Hello everyone,
I have a question regarding Bi-parental QTL mapping. In my genotype data, three parents are involved, e.g., X, Y, Z. All my materials are inbred lines and double-haploids. So, the individuals I have are either X*Y or X*Z. My genotype data is A, B, H translated. So, A= Homozygous for parent A(AA), B= Homozygous for parent B(BB), H=Heterozygous(AB).X was considered to be as parent A and Y/Z was considered as parent B while doing the ABH translation.
I am using RQtl for the QTL mapping. I am confused, which cross type should I use? If I use “cross-type =DH” it shows warning messages as three genotypes are involved. Which cross type should I use? Should I replace all H with missing values so that R can read it as DH or it is ok if I use “F2” as cross-type?
Thank you very much .Any kind of suggestion would be highly appreciated.
I have worked with DH population with very few observations for few markers with H genotype. What I did, I considered them as missing values when I worked with Rqtl. However, you may use Plabqtl program (Utz and Milchinger, 2006). In this program you have more options to solve this problem. Please have a look on page 28 in the attached file.
Regards
Yaser Hasan Thank you.Actually I am using data form a commercial pre-breeding program. It is not unusual for commercial pre-breeding to have some level of heterozygosity in the DH lines (which my populations were) due to the methodology of production and growing those DH lines. In practice, unless every spike (which was not done) is bagged the high amount of sterility allows for outcrossing and therefore the chance of heterozygosity is increased. That´s why I got some H also in my genotype data. I will follow your suggestion.
One of the choices is to use R/qtl2 which is suitable for complex cross designs.
https://github.com/kbroman
Zachary Stansell Thank you very much.I removed all H from my genotype data as my mapping population is a DH and I got some H because of out crossing. After that read.cross function worked! Thank you for your kind help
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