Location: Southern Horticultural ResearchTitle: Transcriptome sequencing of Hydrangea macrophylla to uncover genes related to reblooming and powdery mildew resistance
Submitted to: Acta Horticulture Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 7/24/2013
Publication Date: 9/29/2013
Citation: Rinehart, T.A., Reed, S.M., Scheffler, B.E. 2013. Transcriptome sequencing of Hydrangea macrophylla to uncover genes related to reblooming and powdery mildew resistance. Acta Horticulture Proceedings. 3:30-37.
Interpretive Summary: High throughput DNA sequencing using pyrosequencing technology allows rapid production of sequence data with dramatically reduced time, labor, and cost. Published reports on 454 pyrosequencing have been mostly restricted to model species with genomic or other EST data already available. However, affordable sequencing has enabled whole genome or transcriptome sequencing of non-model plants such as medicinal or ornamental crops that have no prior data. This recent advance in methodology, along with the lower costs, enables functional genomic studies in crops that would otherwise not be explored.Here we used ‘Veitchii’ as a source of tissue for transcriptome sequencing. The genes that confer resistance were presumably being expressed in leaf tissue at the time of collection and should be represented in the resulting data. Gene annotation of the isogroups was used to identify putative genes and gene networks involved in traits such as powdery mildew resistance that are important to breeding new H. macrophylla cultivars.
Technical Abstract: Massively parallel pyrosequencing technology has been used extensively on agronomic crops and model plants. Transcriptome sequencing is a useful first step in functional genomic studies, microarray and gene expression studies, single nucleotide polymorphism (SNP) surveys, quantitative trait loci (QTL) mapping, and genomic scans of diversity. Here we describe annotation and sequence comparison of a normalized expressed sequence tag (EST) library from a non-model crop, Hydrangea macrophylla, which is grown as a woody landscape ornamental plant, forced greenhouse floral crop, and for cut flowers. Transcriptome sequences were generated using 454 GS-FLX Titanium sequencing of a single normalized EST library made from leaf, bud, stem, and flower tissue. Median sequence length was 431 base pairs and sequencing generated 1.1 million high-quality reads. Assembled data include 46,673 contigs that break down into 42,664 isotigs and 24,201 isogroups. BLAST2Go was used for sequence annotation. Transcriptome data was screened for microsatellites regions, which produced primer pairs for more than 4000 new SSR markers to saturate a linkage map for H. macrophylla. SNP discovery is underway as well. Here we provide a list of candidate genes that could be utilized in future experiments to increase flowering, resist powdery mildew, and enhance floral characteristics.