Is a pedigree required?

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Dan Fulop

Feb 6, 2014, 4:50:07 PM2/6/14

I'm interested in using MAPfastR for QTL mapping in 2 different populations, both derived from inbred parents.  One is a mixed BC2/BC3 population (of ~500 lines) for which we have pedigree information for almost all the lines (and we will hopefully get the pedigree for the remaining lines from our collaborators).  If we do get the pedigree for the remaining lines, then I won't have to worry about lacking it.  However, it would be useful to know if we can use MAPfastR without pedigree information or with some missing pedigree information.

The other population is a so-called IL (introgression line) population that's derived from a very complex multiple back-cross design.  The ILs have a single introgression from parent 2 (P2) into parent 1 (P1), and together all the ILs "tile" the P2 genome in the P1 genome.  All the ILs are inbred.  Essentially, several different sets of IL lines have different pedigrees (but they all have just one P2 chromosomal segment introgressed into P1), and this population was made so long ago that I highly doubt we can get the IL's pedigrees.

So, the question again is whether or not one can map QTL with MAPfastR without any pedigree information (as in the IL population) or with some missing pedigrees (as in the BC2/BC3 population)?

It seems to me one could potentially map without any pedigree information by estimating IBD and haplotypes and then mapping using FIA, which can account for the expected covariance in phenotypes given the degree of genome sharing between lines.  Is that correct?

I should note that we have very dense SNP data on both of these populations.  The BC2/BC3 population was sequenced using RADseq and the IL population with RNAseq.  Moreover, parental origin of chromosomal segments (i.e. haplotypes) have been determined for these lines using simple "in-house" HMM code.

I look forward to hearing any suggestions/feedback you may have!

Thanks in advance,

Dan Fulop.
Postdoctoral Scholar
Dept. Plant Biology, UC Davis
Maloof Lab, Rm. 2220
Life Sciences Addition, One Shields Ave.
Davis, CA 95616

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