Identificación de QTL fenológicos utilizando una combinación de secuenciación del genoma completo de alta y baja cobertura en ciruelo japonés ( Prunus salicina Lindl.)

The genetic control of phenological traits in Japanese plum (Prunus salicina Lindl.) was investigated through quantitative trait loci (QTL) analysis in three segregating F1 populations: ‘Black Splendor’ × ‘Pioneer’ (BS×PIO), ‘Red Beaut’ × ‘Black Splendor’ (RB×BS), and ‘Red Beaut’ × ‘Santa Rosa Preco...

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Detalles Bibliográficos
Autores: Nicolás Almansa, María, Ruiz, David, Guevara, Alfonso, Rubio, Manuel, Martínez Gómez, Pedro, Brown, Pat J., Martínez García, Pedro J.
Tipo de recurso: artículo
Fecha de publicación:2025
País:España
Institución:Universidad Miguel Hernández de Elche
Repositorio:REDIUMH. Depósito Digital de la UMH
OAI Identifier:oai:dspace.umh.es:11000/38628
Acceso en línea:https://hdl.handle.net/11000/38628
Access Level:acceso abierto
Palabra clave:Phenology
Prunus salicina
breeding
lcWGS
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spelling Identificación de QTL fenológicos utilizando una combinación de secuenciación del genoma completo de alta y baja cobertura en ciruelo japonés ( Prunus salicina Lindl.)Nicolás Almansa, MaríaRuiz, DavidGuevara, AlfonsoRubio, ManuelMartínez Gómez, PedroBrown, Pat J.Martínez García, Pedro J.PhenologyPrunus salicinabreedinglcWGSThe genetic control of phenological traits in Japanese plum (Prunus salicina Lindl.) was investigated through quantitative trait loci (QTL) analysis in three segregating F1 populations: ‘Black Splendor’ × ‘Pioneer’ (BS×PIO), ‘Red Beaut’ × ‘Black Splendor’ (RB×BS), and ‘Red Beaut’ × ‘Santa Rosa Precoz’ (RB×SRP), comprising 121, 103, and 103 seedlings, respectively. Whole-genome sequencing (~80×) was conducted for the four parents, and progenies were genotyped using a cost-efficient reduced-representation sequencing strategy. SNPs heterozygous in one parent and homozygous in the other were used to build six parental linkage maps. Phenological traits—including beginning, full, and end of flowering (BF, FF, EF), flowering intensity (FI), ripening date (RD), fruit development period (FDP), and productivity (P)—were evaluated over three years. A total of 53 QTLs were identified for flowering stages, 16 for RD, 18 for FDP, 10 for FI, and 16 for P. Many QTLs were stable across years. Major QTLs for flowering traits were mapped to LG1, LG2, LG4, and LG6, with a strong QTL for FF on LG6 of ‘Black Splendor’. In BS×PIO, BF was uncorrelated with FF and EF, indicating distinct genetic control likely inherited from ‘Pioneer’, a low-chill cultivar. RD and FDP were consistently associated with LG4, while productivity QTLs were detected on LG1, LG2, and LG4, often overlapping, suggesting pleiotropic or tightly linked loci. In addition, candidate genes within stable QTLs were detected, providing immediate targets for functional studies. This study provides one of the first genome-wide QTL analyses of phenology in Japanese plum using low-coverage WGS (lcWGS) and offers valuable tools for marker64 assisted breeding in this speciesPrensa de la Universidad de OxfordDepartamentos de la UMH::Biología Aplicada202520252025info:eu-repo/semantics/articleapplication/pdf39application/pdfhttps://hdl.handle.net/11000/38628reponame:REDIUMH. Depósito Digital de la UMHinstname:Universidad Miguel Hernández de ElcheIngléshttps://doi.org/10.1093/hr/uhaf271info:eu-repo/semantics/openAccessAttribution-NonCommercial-NoDerivatives 4.0 Internacionalhttp://creativecommons.org/licenses/by-nc-nd/4.0/oai:dspace.umh.es:11000/386282026-05-27T13:36:21Z
dc.title.none.fl_str_mv Identificación de QTL fenológicos utilizando una combinación de secuenciación del genoma completo de alta y baja cobertura en ciruelo japonés ( Prunus salicina Lindl.)
title Identificación de QTL fenológicos utilizando una combinación de secuenciación del genoma completo de alta y baja cobertura en ciruelo japonés ( Prunus salicina Lindl.)
spellingShingle Identificación de QTL fenológicos utilizando una combinación de secuenciación del genoma completo de alta y baja cobertura en ciruelo japonés ( Prunus salicina Lindl.)
Nicolás Almansa, María
Phenology
Prunus salicina
breeding
lcWGS
title_short Identificación de QTL fenológicos utilizando una combinación de secuenciación del genoma completo de alta y baja cobertura en ciruelo japonés ( Prunus salicina Lindl.)
title_full Identificación de QTL fenológicos utilizando una combinación de secuenciación del genoma completo de alta y baja cobertura en ciruelo japonés ( Prunus salicina Lindl.)
title_fullStr Identificación de QTL fenológicos utilizando una combinación de secuenciación del genoma completo de alta y baja cobertura en ciruelo japonés ( Prunus salicina Lindl.)
title_full_unstemmed Identificación de QTL fenológicos utilizando una combinación de secuenciación del genoma completo de alta y baja cobertura en ciruelo japonés ( Prunus salicina Lindl.)
title_sort Identificación de QTL fenológicos utilizando una combinación de secuenciación del genoma completo de alta y baja cobertura en ciruelo japonés ( Prunus salicina Lindl.)
dc.creator.none.fl_str_mv Nicolás Almansa, María
Ruiz, David
Guevara, Alfonso
Rubio, Manuel
Martínez Gómez, Pedro
Brown, Pat J.
Martínez García, Pedro J.
author Nicolás Almansa, María
author_facet Nicolás Almansa, María
Ruiz, David
Guevara, Alfonso
Rubio, Manuel
Martínez Gómez, Pedro
Brown, Pat J.
Martínez García, Pedro J.
author_role author
author2 Ruiz, David
Guevara, Alfonso
Rubio, Manuel
Martínez Gómez, Pedro
Brown, Pat J.
Martínez García, Pedro J.
author2_role author
author
author
author
author
author
dc.contributor.none.fl_str_mv Departamentos de la UMH::Biología Aplicada
dc.subject.none.fl_str_mv Phenology
Prunus salicina
breeding
lcWGS
topic Phenology
Prunus salicina
breeding
lcWGS
description The genetic control of phenological traits in Japanese plum (Prunus salicina Lindl.) was investigated through quantitative trait loci (QTL) analysis in three segregating F1 populations: ‘Black Splendor’ × ‘Pioneer’ (BS×PIO), ‘Red Beaut’ × ‘Black Splendor’ (RB×BS), and ‘Red Beaut’ × ‘Santa Rosa Precoz’ (RB×SRP), comprising 121, 103, and 103 seedlings, respectively. Whole-genome sequencing (~80×) was conducted for the four parents, and progenies were genotyped using a cost-efficient reduced-representation sequencing strategy. SNPs heterozygous in one parent and homozygous in the other were used to build six parental linkage maps. Phenological traits—including beginning, full, and end of flowering (BF, FF, EF), flowering intensity (FI), ripening date (RD), fruit development period (FDP), and productivity (P)—were evaluated over three years. A total of 53 QTLs were identified for flowering stages, 16 for RD, 18 for FDP, 10 for FI, and 16 for P. Many QTLs were stable across years. Major QTLs for flowering traits were mapped to LG1, LG2, LG4, and LG6, with a strong QTL for FF on LG6 of ‘Black Splendor’. In BS×PIO, BF was uncorrelated with FF and EF, indicating distinct genetic control likely inherited from ‘Pioneer’, a low-chill cultivar. RD and FDP were consistently associated with LG4, while productivity QTLs were detected on LG1, LG2, and LG4, often overlapping, suggesting pleiotropic or tightly linked loci. In addition, candidate genes within stable QTLs were detected, providing immediate targets for functional studies. This study provides one of the first genome-wide QTL analyses of phenology in Japanese plum using low-coverage WGS (lcWGS) and offers valuable tools for marker64 assisted breeding in this species
publishDate 2025
dc.date.none.fl_str_mv 2025
2025
2025
dc.type.none.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://hdl.handle.net/11000/38628
url https://hdl.handle.net/11000/38628
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv https://doi.org/10.1093/hr/uhaf271
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
Attribution-NonCommercial-NoDerivatives 4.0 Internacional
http://creativecommons.org/licenses/by-nc-nd/4.0/
eu_rights_str_mv openAccess
rights_invalid_str_mv Attribution-NonCommercial-NoDerivatives 4.0 Internacional
http://creativecommons.org/licenses/by-nc-nd/4.0/
dc.format.none.fl_str_mv application/pdf
39
application/pdf
dc.publisher.none.fl_str_mv Prensa de la Universidad de Oxford
publisher.none.fl_str_mv Prensa de la Universidad de Oxford
dc.source.none.fl_str_mv reponame:REDIUMH. Depósito Digital de la UMH
instname:Universidad Miguel Hernández de Elche
instname_str Universidad Miguel Hernández de Elche
reponame_str REDIUMH. Depósito Digital de la UMH
collection REDIUMH. Depósito Digital de la UMH
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,811543

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