De Novo Transcriptome Assembly and Single Nucleotide Polymorphism Identification in Three Wild Petunia Spp.

Petunia (Petunia × hybrida), derived from a hybrid between P. axillaris and P. integrifolia, is one of the most economically important bedding plant crops grown in the United States. Traditional breeding approaches have been slow to improve traits such as flowering time and stress resistance, emphasizing the need to develop new genomic tools to improve breeding efficiency. Here we report the de novo assembly, annotation and characterization of transcriptomes from three Petunia species. Petunia axillaris, P. exserta and P. integrifolia transcriptome assemblies comprised of five tissue libraries (callus, 3-week old seedling, shoot apical meristem, mixed floral developmental stages, and trichome) included a total of 281M, 235M and 271M high quality reads, which were initially assembled into 67,813, 58,293 and 87,218 transcripts, respectively. Following assembly, unigenes were extracted for annotation and genes associated with floral development, vegetative growth to reproductive transitions, anthocyanin biosynthesis and temperature response processes were identified. A computational pipeline was developed for single nucleotide polymorphism detection between the species. Short reads from ten commercial petunia cultivars were also sequenced and will be aligned to the reference assembly for SNP identification, allowing evaluation of the population structure. Common SNPs among wild and cultivated genotypes will be further investigated and used for subsequent QTL mapping in two interspecific recombinant inbred line populations. Our research will contribute to both crop improvement and increased greenhouse production efficiency for one of the country's most popular annuals.