CarrotOmics: a genetics and comparative genomics database for carrot (<i>Daucus carota</i>)

Rolling, William; Senalik, Douglas; Iorizzo, Massimo; Ellison, Shelby; Deynze, Allen Van; Simon, Philipp W.

doi:10.1093/database/baac079

Cited by 8 publications

(8 citation statements)

References 50 publications

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“…As with other phytohormones, auxin plays a key role in bud dormancy in carrot taproots. The endogenous levels of auxin, ethylene, cytokinin, ABA, and gibberellic acid (GA 3 ) increase in the taproot up to harvest time and subsequently decrease upon harvest [42,43]. The changes in hormone levels facilitates a short dormancy period after harvest because of preharvest hormonal accumulation.…”

Section: Discussionmentioning

confidence: 99%

Restraining Quiescence Release-Related Ageing in Plant Cells: A Case Study in Carrot

Schulz,

Machaj,

Knox

et al. 2023

Cells

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The blackening of cut carrots causes substantial economic losses to the food industry. Blackening was not observed in carrots that had been stored underground for less than a year, but the susceptibility to blackening increased with the age of the carrots that were stored underground for longer periods. Samples of black, border, and orange tissues from processed carrot batons and slices, prepared under industry standard conditions, were analyzed to identify the molecular and metabolic mechanisms underpinning processing-induced blackening. The black tissues showed substantial molecular and metabolic rewiring and large changes in the cell wall structure, with a decreased abundance of xyloglucan, pectins (homogalacturonan, rhamnogalacturonan-I, galactan and arabinan), and higher levels of lignin and other phenolic compounds when compared to orange tissues. Metabolite profiling analysis showed that there was a major shift from primary to secondary metabolism in the black tissues, which were depleted in sugars, amino acids, and tricarboxylic acid (TCA) cycle intermediates but were rich in phenolic compounds. These findings suggest that processing triggers a release from quiescence. Transcripts encoding proteins associated with secondary metabolism were less abundant in the black tissues, but there were no increases in transcripts associated with oxidative stress responses, programmed cell death, or senescence. We conclude that restraining quiescence release alters cell wall metabolism and composition, particularly regarding pectin composition, in a manner that increases susceptibility to blackening upon processing.

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Section: Discussionmentioning

confidence: 99%

Restraining Quiescence Release-Related Ageing in Plant Cells: A Case Study in Carrot

Schulz,

Machaj,

Knox

et al. 2023

Cells

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“…For this reason, we also scored flowering at 60 DAS, which was the earliest time point at which we observed signs of flowering ( Figure 1 ) in 5% - 10% of plots in two of our three studies, and also at 100 DAS (harvest day or end of season). Phenotypic data are stored at the CarrotOmics database ( www.carrotomics.org/ ) ( Rolling et al., 2022 ).…”

Section: Methodsmentioning

confidence: 99%

“…Recognizing the need for biennial germplasm for breeding and root production in temperate climates, we partitioned some low-flowering mixtures into a predominantly biennial subcategory, which we characterize as having between 1% and 15% flowering at 60 DAS and 100 DAS ( Figure 2 , left panels). This flowering trait ontology ( Table 1 and Figure 3 ) is stored in the CarrotOmics database ( www.carrotomics.org/ ) ( Rolling et al., 2022 ).…”

Section: Methodsmentioning

confidence: 99%

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

Loarca,

Liou,

Dawson

et al. 2024

Front. Plant Sci.

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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.

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“…Additionally, the RoBuST database facilitates comparative genomic investigation of the splicing patterns of 6015 plant species' 659,369 splice signals (Bhasi et al, 2010). A comprehensive, well-curated, open-access database of carrot genomic resources called CarrotOmics (https://carrotomics.org/) is recently developed by MainLab bioinformatics, Washington State University (Rolling et al, 2022) and is timely for exploiting genomic information by…”

Section: Carrot Bioinformatics Toolsmentioning

confidence: 99%

Carrot: Breeding and Genomics

Kalia,

Singh,

et al. 2023

isvs

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The carrot (Daucus carota) is an important cool-season root vegetable grown and consumed globally. The storage root is a rich source of carotenoids, anthocyanins, dietary fiber and vitamins, besides imparting unique flavor and health benefits to consumers. Both classical and modern molecular breeding techniques have contributed to improving the productivity and quality of the crop across temperate, sub-tropical and tropical regions of the world. In this review, we briefly summarize the genetic resources available, progress in carrot breeding for yield, quality and major biotic and abiotic stresses, genomic resources and molecular breeding. The challenges and future perspectives in tropical carrot breeding for improving important traits, mainly beta-carotene, blunt root shape and scar-free smooth roots are also discussed.

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

Cited by 8 publications

References 50 publications

Restraining Quiescence Release-Related Ageing in Plant Cells: A Case Study in Carrot

Restraining Quiescence Release-Related Ageing in Plant Cells: A Case Study in Carrot

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

Carrot: Breeding and Genomics

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