Genotyping-by-Sequencing Derived Genetic Linkage Map and Quantitative Trait Loci for Sugar Content in Onion (<i>Allium cepa</i> L.)

Onion (2n = 2x = 16) has been a nutritional, medicinal and economically valuable vegetable crop all over the world since ancient times. To accelerate the molecular breeding in onion, genetic linkage maps are prerequisite. However, construction of genetic linkage maps of onion remains relatively rudi...

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Autores principales:	Ye-Rin Lee, Cheol Woo Kim, JiWon Han, Hyun Jin Choi, Koeun Han, Eun Su Lee, Do-Sun Kim, Jundae Lee, Muhammad Irfan Siddique, Hye-Eun Lee
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	sugar content GBS genetic linkage map QTL mapping Botany QK1-989
Acceso en línea:	https://doaj.org/article/44f4629090c74efca90bc709d9dc1cfd
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spelling	oai:doaj.org-article:44f4629090c74efca90bc709d9dc1cfd2021-11-25T18:44:30ZGenotyping-by-Sequencing Derived Genetic Linkage Map and Quantitative Trait Loci for Sugar Content in Onion (<i>Allium cepa</i> L.)10.3390/plants101122672223-7747https://doaj.org/article/44f4629090c74efca90bc709d9dc1cfd2021-10-01T00:00:00Zhttps://www.mdpi.com/2223-7747/10/11/2267https://doaj.org/toc/2223-7747Onion (2n = 2x = 16) has been a nutritional, medicinal and economically valuable vegetable crop all over the world since ancient times. To accelerate the molecular breeding in onion, genetic linkage maps are prerequisite. However, construction of genetic linkage maps of onion remains relatively rudimentary due to a large genome (about 16.3 Gbp) as well as biennial life cycle, cross-pollinated nature, and high inbreeding depression. In this study, we constructed single nucleotide polymorphism (SNP)-based genetic linkage map of onion in an F<sub>2</sub> segregating population derived from a cross between the doubled haploid line ‘16P118’ and inbred line ‘Sweet Green’ through genotyping by sequencing (GBS). A total of 207.3 Gbp of raw sequences were generated using an Illumina HiSeq X system, and 24,341 SNPs were identified with the criteria based on 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 216 GBS-based SNPs were constructed comprising eight linkage groups spanning a genetic length of 827.0 cM. Furthermore, we identified the quantitative trait loci (QTLs) for the sucrose, glucose, fructose, and total sugar content across the onion genome. We identified a total of four QTLs associated with sucrose (<i>qSC4.1</i>), glucose (<i>qGC5.1</i>), fructose (<i>qFC5.1</i>), and total sugar content (<i>qTSC5.1</i>) explaining the phenotypic variation (R<sup>2</sup>%) ranging from 6.07–11.47%. This map and QTL information will contribute to develop the molecular markers to breed the cultivars with high sugar content in onion.Ye-Rin LeeCheol Woo KimJiWon HanHyun Jin ChoiKoeun HanEun Su LeeDo-Sun KimJundae LeeMuhammad Irfan SiddiqueHye-Eun LeeMDPI AGarticlesugar contentGBSgenetic linkage mapQTL mappingBotanyQK1-989ENPlants, Vol 10, Iss 2267, p 2267 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	sugar content GBS genetic linkage map QTL mapping Botany QK1-989
spellingShingle	sugar content GBS genetic linkage map QTL mapping Botany QK1-989 Ye-Rin Lee Cheol Woo Kim JiWon Han Hyun Jin Choi Koeun Han Eun Su Lee Do-Sun Kim Jundae Lee Muhammad Irfan Siddique Hye-Eun Lee Genotyping-by-Sequencing Derived Genetic Linkage Map and Quantitative Trait Loci for Sugar Content in Onion (<i>Allium cepa</i> L.)
description	Onion (2n = 2x = 16) has been a nutritional, medicinal and economically valuable vegetable crop all over the world since ancient times. To accelerate the molecular breeding in onion, genetic linkage maps are prerequisite. However, construction of genetic linkage maps of onion remains relatively rudimentary due to a large genome (about 16.3 Gbp) as well as biennial life cycle, cross-pollinated nature, and high inbreeding depression. In this study, we constructed single nucleotide polymorphism (SNP)-based genetic linkage map of onion in an F<sub>2</sub> segregating population derived from a cross between the doubled haploid line ‘16P118’ and inbred line ‘Sweet Green’ through genotyping by sequencing (GBS). A total of 207.3 Gbp of raw sequences were generated using an Illumina HiSeq X system, and 24,341 SNPs were identified with the criteria based on 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 216 GBS-based SNPs were constructed comprising eight linkage groups spanning a genetic length of 827.0 cM. Furthermore, we identified the quantitative trait loci (QTLs) for the sucrose, glucose, fructose, and total sugar content across the onion genome. We identified a total of four QTLs associated with sucrose (<i>qSC4.1</i>), glucose (<i>qGC5.1</i>), fructose (<i>qFC5.1</i>), and total sugar content (<i>qTSC5.1</i>) explaining the phenotypic variation (R<sup>2</sup>%) ranging from 6.07–11.47%. This map and QTL information will contribute to develop the molecular markers to breed the cultivars with high sugar content in onion.
format	article
author	Ye-Rin Lee Cheol Woo Kim JiWon Han Hyun Jin Choi Koeun Han Eun Su Lee Do-Sun Kim Jundae Lee Muhammad Irfan Siddique Hye-Eun Lee
author_facet	Ye-Rin Lee Cheol Woo Kim JiWon Han Hyun Jin Choi Koeun Han Eun Su Lee Do-Sun Kim Jundae Lee Muhammad Irfan Siddique Hye-Eun Lee
author_sort	Ye-Rin Lee
title	Genotyping-by-Sequencing Derived Genetic Linkage Map and Quantitative Trait Loci for Sugar Content in Onion (<i>Allium cepa</i> L.)
title_short	Genotyping-by-Sequencing Derived Genetic Linkage Map and Quantitative Trait Loci for Sugar Content in Onion (<i>Allium cepa</i> L.)
title_full	Genotyping-by-Sequencing Derived Genetic Linkage Map and Quantitative Trait Loci for Sugar Content in Onion (<i>Allium cepa</i> L.)
title_fullStr	Genotyping-by-Sequencing Derived Genetic Linkage Map and Quantitative Trait Loci for Sugar Content in Onion (<i>Allium cepa</i> L.)
title_full_unstemmed	Genotyping-by-Sequencing Derived Genetic Linkage Map and Quantitative Trait Loci for Sugar Content in Onion (<i>Allium cepa</i> L.)
title_sort	genotyping-by-sequencing derived genetic linkage map and quantitative trait loci for sugar content in onion (<i>allium cepa</i> l.)
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/44f4629090c74efca90bc709d9dc1cfd
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Genotyping-by-Sequencing Derived Genetic Linkage Map and Quantitative Trait Loci for Sugar Content in Onion (<i>Allium cepa</i> L.)

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