RIL "Backcross" with original parent

[Marion Pitz]

Hello,

I have a RIL population of Maize recombinant inbred lines, that was generated by intermating the lines B73 and Mo17 for 4 generations, followed by at least 6 generations of selfing. Thus, the RILs themselves are quite homozygous.

We now crossed each RIL once with B73 and once with Mo17, creating hybrids, that are not totally homozygous, but only across ~half the genome. B73 and Mo17 are always the maternal parent.

I am unsure now, which type of cross to use for this setup. Is it still BC, as that type only allows for AA or AB genotypes, but my RILs contain AA and BB?

Thank you very much in advance.

[Karl Broman]

The RIL x B73 lines all have a single RIL chromosome and a fixed B73 chromosome. Similarly, the RIL x Mo17 have one RIL chromosome and a fixed Mo17 chromosome.

For QTL analysis, I would treat the data just as an RIL, though recognizing that rather than comparisons being AA vs BB, they're really AA vs AB in one cross and AB vs BB in the other.

I would treat the data on the two sets (crossed to B73 and crossed to Mo17) as if they were two treatments or environments.

karl

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[Marion Pitz]

Thank you very much for your reply. It seems to work so far.