CarrotOmics: a genetics and comparative genomics database for carrot (Daucus carota)

Authors: Rolling, William; Senalik, Douglas; IORIZZO, MASSIMO - North Carolina State University; ELLISON, SHELBY - University Of Wisconsin; VAN DEYNZE, ALLEN - University Of California, Davis; Simon, Philipp

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/20/2021
Publication Date: 9/7/2022
Citation: Rolling, W.R., Senalik, D.A., Iorizzo, M., Ellison, S., Van Deynze, A., Simon, P.W. 2022. CarrotOmics: a genetics and comparative genomics database for carrot (Daucus carota). Horticulture Research. 2022, 1-8. https://doi.org/10.1093/database/baac079.
DOI: https://doi.org/10.1093/database/baac079

Interpretive Summary: Plant germplasm evaluation and plant breeding and genetics programs generate large datasets to characterize crop traits and their genetic makeup. These big datasets, known as databases, are often grouped by the crop, or family of related crops, that have been characterized. In this manuscript we summarize a database called CarrotOmics developed for carrot and its relatives (cilantro, celery, dill, etc.). The images and genomic data generated constitutes a database that is of vital importance and interest to plant researchers, crop breeders in public and private sector, crop production and processing industries, and consumers.

Technical Abstract: CarrotOmics (https://carrotomics.org/) is a comprehensive, curated, database for genetic, genomic and phenotypic information for carrot (Daucus carota L.) germplasm. Carrot researchers have produced large genomic datasets for genomic-assisted breeding and study of the genetic underpinnings of important traits. The CarrotOmics database was developed to disseminate pertinent ‘omic’ data for these efforts. A valuable resource found on CarrotOmics is the carrot reference genome (v2.0) complete with gene predictions, gene annotation, and sequence assembly. The reference genome sequence and genic sequences can be viewed, analyzed or downloaded. Other genomic resources include descriptions of 8,626 genetic markers to 79 genetic maps and describing 341 mapped loci. There are also 27,691 phenotypic measures and descriptions from 8,368 accessions representing 929 Apiales species. This is a timely resource for the Apiaceae research community and for carrot geneticists to facilitate novel cultivar development addressing challenges including an expanding acreage in tropical climates, an evolving consumer interested in sustainably grown vegetables, and a dynamic environment due to anthropogenic climate change. Breeding efforts targeting these goals are underway; however, carrot biology; including a long generation time, outcrossing, heterozygous breeding lines, and inbreeding depression, can hamper breeding efficiency. Progress in computational analysis, phenomics, and DNA sequencing technology has vastly improved the study of economically and physiologically important traits. Carrot breeders are now positioned to apply genomic-assisted selection in breeding programs and to improve breeding efficiency and/or genetic gains. The resources on CarrotOmics will advance the study of carrot genetics, germplasm improvement, and research on Apiaceae.