An ultra-high density genetic map provides insights into genome synteny, recombination landscape and taproot skin color in radish (Raphanus sativus L.)

Xiaobo Luo, Liang Xu, Yan Wang, Junhui Dong, Yinglong Chen, Mingjia Tang, Lianxue Fan, Yuelin Zhu, Liwang Liu

Research output: Contribution to journalArticle

Abstract

High density genetic map are valuable approach for exploring novel genomic information, quantitative trait locus (QTL) mapping and gene discovery for economically agronomic traits in plant species. However, high-resolution genetic maps applied to gene tagging associated with important traits and examined the genomic features underlying recombination landscape in radish (Raphanus sativus) is not well documented. In this study, an ultra-high dense genetic map with 411891 SNPs covering 1306.8 cM in nine radish linkage groups (LGs) was developed by a whole genome sequencing-based approach. A total of 18 QTLs for 11 horticulture traits were detected. The map-based cloning data indicated that the R2R3-MYB transcription factor RsMYB90 was a crucial candidate gene determining the taproot skin color. Comparative genomics analysis among radish, Brassica rapa and B. oleracea genome revealed several genomic rearrangements existed in the radish genome. The highly uneven distribution of recombination was observed across the nine radish chromosomes. Totally, 504 recombination hot regions were enriched near gene promoters and terminators. The recombination rate in recombination hot regions was positively correlated with SNPs, gene density and GC content, respectively. Functional annotation indicated that genes within recombination hot regions were mainly involved in metabolic process and binding. Three QTLs for three traits were found in the recombination hot regions. The results provide novel insights into the radish genome evolution, recombination landscape and facilitate the development of effective strategies for molecular breeding by targeting and dissecting important traits in radish. This article is protected by copyright. All rights reserved.

Original languageEnglish
JournalPlant Biotechnology Journal
DOIs
Publication statusE-pub ahead of print - 20 Jun 2019

Fingerprint

Skin Pigmentation
Synteny
Raphanus
Raphanus sativus
radishes
Genetic Recombination
Genome
genome
color
genomics
quantitative trait loci
genes
Genes
Single Nucleotide Polymorphism
DNA Shuffling
Molecular Sequence Annotation
Brassica rapa
horticulture
Brassica oleracea
Quantitative Trait Loci

Cite this

@article{661cbc42a468445e9aa6868d0f8d4f98,
title = "An ultra-high density genetic map provides insights into genome synteny, recombination landscape and taproot skin color in radish (Raphanus sativus L.)",
abstract = "High density genetic map are valuable approach for exploring novel genomic information, quantitative trait locus (QTL) mapping and gene discovery for economically agronomic traits in plant species. However, high-resolution genetic maps applied to gene tagging associated with important traits and examined the genomic features underlying recombination landscape in radish (Raphanus sativus) is not well documented. In this study, an ultra-high dense genetic map with 411891 SNPs covering 1306.8 cM in nine radish linkage groups (LGs) was developed by a whole genome sequencing-based approach. A total of 18 QTLs for 11 horticulture traits were detected. The map-based cloning data indicated that the R2R3-MYB transcription factor RsMYB90 was a crucial candidate gene determining the taproot skin color. Comparative genomics analysis among radish, Brassica rapa and B. oleracea genome revealed several genomic rearrangements existed in the radish genome. The highly uneven distribution of recombination was observed across the nine radish chromosomes. Totally, 504 recombination hot regions were enriched near gene promoters and terminators. The recombination rate in recombination hot regions was positively correlated with SNPs, gene density and GC content, respectively. Functional annotation indicated that genes within recombination hot regions were mainly involved in metabolic process and binding. Three QTLs for three traits were found in the recombination hot regions. The results provide novel insights into the radish genome evolution, recombination landscape and facilitate the development of effective strategies for molecular breeding by targeting and dissecting important traits in radish. This article is protected by copyright. All rights reserved.",
author = "Xiaobo Luo and Liang Xu and Yan Wang and Junhui Dong and Yinglong Chen and Mingjia Tang and Lianxue Fan and Yuelin Zhu and Liwang Liu",
year = "2019",
month = "6",
day = "20",
doi = "10.1111/pbi.13195",
language = "English",
journal = "Plant Biotechnology Journal",
issn = "1467-7644",
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An ultra-high density genetic map provides insights into genome synteny, recombination landscape and taproot skin color in radish (Raphanus sativus L.). / Luo, Xiaobo; Xu, Liang; Wang, Yan; Dong, Junhui; Chen, Yinglong; Tang, Mingjia; Fan, Lianxue; Zhu, Yuelin; Liu, Liwang.

In: Plant Biotechnology Journal, 20.06.2019.

Research output: Contribution to journalArticle

TY - JOUR

T1 - An ultra-high density genetic map provides insights into genome synteny, recombination landscape and taproot skin color in radish (Raphanus sativus L.)

AU - Luo, Xiaobo

AU - Xu, Liang

AU - Wang, Yan

AU - Dong, Junhui

AU - Chen, Yinglong

AU - Tang, Mingjia

AU - Fan, Lianxue

AU - Zhu, Yuelin

AU - Liu, Liwang

PY - 2019/6/20

Y1 - 2019/6/20

N2 - High density genetic map are valuable approach for exploring novel genomic information, quantitative trait locus (QTL) mapping and gene discovery for economically agronomic traits in plant species. However, high-resolution genetic maps applied to gene tagging associated with important traits and examined the genomic features underlying recombination landscape in radish (Raphanus sativus) is not well documented. In this study, an ultra-high dense genetic map with 411891 SNPs covering 1306.8 cM in nine radish linkage groups (LGs) was developed by a whole genome sequencing-based approach. A total of 18 QTLs for 11 horticulture traits were detected. The map-based cloning data indicated that the R2R3-MYB transcription factor RsMYB90 was a crucial candidate gene determining the taproot skin color. Comparative genomics analysis among radish, Brassica rapa and B. oleracea genome revealed several genomic rearrangements existed in the radish genome. The highly uneven distribution of recombination was observed across the nine radish chromosomes. Totally, 504 recombination hot regions were enriched near gene promoters and terminators. The recombination rate in recombination hot regions was positively correlated with SNPs, gene density and GC content, respectively. Functional annotation indicated that genes within recombination hot regions were mainly involved in metabolic process and binding. Three QTLs for three traits were found in the recombination hot regions. The results provide novel insights into the radish genome evolution, recombination landscape and facilitate the development of effective strategies for molecular breeding by targeting and dissecting important traits in radish. This article is protected by copyright. All rights reserved.

AB - High density genetic map are valuable approach for exploring novel genomic information, quantitative trait locus (QTL) mapping and gene discovery for economically agronomic traits in plant species. However, high-resolution genetic maps applied to gene tagging associated with important traits and examined the genomic features underlying recombination landscape in radish (Raphanus sativus) is not well documented. In this study, an ultra-high dense genetic map with 411891 SNPs covering 1306.8 cM in nine radish linkage groups (LGs) was developed by a whole genome sequencing-based approach. A total of 18 QTLs for 11 horticulture traits were detected. The map-based cloning data indicated that the R2R3-MYB transcription factor RsMYB90 was a crucial candidate gene determining the taproot skin color. Comparative genomics analysis among radish, Brassica rapa and B. oleracea genome revealed several genomic rearrangements existed in the radish genome. The highly uneven distribution of recombination was observed across the nine radish chromosomes. Totally, 504 recombination hot regions were enriched near gene promoters and terminators. The recombination rate in recombination hot regions was positively correlated with SNPs, gene density and GC content, respectively. Functional annotation indicated that genes within recombination hot regions were mainly involved in metabolic process and binding. Three QTLs for three traits were found in the recombination hot regions. The results provide novel insights into the radish genome evolution, recombination landscape and facilitate the development of effective strategies for molecular breeding by targeting and dissecting important traits in radish. This article is protected by copyright. All rights reserved.

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DO - 10.1111/pbi.13195

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