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Construction of high-resolution recombination maps in Asian seabass

BACKGROUND: A high-density genetic map is essential for de novo genome assembly, fine mapping QTL for important complex traits, comparative genomic studies and understanding the mechanisms of genome evolution. Although a number of genomic resources are available in Asian seabass (Lates calcarifer),...

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Autores principales: Wang, Le, Bai, Bin, Liu, Peng, Huang, Shu Qing, Wan, Zi Yi, Chua, Elaine, Ye, Baoqing, Yue, Gen Hua
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5223582/
https://www.ncbi.nlm.nih.gov/pubmed/28068919
http://dx.doi.org/10.1186/s12864-016-3462-z
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author Wang, Le
Bai, Bin
Liu, Peng
Huang, Shu Qing
Wan, Zi Yi
Chua, Elaine
Ye, Baoqing
Yue, Gen Hua
author_facet Wang, Le
Bai, Bin
Liu, Peng
Huang, Shu Qing
Wan, Zi Yi
Chua, Elaine
Ye, Baoqing
Yue, Gen Hua
author_sort Wang, Le
collection PubMed
description BACKGROUND: A high-density genetic map is essential for de novo genome assembly, fine mapping QTL for important complex traits, comparative genomic studies and understanding the mechanisms of genome evolution. Although a number of genomic resources are available in Asian seabass (Lates calcarifer), a high-density linkage map is still lacking. To facilitate QTL mapping for marker-assisted selection and genome assembly, and to understand the genome-wide recombination rates, we constructed high density linkage maps using three families and genotyping by sequencing. RESULTS: A high-density consensus linkage map consisting of 8, 274 markers was constructed based on sex-averaged genetic maps. The genetic maps were then aligned and integrated with the current genome assembly of Asian seabass. More than 90% of the genome contig sequences were anchored onto the consensus genetic map. Evidence of assembly errors in the current genome assembly was identified. A fragment of up to 2.5 Mb belonging to LG14 was assembled into Chr15. The length of family-specific sex-averaged maps ranged from 1348.96 to 1624.65 cM. Female maps were slightly longer than male maps using common markers. Female-to-male ratios were highly variable both across chromosomes within each family and throughout three families for each chromosome. However, the distribution patterns of recombination along chromosomes were similar between sexes across the whole genome. The overall recombination rates were significantly correlated with genome-wide GC content and the correlations were revealed to be stronger in females than in males. CONCLUSIONS: These high-density genetic maps provide not only essential tools for facilitating de novo genome assembly and comparative genomic studies in teleosts, but also critical resources for fine mapping QTL and genome-wide association mapping for economically important traits in Asian seabass. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-3462-z) contains supplementary material, which is available to authorized users.
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spelling pubmed-52235822017-01-11 Construction of high-resolution recombination maps in Asian seabass Wang, Le Bai, Bin Liu, Peng Huang, Shu Qing Wan, Zi Yi Chua, Elaine Ye, Baoqing Yue, Gen Hua BMC Genomics Research Article BACKGROUND: A high-density genetic map is essential for de novo genome assembly, fine mapping QTL for important complex traits, comparative genomic studies and understanding the mechanisms of genome evolution. Although a number of genomic resources are available in Asian seabass (Lates calcarifer), a high-density linkage map is still lacking. To facilitate QTL mapping for marker-assisted selection and genome assembly, and to understand the genome-wide recombination rates, we constructed high density linkage maps using three families and genotyping by sequencing. RESULTS: A high-density consensus linkage map consisting of 8, 274 markers was constructed based on sex-averaged genetic maps. The genetic maps were then aligned and integrated with the current genome assembly of Asian seabass. More than 90% of the genome contig sequences were anchored onto the consensus genetic map. Evidence of assembly errors in the current genome assembly was identified. A fragment of up to 2.5 Mb belonging to LG14 was assembled into Chr15. The length of family-specific sex-averaged maps ranged from 1348.96 to 1624.65 cM. Female maps were slightly longer than male maps using common markers. Female-to-male ratios were highly variable both across chromosomes within each family and throughout three families for each chromosome. However, the distribution patterns of recombination along chromosomes were similar between sexes across the whole genome. The overall recombination rates were significantly correlated with genome-wide GC content and the correlations were revealed to be stronger in females than in males. CONCLUSIONS: These high-density genetic maps provide not only essential tools for facilitating de novo genome assembly and comparative genomic studies in teleosts, but also critical resources for fine mapping QTL and genome-wide association mapping for economically important traits in Asian seabass. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-3462-z) contains supplementary material, which is available to authorized users. BioMed Central 2017-01-10 /pmc/articles/PMC5223582/ /pubmed/28068919 http://dx.doi.org/10.1186/s12864-016-3462-z Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Wang, Le
Bai, Bin
Liu, Peng
Huang, Shu Qing
Wan, Zi Yi
Chua, Elaine
Ye, Baoqing
Yue, Gen Hua
Construction of high-resolution recombination maps in Asian seabass
title Construction of high-resolution recombination maps in Asian seabass
title_full Construction of high-resolution recombination maps in Asian seabass
title_fullStr Construction of high-resolution recombination maps in Asian seabass
title_full_unstemmed Construction of high-resolution recombination maps in Asian seabass
title_short Construction of high-resolution recombination maps in Asian seabass
title_sort construction of high-resolution recombination maps in asian seabass
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5223582/
https://www.ncbi.nlm.nih.gov/pubmed/28068919
http://dx.doi.org/10.1186/s12864-016-3462-z
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