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?