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Connected populations for detecting quantitative trait loci and testing for epistasis: an application in maize


Quantitative trait loci (QTL) detection experiments have often been restricted to large biallelic populations. Use of connected multiparental crosses has been proposed to increase the genetic variability addressed and to test for epistatic interactions between QTL and the genetic background. We present here the results of a QTL detection performed on six connected F2 populations of 150 F2:3 families each, derived from four maize inbreds and evaluated for three traits of agronomic interest. The QTL detection was carried out by composite interval mapping on each population separately, then on the global design either by taking into account the connections between populations or not. Epistatic interactions between loci and with the genetic background were tested. Taking into account the connections between populations increased the number of QTL detected and the accuracy of QTL position estimates. We detected many epistatic interactions, particularly for grain yield QTL (R 2 increase of 9.6%). Use of connections for the QTL detection also allowed a global ranking of alleles at each QTL. Allelic relationships and epistasis both contribute to the lack of consistency for QTL positions observed among populations, in addition to the limited power of the tests. The potential benefit of assembling favorable alleles by marker-assisted selection are discussed.

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This research program was funded by INRA and Agriobtention. We are grateful to our colleagues involved in marker analyses at le Moulon (D. Madur, V. Combes, F. Dumas), and colleagues involved in material production and field testing at INRA le Moulon (P. Bertin, P. Jamin, D. Coubriche, S. Jouanne), at INRA Dreux, at INRA Rennes, at INRA Lusignan and at INRA Mons. We also thank the BIA unit at INRA Toulouse for the maintenance of MCQTL software (B. Mangin, B. Ngom, J. Marcel). We are grateful to Guy Decoux for the informatic program used for the graphical display of the maps. We are grateful to Rex Bernardo for very helpful advices on the writing of this manuscript.

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Correspondence to L. Moreau.

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Communicated by J.-L. Jannink

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Blanc, G., Charcosset, A., Mangin, B. et al. Connected populations for detecting quantitative trait loci and testing for epistasis: an application in maize. Theor Appl Genet 113, 206–224 (2006). https://doi.org/10.1007/s00122-006-0287-1

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  • Quantitative Trait Locus
  • Epistatic Interaction
  • Epistatic Effect
  • Quantitative Trait Locus Effect
  • Allelic Effect