Comparative Root Transcriptome Profiling and Gene Regulatory Network Analysis between Eastern and Western Carrot (Daucus carota L.) Cultivars Reveals Candidate Genes for Vascular Tissue Patterning

Znanstveni rad - Izvorni znanstveni rad

• Autor: Chaitra C. Kulkarni
• Autor: Sarvamangala S. Cholin
• Autor: Akhilesh K. Bajpai
• Autor: Gabrijel Ondrasek
• Autor: R. K. Mesta
• Autor: Santosha Rathod
• Autor: H. B. Patil
• Autorova ustanova: Sveučilište u Zagrebu; Agronomski fakultet
• Znanstveno / umjetničko područje, polje i grana: BIOTEHNIČKE ZNANOSTI; Poljoprivreda (agronomija)

Sažetak (engleski)

Carrot (Daucus carota L.) is a highly consumed vegetable rich in carotenoids, known for their potent antioxidant, anti-inflammatory, and immune-protecting properties. While genetic and molecular studies have largely focused on wild and Western carrot cultivars (cvs), little is known about the evolutionary interactions between closely related Eastern and Western cvs. In this study, we conducted comparative transcriptome profiling of root tissues from Eastern (UHSBC-23-1) and Western (UHSBC-100)... Više carrot cv. to better understand differentially expressed genes (DEGs) associated with storage root development and vascular cambium (VC) tissue patterning. Through reference-guided TopHat mapping, we achieved an average mapping rate of 73.87% and identified a total of 3544 DEGs (p < 0.05). Functional annotation and gene ontology classification revealed 97 functional categories, including 33 biological processes, 19 cellular components, 45 metabolic processes, and 26 KEGG pathways. Notably, Eastern cv. exhibited enrichment in cell wall, plant-pathogen interaction, and signal transduction terms, while Western cv. showed dominance in photosynthesis, metabolic process, and carbon metabolism terms. Moreover, constructed gene regulatory network (GRN) for both cvs. obtained orthologs with 1222 VC-responsive genes of Arabidopsis thaliana. In Western cv, GRN revealed VC-responsive gene clusters primarily associated with photosynthetic processes and carbon metabolism. In contrast, Eastern cv. exhibited a higher number of stress-responsive genes, and transcription factors (e.g., MYB15, WRKY46, AP2/ERF TF connected via signaling pathways with NAC036) were identified as master regulators of xylem vessel differentiation and secondary cell wall thickening. By elucidating the comparative transcriptome profiles of Eastern and Western cvs. for the first time, our study provides valuable insights into the differentially expressed genes involved in root development and VC tissue patterning. The identification of key regulatory genes and their roles in these processes represents a significant advancement in our understanding of the evolutionary relations and molecular mechanisms underlying secondary growth of carrot and regulation by vascular cambium. Sakrij dio sažetka

• Ključne riječi (engleski): carrot; vascular cambium; candidate genes; gene regulatory network; plant stress response
• Jezik: engleski
• Vrsta publikacije: Znanstveni rad - Izvorni znanstveni rad
• Status objave: Objavljen
• Vrsta recenzije: Recenziran - međunarodna recenzija
• Verzija publikacije: Objavljena verzija rada (izdavačev PDF)
• Naslov časopisa: Plants
• Brojčani podaci: vol. 12, br. 19, 3449
• e-ISSN: 2223-7747
• DOI: https://doi.org/10.3390/plants12193449
• URN:NBN: urn:nbn:hr:204:350054
• Datum objave publikacije: 2023-09-30
• URL dokumenta: https://www.mdpi.com/2223-7747/12/19/3449
• Vrsta resursa: Tekst
• Prava pristupa: Otvoreni pristup
• Javna napomena: This research was funded by the Department of Biotechnology (DBT), Govt of India (DBT-BIOCARe-102/IFD/SAN/3308/2014-15) and Vision Group of Science and Technology, Govt of Karnataka (KSTePS/VGST-RGS-F/2018-19/GRD No. 840/315).
• Datum i vrijeme pohrane: 2025-02-11 07:57:40