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Genetic and QTL analyses of yield and a set of physiological traits in pepper

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Abstract

An interesting strategy for improvement of a complex trait dissects the complex trait in a number of physiological component traits, with the latter having hopefully a simple genetic basis. The complex trait is then improved via improvement of its component traits. As first part of such a strategy to improve yield in pepper, we present genetic and QTL analyses for four pepper experiments. Sixteen traits were analysed for a population of 149 recombinant inbred lines, obtained from a cross between the large-fruited pepper cultivar ‘Yolo Wonder’ (YW) and the small fruited pepper ‘Criollo de Morelos 334’ (CM334). The marker data consisted of 493 markers assembled into 17 linkage groups covering 1,775 cM. The trait distributions were unimodal, although sometimes skewed. Many traits displayed heterosis and transgression. Heritabilities were high (mean 0.86, with a range between 0.43 and 0.96). A multiple QTL mapping approach per trait and environment yielded 24 QTLs. The average numbers of QTLs per trait was two, ranging between zero and six. The total explained trait variance by QTLs varied between 9 and 61 %. QTL effects differed quantitatively between environments, but not qualitatively. For stem-related traits, the trait-increasing QTL alleles came from parent CM334, while for leaf and fruit related traits the increasing QTL alleles came from parent YW. The QTLs on linkage groups 1b, 2, 3a, 4, 6 and 12 showed pleiotropic effects with patterns that were consistent with the genetic correlations. These results contribute to a better understanding of the genetics of yield-related physiological traits in pepper and represent a first step in the improvement of the target trait yield.

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Acknowledgments

The research leading to these results has received funding from the European Community’s Seventh Framework Programme (FP7/2007-2013) under grant agreement n° 211347. We thank the SPICY Industrial Advisory Board for support and discussions. Rik van Wijk and Syngenta are especially acknowledged for their highly valuable help in making available additional SNP markers that strongly improved the quality of the genetic map.

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Authors and Affiliations

  1. Biometris, Wageningen UR, P.O. Box 100, 6700 AC, Wageningen, The Netherlands

    N. A. Alimi, M. C. A. M. Bink, J. Jansen, P. C. Rodrigues, G. W. A. M. van der Heijden & F. A. van Eeuwijk

  2. INRA PACA, GAFL UR 1052, BP 94, 84143, Montfavet Cedex, France

    N. A. Alimi, M. Nicolaï, V. Lefebvre & A. Palloix

  3. Wageningen UR Greenhouse Horticulture, P.O. Box 644, 6700 AP, Wageningen, The Netherlands

    J. A. Dieleman, M. Wubs & E. Heuvelink

  4. Estación Experimental de La Fundación Cajamar, Paraje Las Palmerillas 25, 04710, El Ejido, Spain

    J. Magan

  5. Plant Research International, Wageningen UR, P.O. Box 16, 6700 AA, Wageningen, The Netherlands

    R. E. Voorrips

  6. Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Gent, Belgium

    A. Vercauteren & M. Vuylsteke

  7. Biomathematics and Statistics Scotland, JCMB, The King’s Buildings, Edinburgh, EH9 3JZ, Scotland, UK

    Y. Song & C. Glasbey

  8. Department of Atomic Physics, Budapest University of Technology and Economics, Budafoki 8, Budapest, 1111, Hungary

    A. Barocsi

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  1. N. A. Alimi
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  2. M. C. A. M. Bink
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  3. J. A. Dieleman
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  4. M. Nicolaï
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  7. J. Magan
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  8. R. E. Voorrips
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  9. J. Jansen
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  10. P. C. Rodrigues
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  11. G. W. A. M. van der Heijden
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  12. A. Vercauteren
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  14. Y. Song
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  16. A. Barocsi
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  17. V. Lefebvre
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  18. A. Palloix
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  19. F. A. van Eeuwijk
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Corresponding author

Correspondence to F. A. van Eeuwijk.

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Appendices

Appendix 1: EU-SPICY experimental set-up

See Tables 7 and 8

Table 7 Allocation of genotypes to subsets, plots and blocks in the NL experiments, including the number of genotypes (#gtp) and number of occupied plots (#plots)
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Table 8 Representation of a sample block in SP trials, xx represents the 152 genotypes replicated once each, dd are the dummy genotypes while b stands for border plants
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Appendix 2: phenotypic mean comparison

See Tables 9, 10, 11

Table 9 Phenotypic mean comparison for environment NL1
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Table 10 Phenotypic mean comparison for environment NL2
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Table 11 Phenotypic mean comparison for environment SP1
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Alimi, N.A., Bink, M.C.A.M., Dieleman, J.A. et al. Genetic and QTL analyses of yield and a set of physiological traits in pepper. Euphytica 190, 181–201 (2013). https://doi.org/10.1007/s10681-012-0767-0

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