A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

Iorizzo, Massimo; Ellison, Shelby; Senalik, Douglas; Zeng, Peng; Satapoomin, Pimchanok; Huang, Jiaying; Bowman, Megan J.; Iovene, Marina; Sanseverino, Walter; Cavagnaro, Pablo Federico; Yıldız, Mehtap; Macko-Podgórni, Alicja; Morańska, Emilia; Grzebelus, Ewa; Grzebelus, Dariusz; Ashrafi, Hamid; Zheng, Zhijun; Cheng, Shifeng; Spooner, David M.; Deynze, Allen Van; Simon, Philipp W.

doi:10.1038/ng.3565

Cited by 436 publications

(580 citation statements)

References 125 publications

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“…A cenoura (Daucus carota L.) é a principal espécie dentro da família Apiaceae, que inclui outras hortaliças, como mandioquinha-salsa, aipo, funcho, salsa, coentro, entre outras plantas medicinais ou especiarias (IORIZZO et al, 2016). No Brasil, encontra-se entre as cinco principais hortaliças cultivadas, e todo ano mais de 760 mil toneladas são colhidas em uma área de aproximadamente 24,5 mil hectares (Anuário Brasileiro de Hortaliças, 2015).…”

Section: Introductionunclassified

Divergência genética entre genótipos de cenoura através de caracteres agronômicos

Carvalho

Silva

2017

AGRO@MBIENTE ON-LINE

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Resumo: O objetivo deste trabalho foi quantificar a divergência genética entre 20 genótipos de cenoura com base em testes de agrupamento para caracteres agronômicos. O experimento foi conduzido em Brasília -DF, entre março e julho de 2013. Foram avaliados 20 genótipos de cenoura em experimento em blocos ao acaso com quatro repetições. A parcela experimental foi constituída de um canteiro com 2 x 1 m de comprimento e largura, respectivamente; o plantio foi realizado em linhas transversais ao canteiro, em espaçamento duplo, sendo 20 cm entre fileiras duplas e 10 cm entre fileiras simples. Aos 90 dias após a semeadura, foram avaliados os sintomas da queima das folhas; e aos 110 dias, realizada a colheita das plantas das parcelas e avaliados os caracteres componentes de produção e de qualidade de raízes. Foi realizada análise de variância e por meio da distância generalizada de Mahalanobis foi realizado o teste de agrupamento de Tocher e o teste de agrupamento pela ligação média entre grupos (UPGMA). A análise de variância demonstrou diferenças altamente significativas (P<0,01) para todos os caracteres, e a precisão experimental foi condizente com a relatada na literatura para esses caracteres. Houve a formação de grupos divergentes, porém, os genótipos derivados de Brasília não apresentaram divergência entre eles. Desse modo, os cruzamentos mais indicados são Kuroda ou Nantes, com genótipos derivados de Brasília, para a formação de populações com maior variabilidade genética. Palavras-chave: Daucus carota L. Distância morfológica. Dissimilaridade genética.Abstract: The aim of this study was to quantify genetic divergence among 20 carrot genotypes based on cluster analysis of their agronomic characteristics. The experiment was conducted in Brasilia -Federal District, from March to July of 2013. Twenty carrot genotypes were evaluated in a randomised block design with four replications. An experimental plot consisted of one bed with a length and width of 2 x 1 m. Planting was carried out in rows that were transversal to the bed, at a spacing of 20 cm between each set of double rows, and 10 cm between single rows. At 90 days after sowing, symptoms of leaf burn were evaluated; at 110 days, the plants were harvested, and the components of root production and quality evaluated. Variance analysis was performed, and the Tocher clustering test and the average linkage between groups (UPGMA) test were performed using the Mahalanobis generalised distance. The analysis of variance showed highly significant differences (P<0.01) for all the characteristics, and the experimental precision was consistent to that reported in the literature for these traits. Diverging groups were formed; however, the derived genotypes from Brasília showed no divergence. Kuroda or Nantes, with derived genotypes from Brasília, are therefore the most indicated crosses for the formation of populations of greater genetic variability.

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Section: Introductionunclassified

Divergência genética entre genótipos de cenoura através de caracteres agronômicos

Carvalho

Silva

2017

AGRO@MBIENTE ON-LINE

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“…A third type of DXS-like sequences is usually present in plant genomes but their enzymatic role is still unclear (Rodriguez-Concepcion and Boronat, 2015). In carrot, one gene for DXR (DCAR_026133) and four DXS-encoding genes (type I DCAR_030576, type II DCAR_009911 and DCAR_014178, and type III DCAR_022887) were recently annotated (Iorizzo et al, 2016). Interestingly, only the expression of the type I DXS gene was correlated with high carotenoid content (Iorizzo et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

“…In carrot, one gene for DXR (DCAR_026133) and four DXS-encoding genes (type I DCAR_030576, type II DCAR_009911 and DCAR_014178, and type III DCAR_022887) were recently annotated (Iorizzo et al, 2016). Interestingly, only the expression of the type I DXS gene was correlated with high carotenoid content (Iorizzo et al, 2016). In this work, we aimed to experimentally evaluate the role of DXS and DXR activities in regulating the production of MEP-derived isoprenoids in leaves and storage roots.…”

Section: Introductionmentioning

confidence: 99%

Differential Contribution of the First Two Enzymes of the MEP Pathway to the Supply of Metabolic Precursors for Carotenoid and Chlorophyll Biosynthesis in Carrot (Daucus carota)

et al. 2016

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Carotenoids and chlorophylls are photosynthetic pigments synthesized in plastids from metabolic precursors provided by the methylerythritol 4-phosphate (MEP) pathway. The first two steps in the MEP pathway are catalyzed by the deoxyxylulose 5-phosphate synthase (DXS) and reductoisomerase (DXR) enzymes. While DXS has been recently shown to be the main flux-controlling step of the MEP pathway, both DXS and DXR enzymes have been proven to be able to promote an increase in MEP-derived products when overproduced in diverse plant systems. Carrot (Daucus carota) produces photosynthetic pigments (carotenoids and chlorophylls) in leaves and in light-exposed roots, whereas only carotenoids (mainly α- and β-carotene) accumulate in the storage root in darkness. To evaluate whether DXS and DXR activities influence the production of carotenoids and chlorophylls in carrot leaves and roots, the corresponding Arabidopsis thaliana genes were constitutively expressed in transgenic carrot plants. Our results suggest that DXS is limiting for the production of both carotenoids and chlorophylls in roots and leaves, whereas the regulatory role of DXR appeared to be minor. Interestingly, increased levels of DXS (but not of DXR) resulted in higher transcript abundance of endogenous carrot genes encoding phytoene synthase, the main rate-determining enzyme of the carotenoid pathway. These results support a central role for DXS on modulating the production of MEP-derived precursors to synthesize carotenoids and chlorophylls in carrot, confirming the pivotal relevance of this enzyme to engineer healthier, carotenoid-enriched products.

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“…This indicated the AP2/EREBP gene family was well conserved in genomes of Cucurbitaceae species and A. thaliana. The conservation of TF genes including AP2/EREBP genes was already well demonstrated in many plant genomes, such as Chinese cabbage (Lee et al 2012) and carrot (Iorizzo et al 2016).…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Classification of the AP2/EREBP Gene Family in the Cucurbitaceae Species

Lee

Ali

et al. 2017

Plant Breed. Biotech.

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This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. ABSTRACT AP2/EREBP gene family consists of transcription factor genes with a conserved AP2 DNA-binding domain and is involved in various biological processes. AP2/EREBP gene families were identified through genome-wide searches in five Cucurbitaceae species including cucumber, wild cucumber, melon, watermelon, and bitter gourd, which consisted of more than 100 genes in each of the five species. The gene families were further divided into five groups including four subfamilies (ERF, DREB, AP2 and RAV) and a soloist group. Among the subfamilies, DREB subfamily which is known to be related to abiotic stress response was more analyzed and a total of 25 genes were identified as Cucurbitaceae homologues of Arabidopsis CBF/DREB1 genes which are important for abiotic stress-response and tolerance. In silico expression profiling using RNA-Seq data revealed diverse expression patterns of cucumber AP2/EREBP genes. AP2/EREBP gene families identified in this study will be valuable for understanding the stress response mechanism as well as facilitating molecular breeding in Cucurbitaceae crops.

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A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

Cited by 436 publications

References 125 publications

Divergência genética entre genótipos de cenoura através de caracteres agronômicos

Divergência genética entre genótipos de cenoura através de caracteres agronômicos

Differential Contribution of the First Two Enzymes of the MEP Pathway to the Supply of Metabolic Precursors for Carotenoid and Chlorophyll Biosynthesis in Carrot (Daucus carota)

Genome-Wide Identification and Classification of the AP2/EREBP Gene Family in the Cucurbitaceae Species

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