# Help with gene linkage and mapping!

Here's an interesting question I've been trying to figure out:

My annotations are in red. So far, I've figured out:

• We know 630 colonies survived when plated with ACD antibiotics...meaning they picked up the a/c/d resistance alleles, but remain wild-type for the b allele. The genotype would be "a b+ c d". Because SO MANY (630!) colonies seemed to inherit a/c/d together, and b completely separate from them, I would say b is the gene quite distant from the 3 other genes.

However, I've unsure about how to proceed and determine the probably order of the 3 others genes: a, c, and d.

Here's my hunch: B--------------------C-D-A.

I'll explain:

• Well, I looked and saw 942 (many!!!) picked up A/D together. So A/D are probably adjacent.

• Then, 786 (many, but fewer) picked up C/D together. So C is further from D than A is far from D. The question becomes: is it "C---A-D" or is it "A-D---C"?

• The insight comes in with 640 (still fewer) picked up A/C together. That means A is actually quite FAR from C, because more distance = more recombination events that could split them up. So between the "C---A-D" or "A-D---C" listed above, it's more likely "A-D---C".

• Okay! We know B is far from the other ones, BUT is it like "B-------ADC", or is it like "ADC-------B"? Well, let's look: picked up B/C together is 51, but picked up A/B together is only 46. That means A is a little FURTHER from B than C is further from B, since 46 < 51.

• This led me to my proposed answer: that the order is "ADC---------B", or if you just flip it around, its equivalent: "B---------CDA".

How's my reasoning? This stuff can be pretty confusing; am I approaching it from the right angles? Thanks so much; really appreciate it!

• You were never told that all the genes were on a single plasmid. I think you should treat all those counts < 50 as essentially zero; cells pretty much never get both the ACD and the B plasmid; they get one or the other. Oct 18, 2019 at 16:37