Development and quality of the carrot storage root - a pan-genomics perspective

• Applicant: Professorin Agnieszka Golicz, Ph.D.
• Subject Area: Plant Breeding and Plant Pathology
• Term: since 2025
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 563531597

Structural genome rearrangements constitute a major force behind genetic innovations in plants, leading to new phenotypes. Plant pan-genomes provide a framework for systematic annotation of structural rearrangements which can subsequently be functionally validated. We hypothesize that structural genome rearrangements are the major force driving carrot domestication and improvement. Carrot (Daucus carota L.) is one of the most economically important vegetable crops cultivated in temperate climate regions. It produces a fleshy succulent edible storage root usually rich in reducing sugars and pigments (carotenoids and/or anthocyanins), very different from a thin fibrous and usually highly branched non-pigmented inedible root produced by carrot wild ancestors. We aim to perform an analysis of structural variants and develop D. carota pan-genome including representative accessions of the wild and cultivated plants. Pan-genome based GWAS and expression quantitative trait loci GWAS (eQTL-GWAS) analysis utilizing the information on structural variants, in combination with gene co-expression networks, will be used to search for hub genes governing expression of genes encoding enzymes involved in the key traits: accumulation of sugars, carotenoids and anthocyanins, providing insight to the regulation of those genes manifested by the observed root phenotype. Finally, the CRISPR/Cas system will be used to edit some of those candidate genes to reveal the effect of knock-out mutations on the expression of downstream genes. As a result of the project, the first carrot pan-genome will be developed and used to comprehensively identify and annotate transposable element-associated structural variants, innovative 3D laser scanning will be used to facilitate carrot root phenotyping, spatial transcriptomics will be performed and gene expression in different root tissues will be mapped, and master regulators of the carotenoid, anthocyanin and sugar pathways in carrot roots will be identified. The project will be realized jointly by a Polish team at the University of Agriculture in Krakow and a German team at the Justus-Liebig University, Giessen, in the years 2026-2028.

• DFG Programme: Research Grants
• International Connection: Poland
• Cooperation Partner: Professor Dr. Dariusz Grzebelus