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Bayesian QTL analyses using pedigreed families of an outcrossing species, with application to fruit firmness in apple

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Proof of concept of Bayesian integrated QTL analyses across pedigree-related families from breeding programs of an outbreeding species. Results include QTL confidence intervals, individuals’ genotype probabilities and genomic breeding values.

Abstract

Bayesian QTL linkage mapping approaches offer the flexibility to study multiple full sib families with known pedigrees simultaneously. Such a joint analysis increases the probability of detecting these quantitative trait loci (QTL) and provide insight of the magnitude of QTL across different genetic backgrounds. Here, we present an improved Bayesian multi-QTL pedigree-based approach on an outcrossing species using progenies with different (complex) genetic relationships. Different modeling assumptions were studied in the QTL analyses, i.e., the a priori expected number of QTL varied and polygenic effects were considered. The inferences include number of QTL, additive QTL effect sizes and supporting credible intervals, posterior probabilities of QTL genotypes for all individuals in the dataset, and QTL-based as well as genome-wide breeding values. All these features have been implemented in the FlexQTL™ software. We analyzed fruit firmness in a large apple dataset that comprised 1,347 individuals forming 27 full sib families and their known ancestral pedigrees, with genotypes for 87 SSR markers on 17 chromosomes. We report strong or positive evidence for 14 QTL for fruit firmness on eight chromosomes, validating our approach as several of these QTL were reported previously, though dispersed over a series of studies based on single mapping populations. Interpretation of linked QTL was possible via individuals’ QTL genotypes. The correlation between the genomic breeding values and phenotypes was on average 90 %, but varied with the number of detected QTL in a family. The detailed posterior knowledge on QTL of potential parents is critical for the efficiency of marker-assisted breeding.

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Acknowledgments

This study has been carried out with financial support from the Commission of the European Communities, specific research program “Quality of Life and Management of Living Resource”, QLK5-2002-01492 “High-quality Disease Resistant Apples for a Sustainable Agriculture”, coordinated by L. Gianfranceschi from the University of Milan (It.). The first author and last author also acknowledge the support from the U.S. Department of Agriculture’s National Institute of Food and Agriculture–Specialty Crops Research Initiative project, ‘‘RosBREED: Enabling marker-assisted breeding in Rosaceae’’ (2009-51181-05808) and the European Union-funded project ‘‘FruitBreedomics: Integrated approach for increasing breeding efficiency in fruit tree crops’’ (Grant #FP7- 265582; http://fruitbreedomics.com/). The first author also acknowledges the financial support from Kennisbasis project KB-17-003.01-002 Genomic breeding tools and databases. The INRA experimental unit UE-Horti is also especially thanked for strong support in orchard management and fruit harvest.

Conflict of interest

The authors declare that they have no conflict of interest.

Author information

Author notes

  1. A. B. Kouassi

    Present address: Université Félix Houphhoët-Boigny, Unité de Formation et de Recherche (UFR) ‘Biosciences’, Laboratoire de Génétique, 22BP 582 Abidjan 22, Abidjan, Côte d’Ivoire

  2. F. Mathis

    Present address: Fabienne Mathis, VEGEPOLYS, Pôle de compétitivité, 7 rue Dixmeras, 49044, Angers Cedex 01, France

  3. D. Gobbin

    Present address: Tecan Group Ltd., 8708, Männedorf, Switzerland

  4. A. Boudichevskaia

    Present address: Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Corrensstr. 3, 06466, Gatersleben, Germany

  5. F. Dunemann

    Present address: Julius Kühn-Institut, Institute for Breeding Research on Horticultural Crops, Erwin Baur Str. 27, 06484, Quedlinburg, Germany

  6. K. M. Evans

    Present address: Washington State University (WSU-TFREC), 1100 N. Western Avenue, Wenatchee, WA, 98801, USA

  7. A. Antofie

    Present address: Direction Générale Qualité et Sécurité, Métrologie Légale SPF Economie, PME, Classes Moyennes et Energie, North Gate, Bd du Roi Albert II, 16, 1000, Bruxelles, Belgium

  8. F. Rezzonico

    Present address: Research Group Environmental Genomics and Systems Biology, Institute of Natural Resource Sciences, Zürich University of Applied Sciences ZHAW, Grüental, 8820, Wädenswil, Switzerland

Authors and Affiliations

  1. Biometris, Wageningen University and Research Centre, Droevendaalsesteeg 1, P.O. Box 16, 6700 AA, Wageningen, The Netherlands

    M. C. A. M. Bink & J. Jansen

  2. Plant Breeding, Wageningen UR, Droevendaalsesteeg 1, P.O. Box 16, 6700 AA, Wageningen, The Netherlands

    M. Madduri, R. E. Voorrips & W. E. van de Weg

  3. INRA, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 Quasav, Pres L’UNAM, 49071, Beaucouzé, France

    C.-E. Durel, A. B. Kouassi, F. Laurens & F. Mathis

  4. UMR1345 Institut de Recherche en Horticulture et Semences, Université d’Angers, 49045, Angers, France

    C.-E. Durel, A. B. Kouassi & F. Laurens

  5. UMR1345 Institut de Recherche en Horticulture et Semences, AgroCampus-Ouest, 49045, Angers, France

    C.-E. Durel, A. B. Kouassi & F. Laurens

  6. Plant Pathology, Institute of Integrative Biology (IBZ), ETH Zurich, 8092, Zurich, Switzerland

    C. Gessler, D. Gobbin, F. Rezzonico & A. Patocchi

  7. Research Station Agroscope, Schloss 1, 8820, Wädenswil, Switzerland

    F. Rezzonico, A. Patocchi & M. Kellerhals

  8. Institute for Breeding Research on Horticultural Crops, Julius Kühn-Institut, Pillnitzer Platz 3a, 01326, Dresden, Germany

    A. Boudichevskaia, F. Dunemann & A. Peil

  9. Department of Experimental Design and Bioinformatics, Warsaw University of Life Sciences, SGGW, 02-776, Warsaw, Poland

    A. Nowicka

  10. Laboratory of Basic Research in Horticulture, Faculty of Horticulture, Biotechnology, and Landscape Architecture, Warsaw University of Life Sciences SGGW, 02-776, Warsaw, Poland

    B. Lata & M. Stankiewicz-Kosyl

  11. Department of Pomology, Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, SGGW, 02-776, Warsaw, Poland

    K. Jeziorek, E. Pitera, A. Soska & K. Tomala

  12. East Malling Research, New Road, East Malling, Kent, ME19 6BJ, UK

    K. M. Evans & F. Fernández-Fernández

  13. Research Centre for Agriculture and Forestry Laimburg, 39040, Vadena, BZ, Italy

    W. Guerra

  14. Research Institute of Horticulture, 96-100, Skierniewice, Poland

    M. Korbin, S. Keller, M. Lewandowski, W. Plocharski, K. Rutkowski & E. Zurawicz

  15. Department of Fruit and Woody Plant Science, Current Department of Agricultural Sciences, University of Bologna, Via Fanin 46, 40127, Bologna, Italy

    F. Costa, S. Sansavini & S. Tartarini

  16. Department of Genetics and Biology of Fruit Crops, Research and Innovation Centre, Foundation Edmund Mach, Via Mach 1, 38010, Trento, Italy

    F. Costa, M. Komjanc & D. Mott

  17. Walloon Agricultural Research Centre (CRA-W), Liroux 9, 5030, Gembloux, Belgium

    A. Antofie, M. Lateur & A. Rondia

  18. Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milan, Italy

    L. Gianfranceschi

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  1. M. C. A. M. Bink
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Corresponding author

Correspondence to M. C. A. M. Bink.

Additional information

Communicated by M. J. Sillanpaa.

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Bink, M.C.A.M., Jansen, J., Madduri, M. et al. Bayesian QTL analyses using pedigreed families of an outcrossing species, with application to fruit firmness in apple. Theor Appl Genet 127, 1073–1090 (2014). https://doi.org/10.1007/s00122-014-2281-3

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  • DOI: https://doi.org/10.1007/s00122-014-2281-3

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