ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Plant Breeding
Volume 16 - 2025 | doi: 10.3389/fpls.2025.1591861
Beyond Bloom: Validated marker-trait discovery for polyploid roses via GWAS
Provisionally accepted
- Department Molecular Plant Breeding, Leibniz University Hannover, Hanover, Germany
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Breeding roses with ideal ornamental characteristics, such as beautiful flowers, a pleasant fragrance and attractive growth characteristics, is a complex and time-consuming task that can be accelerated through the use of molecular markers. Here, we analysed nine ornamental traits in roses in a genome-wide association study using the RhWagSNP chip in a panel of 285 cultivars and varieties. For six of these traits ('Young shoot: intensity of anthocyanin coloration', 'Stem: number of prickles', 'Leaf: glossiness of upper side', 'Flower: number of petals', 'Flower: fragrance' and 'Petal: length'), we detected marker-trait associations for major QTLs, which we validated in subsequent single-marker analyses using PACE technology in independent panels of up to 182 genotypes. For two traits ('Leaf: anthocyanin coloration' and 'Leaf: intensity of green colour on the upper side'), we could not validate marker-trait associations, and for the trait 'Leaf: size', we found no significant associations at all. Loci that affect petal size, petal number and fragrance have been previously studied. We were able to detect associated markers with increased effect sizes for all three traits. Even greater effects were observed when we combined markers from independent loci for petal number and fragrance. Associated markers for some of the analysed traits largely colocalise with markers previously identified in QTL analyses of biparental populations. Our validation strategy using PACE as an alternative marker technology in independent panels and different environments supports the robustness of our data, irrespective of our limited panel sizes. For the six traits for which we could validate marker-trait associations, our data can be interpreted cautiously as indicating high complexity of inheritance, with few large-effect QTLs influencing the traits. For the other four traits, either greater genetic complexity and/or stronger environmental effects may have confounded our analyses. We believe that the markers presented here can serve as valuable tools for marker-assisted selection and for further genetic analysis of the traits we have analysed.
Keywords: MAS, SNP array, rose ornamental traits, polyploid, Molecular markers, genome-wide association studies, QTL, Breeding
Received: 11 Mar 2025; Accepted: 14 Apr 2025.
Copyright: © 2025 Patzer, Schulz, Ezeoke, Linde and Debener. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Thomas Debener, Department Molecular Plant Breeding, Leibniz University Hannover, Hanover, Germany
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