Small RNA and transcriptome deep sequencing proffers insight into floral gene regulation in Rosa cultivars

Abstract

BackgroundRoses (Rosa sp.), which belong to the family Rosaceae, are the most economically important ornamental plants—making up 30% of the floriculture market. However, given high demand for roses, rose breeding programs are limited in molecular resources which can greatly enhance and speed breeding efforts. A better understanding of important genes that contribute to important floral development and desired phenotypes will lead to improved rose cultivars. For this study, we analyzed rose miRNAs and the rose flower transcriptome in order to generate a database to expound upon current knowledge regarding regulation of important floral characteristics. A rose genetic database will enable comprehensive analysis of gene expression and regulation via miRNA among different Rosa cultivars.ResultsWe produced more than 0.5 million reads from expressed sequences, totalling more than 110 million bp. From these, we generated 35,657, 31,434, 34,725, and 39,722 flower unigenes from Rosa hybrid: ‘Vital’, ‘Maroussia’, and ‘Sympathy’ and Rosa rugosa Thunb. , respectively. The unigenes were assigned functional annotations, domains, metabolic pathways, Gene Ontology (GO) terms, Plant Ontology (PO) terms, and MIPS Functional Catalogue (FunCat) terms. Rose flower transcripts were compared with genes from whole genome sequences of Rosaceae members (apple, strawberry, and peach) and grape. We also produced approximately 40 million small RNA reads from flower tissue for Rosa, representing 267 unique miRNA tags. Among identified miRNAs, 25 of them were novel and 242 of them were conserved miRNAs. Statistical analyses of miRNA profiles revealed both shared and species-specific miRNAs, which presumably effect flower development and phenotypes.ConclusionsIn this study, we constructed a Rose miRNA and transcriptome database, and we analyzed the miRNAs and transcriptome generated from the flower tissues of four Rosa cultivars. The database provides a comprehensive genetic resource which can be used to better understand rose flower development and to identify candidate genes for important phenotypes.

An NAC Transcription Factor Controls Ethylene-Regulated Cell Expansion in Flower Petals

“…The sequence of rhy-miR164 was identical to the miR164 sequence in Arabidopsis ( Fig. 2A) and was consistent with a recent report in rose (Kim et al, 2012). The rhy-miR164 abundance in ethylene-treated rose petals was reduced to 48.8% of that of control petals.…”

“…Moreover, application of next-generation sequencing technologies greatly promoted the study on rose genomics. A rose transcriptome database was reported recently, which contained more than 30,000 transcripts from three modern rose cultivars and Rosa rugosa (Kim et al, 2012). Lately, a transcriptome data set containing 80,714 transcript clusters was generated by using the RNA from various tissues of Rosa chinensis 'Old Blush' and in response to biotic and abiotic stresses (Dubois et al, 2012).…”

Recent Progress in Genomic Analysis of Ornamental Plants, with a Focus on Carnation

“…transcripts based on this cultivar. Kim et al (2012) collected transcripts from three rose cultivars and R. rugosa Thunb., and Yan et al (2014) acquired transcript data from another R. chinensis cultivar. Pei et al (2013) created a rose floral transcriptome using 454 technology and exploited the transcriptome to identify potential key regulators of ethylene-influenced cell expansion.…”

Transcriptional regulators of flavonoid biosynthesis and their application to flower color modification in Japanese gentians

“…This approach to creating desirable flower colors will also have a significant impact on plant biotechnology and may be used in breeding programs for most flowers. Recent nextgeneration sequencing technologies have been applied to several flower species including petunia (Zenoni et al 2011), rose (Kim et al 2012), carnation (Tanase et al 2012), and orchid (Chou et al 2013), yielding data that have provided a foundation for novel research. It is noteworthy that the whole genome sequence of carnation, one of the major cut-flowers sold worldwide, has recently been reported (Yagi et al 2013); the data will be useful for the discovery of novel genes and the elucidation of the complex metabolic networks of flavonoid biosynthesis in flowers.…”