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Population structure and marker–trait associations for pomological traits in peach and nectarine cultivars

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Abstract

Marker–trait associations based on populations from controlled crosses have been established in peach using markers mapped on the peach consensus map. In this study, we explored the utility of unstructured populations for association mapping to determine useful marker–trait associations in peach/nectarine cultivars. We used 94 peach cultivars representing local Spanish and modern cultivars from international breeding programs that are maintained at the Experimental Station of Aula Dei, Spain. This collection was characterized for pomological traits and was screened with 40 SSR markers that span the peach genome. Population structure analysis using STRUCTURE software identified two subpopulations, the local and modern cultivars, with admixture within both groups. The local Spanish cultivars were somewhat less diverse than modern cultivars. Marker–trait associations were determined in TASSEL with and without modelling coefficient of membership (Q) values as covariates. The results showed significant associations with pomological traits. We chose three markers on LG4 because of their proximity to the endoPG locus (freestone–melting flesh) that strongly affects pomological traits. Two genotypes of BPPCT015 marker showed significant associations with harvest date, flavonoids and sorbitol. Also, two genotypes of CPPCT028 showed associations with harvest date, total phenolics, RAC, and total sugars. Finally, two genotypes of endoPG1 showed associations with flesh firmness and total sugars. The analysis of linkage disequilibrium (LD) revealed a high level of LD up to 20 cM, and decay at farther distances. Therefore, association mapping could be a powerful tool for identifying marker–trait associations and would be useful for marker-assisted selection in peach breeding.

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Acknowledgments

We thank Blessing Athanson (Washington State University-IAREC USA), Rosa Giménez, Elvira Sierra, and Silvia Segura for technical assistance and plant management in the field. We gratefully acknowledge Dr. Chuck Brown (USDA-ARS, Prosser) for allowing us to use his ABI machine for fragment analyses and Dr. Ana Casas for assistance and support on the statistical analysis. This study was funded by the Spanish MICINN (Ministry of Science and Innovation) grants AGL-2008-00283 and RFP 2009-00016 and co-funded by FEDER and the Regional Government of Aragón (A44). C. Font was supported by a JAE-Pre fellowship from CSIC (Consejo Superior de Investigaciones Científicas) which enabled her to visit Washington State University, USA, to undertake a preliminary study of association genetics.

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Authors and Affiliations

  1. Departamento de Pomología, Estación Experimental de Aula Dei-CSIC, P.O. Box 13034, 50080, Zaragoza, Spain

    Carolina Font i Forcada, María Ángeles Moreno & Yolanda Gogorcena

  2. Irrigated Agriculture Research and Extension Center, Washington State University, 24106 N Bunn Road, Prosser, WA, 99350, USA

    Nnadozie Oraguzie

  3. Departamento de Genética y Producción Vegetal, Estación Experimental de Aula Dei-CSIC, P.O. Box 13034, 50080, Zaragoza, Spain

    Ernesto Igartua

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  1. Carolina Font i Forcada
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  2. Nnadozie Oraguzie
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  3. Ernesto Igartua
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  4. María Ángeles Moreno
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  5. Yolanda Gogorcena
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Correspondence to Yolanda Gogorcena.

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Font i Forcada, C., Oraguzie, N., Igartua, E. et al. Population structure and marker–trait associations for pomological traits in peach and nectarine cultivars. Tree Genetics & Genomes 9, 331–349 (2013). https://doi.org/10.1007/s11295-012-0553-0

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