Can someone simply explain the mechanisms underlying recombinant strain formation and analysis?

[danaz123]

Hi - I am just learning genetics, as my lab will be incorporating genetic analysis into future work. I have a decent understanding of basic topics (meiosis, mutations, simple epigenetics), but I have of trouble visualizing the concepts underlying genomic analysis. Specifically, I can't seem to figure out how recombinant strains are formed.

 

Here is an excerpt from a site describing recombinant strain formation:

 

"The construction of a set of RI strains is quite simple in theory and is illustrated in Figure 9.4. One begins with an outcross between two well-established highly inbred strains of mice, such as B6 and DBA in the example shown. These are considered the progenitor strains. The F₁ progeny from this cross are all identical, and thus in genetic terms, they are all interchangeable. F₁ hybrid animals are bred to each other to produce a large set of F₂ animals. At this generation, siblings and cousins are no longer identical because of the segregation of B6 and DBA alleles from the heterozygous F₁parents. As illustrated in Figure 9.4 for a single pair of homologs, each of the F₂ animals will have a unique genotype with some loci homozygous for the B6 allele, some homozygous for the DBA allele, and some heterozygous with both alleles. At this stage, pairs of F₂ animals are chosen at random to serve as the founders for new inbred strains of mice. The offspring from each F₂ founder pair are maintained separately from all other offspring, and just two are chosen randomly for brother-sister mating to produce the next generation. The same process is repeated at each subsequent generation until at least 20 sequential rounds of strict brother-sister matings have been completed and a new inbred strain with special properties is established. "

My questions:

1) Why is the F1 progeny of the B6 and DBA cross genetically identical? Doesn't meiosis shuffle chromosomes so that all siblings are different? And what about crossing over during meiosis?

2) Why is the F2 generation "no longer identical"?

3) How is this info used for linkage analyses?

I realize this questions might be really off-base. A really basic explanation of the construction of recombinant strains would be great.