Springer Nature is making SARS-CoV-2 and COVID-19 research free. View research | View latest news | Sign up for updates

QTL mapping under truncation selection in homozygous lines derived from biparental crosses

Abstract

In plant breeding, a large number of progenies that will be discarded later in the breeding process must be phenotyped and marker genotyped for conducting QTL analysis. In many cases, phenotypic preselection of lines could be useful. However, in QTL analyses even moderate preselection can have a significant effect on the power of QTL detection and estimation of effects of the target traits. In this study, we provide exact formulas for quantifying the change of allele frequencies within marker classes, expectations of marker contrasts and the variance of the marker contrasts under truncation selection, for the general case of two QTL affecting the target trait and a correlated trait. We focused on homozygous lines derived at random from biparental crosses. The effects of linkage between the marker and the QTL under selection as well as the effect of selection on a correlated trait can be quantified with the given formulas. Theoretical results clearly show that depending on the magnitude of QTL effects, high selection intensities can lead to a dramatic reduction in power of QTL detection and that approximations based on the infinitesimal model deviate substantially from exact solutions. The presented formulas are valuable for choosing appropriate selection intensity when performing QTL mapping experiments on the data on phenotypically preselected traits and enable the calculation and bias correction of the effects of QTL under selection. Application of our theory to experimental data revealed that selection-induced bias of QTL effects can be successfully corrected.

This is a preview of subscription content, log in to check access.

Fig. 1

References

  1. Bovenhuis H, Spelman R (2000) Selective genotyping to detect quantitative trait loci for multiple traits in outbred populations. J Dairy Sci 83:173

  2. Cochran W (1951) Improvement by means of selection. In: Proceedings of the second Berkeley symposium on mathematical statistics and probability, vol 8950, pp 449–470

  3. Darvasi A, Soller M (1992) Selective genotyping for determination of linkage between a marker locus and a quantitative trait locus. Theor Appl Genet 85:353–359

  4. Deuflhard P (2004) Newton methods for nonlinear problems. Affine invariance and adaptive algorithms. Springer series in computational mathematics, vol 35. Springer, Berlin

  5. Falconer D (1989) Introduction to quantitative genetics, 3rd edn. Longman Scientific & Technical, England

  6. Foody GM, Warner TA, Nellis MD (2009) The SAGE handbook of remote sensing. Sage Publications Ltd, London, pp 105–110; 297–307

  7. Frisch M, Melchinger A (2007) Variance of the parental genome contribution to inbred lines derived from biparental crosses. Genetics 176:477–488

  8. Gallais A, Moreau L, Charcosset A (2007) Detection of marker QTL associations by studying change in marker frequencies with selection. Theor Appl Genet 114:669–681

  9. Graybill F (1976) Theory and application of the linear model, 5th edn. Duxbury Press, California

  10. Haley C, Knott S (1992) A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 69:315–324

  11. Kendall M, Stuart A (1979) The advanced theory of statistics. Inference and relationship, vol 2, 4th edn. Butler and Tanner LTD, Frome and London

  12. Lander E, Botstein D (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121:185–199

  13. Lebowitz R, Soller M, Beckmann J (1987) Trait-based analyses for the detection of linkage between marker loci and quantitative trait loci in crosses between inbred lines. Theor Appl Genet 73:556–562

  14. Mackinnon M, Georges M (1992) The effects of selection on linkage analysis for quantitative traits. Genetics 132:1177–1185

  15. Martin M, Miedaner T, Dhillon BS, Ufermann U, Kessel B, Ouzunova M, Schipprack W, Melchinger AE (2011) Colocalization of QTL for Giberella ear rot resistance and low mycotoxin contamination in early European flint maize. Crop Sci 51:1935–1945

  16. Martinez O, Curnow R (1992) Estimating the locations and the sizes of the effects of quantitative trait loci using flanking markers. Theor Appl Genet 85:480–488

  17. Mood MA, Graybill AF, Boes DC (1974) Introduction to the theory of statistics, 3th edn. MacGraw-Hill Book Company, Singapore

  18. Moreau L, Charcosset A, Gallais A (2004) Experimental evaluation of several cycles of marker-assisted selection in maize. Euphytica 137:111–118

  19. Navabi A, Mather D, Bernier J, Spaner D, Atlin G (2009) QTL detection with bidirectional and unidirectional selective genotyping: marker-based and trait-based analyses. Theor Appl Genet 118:347–358

  20. Satterthwaite F (1946) An approximate distribution of estimates of variance components. Biometrics Bulletin 2:110–114

  21. Schnell F (1961) Some general formulations of linkage effects in inbreeding. Genetics 46:947–957

  22. Schön C, Utz H, Groh S, Truberg B, Openshaw S, Melchinger A (2004) Quantitative trait locus mapping based on resampling in a vast maize testcross experiment and its relevance to quantitative genetics for complex traits. Genetics 167:485–498

  23. Soller M, Brody T, Genizi A (1976) On the power of experimental designs for the detection of linkage between marker loci and quantitative loci in crosses between inbred lines. Theor Appl Genet 47:35–39

  24. Tanksley S, Nelson J (1996) Advanced backcross QTL analysis: a method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines. Theor Appl Genet 92:191–203

  25. Utz H, Melchinger A (1996) PLABQTL: a program for composite interval mapping of QTL. J Quant Trait Loci 2:1–5

Download references

Acknowledgments

This research was financed by the Deutsche Forschungsgemeinschaft (DFG) research grant SCHO 690/2-1. We are indebted to Dr. Xuefei Mi for his support in preparing the graphics. This paper is dedicated to Prof. Dr. Adolf Martin Steiner on the occasion of his 75th birthday, to whom A.E.M. and C.C.S. owe big gratitude for advice and support in their professional career.

Conflict of interest

The authors declare no conflict of interest.

Author information

Correspondence to Albrecht E. Melchinger.

Additional information

Communicated by M. Frisch.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material (DOC 601 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Melchinger, A.E., Orsini, E. & Schön, C.C. QTL mapping under truncation selection in homozygous lines derived from biparental crosses. Theor Appl Genet 124, 543–553 (2012). https://doi.org/10.1007/s00122-011-1727-0

Download citation

Keywords

  • Quantitative Trait Locus
  • Quantitative Trait Locus Analysis
  • Truncation Selection
  • Quantitative Trait Locus Mapping
  • Marker Contrast