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Fine Mapping, Transcriptome Analysis, and Marker Development for Y(2), the Gene That Conditions β-Carotene Accumulation in Carrot (Daucus carota L.)
Domesticated carrots, Daucus carota subsp. sativus, are the richest source of β-carotene in the US diet, which, when consumed, is converted into vitamin A, an essential component of eye health and immunity. The Y(2) locus plays a significant role in beta-carotene accumulation in carrot roots, but a...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Genetics Society of America
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5555471/ https://www.ncbi.nlm.nih.gov/pubmed/28663343 http://dx.doi.org/10.1534/g3.117.043067 |
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author | Ellison, Shelby Senalik, Douglas Bostan, Hamed Iorizzo, Massimo Simon, Philipp |
author_facet | Ellison, Shelby Senalik, Douglas Bostan, Hamed Iorizzo, Massimo Simon, Philipp |
author_sort | Ellison, Shelby |
collection | PubMed |
description | Domesticated carrots, Daucus carota subsp. sativus, are the richest source of β-carotene in the US diet, which, when consumed, is converted into vitamin A, an essential component of eye health and immunity. The Y(2) locus plays a significant role in beta-carotene accumulation in carrot roots, but a candidate gene has not been identified. To advance our understanding of this locus, the genetic basis of β-carotene accumulation was explored by utilizing an advanced mapping population, transcriptome analysis, and nucleotide diversity in diverse carrot accessions with varying levels of β-carotene. A single large effect Quantitative Trait Locus (QTL) on the distal arm of chromosome 7 overlapped with the previously identified β-carotene accumulation QTL, Y(2). Fine mapping efforts reduced the genomic region of interest to 650 kb including 72 genes. Transcriptome analysis within this fine mapped region identified four genes differentially expressed at two developmental time points, and 13 genes differentially expressed at one time point. These differentially expressed genes included transcription factors and genes involved in light signaling and carotenoid flux, including a member of the Di19 gene family involved in Arabidopsis photomorphogenesis, and a homolog of the bHLH36 transcription factor involved in maize carotenoid metabolism. Analysis of nucleotide diversity in 25 resequenced carrot accessions revealed a drastic decrease in diversity of this fine-mapped region in orange cultivated accessions as compared to white and yellow cultivated and to white wild samples. The results presented in this study provide a foundation to identify and characterize the gene underlying β-carotene accumulation in carrot. |
format | Online Article Text |
id | pubmed-5555471 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Genetics Society of America |
record_format | MEDLINE/PubMed |
spelling | pubmed-55554712017-08-17 Fine Mapping, Transcriptome Analysis, and Marker Development for Y(2), the Gene That Conditions β-Carotene Accumulation in Carrot (Daucus carota L.) Ellison, Shelby Senalik, Douglas Bostan, Hamed Iorizzo, Massimo Simon, Philipp G3 (Bethesda) Investigations Domesticated carrots, Daucus carota subsp. sativus, are the richest source of β-carotene in the US diet, which, when consumed, is converted into vitamin A, an essential component of eye health and immunity. The Y(2) locus plays a significant role in beta-carotene accumulation in carrot roots, but a candidate gene has not been identified. To advance our understanding of this locus, the genetic basis of β-carotene accumulation was explored by utilizing an advanced mapping population, transcriptome analysis, and nucleotide diversity in diverse carrot accessions with varying levels of β-carotene. A single large effect Quantitative Trait Locus (QTL) on the distal arm of chromosome 7 overlapped with the previously identified β-carotene accumulation QTL, Y(2). Fine mapping efforts reduced the genomic region of interest to 650 kb including 72 genes. Transcriptome analysis within this fine mapped region identified four genes differentially expressed at two developmental time points, and 13 genes differentially expressed at one time point. These differentially expressed genes included transcription factors and genes involved in light signaling and carotenoid flux, including a member of the Di19 gene family involved in Arabidopsis photomorphogenesis, and a homolog of the bHLH36 transcription factor involved in maize carotenoid metabolism. Analysis of nucleotide diversity in 25 resequenced carrot accessions revealed a drastic decrease in diversity of this fine-mapped region in orange cultivated accessions as compared to white and yellow cultivated and to white wild samples. The results presented in this study provide a foundation to identify and characterize the gene underlying β-carotene accumulation in carrot. Genetics Society of America 2017-06-29 /pmc/articles/PMC5555471/ /pubmed/28663343 http://dx.doi.org/10.1534/g3.117.043067 Text en Copyright © 2017 Ellison et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Investigations Ellison, Shelby Senalik, Douglas Bostan, Hamed Iorizzo, Massimo Simon, Philipp Fine Mapping, Transcriptome Analysis, and Marker Development for Y(2), the Gene That Conditions β-Carotene Accumulation in Carrot (Daucus carota L.) |
title | Fine Mapping, Transcriptome Analysis, and Marker Development for Y(2), the Gene That Conditions β-Carotene Accumulation in Carrot (Daucus carota L.) |
title_full | Fine Mapping, Transcriptome Analysis, and Marker Development for Y(2), the Gene That Conditions β-Carotene Accumulation in Carrot (Daucus carota L.) |
title_fullStr | Fine Mapping, Transcriptome Analysis, and Marker Development for Y(2), the Gene That Conditions β-Carotene Accumulation in Carrot (Daucus carota L.) |
title_full_unstemmed | Fine Mapping, Transcriptome Analysis, and Marker Development for Y(2), the Gene That Conditions β-Carotene Accumulation in Carrot (Daucus carota L.) |
title_short | Fine Mapping, Transcriptome Analysis, and Marker Development for Y(2), the Gene That Conditions β-Carotene Accumulation in Carrot (Daucus carota L.) |
title_sort | fine mapping, transcriptome analysis, and marker development for y(2), the gene that conditions β-carotene accumulation in carrot (daucus carota l.) |
topic | Investigations |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5555471/ https://www.ncbi.nlm.nih.gov/pubmed/28663343 http://dx.doi.org/10.1534/g3.117.043067 |
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