When chromosomal crossover occurs, two matched chromosomes swap matched sections of their chromosomes. My question is: how does the cell select where to to make the break on both chromosomes? Is it based on some attempt to match sequences on the two chromosomes, or purely on distance from the centromere? The mechanics of the former could be achieved by breaking the two strands of each chromosome at different places. The mechanics of the second is a simple walk from the centromere with a random(?) selection of where to cut.
The purpose of this question: if the process is based on distance from the centromere then it would provide an explanation the presence of junk DNA. Successful crossover requires that the number of functioning genes on the two chromosomes not be radically altered in quantity. A failed crossover would result in at least one of the gametes being non-viable, reducing fertility. If crossover is based on centromere distance then the location of genes becomes a factor in the success of a crossover, erecting a fitness barrier between populations with radically different gene placement, even if gene content is identical.
If this is a question without an answer, currently, one way to address it would be to try to cross breed knockout mice that don't have junk DNA with ordinary mice that do. If the fertility of the cross breeding is significantly lower than than knockout with knockout and normal with normal, or if the cross breeds are less fecund, then that would provide evidence for position based crossovers, and a function for junk DNA in the crossover process.