Molecular Breeding

, Volume 29, Issue 3, pp 661–673 | Cite as

On the use of mathematically-derived traits in QTL mapping

  • Yu Wang
  • Huihui Li
  • Luyan Zhang
  • Wenyan Lü
  • Jiankang Wang


Mathematically-derived traits from two or more component traits, either by addition, subtraction, multiplication, or division, have been frequently used in genetics and breeding. When used in quantitative trait locus (QTL) mapping, derived traits sometimes show discrepancy with QTL identified for the component traits. We used three QTL distributions and three genetic effects models, and an actual maize mapping population, to investigate the efficiency of using derived traits in QTL mapping, and to understand the genetic and biological basis of derived-only QTL, i.e., QTL identified for a derived trait but not for any component trait. Results indicated that the detection power of the four putative QTL was consistently greater than 90% for component traits in simulated populations, each consisting of 200 recombinant inbred lines. Lower detection power and higher false discovery rate (FDR) were observed when derived traits were used. In an actual maize population, simulations were designed based on the observed QTL distributions and effects. When derived traits were used, QTL detected for both component and derived traits had comparable power, but those detected for component traits but not for derived traits had low detection power. The FDR from subtraction and division in the maize population were higher than the FDR from addition and multiplication. The use of derived traits increased the gene number, caused higher-order gene interactions than observed in component traits, and possibly complicated the linkage relationship between QTL as well. The increased complexity of the genetic architecture with derived traits may be responsible for the reduced detection power and the increased FDR. Derived-only QTL identified in practical genetic populations can be explained either as minor QTL that are not significant in QTL mapping of component traits, or as false positives.


Derived trait Component trait QTL mapping Power analysis 



This work was supported by the National 973 Program of China (Project no. 2011CB100100), and the Natural Science Foundation of China (Project no. 31000540).

Supplementary material

11032_2011_9580_MOESM1_ESM.doc (3.6 mb)
Supplementary material 1 (DOC 3648 kb)


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Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Yu Wang
    • 1
    • 2
  • Huihui Li
    • 2
  • Luyan Zhang
    • 2
  • Wenyan Lü
    • 1
  • Jiankang Wang
    • 2
  1. 1.College of AgronomyShenyang Agricultural UniversityLiaoningChina
  2. 2.Institute of Crop ScienceThe National Key Facility for Crop Gene Resources and Genetic Improvement, and CIMMYT China, Chinese Academy of Agricultural SciencesBeijingChina

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