Construction of an Onion (<i>Allium cepa</i> L.) Genetic Linkage Map using Genotyping-by-Sequencing Analysis with a Reference Gene Set and Identification of QTLs Controlling Anthocyanin Synthesis and Content

Anthocyanins, the pigmented flavonoids responsible for red and blue colors in horticultural products, promote human health by preventing cancers and lowering the risk of cardiovascular disease. Red onions contain several cyanidin- and peonidin-based anthocyanins. In this study, we constructed a sing...

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Main Authors: Yousoo Choi, Sunggil Kim, Jundae Lee
Format: Article
Language:English
Published: MDPI AG 2020-05-01
Series:Plants
Subjects:
GBS
HRM
QTL
Online Access:https://www.mdpi.com/2223-7747/9/5/616
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spelling doaj-eb39d1f84b59401bb3530e336ede0fe42020-11-25T02:10:09ZengMDPI AGPlants2223-77472020-05-01961661610.3390/plants9050616Construction of an Onion (<i>Allium cepa</i> L.) Genetic Linkage Map using Genotyping-by-Sequencing Analysis with a Reference Gene Set and Identification of QTLs Controlling Anthocyanin Synthesis and ContentYousoo Choi0Sunggil Kim1Jundae Lee2Department of Horticulture, Institute of Agricultural Science & Technology, Jeonbuk National University, Jeonju 54896, KoreaDepartment of Plant Biotechnology, Biotechnology Research Institute, Chonnam National University, Gwangju 61186, KoreaDepartment of Horticulture, Institute of Agricultural Science & Technology, Jeonbuk National University, Jeonju 54896, KoreaAnthocyanins, the pigmented flavonoids responsible for red and blue colors in horticultural products, promote human health by preventing cancers and lowering the risk of cardiovascular disease. Red onions contain several cyanidin- and peonidin-based anthocyanins. In this study, we constructed a single-nucleotide polymorphism (SNP)-based genetic linkage map in an F<sub>2</sub> segregating population derived from a cross between the inbred line ‘SP3B’ (yellow bulb) and the doubled haploid line ‘H6′ (red bulb) to identify quantitative trait loci (QTLs) for total anthocyanin content of onion bulbs using a genotyping-by-sequencing (GBS) analysis based on a reference gene set. A total of 101.9 Gbp of raw sequences were generated using an Illumina HiSeq 2500 system and a total of 1625 SNP loci were identified with the criteria of three minimum depths, lower than 30% missing rate, and more than 5% minor allele frequency. As a result, an onion genetic linkage map consisting of 319 GBS-based SNP loci and 34 high-resolution melting (HRM) markers was constructed with eight linkage groups and a total genetic distance of 881.4 cM. In addition, the linkage groups were assigned to corresponding chromosomes by comparison with the reference genetic map OH1×5225 through marker development based on common transcripts. The analysis revealed one major QTL, <i>qAS7.1</i>, for anthocyanin synthesis and two significant QTLs, <i>qAC4.1</i> and <i>qAC4.2</i>, for anthocyanin content. The QTL <i>qAS7.1</i>, located on chromosome 7 with a phenotypic variation of 87.61%, may be a dihydroflavonol 4-reductase (<i>DFR</i>) gene that determines whether the bulb color is red or yellow. The QTLs <i>qAC4.1</i> and <i>qAC4.2</i> are separately positioned on chromosome 4 with <i>R<sup>2</sup></i> values of 19.43% and 26.28%, respectively. This map and QTL information will contribute to marker development and breeding for high anthocyanin content in bulb onion.https://www.mdpi.com/2223-7747/9/5/616anthocyaninbulb colorGBSHRMQTLtranscriptome
collection DOAJ
language English
format Article
sources DOAJ
author Yousoo Choi
Sunggil Kim
Jundae Lee
spellingShingle Yousoo Choi
Sunggil Kim
Jundae Lee
Construction of an Onion (<i>Allium cepa</i> L.) Genetic Linkage Map using Genotyping-by-Sequencing Analysis with a Reference Gene Set and Identification of QTLs Controlling Anthocyanin Synthesis and Content
Plants
anthocyanin
bulb color
GBS
HRM
QTL
transcriptome
author_facet Yousoo Choi
Sunggil Kim
Jundae Lee
author_sort Yousoo Choi
title Construction of an Onion (<i>Allium cepa</i> L.) Genetic Linkage Map using Genotyping-by-Sequencing Analysis with a Reference Gene Set and Identification of QTLs Controlling Anthocyanin Synthesis and Content
title_short Construction of an Onion (<i>Allium cepa</i> L.) Genetic Linkage Map using Genotyping-by-Sequencing Analysis with a Reference Gene Set and Identification of QTLs Controlling Anthocyanin Synthesis and Content
title_full Construction of an Onion (<i>Allium cepa</i> L.) Genetic Linkage Map using Genotyping-by-Sequencing Analysis with a Reference Gene Set and Identification of QTLs Controlling Anthocyanin Synthesis and Content
title_fullStr Construction of an Onion (<i>Allium cepa</i> L.) Genetic Linkage Map using Genotyping-by-Sequencing Analysis with a Reference Gene Set and Identification of QTLs Controlling Anthocyanin Synthesis and Content
title_full_unstemmed Construction of an Onion (<i>Allium cepa</i> L.) Genetic Linkage Map using Genotyping-by-Sequencing Analysis with a Reference Gene Set and Identification of QTLs Controlling Anthocyanin Synthesis and Content
title_sort construction of an onion (<i>allium cepa</i> l.) genetic linkage map using genotyping-by-sequencing analysis with a reference gene set and identification of qtls controlling anthocyanin synthesis and content
publisher MDPI AG
series Plants
issn 2223-7747
publishDate 2020-05-01
description Anthocyanins, the pigmented flavonoids responsible for red and blue colors in horticultural products, promote human health by preventing cancers and lowering the risk of cardiovascular disease. Red onions contain several cyanidin- and peonidin-based anthocyanins. In this study, we constructed a single-nucleotide polymorphism (SNP)-based genetic linkage map in an F<sub>2</sub> segregating population derived from a cross between the inbred line ‘SP3B’ (yellow bulb) and the doubled haploid line ‘H6′ (red bulb) to identify quantitative trait loci (QTLs) for total anthocyanin content of onion bulbs using a genotyping-by-sequencing (GBS) analysis based on a reference gene set. A total of 101.9 Gbp of raw sequences were generated using an Illumina HiSeq 2500 system and a total of 1625 SNP loci were identified with the criteria of three minimum depths, lower than 30% missing rate, and more than 5% minor allele frequency. As a result, an onion genetic linkage map consisting of 319 GBS-based SNP loci and 34 high-resolution melting (HRM) markers was constructed with eight linkage groups and a total genetic distance of 881.4 cM. In addition, the linkage groups were assigned to corresponding chromosomes by comparison with the reference genetic map OH1×5225 through marker development based on common transcripts. The analysis revealed one major QTL, <i>qAS7.1</i>, for anthocyanin synthesis and two significant QTLs, <i>qAC4.1</i> and <i>qAC4.2</i>, for anthocyanin content. The QTL <i>qAS7.1</i>, located on chromosome 7 with a phenotypic variation of 87.61%, may be a dihydroflavonol 4-reductase (<i>DFR</i>) gene that determines whether the bulb color is red or yellow. The QTLs <i>qAC4.1</i> and <i>qAC4.2</i> are separately positioned on chromosome 4 with <i>R<sup>2</sup></i> values of 19.43% and 26.28%, respectively. This map and QTL information will contribute to marker development and breeding for high anthocyanin content in bulb onion.
topic anthocyanin
bulb color
GBS
HRM
QTL
transcriptome
url https://www.mdpi.com/2223-7747/9/5/616
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