Falsely Declaring a Marker-QTL Association

Case 1
                         Lines                         Lines         
Locus         1         2         3         4         5         6
   1           AA       AA       AA       aa        aa       aa
   2           BB        BB       BB       bb        bb       bb
   3           cc        cc       cc       cc        cc       cc
   4           MM       MM     MM      mm       mm      mm
Mean         6/3=2         0/3=0

Case 2
                         Lines                         Lines         
Locus         1         2         3         4         5         6
   1           AA       AA       AA       aa        aa       aa
   2           BB        BB       BB       bb        bb       bb
   3           CC       CC       CC       cc        cc       cc
   4           MM      MM      MM      mm       mm      mm
Mean         9/3=3        0/3=0

In Case 1, a Type I error would occur because the lines with the MM marker genotype have a mean of 2 and the lines with the mm marker genotype have a mean of zero. Locus 3 is linked to the marker, but there is no segregation for the QTL in that population. In Case 2, locus 3 is segregating and the lines with the MM marker genotype have the CC genotype for the QTL. Lines 4, 5, and 6 have the mm marker genotype and the cc genotype for the QTL. A correct decision is made in rejection of Ho: no marker QTL association or no QTL present for Case 2.

Case 3

                         Lines                         Lines         
Locus         1         2         3         4         5         6
   1           AA       AA       aa       aa        AA      aa
   2           bb        bb       BB       BB        bb       BB
   3           CC        CC      CC       cc        cc       cc
   4           MM       MM     MM      mm       mm      mm
Mean         6/3=2         3/3=1

In Case 3, the correct decision is made to reject Ho and declare the presence of a marker-QTL association. All the lines with the MM marker genotype have the CC QTL genotype and all the lines with the mm marker genotype have the cc QTL genotype. The background genes average out to 4 positive alleles for each set of lines. This is what would be expected in most cases.