Genomic analysis of fruit size and shape traits in apple: unveiling candidate genes through GWAS analysis
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Publication date
2023-12-19ISSN
2052-7276
Abstract
Genomic tools facilitate the efficient selection of improved genetic materials within a breeding program. Here, we focus on two apple fruit quality traits: shape and size. We utilized data from 11 fruit morphology parameters gathered across three years of harvest from 355 genotypes of the apple REFPOP collection, which serves as a representative sample of the genetic variability present in European-cultivated apples. The data were then employed for genome-wide association studies (GWAS) using the FarmCPU and the BLINK models. The analysis identified 59 SNPs associated with fruit size and shape traits (35 with FarmCPU and 45 with BLINK) responsible for 71 QTNs. These QTNs were distributed across all chromosomes except for chromosomes 10 and 15. Thirty-four QTNs, identified by 27 SNPs, were related for size traits, and 37 QTNs, identified by 26 SNPs, were related to shape attributes. The definition of the haploblocks containing the most relevant SNPs served to propose candidate genes, among them the genes of the ovate family protein MdOFP17 and MdOFP4 that were in a 9.7kb haploblock on Chromosome 11. RNA-seq data revealed low or null expression of these genes in the
oblong cultivar “Skovfoged” and higher expression in the flat “Grand’mere.” The Gene Ontology enrichment analysis support a role of OFPs and hormones in shape regulation. In conclusion, this comprehensive GWAS analysis of the apple REFPOP collection has revealed promising genetic markers and candidate genes associated with apple fruit shape and size attributes, providing valuable insights that could enhance the efficiency of future breeding programs.
Document Type
Article
Document version
Published version
Language
English
Subject (CDU)
633 - Field crops and their production
Pages
14
Publisher
Oxford University Press
Is part of
Horticulture Research
Citation
Dujak, Christian, Veredas Coleto-Alcudia, and Maria José Aranzana. 2023. “Genomic Analysis of Fruit Size and Shape Traits in Apple: Unveiling Candidate Genes through GWAS Analysis.” OUP Academic. Oxford University Press. December 19. https://academic.oup.com/hr/article/11/2/uhad270/7480138.
Grant agreement number
MC/Programa Estatal para impulsar la investigación científico-técnica y su transferencia/PID2021-128885OB-I00/ES/ /
EC/H2020/817970/EU/INnovations in plant VarIety Testing in Europe to foster the introduction of new varieties better adapted to varying biotic and abiotic conditions and to more sustainable crop management practices/INVITE
MINECO/Programa Estatal de fomento de la investigación científica y técnica de excelencia/SEV-2015-0533/ES/ /
MICIU/Programa Estatal de generación del conocimiento y fortalecimiento científico y tecnológico del sistema I+D+I/CEX2019-000902-S/ES/ /
Program
Genòmica i Biotecnologia
This item appears in the following Collection(s)
- ARTICLES CIENTÍFICS [2555]
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Except where otherwise noted, this item's license is described as http://creativecommons.org/licenses/by/4.0/