15. Mapping and Characterizing QTL: Inbred Line Crosses

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Updated notes

Comments (and corrections) on our discussion on pages 441-442 of the Bonferroni correction from Stan Sawyer (Washington University St.Louis).
Updated reference: on F2:3 designs (p432) we give Fisch, Ragot and Gay (1996) as a reference. Stephanie Monks (Univ. Washington) reminded us that this was generalized and improved (as far as probability calculation of the QTL genotypes) by Jiang, C. and Z.-B. Zeng (1997) Mapping quantitative trait loci with dominant and missing markers in various crosses from two inbred lines. Genetica 101:47-58. A copy of the article and the abstract is available from Zhao-Bang's website.
Summary table and figures (pdf file) of roughly 100 QTL mapping experiments using inbred line crosses. These were used to generate figures 15.13 and 15.14.
LOD scores (pg. 447-448) where original introduced by Barnard (1949 J. R. Stat. Soc B 11:116-139). We introduce them in the book as log of the likelihood ratio, which is also sometimes called the backwards lod. They are also introduced as the ratio of two probabilities, and this is called the Forward lod. See Elston (1997, American Journal of Human Genetics 60:255-262) for further discussion. [Thanks to Bruce Southey, Iowa State]

Tests of Associations between QTLs detected in different experiments and QTL-Candidate locus associations

(Posted 13 May 1999)

Background: As more QTL mapping studies appear, attempts are being made to ascertain whether the same QTLs are being detected in different experiments. A related issue is testing whether mapped QTLs are nonrandomly associated with the map positions of candidate loci. Resampling tests provide a nice approach to testing for significance.

Some recent references

Keightley et al. 1998. Test of candidate trait loci in line crosses using flanking markers. Heredity 81: 630-637. [Resampling test looking at wether detected QTLs for fatness in mice are associated with the map positions of 5 candidate loci .]

Nuzhdin et al. 1998. Mapping quantitative trait loci affecting Drosophila melanogaster sternopleural bristle number using changes of marker allele frequencies in divergently selected lines. Genetical Research 72: 79--91. [Resampling test of whether detected bristle QTLs correspond to the positions of candidate genes]

Lin, Schertz, and Paterson. 1995. Comparative analysis of QTLs affecting plant height and maturity across the Poasceae, in reference to an interspecific sorghum population. Genetics 141: 391-411

Lyman and Mackay. 1998. Candidate quantitative trait loci and naturally occuring phenotypic variation for bristle number in Drosophila melanogaster: The delta-hairless gene region. Genetics 149: 983-998.

Course notes

Lecture notes from the course of Detection of QTLs and Marker-assisted Selection by J. Weller, M. Sollor, and A. B. Korol, 24 August - 7 Sept 1997, Jerusalem.

Journals

The Journal of Quantitative Trait Loci (JQTL),, an electronic journal sponsored by the Crop Science Society of America

WWW pages related to QTL mapping

Genetic Linkage Analysis Report on Quantitative Trait Loci (QTL) Mapping Software for Crosses Between Inbred Lines (From the Feb 1997 Gordon Conference), by Steve J. Knapp (ed. by Brian S. Yandell)
Brian Yandell's (U Wisconsin) Genetic Linkage Analysis Web page has lots of nice links related to linkage and gene mapping.
Carol Bult's (informatics) Quantitative Trait Locus (QTL) Mapping Resource Page

Programs

QTL Express -- Web-based user-friendly QTL mapping software from Chris Haley, Mike Kearsey, Sara Knott, George Seaton, and Peter Visscher, A simple-to-use web-based package for QTL analysis using regression interval mapping techniques. QTL Express currently supports analyses of F2 data from crosses between inbred or outbred lines, and data from outbred half-sib populations. Modules allowing analysis of other data-structures and further enhancements will be added in due course.
Special features include,

Error checking
Help files
Example data files
Marker segregation distortion test
Inclusion of fixed effects / covariates
Permutation tests to set significance thresholds
Bootstrapping to determine confidence intervals
Single and linked QTL models

QTL cartographer is a suite of programs out of North Carolina State University (by Chris Basten, Bruce Weir, and Shaobang Zeng) designed to map quantitative trait loci (QTLs) onto a genetic linkage map using linear regression and interval or composite interval mapping. It includes programs to simulate or translate data files, do analyses and reformat the analytical results for graphical presentation.

Web site
FTP site

Jim Holland's (Department of Crop Science, North Carolina State University) SAS code for testing marker pairs for QTL epistatic interactions. Reference is Journal of Heredity 1998, Vol 89:374-375.

Epistat This program from the University of Utah (by K. Chase, F. R. Alder, and K. G. Lark) for identifying and testing interactions between pairs of QTLs. Details can be found in Theoretical and Applied Genetics (1997) 94: 724--730. It runs on DOS 3.0 or higher, and more information can be found at http://208.214.31.206/epistat.htm

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Created 25 February 1995, last updated 14 April 2003

Bruce Walsh. jbwalsh@u.arizona.edu . Comments welcome.