BackgroundLilium lancifolium, a very important cold-resistant wild flower for lily cold resistance breeding, is widely distributed in southwestern and northeastern China. To gain a better understanding of the cold signaling pathway and the molecular metabolic reactions involved in the cold response, we performed a genome-wide transcriptional analysis using RNA-Seq.ResultsApproximately 104,703 million clean 90- bp paired-end reads were obtained from three libraries (CK 0 h, Cold-treated 2 h and 16 h at 4°C); 18,736 unigenes showed similarity to known proteins in the Swiss-Prot protein database, and 15,898, 13,705 and 1849 unigenes aligned to existing sequences in the KEGG and COG databases (comprising 25 COG categories) and formed 12 SOM clusters, respectively. Based on qRT-PCR results, we studied three signal regulation pathways —the Ca2+ and ABA independent/dependent pathways —that conduct cold signals to signal transduction genes such as LlICE and LlCDPK and transcription factor genes such as LlDREB1/CBF, LlAP2/EREBP, LlNAC1, LlR2R3-MYB and LlBZIP, which were expressed highly in bulb. LlFAD3, Llβ-amylase, LlP5CS and LlCLS responded to cold and enhanced adaptation processes that involve changes in the expression of transcripts related to cellular osmoprotectants and carbohydrate metabolism during cold stress.ConclusionsOur study of differentially expressed genes involved in cold-related metabolic pathways and transcription factors facilitated the discovery of cold-resistance genes and the cold signal transcriptional networks, and identified potential key components in the regulation of the cold response in L lancifolium, which will be most beneficial for further research and in-depth exploration of cold-resistance breeding candidate genes in lily.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-203) contains supplementary material, which is available to authorized users.
Plants have continually confrontation with different abiotic stresses, including salt, low temperature, drought or hormone stress. The plants acclimate to the environmental stresses relating with the falls of the molecular mesh including the stress signal receiver, signal transcriptional regulation and the expression of functional and structure genes. Using the RNA-seq, we carried out a transcriptional analysis under cold treatment for investigating a profound comprehension of the signal network and molecular metabolisms reaction included in abiotic stress reaction for Lilium lancifolium. Our study identified 18,722 unigenes had demonstrated the resemblance to the known exact proteins in the Swiss-Prot protein database and classified them by Gene ontology into three primary kinds: cellular component, biological process, and molecular function, and then 15,898 unigenes aligned to existing sequences in the KEGG databases. Based on the transcriptome results of cold stress, more stress-related genes were identified and analyzed of their expressions in other abiotic stress treatments as 37 °C, ABA, JA and Na. Meanwhile, bioinformatics qRT-PCR analyses of stress genes as LlDREB1, LlAP2, LlNAC1, LlHOT, LlR2R3-MYB and LlCDPK revealed that novel candidate genes encoding ethylene responsive transporters and serine/threonine receptor-like kinases, which contributed to speculate the signal regulation pathway during the abiotic stresses; engineering genes could also boost the tolerance to stress, as protected and maintained the function and structure of cellular components. Our research conjectured the abiotic stress signal transduction pathway and identified the expected key ingredients regulating the stress tolerance in Lilium lancifolium, which would enable the in-depth molecular exploration of stress-tolerance mechanisms in lily.
The new transcriptomes provided comprehensive sequence profiling data of transcriptomic variation during vernalization in Lily Asiatic Hybrids 'Tiny ghost'. A number of 52,277,184 sequencing raw reads totaling 5.11 Gbp of the chilling treatment (4 °C) sample and 39,466,176 sequencing raw reads totaling 3.85 Gbp of room temperature control (25 °C) sample were assembled de novo into 68,718 unigenes with a mean length of 984 bp, and a total of 33,208 (45.6%) unigenes were annotated by using public protein databases with a cut-off E value about 10(-5). There are 6,153 unigenes of which were assigned to specific metabolic pathways by the Kyoto encyclopedia of genes and genomes. Gene Ontology analysis of the annotated unigenes revealed that the majority of sequenced genes were associated with signal transduction mechanisms, posttranslational modification, protein turnover and chaperones. In addition, the genes expression levels were compared just after vernalization completion between the cold treatment and room temperature control. There are 68,116 unigenes were differentially expressed, and hierarchical clustering analysis arranged 7,301 significantly differentially-expressed unigenes into 56 groups. Six genes related to the vernalization were selected to confirm their expression levels by using quantitative real-time polymerase chain reaction. Furthermore, typical vernalization unigenes VRN1 and VRN2 were identified, and also some vernalization-associated unigenes, such as CBF, SOC, TaAGL, AP2, LEA, LIM et al. were also annotated in the present study. As for VRN1 and VRN2, their expressions were consistent with some previous related studies. Also, this was the first time the vernalization genes VRN1 and VRN2 were founded in lily. According to the results of the present studies, we predicted that they would play an important role during vernalization in Lily Asiatic Hybrids; these data provided the foundation for the future studies of metabolism during vernalization of Asiatic lily.
In our review, we highlighted the progresses made in molecular breeding of lily's flowering, including the ABCDE models, the gene cloning, the establishment of regeneration system, the gene transformation methods, the transgene technology application in lily. Meanwhile, questions that were met at present in molecular breeding in flowering of lily were underlined, and we provide viable solutions. Although many researches on lily literature had been published in the world, in our review, we provided a valuable and unique resource and spring-board from which to understand or further study the molecular breeding in flowering of lily.
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