Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2015 Sep 24;16(1):726.
doi: 10.1186/s12864-015-1931-4.

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

Yufang Guo  1 , Krystle E Wiegert-Rininger  1 , Veronica A Vallejo  1 , Cornelius S Barry  1 , Ryan M Warner  2
Affiliations

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

Yufang Guo et al. BMC Genomics. .

Abstract

Background: 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. 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.

Results: Here 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.

Conclusions: The 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.

PubMed Disclaimer

Figures

Fig. 1
Fig. 1
Quality metrics of the Petunia spp. transcriptome assemblies. a Size distribution of assembled transcripts. b CEGMA completeness assessment of the transcriptome assemblies. c Percentage of P. axillaris, P. exserta, and P. integrifolia unigenes with assigned functional annotations from UniRef100, TAIR10, RefSeq, the Pfam domain database, and NCBI GenBank non-redundant protein set. In addition, the total percentage of annotated unigenes per species is presented
Fig. 2
Fig. 2
OrthoMCL identified orthologous gene clusters in the three Petunia species. A total of 21,272 orthologous clusters were identified among all comparisons. Unique and species specific OrthoMCL clusters are shown
Fig. 3
Fig. 3
Biological Process GO annotation comparisons among species
Fig. 4
Fig. 4
Summary of SNP loci between three Petunia spp. a Total number of SNP loci between P. axillaris, P. exserta and P. integrifolia; b number of homozygous SNP loci between P. axillaris, P. exserta and P. integrifolia. The intersecting portions of the Venn diagram illustrate the number of common loci between the comparisons
Fig. 5
Fig. 5
Distribution of transcripts with different number of SNPs. The x-axis indicates the number of SNPs within each transcript and the y-axis indicates the number of transcripts within the category. The percentage on top of each bar indicates the percentage of total transcripts fall into the category. All – all three species, A × E (P. axillaris × P. exserta), I × A (P. integrifolia × P. axillaris), I × E (P. integrifolia × P. exserta)
Fig. 6
Fig. 6
Minor allele reads count frequency distribution for SNPs among P. axillaris, P. exserta, and P. integrifolia
Fig. 7
Fig. 7
Genetic linkage map of a P. integrifolia × P. axillaris F2 population. Markers developed from plastochron-related genes are highlighted in red. QTL for development rate (DR) are indicated along with the corresponding LOD score along the linkage group
See this image and copyright information in PMC

References

    1. Reck-Kortmann M, Silva-Arias GA, Segatto ALA, Mader C, Bonatto SL, de Freitas LB. Multilocus phylogeny reconstruction: New insights into the evolutionary history of the genus Petunia. Mol Phylogenet Evol. 2014;81:19–28. doi: 10.1016/j.ympev.2014.08.022. - DOI - PubMed
    1. Stehmann JR, Lorenz-Lemke AP, Freitas LB, Semir J. The genus Petunia. In: Gerats T, Strommer J, editors. Petunia Evolutionary, Developmental and Physiological Genetics. New York: Springer; 2009. pp. 1–28.
    1. Morita Y, Saito R, Ban Y, Tanikawa N, Kuchitsu K, Ando T, Yoshikawa M, Habu Y, Ozeki Y, Nakayama M. Tandemly arranged chalcone synthase A genes contribute to the spatially regulated expression of siRNA and the natural bicolor floral phenotype in Petunia hybrida. Plant J. 2012;70(5):739–49. doi: 10.1111/j.1365-313X.2012.04908.x. - DOI - PubMed
    1. Kelly RO, Deng ZA, Harbaugh BK. Evaluation of 125 petunia cultivars as bedding plants and establishment of class standards. Horttechnology. 2007;17(3):386–96.
    1. Kroon J, Souer E, Degraaff A, Xue YB, Mol J, Koes R. Cloning and structural analysis of the anthocyanin pigmentation locus Rt of Petunia hybrida: Characterization of insertion sequences in two mutant alleles. Plant J. 1994;5(1):69–80. doi: 10.1046/j.1365-313X.1994.5010069.x. - DOI - PubMed

Publication types

Substances

LinkOut - more resources