همایش ملی بیوانفورماتیک ایران

صفحه اصلی / 4th international edition and 13th Iranian Conference on Bioinformatics

Bioinformatic Approach to Predict the Regulatory Mechanisms: TF–miRNA–mRNA–lncRNA Network during Cluster Development in Grape

نویسندگان :

Shahla Sahraei¹ Nafiseh Mahdinezhad² Abbasali Emamjomeh³ Kaveh Kavousi⁴ Mahmood Solouki⁵ Massimo Delledonne⁶

1- Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran 2- Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran 3- Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran 4- 3 Institute of Biochemistry and Biophysics (IBB), Department of Bioinformatics, Laboratory of Complex Biological Systems and Bioinformatics (CBB), University of Tehran, Tehran, Iran 5- Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran 6- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy

کلمات کلیدی :

Grapevine،lncRNAs،miRNA،TF،RNA-seq

چکیده :

Plants employ complex mechanisms to regulate growth processes at various transcriptional levels. Recent studies highlight the critical role of the lncRNA-miRNA-mRNA interaction in plant growth and their response to biotic and abiotic stresses. Yaghooti grapes are among the most significant Iranian grape cultivars, known for their dense clusters. This study aimed to investigate miRNA-TF-mRNA-lncRNA interactions during the development of Yaghooti grape clusters using RNA-seq data. The computational analysis identified 1,549 lncRNAs, 637 mRNAs, 166 miRNAs, and 30 TFs. The target genes AG, DES1, ABCC1, LDOX, F3H, CTR8, FCA, CBLS, ERF, MyB, LOB, and WRKY exhibited the most significant expression changes during cluster development. The enrichment analysis of target genes revealed a relationship between lncRNAs and grape growth, secondary metabolite synthesis, and the response to biotic and abiotic stresses. The important roles of vvi-miR166, vvi-miR156, vvi-miR159, vvi-miR172, and vvi-miR319 have been confirmed in various plant growth processes. STRG.22437.1, rna-XR_002029069.1, rna-XR_002032260.1, and rna-XR_787124.2 were considered as precursors of vvi-miR845a, vvi-MIR156g, vvi-MIR172b, and vvi-MIR477a, respectively. The specific molecular roles of lncRNAs, along with understanding their interactions with other regulatory components affecting cluster density, could lead to the improvement of this cultivar with looser clusters.