Transcriptome comparison reveals key candidate genes in response to vernalization of Oriental lily

Li et al. BMC Genomics (2016) 17:664 DOI 10.1186/s12864-016-2955-0 RESEARCH ARTICLE Open Access Transcriptome comparison reveals key candidate genes in response to vernalization of Oriental lily Wenqi Li, Xiaohua Liu and Yingmin Lu* Abstract Background: Oriental hybrid lily ‘Sorbonne’, a very important cut flower for lily, is enjoyed great popularity in the world, but it must experience a period of low winter temperature to initiate or accelerate the flowering process. To gain a better understanding of the temperature signaling pathway and the molecular metabolic reactions involved in the vernalization response, a genome-wide transcriptional analysis using RNA-Seq was performed. Results: 188,447,956 sequencing reads was assembled into 66,327 unigenes and showed similarity to known proteins in the Swiss-Prot protein database, and 2,893, 30,406 and 60,737 unigenes aligned to existing sequences in the KEGG, COG, and GO databases. Based on qRT-PCR results, we studied the expression of three signal regulation pathways genes–the plant hormones signal transduction (LoAP2, LoIAA1, LoARF10), the DNA methylation (LoCMT, LoFLD), and vernalizatin pathway (LoFLC, LoVRN1, LoVRN2, LoFT, LoSOC1, LoLFY, LoSVP) in the immature flower buds of Oriental hybrid lily. In addition, we identified two vernalizaiton–related genes (LoSVP and LoVRN1) from the cDNA library, which appear to be promising candidates for playing key roles in the development and response of flowering in Oriental lily plants, and LoSVP had a function in delaying flowering but LoVRN1could promote flowering early. Conclusions: We collected a sample for transcriptome sequencing and comparison when the bulb’s apical meristem was in the time of floral transition when the apical meristem had not converted into the morphological differentiation process, which helped to obtain more genes playing key roles in the floral induction pathways. The upstream and downstream relationship between different genes were forecasted by the analysis of genes’ expression levels in a wide range of time. Future research that is targeted towards how genes interact on each other, which will promote establishing and perfecting the molecular mechanisms of floral induction pathway by vernalization. Keywords: Vernalization, Lily, Transcriptome, RNA-Seq, Flower differentiation Abbreviations: BLAST, Basic Local Alignment Search Tool; COG, Clusters of Orthologous Groups; DGE, Digital Gene Expression; EST, Expressed Sequence Tag; FDR, False Discovery Rate; GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes Pathway; NCBI, National Center for Biotechnology Information; qRT-PCR, Real-time Quantitative Reverse Transcription Polymerase Chain Reaction; RACE, Rapid Amplification of cDNA Ends; RPKM, Number of Reads per Kilobase per Million Clean Reads; SAM, Shoot Apical Meristem * Correspondence: College of Landscape Architecture & China National Engineering Research Center for Floriculture, Beijing Forestry University, No.35 Qinghua East Road, Haidian District, Beijing 100083, China © 2016 The Author(s). Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Li et al. BMC Genomics (2016) 17:664 Background Vernalization is a complicated process of plant development that is essential for plants to grow in unfavorable environmental conditions, which occurs during cold environment, and flowering only occurs some weeks or even some months later when some other conditions, including the presence of certain photoperiods and ambient temperatures, are met [1]. It is a temporary suspension of vernalization for plants of obvious growth containing meristems. The transitions of vernalization are regulated by chilling temperatures and/or short photoperiods. We have learnt some knowledge about the molecular mechanisms indicating vernalization from the model plant Arabidopsis thaliana and cereals. In Arabidopsis thaliana, the progressive repression and stable silencing of FLOWERING LOCUS C (FLC), is central to the vernalization mechanism. FLC encoded a MADS domain protein acting as a repressor of flowering [2, 3]. There were also some other genes been found to related to vernalization-responsiveness in Arabidopsis [4]. FLOWERING LOCUS T (FT) and SUPPRESSOR OF OVER-EXPRESSION OF CONSTANS 1 (SOC1), two floral promoters, were repressed transcription by FLC [5]. That is, FLC is highly expressed in plants that have not experienced vernalization [6, 7], and then FLC protein was binded to the promoter of SOC1 and sequences in an FT intron to repress transcription of both these genes [6, 7], which delays flowering. In addition, some other target genes or FLC orthologues were key to the developmental release that enables flowering [8, 9] in other plant species. In cereals, there were two main regulatory pathways leading to the transition to reproductive development at the molecular levels–the vernalization pathway and the photoperiod pathway [10–12]. One of the major genes controlling vernalization-induced flowering is VERNALIZATION 1 (VRN1). VRN1 is similar to Arabidopsis thaliana APETALA1 (AP1), CAULIFLOWER (CAL) and FRUITFULL (FUL), which are MADS-box transcription factors and identity genes in meristem [13]. VRN1 was a major determinant of winter/spring growth habit in cereals. Neither the mechanism behind repression of VRN1 prior to vernalization in vernalization-requiring plants nor the mechanism by which VRN1 leads to transition to reproductive development was fully understood. Another major gene controlling vernalization-induced flowering in cereals is VERNALIZATION 2 (VRN2), which is a floral repressor that delays flowering until plants are vernalized [14]. Besides, there was another group of MADS-box genes that have a putative function in the transition to flowering belong to the SHORT VEGETATIVE PHASE (SVP)like MADS-box genes. SVP-like genes in A. thaliana, Hordeum vulgare, and T. aestivum act as negative regulators of flowering [15, 16]. In T. aestivum, TaVRT2, a Page 2 of 21 SVP-like gene is down-regulated by vernalization and can bind the CArG-box in the VRN1 promoter and interacts with VRN1 and VRN2 proteins [17]. Lilies, monocotyledonous ornamental plants, are one of the most important flowering crops [18], which flowering relies on a combination of integrating effects of endogenous and external signals [19]. Vernalization in Oriental Lilies, which are perennial plants, generally requires a minimum of eight weeks at low tempe (...truncated)