Dominant or additive locus

[Neda Rahnamae]

Dear Karl, 

I would be very grateful if you could help me interpret the results of the estimated effects. 

I worked on an F2 population and detected 4 QTLs for flowering time. 

Here is the result:

Estimated effects:
-----------------
               est       SE       t
Intercept 189.1491   0.2859 661.617
1...@51.4a     1.6292   0.3904   4.173
1...@51.4d     0.9598   0.5286   1.816
3...@67.7a     3.0486   0.4414   6.907
3...@67.7d    -0.2015   0.5432  -0.371
8...@8.9a     -5.2433   0.3940 -13.308
8...@8.9d      1.8724   0.5307   3.528
8...@153.9a    2.4347   0.4352   5.594
8...@153.9d   -0.5190   0.5358  -0.969

the highlighted QTL is the major QTL with LOD score close to 40. 

[Karl Broman]

What is your question? I din’t understand what help you need.

karl

On Jan 30, 2024, at 7:42 AM, Neda Rahnamae <nrahn...@gmail.com> wrote:

Dear Karl, 

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[Neda Rahnamae]

Dear Karl,

I am sorry. My question is, because I cannot see d = -a or d = +a for any of these QTLs, does it mean that I have a dominant allele for all of them? 

Thank you and best,

Neda

[Amir FARTASH]

Hi , 

I think that here the + and negative relates to the parental lines. for example it means that the the + it comes from maternal and the - is from paternal 

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École Nationale Supérieure Agronomique de Toulouse (INP- ENSAT)

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[Karl Broman]

Think of AA, AB, and BB genotypes having average phenotypes -a, +d, and +a, respectively.

For a couple of QTL, (3@67.7 and 8@153.9), the estimates are consistent with additive alleles (d could reasonably be 0).

For others, d is bigger than 0 but not quite |a|, so you would maybe say incompletely dominant.

karl