Finding a gene within an introgression

[arnon77]

Hi
I have 2 Nearly Isogenic Lines (NILs) in pepper. The NILs are different in phenotype and segregate in a mendelian pattern. The introgression is few Mbp long and I need a gene!
Be aware that capsicum is poor in markers and a genomic sequence so I'm kind of stuck here.
I thought about 2 strategies:

• From an F2:NIL-1xNIL-2 population- take 2 phenotypic pools of RNA and sequence them in order to find few differential genes which might include my gene within the introgression.
• Same as previous only make a DNA pool and sequence in order to produce new markers based on polymorphism within the introgression.

Has anyone been dealing practically with such? and could recommend a short path towards a gene?
Thanx

[JackBean]

few Mbp will probably contain more than one gene.

With RNA sequencing, you will see also differences in genes not included in your introgression. Thus, the question is, are you interested only in that part or do you want all differences?

[arnon77]

It's my PhD thesis, so I need a gene in the shortest time=most efficient method.
and true probably there are few dozens of genes within that segment.

[JackBean]

The question stays, are you interested in what makes the lines different or in what is in the introgression?

[arnon77]

sorry for bein away...
I wish i could find the actual gene that is the cause of the difference.

[JackBean]

then go for the mRNA profiling