Quantitative Genetics Resources (original) (raw)

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This list of resources is maintained as an electronic supplement to our forthcoming two volume textbook on Quantitative Genetics to be published by Sinauer Associates. Links to web pages, particular programs, and notes/comments on all issues in quantitative genetics (i.e., animal breeding, plant breeding, evolutionary genetics, human genetics) can be found under the appropriate chapters for each volume.

The authors are Mike Lynch(in the Department of Biology at Indiana University at Bloomington) and myself ( Bruce Walsh in the Department of Ecology and Evolutionary Biology at the University of Arizona). E-mail the authors.

• Home pages for our two volumes. (Links to programs, ftp sites, and web pages, as well as notes giving updated material are given in the webpage for the appropriate chapter.)
  1. Genetics and Analysis of Quantitative Traits
  2. Evolution and Selection of Quantitative Traits
• List of Quantitative Genetic Websites
  1. Online Class Notes
  2. Genomes
  3. Software
  4. Meetings
  5. Advanced Classes/Workshops
  6. Quantitative-Genetics related listserves
  7. Directories for Finding People
  8. Animal Breeding and Genetics
  9. Plant Breeding
  10. Forest Breeding
  11. Evolution
  12. Human Genetics
  13. Departments and Programs
  14. Journals
  15. Searchable bibliographices
• Class notes for Genetics 320 (general information about genetics).

Volume 1: Genetics and Analysis of Quantitative Traits

Published December 1997. Deals with basic biology and estimation of quantitiative characters.

Expanded Table of Contents

Current list of Typos and Other Still Errors (last updated 25 August 2003)

• Sorted by date reported

Details and Ordering information

Topics Covered (Complete list of chapters)

• Resemblance between relatives
• Genetic variance components
• Detecting major genes
• Polygenes and polygenetic mutation
• QTL mapping in inbred and outbred populations
• Line cross analysis, inbreeding and outbreeding depression
• Distribution theory, matrix methods, scaling and transformation
• Estimation: regression, ANOVA, BLUP, and REML
• Sibs, dialleles, correlated characters, GxE, maternal effects, sex-linked, threshold characters

For updates, programs, notes on new material, see the webpage for the appropriate chapter

Comments to the publisher from original reviewers of the manuscript (W. G. Hill, James Crow, Ruth Shaw) Reviews: Warren Ewens, American Journal of Human Biology 11: 798-800. [ review Trudy MacKay, Evolution 53: 307-309. [ review ] Jim Cheverud, Am. J. Phys. Anthrop. 108: 375-376. [ review ] J. J. Colleau, Genetics, Selection, Evolution 30: 203-204. [ review ] Nick Barton, Genetical Research 72: 73. [ review ] Paul Siegel, Journal of Heredity 90: 256-257. [ review ] Mary Marazita, Trends in Genetics 15: 120. [ review ] Outi Savolainen, Forest Genetics 6: 88 [ review ] William A. Nelson and Elizabeth E. Crone, The Quarterly Review of Biology 74: 225. [review ] Christopher Basten, Theoretical Population Biology 57: 307 [review ] Suzanne Leal, American Journal of Human Genetics 68: 548-549. [ review ]

Courses using Volume 1 (partial list):

[ Please drop us an e-mail so we can add your course to this list! ]

1. BioStatistics 578, Statistical Methods in Quantitative Genetics. Stephanie Monks, University of Washington (Winter Quarter, 2000).
2. Biometrical Genetics and Plant Breeding, Chris Cramer, New Mexico State University.
3. Module 8: Quantitative Trait Gene Mapping I, NCSU Summer Institute in Statistical Genetics, Z-B. Zeng, C. J. Basten, and R. Doerge.
4. Module 10: Quantitative Trait Gene Mapping II , NCSU Summer Institute in Statistical Genetics, Z-B Zeng, C.J. Basten, B. Yandell and I. Hoeschele.
5. Short Course in QTL mapping, as part of the Quantitative Genetics and Genome Analysis MSc degree at the University of Edinburgh. S. Knott (and others).

Volume 2: Evolution and Selection of Quantitative Traits

This is about 70 percent finished) will follow, and deals with natural and artificial selection on quantitative characters. Draft chapters can be downloaded from the Vol. 2 webpage.

Topics Covered (Complete list of chapters)

• Genetic drift, including changes in non-additive variances
• Selection theory: changes in means and variances, short and long-term response, effects of finite population size, index selection.
• Measuring selection in natural populations
• Phenotypic evolution models: applications to ecology, paleobiology, marcoevolution, sexual selection
• Maintenance of quantitative genetic variability

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Notes on Program Links

• Most programs are listed under the appropriate chapters.
• There is a seperate list of general-purpose educational programs .
• Only programs that are available free to the general community will be listed!!
• To include your listing or report of errors, please e-mail me. Thanks!

Recent Books on Quantitative Genetics

Recent books not cited in our book.

• Gallais, A. 2003. Quantitative Genetics and Breeding Methods in Autopolyploid Plants INRA, Paris 513 pp.
• Sorensen, D., and D. Gianola. 2002 Likelihood, Bayesian, and MCMC Methods in Quantitative Genetics. Springer 739 pp. ISBN 0-387-95440-6. $89.95 webpage
• Bernardo, Rex 2002Breeding for Quantitative Traits in Plants. Stemma Press 369 pp. ISBN 0-9720724-0-5. $65. Webpage
• Knoury, Muin J., Terri H. Beaty, and Bernice H. Cohen. 1993.Fundamentals of Genetic Epidemiology. Oxford. 383 pp. ISBN 0-19-505288-9. $59.50
• Lange, K. 1997. Mathematical and statistical methods for genetic analysis. Springer. 288PP. HARDCOVER $54.95 ISBN 0-387-94909-7 (Available at amazon.com)
  • An excellent short text with a strong emphasis on probablistic and statistical issues, with a focus on human applications.
  • **Introduction:**During the past decade, geneticists have constructed detailed maps of the human genome and cloned scores of Mendelian disease genes. They now stand on the threshold of sequencing the genome in its entirety. The unprecedented insights into human disease and evolution offered by mapping and sequencing will transform medicine and agriculture. This revolution depends vitally on the contributions of applied mathematicians, statisticians, and computer scientists.Mathematical and Statistical Methods for Genetic Analysis is written to equip graduate students in the mathematical sciences to understand and model the epidemiological and experimental data encountered in genetics research. Mathematical, statistical, and computational principles relevant to this task are developed hand in hand with applications to gene mapping, risk prediction, and the testing of epidemiological hypotheses. The book includes many topics currently accessible only in journal articles, including pedigree analysis algorithms, Markov chain Monte Carlo methods, reconstruction of evolutionary trees, radiation hybrid mapping, and models of recombination. Exercise sets are included.
  • **Contents:**1. Basic principles of population genetics; 2. Counting methods and the EM algorithm; 3. Newton's method and scoring; 4. Hypothesis testing and categorical data; 5; Genetic identity coefficients; 6. Applications of identity coefficients; 7. Computation of Mendelian likelihoods; 8. The polygenic model; 9. Markov chain Monte Carlo methods; 10. Reconstruction of evolutionary trees; 11. Radiation hybrid mapping; 12. Models of recombination; 13. Poisson approximation; Appendix A: Molecular genetics in brief.
• Simm, G. 1998. Genetic Improvement of Cattle and Sheep. Farming Press. ISBN 0-85236-351-6. Softcover $49.95 (Available at amazon.com, search on title, not author)
• Haines, J. L. and M. A. Pericak-Vance (eds). 1998 .Approaches to Gene Mapping in Complex Human Diseases . ISBN 0-471-17195-6. Softcover $79.95. 320 pages. (Available at amazon.com )
• Sham, Pak. 1998. Statistics in Human Genetics ISBN 0-340-662417 Softcover $44.95 (Available at amazon.com ). 304 pages. Topics covered include the estimation of allele frequencies; the testing for Hardy-Weinberg equilibrium; classical and complex segregation analysis; linkage analysis for Mendelian and complex diseases and quantitative traits; the detection of allelic associations; the estimation of heritability for multifactorial traits; and path analysis.
• Ott, Jurg. 1999. Analysis of Human Genetic Linkage (3rd ed). ISBN 0-801-861403. Johns Hopkins Univ Press. Softcover $55.00. 424 pages. (Available at amazon.com )
• Plomin, Robert, John C. DeFries, Gerlad E. McClearn, and Peter McGuffin. Behavioral Genetics (4th ed). ISBN 0-7167-5159-3. Worth Publishers, New York. $89.50 449 pages. (Available at amazon.com )
• Thompson, Elizabeth A. 2000.Statistical Inferences from Genetic Data on Pedigrees . ISBN 0-940600-49-8 .
  • This monograph is based on lectures presented at a 1999 CBMS Summer Research Conference. It develops the probability models for genetic data on related individuals, from the meiosis level to data on extended pedigrees. The focus is on simple Mendelian traits, such as DNA markers, but on joint models for data at multiple genetic loci, such as arise in modern genome scan studies. The statistical approach is that of likelihood, maximum likelihood estimation, and methods for the analysis of latent-variable and hidden-Markov models including the EM algorithm, the Baum algorithm, and Monte Carlo imputation methods. The first half of the monograph develops the basic concepts and approaches, focusing on the ideas of gene identity by descent and the tracing of gene descent in pedigrees using meiosis indicators or inheritance vectors. This material should be accessible to first-year graduate students in statistics or biostatistics. Only a basic understanding of discrete probability and mathematical statistics (likelihood inference) are assumed. No genetic knowledge is presupposed, although some familiarity with basic terminology will be helpful. Building on these foundations, the second half of the monograph develops Markov chain Monte Carlo (MCMC) and Monte Carlo likelihood methods for the analysis of data on individuals in a known pedigree structure. This material is more specialized, but should be accessible to those who have mastered the earlier chapters, or who have studied hidden Markov models and MCMC methods. The objective is Monte Carlo estimation of likelihood surfaces and conditional probabilities, rather than Bayesian sampling of parameter spaces and posterior distributions. The penultimate chapter illustrates the methods presented, through detailed analysis of two examples, using recently implemented MCMC samplers and likelihood estimation procedures. The final chapter discusses related research areas and the potential for further development of methods.
  • Ordering information ($30.00)
• Quantitative Trait Loci Analysis in Animals , by Joel Weller. $50.00 (US) 304 pages. More details

Links to webpages on Quantitative Genetics

• Class Notes (Some of these links appear to only be active when the class is taught)

1. Statistical Genetics, with a focus on Animal and Plant Breeding . Wyman Nyquist, Purdue University. Very extensive notes (essentially an on-line textbook)
2. Armidale Animal Breeding Summer Course 2003 . David Lindsay, Julius van der Werf, Mike Goddard, Ben Hayes, University of New England, Armidale NSW.
3. Armidale Animal Breeding Summer Course 2004.
4. 2003 Nordic postgraduate course: Quantitative Genetics in Animal Breeding. Bruce Walsh and Bill Muir, Helsinki, Finland.
5. Quantitative Genetics and Animal Models . L. R. Schaeffer, University of Guelph.
6. Estimation of Genetic Parameters . L. R. Schaeffer, University of Guelph.
7. EEB 348: Population Genetics . Kent Holsinger, Univ. Conn.

• Genomes

1. AnimalGenome Size Database ( C-values for over 2,100 species and subspecies of vertebrates and 800 invertebrates)
2. Human
   • Nature site
   • Science site
3. Mouse
4. Fugu (Puffer fish)
5. Arabidopsis
6. Flybase (Drosophila)
7. Mosquito
8. Wormbase (C. elegans)
9. Dictyostelium
10. TIGR Microbial Database

• Karen Ayres (University of Reading ) very extensive Statistical Genetics webpage
• Software
• For software for a particular topic, see the appropriate chapter in the Volume 1 webpage
• Websites with lists of programs:
  1. Genetics
     1. Software for Animal Breeding
     2. National Biotechnology Information FacilityGeneral list of genetic-analysis software
     3. Pedigree drawing software.
     4. Pedigree tools.
     5. Genetic Analysis Software, a massive list (largely human genetic) from Rockerfeller University.
     6. Linkage & QTL Mapping.
     7. Genetic calculation applets, from Knud Christensen at The Royal Veterinary & Agricultural University, Denmark.
  2. Statistics
     1. StatLib---General Archive Massive listing of programs, hosted by the Department of Statistics at Carnegie Mellon University.
     2. Statistical power analysis .
     3. VassarStats web site , a collection from Richard Lowry, Department of Psychology, Vassar College,
• Meetings
• Upcoming
• Recent Past
  1. Gordon Conference on Quantitative Genetics , February 9 - 14, 2003. Ventura, California.
  2. Conference on Long term selection . June 17 - 19, 2002, Urbana, Illinois.
  3. Seventh World Congress on Genetics Applied to Livestock Production (7th WCGALP) August 19-23, 2002. Montpellier, France.
  4. Population and Evolutionary Genetics of Forest Tree Species Star� Lesn�, Slovakia, August 25-29, 2002
  5. Gordon Conference on Quantitative Genetics , February 18-23, 2001. Ventura, California.
  6. Quantitative Genetics and Plant Breeding in the 21st Century. A Symposium held by the LSU Chapter of Sigma Xi from March 26 thru March 28, 2001 in Baton Rouge, Louisiana.
• Summaries from Previous meetings
  1. Report and Recommendations from the NIH meeting on The Genetic Architecture of Complex Traits held at the (US) National Institutes of Health on December 10-11, 1997.
  2. Reports from Sixth World Congress on Genetics Applied to Livestock Production, University of New England, Australia (January 11-16th 1998).
• Advanced Classes/Workshops

1. Summer Institute in Statistical Genetics, from University of Washington
2. The M.Sc./Diploma in Quantitative Genetics and Genome Analysis at the University of Edinburgh.

• Quantitative-Genetics related listserves
• ANGENMAP(ANimal GENe MAPpers) is an internet discussion group for all gene mappers and interested parties
• Directories for Finding People

1. Evolution and population genetics
2. Animal Breeders and Geneticists
3. Animal Gene Mapping Community Directory

• Animal Breeding and Genetics
• Online Mendelian Inheritance in Animals (OMIA)
• Animal Geneticists Discussion Group.
• ANGENMAP Discussion Group (Animal Gene Mappers).
• Animal Breeding and Genetics Group Wageningen University .
• Animal Genetics and Breeding Unit University of New England (Armidale, New South Wales, Australia).
• Domestic Animal Diversity Information System.
• The Association for the Advancement of Animal Breeding and Genetics
• AAABG (The Association for the Advancement of Animal Breeding and Genetics Inc)Genetic parameter site for traits in Pigs and beef cattle
• American Society of Animal Science .
• American Dairy Science Association (ADSA).
• FABA, FABA - Finnish Animal Breeding Association.
• Institute for Animal Science and Health (ID-DLO), in The Netherlands.
• Animal Breeding and Genetics at University of Illinois (ADSA).
• Animal Improvement Programs Laboratory (AIPL) , (Beltsville, Maryland)
• CGIL, Centre for genetic improvement of livestock (Cananda)
• The South African Stud Book and Livestock Improvement Association
• STAGES Swine Testing and Genetic Evaluation System
• Plant Breeding
• Plant Genome information
• WWW Pages of Agronomic Information
• Institute of Plant Breeding, Wageningen Agricultural University
• Forest Breeding
• Breeding theory and progeny testing working group of the International Union of Forest Research Organizations
• Evolution
• List of Evolution related web sites.
• EVOL message homepage
• Human Genetics
• Online Mendelian Inheritance in Man. This database is a catalog of human genes and genetic disorders authored and edited by Dr. Victor A. McKusick and his colleagues at Johns Hopkins and elsewhere, and developed for the World Wide Web by NCBI, the National Center for Biotechnology Information. The database contains textual information, pictures, and reference information. It also contains copious links to NCBI's Entrez database of MEDLINE articles and sequence information.
• Genetic Linkage Analysis server at Rockerfeller.
• Statistical Genetics Group at the University of Michigan
• SAGEStatistical Analysis for Genetic Epidemiology package
• USCF's bigEpidemiology page
• American Society of Human Genetics
• Departments and Programs
• NCSU Program in Statistical Genetics (USA)
• Quantitative Genetics and Genome Analysis at the University of Edinburgh (UK).
• Genetics for Animal Breeding at the University of New England (Armidale, Australia).
• Journals
• The Journal of Quantitative Trait Loci (JQTL), an electronic journal sponsored by the Crop Science Society of America.
• Genome
• Nature Genetics
• Journal of Animal Science
• Journal of Dairy Science
• Crop Science
• Proceedings of the National Academy of Sciences
• Evolution
• Genetics
• Searchable bibliographices
• Joe Felsenstein's Bibliography of Theoretical Population Genetics (to 1981), in searchable gopher format
• Fred Allendorf's Bibliography of Genetic Variation in Natural Populations

Home Pages: [** Walsh**] - [** Volume One**] - [** Volume Two**] - [** What's new **]

Created 25 February 1995, last updated 31 Jan 2002
Bruce Walsh. jbwalsh@u.arizona.edu . Comments welcome.
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