A question on mouse crossing: Do you think it is possible to breed two genetic mutations (6kb apart) at a homologous locus onto a same chromosome, or in cis? Because the crossover between two mutations may require meiosis recombination, I thus plan to interbreed heterozygous A-b/a-B littermates, and genotyping all pups with long range PCR. Do you think this is a feasible plan? How many breeding pairs / scale would you recommend? Thanks!
It's genetically possible, but you'd have to ask a mouse person if it's practical.
6 kb is a rather short genetic distance. Looks like on average there are 2 kb per centiMorgan. http://www.informatics.jax.org/silver/frames/frame5-1.shtml
But that can very a LOT depending on exact location, mouse strain, etc.
So, if you are fortunate that this is about 3 cMorgans in distance, then you might get 3 recombinant offspring in 100. I'd plan on genotyping more than that - 300? 500?
Better ask a mouse expert how many breeding pairs that would take. And see if the recombination rate for your particular locus and mouse strain are known.
Good luck!