Jose Luis Zambrano Mendoza, The Ohio State University
This selective mapping tutorial, presented in pdf and slideshare formats, introduces selective QTL mapping based on analysis of subsets of a population. The subsets are chosen based on genotype or phenotype. MapPop v. 1.0 software is used to select individuals based on genotype. This tutorial also includes comparison of QTL detection for maize virus resistance based on selective mapping and the whole population.
This selective mapping tutorial:
- Introduces selective mapping, and why one would want to use it
- Explains how to perform selective mapping based on phenotype and genotype using MapPop
- Provides a case study in maize that compares quantitative trait locus (QTL) detection based on all individuals in an F2 mapping population and all marker genotypes and the two selective mapping approaches
- Gallais, A., L. Moreau, and L. Charcosset. 2007. Detection of marker-QTL association by studying changing in marker frequencies with selection. Theoretical and Applied Genetics 114: 669-681. (Available online at: http://dx.doi.org/10.1007/s00122-006-0467-z) (verified 29 Nov 2011).
- Jones, M. W., M. G. Redinbaugh, R. J. Anderson, and R. Louie. 2004. Identification of quantitative trait loci controlling resistance to maize chlorotic dwarf virus. Theoretical and Applied Genetics 110: 48-57. (Available online at: http://dx.doi.org/10.1007/s00122-004-1757-y) (verified 29 Nov 2011).
- Lander, E. S., and D. Bostein. 1989. Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121: 185-199.
- Sun, Y. P., J. K. Wang, J. H. Crouch, and Y. B. Xu. 2010. Efficiency of selective genotyping for genetic analysis of complex traits and potential applications in crop improvements. Molecular Breeding 26: 493-511. (Available online at: http://dx.doi.org/10.1007/s11032-010-9390-8) (verified 29 Nov 2011).
- Vision, T. J., D. G. Brown, D. B. Shmoys, R. T. Durrett, and S. D. Tanksley. 2000. Selective mapping: A strategy for optimizing the construction of high-density linkage maps. Genetics 155: 407-420.
- Brown, D., and T. Vision. MapPop 1.0: Software for selective mapping and bin mapping [Online]. Department of Biology, The University of North Carolina at Chapel Hill. Available at: http://www.bio.unc.edu/faculty/vision/lab/mappop/manual.pdf (verified 29 Nov 2011).
- MaizeGDB: Maize genetics and genomics database [Online]. Available at: www.maizegdb.org (verified 28 Nov 2011).
Development of this page was supported in part by the National Institute of Food and Agriculture (NIFA) Solanaceae Coordinated Agricultural Project, agreement 2009-85606-05673, administered by Michigan State University. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the United States Department of Agriculture.
Selective Mapping Tutorial.pdf (1.69 MB)