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Construction of a high-resolution genetic map and identification of single nucleotide polymorphism markers relevant to flower stalk height in onion

INTRODUCTION: Onion (Allium cepa L., 2n=16) is an economically and nutritionally important vegetable crop worldwide. Construction of a high-resolution genetic map and map-based gene mining in onion have lagged behind other vegetable crops such as tomato and pepper. METHODS: In this study, we constru...

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Autores principales: Li, Yanwei, Huo, Yumeng, Yang, Yanyan, Wang, Zhenbao, Sun, Yaling, Liu, Bingjiang, Wu, Xiong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9928573/
https://www.ncbi.nlm.nih.gov/pubmed/36818885
http://dx.doi.org/10.3389/fpls.2023.1100691
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author Li, Yanwei
Huo, Yumeng
Yang, Yanyan
Wang, Zhenbao
Sun, Yaling
Liu, Bingjiang
Wu, Xiong
author_facet Li, Yanwei
Huo, Yumeng
Yang, Yanyan
Wang, Zhenbao
Sun, Yaling
Liu, Bingjiang
Wu, Xiong
author_sort Li, Yanwei
collection PubMed
description INTRODUCTION: Onion (Allium cepa L., 2n=16) is an economically and nutritionally important vegetable crop worldwide. Construction of a high-resolution genetic map and map-based gene mining in onion have lagged behind other vegetable crops such as tomato and pepper. METHODS: In this study, we constructed a high-resolution genetic map of onion using 321 F2 individuals from a cross between two double haploid lines DH-1×DH-17 and employing specific length amplified fragment (SLAF)-seq technology. The genetic map containing 10,584 polymorphic SLAFs with 21,250 single nucleotide polymorphism (SNP) markers and 8 linkage groups was developed for onion, which spanned 928.32 cM, with an average distance of 0.09 cM between adjacent markers. RESULTS: Using this map, we carried out QTL mapping of Ms locus related to the male-fertile trait and reproduced previous mapping results, which proved that this map was of good quality. Then, four QTLs (located on LG2, LG5, and LG8) were detected for flower stalk height, explaining 26.60% of the phenotypic variance. Among them, we proposed that 20 SLAF markers (in three QTLs) of flower stalk height trait were effective favorable allelic variant markers associated with heterosis. DISCUSSION: Overall, the genetic map was structured using SLAF-seq based on DH lines, and it is the highest-quality and highest-resolution linkage map of onion to date. It lays a foundation for the fine mapping and candidate gene identification of flower stalk height, and provides new insights into the developmental genetic mechanisms in onion breeding.
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spelling pubmed-99285732023-02-16 Construction of a high-resolution genetic map and identification of single nucleotide polymorphism markers relevant to flower stalk height in onion Li, Yanwei Huo, Yumeng Yang, Yanyan Wang, Zhenbao Sun, Yaling Liu, Bingjiang Wu, Xiong Front Plant Sci Plant Science INTRODUCTION: Onion (Allium cepa L., 2n=16) is an economically and nutritionally important vegetable crop worldwide. Construction of a high-resolution genetic map and map-based gene mining in onion have lagged behind other vegetable crops such as tomato and pepper. METHODS: In this study, we constructed a high-resolution genetic map of onion using 321 F2 individuals from a cross between two double haploid lines DH-1×DH-17 and employing specific length amplified fragment (SLAF)-seq technology. The genetic map containing 10,584 polymorphic SLAFs with 21,250 single nucleotide polymorphism (SNP) markers and 8 linkage groups was developed for onion, which spanned 928.32 cM, with an average distance of 0.09 cM between adjacent markers. RESULTS: Using this map, we carried out QTL mapping of Ms locus related to the male-fertile trait and reproduced previous mapping results, which proved that this map was of good quality. Then, four QTLs (located on LG2, LG5, and LG8) were detected for flower stalk height, explaining 26.60% of the phenotypic variance. Among them, we proposed that 20 SLAF markers (in three QTLs) of flower stalk height trait were effective favorable allelic variant markers associated with heterosis. DISCUSSION: Overall, the genetic map was structured using SLAF-seq based on DH lines, and it is the highest-quality and highest-resolution linkage map of onion to date. It lays a foundation for the fine mapping and candidate gene identification of flower stalk height, and provides new insights into the developmental genetic mechanisms in onion breeding. Frontiers Media S.A. 2023-01-31 /pmc/articles/PMC9928573/ /pubmed/36818885 http://dx.doi.org/10.3389/fpls.2023.1100691 Text en Copyright © 2023 Li, Huo, Yang, Wang, Sun, Liu and Wu https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Li, Yanwei
Huo, Yumeng
Yang, Yanyan
Wang, Zhenbao
Sun, Yaling
Liu, Bingjiang
Wu, Xiong
Construction of a high-resolution genetic map and identification of single nucleotide polymorphism markers relevant to flower stalk height in onion
title Construction of a high-resolution genetic map and identification of single nucleotide polymorphism markers relevant to flower stalk height in onion
title_full Construction of a high-resolution genetic map and identification of single nucleotide polymorphism markers relevant to flower stalk height in onion
title_fullStr Construction of a high-resolution genetic map and identification of single nucleotide polymorphism markers relevant to flower stalk height in onion
title_full_unstemmed Construction of a high-resolution genetic map and identification of single nucleotide polymorphism markers relevant to flower stalk height in onion
title_short Construction of a high-resolution genetic map and identification of single nucleotide polymorphism markers relevant to flower stalk height in onion
title_sort construction of a high-resolution genetic map and identification of single nucleotide polymorphism markers relevant to flower stalk height in onion
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9928573/
https://www.ncbi.nlm.nih.gov/pubmed/36818885
http://dx.doi.org/10.3389/fpls.2023.1100691
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