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Open Access Highly Accessed Research article

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

Jungeun Kim12, June Hyun Park7, Chan Ju Lim1, Jae Yun Lim7, Jee-Youn Ryu34, Bong-Woo Lee1, Jae-Pil Choi1, Woong Bom Kim1, Ha Yeon Lee1, Yourim Choi7, Donghyun Kim7, Cheol-Goo Hur12, Sukweon Kim5, Yoo-Sun Noh3, Chanseok Shin7* and Suk-Yoon Kwon16*

Author Affiliations

1 Green Bio Research Center, 125 Gwahak-ro, Yuseong-gu, Daejeon, 305-806, Republic of Korea

2 Bioinformatics, University of Science & Technology, 217 Gajung-ro, Yuseong-gu, Daejeon, 305-350, Republic of Korea

3 School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 151-747, Republic of Korea

4 Korea Ocean Research & Development Institute, 787 Haeanro, Sangrok-gu, Ansan, 426-744, Republic of Korea

5 Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 305-806, Republic of Korea

6 Biosystems and Bioengineering Program, University of Science & Technology, 217 Gajungno, Yuseong-gu, Daejeon, 305-350, Republic of Korea

7 Department of Agricultural Biotechnology, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-921, Republic of Korea

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BMC Genomics 2012, 13:657  doi:10.1186/1471-2164-13-657

Published: 21 November 2012

Abstract

Background

Roses (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.

Results

We 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.

Conclusions

In 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.