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Identification of QTLs for root color and carotenoid contents in Japanese orange carrot F(2) populations

Carrot is a major source of provitamin A in a human diet. Two of the most important traits for carrot breeding are carotenoid contents and root color. To examine genomic regions related to these traits and develop DNA markers for carrot breeding, we performed an association analysis based on a gener...

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Autores principales: Shibaya, Taeko, Kuroda, Chika, Tsuruoka, Hisano, Minami, Chiharu, Obara, Akiko, Nakayama, Shinobu, Kishida, Yoshie, Fujii, Takayoshi, Isobe, Sachiko
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9110420/
https://www.ncbi.nlm.nih.gov/pubmed/35577860
http://dx.doi.org/10.1038/s41598-022-11544-7
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author Shibaya, Taeko
Kuroda, Chika
Tsuruoka, Hisano
Minami, Chiharu
Obara, Akiko
Nakayama, Shinobu
Kishida, Yoshie
Fujii, Takayoshi
Isobe, Sachiko
author_facet Shibaya, Taeko
Kuroda, Chika
Tsuruoka, Hisano
Minami, Chiharu
Obara, Akiko
Nakayama, Shinobu
Kishida, Yoshie
Fujii, Takayoshi
Isobe, Sachiko
author_sort Shibaya, Taeko
collection PubMed
description Carrot is a major source of provitamin A in a human diet. Two of the most important traits for carrot breeding are carotenoid contents and root color. To examine genomic regions related to these traits and develop DNA markers for carrot breeding, we performed an association analysis based on a general liner model using genome-wide single nucleotide polymorphism (SNPs) in two F(2) populations, both derived from crosses of orange root carrots bred in Japan. The analysis revealed 21 significant quantitative trait loci (QTLs). To validate the detection of the QTLs, we also performed a QTL analysis based on a composite interval mapping of these populations and detected 32 QTLs. Eleven of the QTLs were detected by both the association and QTL analyses. The physical position of some QTLs suggested two possible candidate genes, an Orange (Or) gene for visual color evaluation, and the α- and β-carotene contents and a chromoplast-specific lycopene β-cyclase (CYC-B) gene for the β/α carotene ratio. A KASP marker developed on the Or distinguished a quantitative color difference in a different, related breeding line. The detected QTLs and the DNA marker will contribute to carrot breeding and the understanding of carotenoid biosynthesis and accumulation in orange carrots.
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spelling pubmed-91104202022-05-18 Identification of QTLs for root color and carotenoid contents in Japanese orange carrot F(2) populations Shibaya, Taeko Kuroda, Chika Tsuruoka, Hisano Minami, Chiharu Obara, Akiko Nakayama, Shinobu Kishida, Yoshie Fujii, Takayoshi Isobe, Sachiko Sci Rep Article Carrot is a major source of provitamin A in a human diet. Two of the most important traits for carrot breeding are carotenoid contents and root color. To examine genomic regions related to these traits and develop DNA markers for carrot breeding, we performed an association analysis based on a general liner model using genome-wide single nucleotide polymorphism (SNPs) in two F(2) populations, both derived from crosses of orange root carrots bred in Japan. The analysis revealed 21 significant quantitative trait loci (QTLs). To validate the detection of the QTLs, we also performed a QTL analysis based on a composite interval mapping of these populations and detected 32 QTLs. Eleven of the QTLs were detected by both the association and QTL analyses. The physical position of some QTLs suggested two possible candidate genes, an Orange (Or) gene for visual color evaluation, and the α- and β-carotene contents and a chromoplast-specific lycopene β-cyclase (CYC-B) gene for the β/α carotene ratio. A KASP marker developed on the Or distinguished a quantitative color difference in a different, related breeding line. The detected QTLs and the DNA marker will contribute to carrot breeding and the understanding of carotenoid biosynthesis and accumulation in orange carrots. Nature Publishing Group UK 2022-05-16 /pmc/articles/PMC9110420/ /pubmed/35577860 http://dx.doi.org/10.1038/s41598-022-11544-7 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Shibaya, Taeko
Kuroda, Chika
Tsuruoka, Hisano
Minami, Chiharu
Obara, Akiko
Nakayama, Shinobu
Kishida, Yoshie
Fujii, Takayoshi
Isobe, Sachiko
Identification of QTLs for root color and carotenoid contents in Japanese orange carrot F(2) populations
title Identification of QTLs for root color and carotenoid contents in Japanese orange carrot F(2) populations
title_full Identification of QTLs for root color and carotenoid contents in Japanese orange carrot F(2) populations
title_fullStr Identification of QTLs for root color and carotenoid contents in Japanese orange carrot F(2) populations
title_full_unstemmed Identification of QTLs for root color and carotenoid contents in Japanese orange carrot F(2) populations
title_short Identification of QTLs for root color and carotenoid contents in Japanese orange carrot F(2) populations
title_sort identification of qtls for root color and carotenoid contents in japanese orange carrot f(2) populations
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9110420/
https://www.ncbi.nlm.nih.gov/pubmed/35577860
http://dx.doi.org/10.1038/s41598-022-11544-7
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