Re: genetic analysis - categorical trait

Dear Sang

re:

I am one of ASReml user and a student at UMB, Norway.
Could you please show me how to estimate heritability
of categorical trait and the genetic correlation
between this trait with other continuous traits? I
couldn't find those information in Manual or tutorial
in ASReml guides.

the case:
Fish fillet color: scores: 1,2,3
Fixed effect: batches, growout period
Random effect: animal, dam, family
Continuous traits: body weight

UNFORTUNATELY ASReml cannot fit the model you propose as it cannot
model a multiple threshold process.

It can fit a BIVARIATE analysis of a BINARY trait and a NORMAL trait (see
the enclosed test example binnor.as).

ASReml 3 is in development and can fit a multiple threshold (scored)
trait albiet
it is a bit untidy at present, but has not been extended to Threshld +
Normal

My strategy for this data would depend on the general cell frequencies.
If all classes have at least 10% then a Normal analysis should be
reasonable.

Maybe as a student, you want to explore a range of models and the
efficiency of various forms
of analysis. Feel free to contact me for further detail.

Text of BINNOR.AS follows (The data [binnor.asd] is too big to send to the
list
but I will put it at ftp://asreml:asreml@ftp.dpi.nsw.gov.au if I can.

Lamb data from ARG thesis page 177-8
 record
 CYR GRP 5
  SEX SIRE 18

  Score5 # Express as a proportion
  Score4 Scald FootRot
  rand
binnor.asd !skip 1 !DOPART $4 !ASUV !MAXIT 40
!DDF $1 !FCON $2 !KADJ $3
!PART 1
Score5 !bin !disp ~ SEX GRP !r SIRE .16783

!PART 2
Score5 ~ SEX GRP !r SIRE .16783

!PART 3
rand ~ SEX GRP !r SIRE .16783

# ---------------------------------------------------------------
!PART 4 # Binomial + Normal bivariate
# !ASUV required so that weights are correctly used.
# !disp omitted in this example because variance explicitly set
# GLMM qualifiers only apply to the first trait.
# There is no syntax yet for specyfying GLMM qualifiers on
second trait

Score5 rand !bin ~ Trait.SEX Trait.GRP !r Trait.SIRE
1 2 1
2513
2 0 US 1 -.01 0.25

Trait.SIRE 2
Trait 0 US 0.067 .05 1.20
SIRE

# ---------------------------------------------------------------
!PART 40
Score5 rand !bin ~ Trait.SEX Trait.GRP !r Trait.SIRE
1 2 1
2513
2 0 US 1 0.00 0.25 !GUFP

Trait.SIRE 2
Trait 0 US 0.067 .00 1.20 !GUFP
SIRE

# ---------------------------------------------------------------
!PART 5
Score5 rand ~ Trait.SEX Trait.GRP !r Trait.SIRE
1 2 1
2513 !S2==1
2 0 US 0.2 .01 0.25

Trait.SIRE 2
Trait 0 US 0.015 0.01 1.05
SIRE

May you know Jesus Christ and His blessing in 2007,

Arthur Gilmour, His servant .

Mixed model regression mapping for QTL detection in experimental crosses.
Computational Statistics and Data Analysis 51:3749-3764 now available at
http://dx.doi.org/10.1016/j.csda.2006.12.031

Profile: http://www.dpi.nsw.gov.au/reader/17263
Personal website: http://www.cargovale.com.au/

mailto:Arthur.Gilmour_at_dpi.nsw.gov.au, arthur_at_cargovale.com.au
Principal Research Scientist (Biometrics)
NSW Department of Primary Industries
Orange Agricultural Institute, Forest Rd, ORANGE, 2800, AUSTRALIA

fax: 02 6391 3899; 02 6391 3922 Australia +61
telephone work: 02 6391 3815; home: 02 6364 3288; mobile: 0438 251 426

ASREML 2 is now available from http://www.VSNi.co.uk/products/asreml
The ASReml discussion group is at ASREML-L_at_dpi.nsw.gov.au
To join it, mailto:arthur.gilmour_at_dpi.nsw.gov.au
Cookbook: http://uncronopio.org/ASReml

Proposed travel:
ASReml workshop (Forestry) 16-18 April Tasmania
Rec leave 19-20 April
ASReml planning at Tumut 23-27 April
Biom Brch meet 2-4 May
ASReml workshop (Animal Breeding) 8-26 May South Africa
AAABG 24-26 September Armidale
      <><><><><><><><><><><><><><><><><><><><><><><><><>

nguyen sang <nguyenvansang1973_at_YAHOO.COM>
Sent by: ASReml users discussion group <ASREML-L_at_AGRIC.NSW.GOV.AU>
20/04/2007 06:58 PM
Please respond to ASReml users discussion group

        To: ASREML-L_at_AGRIC.NSW.GOV.AU
        cc:
        Subject: Re: genetic analysis - categorical trait

Dear Sir/Madam,

I am one of ASReml user and a student at UMB, Norway.
Could you please show me how to estimate heritability
of categorical trait and the genetic correlation
between this trait with other continuous traits? I
couldn't find those information in Manual or tutorial
in ASReml guides.

the case:
Fish fillet color: scores: 1,2,3
Fixed effect: batches, growout period
Random effect: animal, dam, family
Continuous traits: body weight

I greatly appreciate if you can guide me on it.

Best regards,
Sang

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Received on Thu Apr 22 2007 - 20:58:38 EST