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Differentially Expressed Small RNAs And Target Genes Related To Fruit Development In Tomato Grafted On Gouqi (Lycium Chinense) Rootstock

Posted on:2016-06-21Degree:DoctorType:Dissertation
Country:ChinaCandidate:A.B.M.KhaldunFull Text:PDF
GTID:1220330470974492Subject:Botany
Abstract/Summary:PDF Full Text Request
Local translocation of small RNAs between cells has been proved. Long distance translocation between rootstock and scion has also been well documented in homo-grafting system, but the process in distant-grafting is widely unexplored where rootstock and scion belonging to different genera.Micro RNAs are a class of small, endogenous, noncoding, gene silencing RNAs that regulate target genes of a wide range of important biological pathways in plants. In this study, tomato was grafted onto gouqi (Lycium chinense Mill.) to reveal the insight of miRNAs regulation and expression patterns in a distant-grafting system. Gouqi is an important traditional Chinese medicinal plant with enriched phytochemicals but a little genome information is available for this plant, particularly at the small-RNA level. Recent findings indicate that the evolutionary role of miRNAs is very important for a better understanding of gene regulation in different plant species.To elucidate small RNAs and their potential target genes in fruit and shoot tissues of control gouqi, control tomato and grafted tomato, high-throughput RNA sequencing technology was used followed by qRT-PCR and RLM 5’-RACE validation experiments. In the first set of the study on gouqi control plant, a total of 60 conserved miRNAs belonging to 31 families and 30 putative novel miRNAs were identified from fruit and shoot tips. A total of 62 significantly differentially expressed miRNAs were identified, of which 15 (14 known and 1 novel) were shoot-specific, and 12 (seven known and five novels) were fruit-specific. Additionally,28 differentially expressed miRNAs were recorded as up-regulated in fruit tissues. The predicted potential targets were involved in a wide range of metabolic and regulatory pathways. GO (Gene Ontology) enrichment analysis and the KEGG (Kyoto Encyclopedia of Genes and Genomes) database revealed that "metabolic pathways" is the most significant pathway with respect to the rich factor and gene numbers. Moreover, five miRNAs were related to fruit maturation, lycopene biosynthesis and signaling pathways, which might be important for the further study of fruit development. This study is the first, to detect known and novel miRNAs, and their potential targets, of L. chinense (gouqi). The data and findings that are presented here will be a good source for the functional genomic study of medicinal plants and for understanding the links among diversified biological pathways.On the other hand, in the second part of our study,68 evolutionary known miRNAs of 37 miRNA families have been identified from fruits and shoot tissues of tomato control and grafted tomato on gouqi root stock. Moreover,168 putative novel miRNAs were also identified. Compared with control tomato,43 (11 known and 32 novels) and 163 (33 known and 130 novels) miRNAs were expressed significantly different in shoot and fruit of grafted tomato, respectively. The fruiting stage was identified as the most responsive in the distant-grafting approach and 123 miRNAs were found as up-regulating in the grafted fruit which is remarkably higher comparing to the grafted shoot tip (28). Potential targets of differentially expressed miRNAs were found to be involved in diverse metabolic and regulatory pathways. ADP binding activities, molybdopterin synthase complex and RNA helicase activity were found as enriched terms in GO analysis. Additionally,’metabolic pathways’revealed as the most significant pathway in KEGG analysis.The information of the small RNA transcriptomes that are obtained from this grafting study might be the first miRNAs elucidation for a distant-grafting system, particularly between gouqi and tomato. The results of this study will provide the insights into the molecular aspects of miRNA-mediated regulation in the medicinal plant gouqi, and in grafted tomato. The further and exclusive studies on the target genes related to the significant biological pathways will open a new window for studying the medicinally important phyto-chemicals. Noteworthy, it would provide a basis for illustrating how miRNA signals could exchange between rootstock and scion and affecting various biological processes.
Keywords/Search Tags:Lycium, Tomato, Distant-grafting, miRNA, High-throughput RNA sequencing
PDF Full Text Request
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