecture. 454 sequencing technology was applied on 4 libraries of azalea flowers and leaves in different growth stages. In total, 1.2 million reads were obtained. Reads from all 4 libraries were assembled together into 84357 contigs. A total of 516 EST-SSRs were extracted from the database, 357 of which were functionally annotated. A subset of 88 EST-SSRs were present in candidate genes for the traits under study at ILVO. High quality EST-SSR markers could be developed for 21 of these genes, 11 of which were implemented on our mapping population to enrich the existing genetic map with co-dominant functional markers. QTL analysis is now being performed for the traits of interest.
Meanwhile, a candidate gene survey resulted in the identification of a set of genes for different pathways under study (jasmonic acid, salicylic acid and flavonoid biosynthesis). The expression of these genes was quantified in several experiments to validate the involvement of the genes in specific biological processes. We also plan to incorporate gene expression data as eQTLS on our genetic map in the near future.
To improve the quality of the database, we are now scheduling Illumina HiSeq analysis on RNA samples isolated under different conditions of both parents of the mapping population .