ASReml · General Resources

This page was last modified on 02 February 2009, at 15:18 NZST

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Other ASReml sites

  • Steve Kachman’s ASReml Workshop notes present examples of code, including .pin files for functions of variance components.
  • Julius van der Werf organises the Armidale Animal Breeding Summer Courses (University of New England, Australia). Module C of the 2005 course includes PowerPoint presentations by Arthur Gilmour. The page contains links to four sets of slides (around 3MB each set).
  • A simple example of fitting a model with asreml-R in the R wiki.
  • A PDF version of a presentation on using the asreml library in R by David Butler.

Race classification

One of the assumptions of genetics analyses is that all individuals come from a single population with common mean and variance. It is clear that in several species of Eucalyptus there are large population differences. Therefore, it is necessary to fit the population of origin in the model equation, either as a fixed effect (e.g. when you have first generation selections, so trees come from only one population) or using genetic groups (e.g. advanced generations, when there are crosses between populations). We are trying to standardise the populations used for the analyses of E. globulus using the subraces shown in the race classification map devised by Dutkowski & Potts (Australian Journal of Botany 47:237–263. 1999).

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CRC-SPF general

If you are interested in research material generated by the CRC-SPF check the publications database, where you will find references and electronic copies of papers, reports and presentations. This database covers not only genetics but also all the other research areas of the CRC for Sustainable Production Forestry. Note: access to CRC resources requires login in the publications management system. Please login using username = guest, password = guest.

There is a large number of courses, presentations, seminars, meetings going on at the CRC for Sustainable Production Forestry. Check the calendar to see all public events.

ENV (freely available) is a program for plotting spatial residuals to monitor analyses using ASReml.

Blockit (freely available) is a DOS (windows terminal) program which creates complete rectangular arrays of data for spatial analysis for one or many blocks/sites.

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References

If you are interested in genetic analysis of progeny tests, and don’t know where to start, browse a few books and sets of notes until you find the ones you feel more comfortable with. You will probably need to start with a quantitative genetics book, then with books or notes on breeding value prediction using BLUP, as well as some papers to have a look at what is going on in your area of research.

  • Books
    • Lynch, M. and Walsh, B. 1998. Genetics and analysis of quantitative traits. Sinauer Associates. 980 p (ISBN 0–87893–481–2). This is the ‘new classic’ for quantitative genetics, and a wonderful place to start learning about the topic. You can also visit the web site for the book, with plenty of references, software and drafts for the second volume (Amazon price).
    • Falconer, D.S. and MacKay, T.F.C. 1996. Introduction to quantitative genetics. Longman. 464 p (ISBN 0582–24302–5). The ‘old classic’ that has been around since 1960. A very good book, although I prefer Lynch and Walsh’s (Amazon price).
    • Mrode, R.A. 1996. Linear models for the prediction of animal breeding values. CAB International. 187 p (ISBN 0–85198–996–9). An excellent introduction to BLUP, with a large number of small examples with all the details of the calculations (Amazon price).
    • Henderson, C.R. 1984. Applications of linear models in animal breeding. University of Guelph. 423 p (ISBN 0–88955–030–1). This is more for consulting specific details, rather than a cover-to-cover book. Not for the faint hearted. It is good to have Searle’s notes as a companion volume if you want to get your hands dirty. To obtain this and the following book please contact Larry Schaeffer.
    • Searle, S.R. 1998. A mathematical supplement to C.R. Henderson’s book “Applications of linear models in animal breeding”. University of Guelph. 254 p.
  • Notes (some of my copies are photocopy of a photocopy)
    • Kennedy, B.W. 1989. Animal model BLUP. Erasmus intensive graduate course. Trinity College Dublin. 141 p. As most of Brian Kennedy’s stuff, it is extremely clear and a real pleasure to read.
    • Quaas, R.L., Anderson, R.D. and Gilmour, A.R. 1984. BLUP School Handbook. Animal Genetics and Breeding Unit, University of New England. 158 p. Nice notes and there is even a reference to autoregressive processes. I think this is just after Arthur finished his PhD at Massey.
  • Sites
    • Larry Schaeffer has lots of course material in BLUP and related topics. He also maintains some of Brian Kennedy’s notes. He has the dubious honour of having a web page where the menu looks like mixed model equations.
    • Is it a fixed or a random effect? Read a very short description at Bob Barker’s site.
    • The Virtual Library of Forest Genetics maintained by Matti Haapanen has a large number of links to forest geneticists, software, organizations, etc.
    • Ever wanted to have a look to Sir Ronald Fisher’s papers? Your library doesn’t hold the journals or books with his work? No worries, have a look at the Collected papers made available by the University of Adelaide.

When I have some time I will be adding more references to other pages and written material. If you know of any material that should be here, please let me know.