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

Chaitra C Kulkarni; Sarvamangala S Cholin; Akhilesh K Bajpai; Gabrijel Ondrasek; R K Mesta; Santosha Rathod; H B Patil

doi:10.3390/plants12193449

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

Plants (Basel). 2023 Sep 30;12(19):3449. doi: 10.3390/plants12193449.

Authors

Chaitra C Kulkarni^{1

2

3}, Sarvamangala S Cholin^{1

3}, Akhilesh K Bajpai⁴, Gabrijel Ondrasek⁵, R K Mesta³, Santosha Rathod⁶, H B Patil³

Affiliations

¹ Plant Molecular Biology Lab (DBT-BIOCARe), Department of Biotechnology & Crop Improvement, College of Horticulture, University of Horticultural Sciences, Bagalkot 587103, Karnataka, India.
² Kittur Rani Chennamma College of Horticulture, Arabhavi, Gokak 591218, Belgaum Dt., Karnataka, India.
³ University of Horticultural Sciences, Bagalkot 587103, Karnataka, India.
⁴ Shodhaka Life Sciences Pvt. Ltd., Electronic City, Phase-I, Bengaluru 560100, Karnataka, India.
⁵ Department of Soil Amelioration, Faculty of Agriculture, University of Zagreb, 10000 Zagreb, Croatia.
⁶ Indian Institute of Rice Research, Hyderabad 500030, Telangana, India.

Abstract

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) 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.

Keywords: candidate genes; carrot; gene regulatory network; plant stress response; vascular cambium.

Grants and funding

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).