Abstract
BackgroundPetunia (Petunia × hybrida), derived from a hybrid between P. axillaris and P. integrifolia, is one of the most economically important bedding plant crops and Petunia spp. serve as model systems for investigating the mechanisms underlying diverse mating systems and pollination syndromes. In addition, we have previously described genetic variation and quantitative trait loci (QTL) related to petunia development rate and morphology, which represent important breeding targets for the floriculture industry to improve crop production and performance. Despite the importance of petunia as a crop, the floriculture industry has been slow to adopt marker assisted selection to facilitate breeding strategies and there remains a limited availability of sequences and molecular markers from the genus compared to other economically important members of the Solanaceae family such as tomato, potato and pepper.ResultsHere we report the de novo assembly, annotation and characterization of transcriptomes from P. axillaris, P. exserta and P. integrifolia. Each transcriptome assembly was derived from five tissue libraries (callus, 3-week old seedlings, shoot apices, flowers of mixed developmental stages, and trichomes). A total of 74,573, 54,913, and 104,739 assembled transcripts were recovered from P. axillaris, P. exserta and P. integrifolia, respectively and following removal of multiple isoforms, 32,994 P. axillaris, 30,225 P. exserta, and 33,540 P. integrifolia high quality representative transcripts were extracted for annotation and expression analysis. The transcriptome data was mined for single nucleotide polymorphisms (SNP) and simple sequence repeat (SSR) markers, yielding 89,007 high quality SNPs and 2949 SSRs, respectively. 15,701 SNPs were computationally converted into user-friendly cleaved amplified polymorphic sequence (CAPS) markers and a subset of SNP and CAPS markers were experimentally verified. CAPS markers developed from plastochron-related homologous transcripts from P. axillaris were mapped in an interspecific Petunia population and evaluated for co-localization with QTL for development rate.ConclusionsThe high quality of the three Petunia spp. transcriptomes coupled with the utility of the SNP data will serve as a resource for further exploration of genetic diversity within the genus and will facilitate efforts to develop genetic and physical maps to aid the identification of QTL associated with traits of interest.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1931-4) contains supplementary material, which is available to authorized users.
Highlights
Petunia (Petunia × hybrida), derived from a hybrid between P. axillaris and P. integrifolia, is one of the most economically important bedding plant crops and Petunia spp. serve as model systems for investigating the mechanisms underlying diverse mating systems and pollination syndromes
We have previously documented that accessions of P. axillaris and P. integrifolia possess increased development rate when compared to a diverse pool of commercial petunia germplasm, suggesting genetic variation for this trait within the genus [10]
Transcriptome assembly and annotation Transcriptome sequencing of five tissue libraries, including callus, flowers, shoot apex, seedlings, and trichomes, from P. axillaris, P. exserta, and P. integrifolia yielded between ~248 and 294 M 100 nt reads, of which greater than 94 % passed quality and trimming filters (Table 1)
Summary
Petunia (Petunia × hybrida), derived from a hybrid between P. axillaris and P. integrifolia, is one of the most economically important bedding plant crops and Petunia spp. serve as model systems for investigating the mechanisms underlying diverse mating systems and pollination syndromes. We have previously documented that accessions of P. axillaris and P. integrifolia possess increased development rate when compared to a diverse pool of commercial petunia germplasm, suggesting genetic variation for this trait within the genus [10]. This was confirmed in an interspecific F2 population of a cross between P. axillaris and P. integrifolia that identified three quantitative trait loci (QTL) on chromosomes 1, 2 and 5 that affected development rate and explained 34 % of the observed variation [11]. The molecular basis underlying these QTL remains to be identified
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