A reproducible ddRAD-seq protocol reveals novel genomic association signatures for fruit-related traits in peach

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dc.contributor.authorKsouri, Najla
dc.contributor.authorSanchez, Gerardo
dc.contributor.authorFont i Forcada, Carolina
dc.contributor.authorContreras Moreira, Bruno
dc.contributor.authorGogorcena Aoiz, Yolanda
dc.contributor.funderAgencia Estatal de Investigación
dc.contributor.funderGobierno de Aragón
dc.contributor.orcidKsouri, Najla [0000-0001-8956-2920]
dc.date.accessioned2025-08-01T08:25:55Z
dc.date.available2025-08-01T08:25:55Z
dc.date.issued2025-07-22
dc.date.updated2025-08-01T08:08:11Z
dc.description.abstractImproving peach cultivars with superior traits is a primary objective of breeding initiatives. In this study, we aimed to elucidate the genetic basis of key agronomic and fruit-related traits using a reproducible ddRAD-seq protocol applied to a discovery panel of 90 peach accessions. Our customized workflow (available at https://github.com/najlaksouri/GWAS-Workflow) integrates three variant callers and tests up to seven models to perform a robust genome-wide association analysis (GWAS). This approach produced 13,045 high-confidence SNPs and identified Blink as the most suitable model, effectively balancing false positive and negative associations. A total of 16 significant associations signals were unveiled for six highly heritable traits (H2 > 0.5), including harvest date, fruit weight, flesh firmness, contents of flavonoids, anthocyanins and sorbitol. By assessing the allelic effect of significant markers on phenotypic attributes, nine SNP alleles were deemed favorable. Notably, a promising marker (SNC_034014.1_7012470) demonstrated simultaneous association with harvest date and fruit firmness, displaying a positive allelic effect on both traits. We anticipate that this marker can serve as a good predictor of firmer varieties. Candidate causal genes were shortlisted when fulfilling the following criteria: (i) position within the linkage disequilibrium block, (ii) functional annotation and (iii) expression pattern. A comprehensive bibliographic review of previously reported QTLs mapping nearby the associated markers allowed us to benchmark the accuracy of our approach. Despite the moderate germplasm size, ddRAD-seq allowed us to produce an accurate representation of the peach genome, resulting in SNP markers suitable for empirical association studies. Together with candidate genes, they lay the foundation for further genetic dissection of peach key traits.
dc.description.sponsorshipThis work was funded by Spanish Research Agency [grants AGL2014-52063-R, AGL2017-83358-R, PID2023-146749OB-I00 MCIN/AEI/https://doi.org/10.13039/501100011033 and by “ERDF A way of making Europe”] and the Government of Aragón [grantsA09_20R, A09_23R, A10_20R], which were co-financed with FEDER funds and the CSIC [grant2020AEP119]. N.K. was funded with a pre-doctoral contract awarded by the Government of Aragón (2018–2023) and C.F-i-F. by a JAE-Pre fellowship from CSIC (2008–2013)
dc.identifier.citationKsouri, N., Sánchez, G., Font i Forcada, C., Contreras-Moreira, B., & Gogorcena, Y. (2025). A reproducible ddRAD-seq protocol reveals novel genomic association signatures for fruit-related traits in peach. Plant Methods, 21(1), 101. https://doi.org/10.1186/s13007-025-01415-3
dc.identifier.doi10.1186/s13007-025-01415-3
dc.identifier.issn1746-4811
dc.identifier.urihttps://hdl.handle.net/10532/7730
dc.language.isoen
dc.publisherSpringer Nature
dc.relationinfo:eu-repo/grantAgreement/MINECO/Programa Programa Estatal de I+D+I Orientada a los Retos de la Sociedad/AGL2014-52063-R
dc.relationinfo:eu-repo/grantAgreement/AEI/Programa Programa Estatal de I+D+I Orientada a los Retos de la Sociedad/AGL2017-83358-R
dc.relationinfo:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PID2023-146749OB-I00
dc.relation.citaSi
dc.rightsAttribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subject.agrovocGenotipado SNP
dc.subject.agrovocLocalización de genes
dc.subject.agrovocPrunus persica
dc.subject.agrovocLigamiento genético
dc.subject.sdgHambre cero
dc.subject.sdgProducción y consumo responsables
dc.subject.sdgVida de ecosistemas terrestres
dc.titleA reproducible ddRAD-seq protocol reveals novel genomic association signatures for fruit-related traits in peach
dc.typetexto
dc.typerevista
dc.typeartículo
dc.typeartículo original
dc.type.hasVersionversión publicada

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