JOINT ANALYSIS OF PROGENY AND CLONES

Dear Folks

I have a trial at 2 sites of macadamia that contains both progeny
procued by crossing and clones of the parents of the progeny. We have
used trained assessors to assess a visual atribute of the kernel, basal
discolouration. We selected 550 progeny form across the 55 familes
available (i.e usually 10 progeny per family), and 5 ramets of each of
the 10 clones. 11 parents were used to make the crossings.

From each individual plants we took 2 samples of 10 kernel. Two
assessors each assessed one of the samples of 10 kernel. The trait was
assessed on a scale from 0 (absent) to 3 (extreme).

My interested is to include both plants types in the genetic analysis to
estimate both additive and non-addtive effects so I can compare progeny
performance against clonal performance. I have chated to Arthur and
Joao Costa e Silva about this last year but without the complication of
the hierarchy in the design.

I have attached the the command file and the output file.
<<bd06cs_t23_test04.as>> <<bd06cs_t23_test04.asr>> I get a message that
the message is too big when I include the zipped data file. I can send
that individually if anyone wishes.

The model is

SS1IKBD ~ mu SITE AGROUP ASSESSOR,
         !r ,
            AGROUP.TREE, # additive covariance matrix for both groups
            at(AGROUP,2).FAM, # to estimate family effects for seedlings
            at(AGROUP,1).ide(TREE), # to estimate non-additive variance
among clones
            PLANT, # to estimate common between plants non-additive and
non-family variance (i.e. within family VD for seedlings and E
            at(AGROUP,1).PLANT, # to estimate difference between VPLANT
and within clone variance
            PLANT.ASSESSOR, # interaction between assessor and plant
             !f mv

0 0 1 !STEP 0.1
AGROUP.TREE 2
AGROUP 0 CORGH 0.99 0.1 0.2 !GFUU # correlation =1 forces Vtree in
group,1 to be additive variance
TREE 0 AINV

I am getting a singularity in the analysis which may be limited data but
would appreaciate feedback about the model to see if there is somethere
I have missed.

Any coments greatly appreciated

Thanks for your time

Dr Craig Hardner
Project Leader Macadamia Improvement and Conservation
CSIRO Plant Industry
Queensland Bioscience Precinct
306 carmody Road
St lucia QLD 4067
ph: 07 3214 2659
fax: 07 3214 2920
email: craig.hardner_at_csiro.au