Advancing utilization of diverse global carrot (Daucus carota L.) germplasm with flowering habit trait ontology

Abstract

Biennial vegetable crops are challenging to breed due to long breeding cycle times. At the same time, it is important to preserve a strong biennial growth habit, avoiding premature flowering that renders the crop unmarketable. Gene banks carry important genetic variation which may be essential to improve crop resilience, but these collections are underutilized due to lack of characterization for key traits like bolting tendency for biennial vegetable crops. Due to concerns about introducing undesirable traits such as premature flowering into elite germplasm, many accessions may not be considered for other key traits that benefit growers, leaving crops more vulnerable to pests, diseases, and abiotic stresses. In this study, we develop a method for characterizing flowering to identify accessions that are predominantly biennial, which could be incorporated into biennial breeding programs without substantially increasing the risk of annual growth habits. This should increase the use of these accessions if they are also sources of other important traits such as disease resistance. We developed the CarrotOmics flowering habit trait ontology and evaluated flowering habit in the largest (N=695), and most diverse collection of cultivated carrots studied to date. Over 80% of accessions were collected from the Eurasian supercontinent, which includes the primary and secondary centers of carrot diversity. We successfully identified untapped genetic diversity in biennial carrot germplasm (n=197 with 0% plants flowering) and predominantly-biennial germplasm (n=357 with <15% plants flowering). High broad-sense heritability for flowering habit (0.81 < H2< 0.93) indicates a strong genetic component of this trait, suggesting that these carrot accessions should be consistently biennial. Breeders can select biennial plants and eliminate annual plants from a predominantly biennial population. The establishment of the predominantly biennial subcategory nearly doubles the availability of germplasm with commercial potential and accounts for 54% of the germplasm collection we evaluated. This subcollection is a useful source of genetic diversity for breeders. This method could also be applied to other biennial vegetable genetic resources and to introduce higher levels of genetic diversity into commercial cultivars, to reduce crop genetic vulnerability. We encourage breeders and researchers of biennial crops to optimize this strategy for their particular crop.

Evaluation of shoot-growth variation in diverse carrot (Daucus carota L.) germplasm for genetic improvement of stand establishment

“…Consequently, flowering habit was not a criterion used in curating this cultivated diversity panel. However, flowering habit data was collected during the course of this study and is the subject of this article's companion paper (Loarca et al, 2024). A list of accessions used in this study from GRIN-Global is available (Supplementary Table 6) and raw data for each accession is available on the CarrotOmics database (Rolling et al, 2022).…”

“…Public availability of multi-year or multi-environment phenotypic data facilitates selection of accessions with desirable agronomic traits and can be used by researchers to create core collections (Berger et al, 2013;Byrne et al, 2018). The wealth of data available on this carrot germplasm collection enables identification of germplasm across a suite of agronomically important traits, such as flowering habit (Loarca et al, 2024), ALB resistance (Tas, 2016), beta-carotenes (Ellison et al, 2018), plant growth traits (Acosta-Motos et al, 2021), taproot shape (Brainard et al, 2021), antioxidant capacity (Peŕez et al, 2023), and seed germination under abiotic stress (Simon et al, 2021). While results are specific to central Wisconsin, ranked correlations were high for two out of three years of our studies.…”

“…This cultivated diversity panel was curated from a Daucus collection to increase the relevance of our germplasm evaluation to commercial breeders. In addition to variation for shoot growth phenotypes, this collection contains annual, biennial, and mixed flowering habits and has now been characterized with the CarrotOmics flowering habit trait ontology in the companion to this article (Loarca et al, 2024), in which relationships between carrot shoot vigor and flowering habit have also been elucidated. We have locally adapted accessions with consistent performance over multiple years to start breeding pools for stand establishment, thereby lowering the barrier to utilization of carrot genetic resources.…”

“…The carrot accessions (also known as plant introductions) in this study are maintained by the United States Department of Agriculture National Plant Germplasm System (USDA-NPGS), which is a major source of useful plant genetic resources (PGR) for breeding programs, and yet one of the major barriers to using PGR is accession evaluation (Byrne et al, 2018). All or parts of this global USDA germplasm collection have previously been evaluated in studies on canopy vigor (Loarca et al, 2024), core collection curation (Corak et al, 2019), demographic history of carrot domestication and breeding (Coe et al, 2023), genetic structure, phyologeny, and carotenoid presence (Ellison et al, 2018), taproot shape (Brainard et al, 2021), plant growth traits (Acosta-Motos et al, 2021), antioxidant capacity (Peŕez et al, 2023), resistance to the necrophytic fungal pathogen Alternaria dauci (Tas, 2016), and several studies on seed germination under abiotic stress (Bolton et al, 2019;Bolton and Simon, 2019;Simon, 2019;Simon et al, 2021). In addition, the collection has been used for ecogeographic variation analysis (Mezghani et al, 2019), genomic core collection curation (Corak et al, 2019), and evaluation of genomic prediction strategies (Corak et al, 2023), as well as in studies of carrot CWR on subspecies identification (Spooner et al, 2014).…”