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Highly dense linkage maps from 31 full-sibling families of turbot (Scophthalmus maximus) provide insights into recombination patterns and chromosome rearrangements throughout a newly refined genome assembly

Highly dense linkage maps enable positioning thousands of landmarks useful for anchoring the whole genome and for analysing genome properties. Turbot is the most important cultured flatfish worldwide and breeding programs in the fifth generation of selection are targeted to improve growth rate, obta...

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Autores principales: Maroso, F, Hermida, M, Millán, A, Blanco, A, Saura, M, Fernández, A, Dalla Rovere, G, Bargelloni, L, Cabaleiro, S, Villanueva, B, Bouza, C, Martínez, P
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6105115/
https://www.ncbi.nlm.nih.gov/pubmed/29897548
http://dx.doi.org/10.1093/dnares/dsy015
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author Maroso, F
Hermida, M
Millán, A
Blanco, A
Saura, M
Fernández, A
Dalla Rovere, G
Bargelloni, L
Cabaleiro, S
Villanueva, B
Bouza, C
Martínez, P
author_facet Maroso, F
Hermida, M
Millán, A
Blanco, A
Saura, M
Fernández, A
Dalla Rovere, G
Bargelloni, L
Cabaleiro, S
Villanueva, B
Bouza, C
Martínez, P
author_sort Maroso, F
collection PubMed
description Highly dense linkage maps enable positioning thousands of landmarks useful for anchoring the whole genome and for analysing genome properties. Turbot is the most important cultured flatfish worldwide and breeding programs in the fifth generation of selection are targeted to improve growth rate, obtain disease resistant broodstock and understand sex determination to control sex ratio. Using a Restriction-site Associated DNA approach, we genotyped 18,214 single nucleotide polymorphism in 1,268 turbot individuals from 31 full-sibling families. Individual linkage maps were combined to obtain a male, female and species consensus maps. The turbot consensus map contained 11,845 markers distributed across 22 linkage groups representing a total normalised length of 3,753.9 cM. The turbot genome was anchored to this map, and scaffolds representing 96% of the assembly were ordered and oriented to obtain the expected 22 megascaffolds according to its karyotype. Recombination rate was lower in males, especially around centromeres, and pairwise comparison of 44 individual maps suggested chromosome polymorphism at specific genomic regions. Genome comparison across flatfish provided new evidence on karyotype reorganisations occurring across the evolution of this fish group.
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spelling pubmed-61051152018-08-27 Highly dense linkage maps from 31 full-sibling families of turbot (Scophthalmus maximus) provide insights into recombination patterns and chromosome rearrangements throughout a newly refined genome assembly Maroso, F Hermida, M Millán, A Blanco, A Saura, M Fernández, A Dalla Rovere, G Bargelloni, L Cabaleiro, S Villanueva, B Bouza, C Martínez, P DNA Res Full Papers Highly dense linkage maps enable positioning thousands of landmarks useful for anchoring the whole genome and for analysing genome properties. Turbot is the most important cultured flatfish worldwide and breeding programs in the fifth generation of selection are targeted to improve growth rate, obtain disease resistant broodstock and understand sex determination to control sex ratio. Using a Restriction-site Associated DNA approach, we genotyped 18,214 single nucleotide polymorphism in 1,268 turbot individuals from 31 full-sibling families. Individual linkage maps were combined to obtain a male, female and species consensus maps. The turbot consensus map contained 11,845 markers distributed across 22 linkage groups representing a total normalised length of 3,753.9 cM. The turbot genome was anchored to this map, and scaffolds representing 96% of the assembly were ordered and oriented to obtain the expected 22 megascaffolds according to its karyotype. Recombination rate was lower in males, especially around centromeres, and pairwise comparison of 44 individual maps suggested chromosome polymorphism at specific genomic regions. Genome comparison across flatfish provided new evidence on karyotype reorganisations occurring across the evolution of this fish group. Oxford University Press 2018-08 2018-06-11 /pmc/articles/PMC6105115/ /pubmed/29897548 http://dx.doi.org/10.1093/dnares/dsy015 Text en © The Author(s) 2018. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Full Papers
Maroso, F
Hermida, M
Millán, A
Blanco, A
Saura, M
Fernández, A
Dalla Rovere, G
Bargelloni, L
Cabaleiro, S
Villanueva, B
Bouza, C
Martínez, P
Highly dense linkage maps from 31 full-sibling families of turbot (Scophthalmus maximus) provide insights into recombination patterns and chromosome rearrangements throughout a newly refined genome assembly
title Highly dense linkage maps from 31 full-sibling families of turbot (Scophthalmus maximus) provide insights into recombination patterns and chromosome rearrangements throughout a newly refined genome assembly
title_full Highly dense linkage maps from 31 full-sibling families of turbot (Scophthalmus maximus) provide insights into recombination patterns and chromosome rearrangements throughout a newly refined genome assembly
title_fullStr Highly dense linkage maps from 31 full-sibling families of turbot (Scophthalmus maximus) provide insights into recombination patterns and chromosome rearrangements throughout a newly refined genome assembly
title_full_unstemmed Highly dense linkage maps from 31 full-sibling families of turbot (Scophthalmus maximus) provide insights into recombination patterns and chromosome rearrangements throughout a newly refined genome assembly
title_short Highly dense linkage maps from 31 full-sibling families of turbot (Scophthalmus maximus) provide insights into recombination patterns and chromosome rearrangements throughout a newly refined genome assembly
title_sort highly dense linkage maps from 31 full-sibling families of turbot (scophthalmus maximus) provide insights into recombination patterns and chromosome rearrangements throughout a newly refined genome assembly
topic Full Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6105115/
https://www.ncbi.nlm.nih.gov/pubmed/29897548
http://dx.doi.org/10.1093/dnares/dsy015
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