Development of whole-genome multiplex assays and construction of an integrated genetic map using SSR markers in Senegalese sole

Abstract The Senegalese sole (Solea senegalensis) is an economically important flatfish species. In this study, a genome draft was analyzed to identify microsatellite (SSR) markers for whole-genome genotyping. A subset of 224 contigs containing SSRs were preselected and validated by using a de novo...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Israel Guerrero-Cózar, Cathaysa Perez-Garcia, Hicham Benzekri, J. J. Sánchez, Pedro Seoane, Fernando Cruz, Marta Gut, Maria Jesus Zamorano, M. Gonzalo Claros, Manuel Manchado
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2020
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/622ae00987114c2381248540e95d2270
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:622ae00987114c2381248540e95d2270
record_format	dspace
spelling	oai:doaj.org-article:622ae00987114c2381248540e95d22702021-12-02T13:58:11ZDevelopment of whole-genome multiplex assays and construction of an integrated genetic map using SSR markers in Senegalese sole10.1038/s41598-020-78397-w2045-2322https://doaj.org/article/622ae00987114c2381248540e95d22702020-12-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-78397-whttps://doaj.org/toc/2045-2322Abstract The Senegalese sole (Solea senegalensis) is an economically important flatfish species. In this study, a genome draft was analyzed to identify microsatellite (SSR) markers for whole-genome genotyping. A subset of 224 contigs containing SSRs were preselected and validated by using a de novo female hybrid assembly. Overall, the SSR density in the genome was 886.7 markers per megabase of genomic sequences and the dinucleotide motif was the most abundant (52.4%). In silico comparison identified a set of 108 SSRs (with di-, tetra- or pentanucleotide motifs) widely distributed in the genome and suitable for primer design. A total of 106 markers were structured in thirteen multiplex PCR assays (with up to 10-plex) and the amplification conditions were optimized with a high-quality score. Main genetic diversity statistics and genotyping reliability were assessed. A subset of 40 high polymorphic markers were selected to optimize four supermultiplex PCRs (with up to 11-plex) for pedigree analysis. Theoretical exclusion probabilities and real parentage allocation tests using parent–offspring information confirmed their robustness and effectiveness for parental assignment. These new SSR markers were combined with previously published SSRs (in total 229 makers) to construct a new and improved integrated genetic map containing 21 linkage groups that matched with the expected number of chromosomes. Synteny analysis with respect to C. semilaevis provided new clues on chromosome evolution in flatfish and the formation of metacentric and submetacentric chromosomes in Senegalese sole.Israel Guerrero-CózarCathaysa Perez-GarciaHicham BenzekriJ. J. SánchezPedro SeoaneFernando CruzMarta GutMaria Jesus ZamoranoM. Gonzalo ClarosManuel ManchadoNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 10, Iss 1, Pp 1-16 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Israel Guerrero-Cózar Cathaysa Perez-Garcia Hicham Benzekri J. J. Sánchez Pedro Seoane Fernando Cruz Marta Gut Maria Jesus Zamorano M. Gonzalo Claros Manuel Manchado Development of whole-genome multiplex assays and construction of an integrated genetic map using SSR markers in Senegalese sole
description	Abstract The Senegalese sole (Solea senegalensis) is an economically important flatfish species. In this study, a genome draft was analyzed to identify microsatellite (SSR) markers for whole-genome genotyping. A subset of 224 contigs containing SSRs were preselected and validated by using a de novo female hybrid assembly. Overall, the SSR density in the genome was 886.7 markers per megabase of genomic sequences and the dinucleotide motif was the most abundant (52.4%). In silico comparison identified a set of 108 SSRs (with di-, tetra- or pentanucleotide motifs) widely distributed in the genome and suitable for primer design. A total of 106 markers were structured in thirteen multiplex PCR assays (with up to 10-plex) and the amplification conditions were optimized with a high-quality score. Main genetic diversity statistics and genotyping reliability were assessed. A subset of 40 high polymorphic markers were selected to optimize four supermultiplex PCRs (with up to 11-plex) for pedigree analysis. Theoretical exclusion probabilities and real parentage allocation tests using parent–offspring information confirmed their robustness and effectiveness for parental assignment. These new SSR markers were combined with previously published SSRs (in total 229 makers) to construct a new and improved integrated genetic map containing 21 linkage groups that matched with the expected number of chromosomes. Synteny analysis with respect to C. semilaevis provided new clues on chromosome evolution in flatfish and the formation of metacentric and submetacentric chromosomes in Senegalese sole.
format	article
author	Israel Guerrero-Cózar Cathaysa Perez-Garcia Hicham Benzekri J. J. Sánchez Pedro Seoane Fernando Cruz Marta Gut Maria Jesus Zamorano M. Gonzalo Claros Manuel Manchado
author_facet	Israel Guerrero-Cózar Cathaysa Perez-Garcia Hicham Benzekri J. J. Sánchez Pedro Seoane Fernando Cruz Marta Gut Maria Jesus Zamorano M. Gonzalo Claros Manuel Manchado
author_sort	Israel Guerrero-Cózar
title	Development of whole-genome multiplex assays and construction of an integrated genetic map using SSR markers in Senegalese sole
title_short	Development of whole-genome multiplex assays and construction of an integrated genetic map using SSR markers in Senegalese sole
title_full	Development of whole-genome multiplex assays and construction of an integrated genetic map using SSR markers in Senegalese sole
title_fullStr	Development of whole-genome multiplex assays and construction of an integrated genetic map using SSR markers in Senegalese sole
title_full_unstemmed	Development of whole-genome multiplex assays and construction of an integrated genetic map using SSR markers in Senegalese sole
title_sort	development of whole-genome multiplex assays and construction of an integrated genetic map using ssr markers in senegalese sole
publisher	Nature Portfolio
publishDate	2020
url	https://doaj.org/article/622ae00987114c2381248540e95d2270
work_keys_str_mv	AT israelguerrerocozar developmentofwholegenomemultiplexassaysandconstructionofanintegratedgeneticmapusingssrmarkersinsenegalesesole AT cathaysaperezgarcia developmentofwholegenomemultiplexassaysandconstructionofanintegratedgeneticmapusingssrmarkersinsenegalesesole AT hichambenzekri developmentofwholegenomemultiplexassaysandconstructionofanintegratedgeneticmapusingssrmarkersinsenegalesesole AT jjsanchez developmentofwholegenomemultiplexassaysandconstructionofanintegratedgeneticmapusingssrmarkersinsenegalesesole AT pedroseoane developmentofwholegenomemultiplexassaysandconstructionofanintegratedgeneticmapusingssrmarkersinsenegalesesole AT fernandocruz developmentofwholegenomemultiplexassaysandconstructionofanintegratedgeneticmapusingssrmarkersinsenegalesesole AT martagut developmentofwholegenomemultiplexassaysandconstructionofanintegratedgeneticmapusingssrmarkersinsenegalesesole AT mariajesuszamorano developmentofwholegenomemultiplexassaysandconstructionofanintegratedgeneticmapusingssrmarkersinsenegalesesole AT mgonzaloclaros developmentofwholegenomemultiplexassaysandconstructionofanintegratedgeneticmapusingssrmarkersinsenegalesesole AT manuelmanchado developmentofwholegenomemultiplexassaysandconstructionofanintegratedgeneticmapusingssrmarkersinsenegalesesole
_version_	1718392202940383232

Development of whole-genome multiplex assays and construction of an integrated genetic map using SSR markers in Senegalese sole

Ejemplares similares