Hi Anil,
The isogenic lines usually refer to two lines have exact same genetic makeup, with one gene in difference. Some researchers refer the 'wild type (non-transgenic)' line and the transgenic line derived from this wild type line as isogenic lines. They basically have only 1 gene different (the genetically transformed one, assuming that no other genomic mutations during tissue culture). In animal research, researchers generate isogenic cell lines by using 'Homologous recombination technology' to 'knock-in' or 'knock-out' a gene to study/compare side-by-side the difference between the normal cells and the mutated cells.
The near-isogenic lines (NILs) [inbred lines] are usually developed for QTL mapping purpose. To develop the NIL mapping population, cross of a donor line (with a trait of interest) and a reference line is initiated. The progeny with the trait-of-interest are then selected for 'backcrossing' to the reference line. This process (backcrossing and genotyping) is repeated for many generations. Eventually, the NIL lines within the mapping population consist of a single fragment or a small number of genomic introgression fragments from a donor parent into an otherwise homogeneous genetic background. See attachment for an example.
Best,
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