Transcriptome-enabled marker discovery and mapping of plastochron-related genes in Petunia spp.

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.

Characterization of Trichome-Expressed BAHD Acyltransferases in Petunia axillaris Reveals Distinct Acylsugar Assembly Mechanisms within the Solanaceae

“…The four candidate P. axillaris ASATs are highly divergent at the nucleotide level, and it was possible to identify fragments of each gene ranging from 247 to 375 nucleotides in length that are highly specific for each target. For example, BLASTN searches against P. axillaris transcriptome and genome assemblies (Guo et al, 2015;Bombarely et al, 2016) failed to identify any additional nucleotide sequences longer than 19 bp that share 100% identity with each VIGS fragment, indicating that there is very limited potential for off-target silencing. Upon silencing, the abundance of each target transcript was reduced by approximately 80% to 90% in silenced lines when compared with those of TRV2 empty vector controls (Supplemental Fig.…”

“…A P. axillaris transcriptome assembly and associated sequences are available under GenBank/EMBL/DDBJ BioProject PRJNA261953 (Guo et al, 2015). Sequences of P. axillaris ASATs are deposited in GenBank under the following accession numbers: PaxASAT1 (KT716258), PaxASAT2 (KT716259), PaxASAT3 (KT716260), and PaxASAT4 (KT716261).…”

“…The four ASATs from S. lycopersicum, SlASAT1 (Solyc12g006330), SlASAT2 (Solyc04g012020), SlASAT3 (Solyc11g067270), and SlASAT4 (Solyc01g105580), were used as query sequences in tBLASTN searches against a de novo transcriptome assembly of P. axillaris that includes transcripts generated from trichomes (Guo et al, 2015). Two P. axillaris unigenes, Pax36474 and Pax31629, were recovered that share 68% and 61% amino acid identity with SlASAT1 and SlASAT2, respectively.…”

Genetic Determinants of Crop Timing and Quality Traits in Two Interspecific Petunia Recombinant Inbred Line Populations

“…axillaris 6 . A total of 209 unique transcripts were differentially expressed between fast- and slow-developing individuals in the IA population (Fig.…”

“…axillaris and P . exserta 6 . Even though, it remains unclear why the reduced IA LG coverage was found only on certain chromosomes.…”