Differentiation of organs and tissues in a developing organism, is associated with

All the cells of a developing organism arise from the zygote by mitosis, so all of them contain the same set of genes.
The zygote and its very early descendants are totipotent; as development proceeds the cells become determined and then differentiate into types with clear-cut identities, such as muscle cells, nerve cells and skin cells.
Cells become different from one another not because they lose genes, but because different sets of genes are switched on or off in different cells at different times.
This is called differential expression of genes; it results in the synthesis of different proteins, which give each cell type its special structure and function.
Genes are not deleted during normal development, which is shown by the fact that a differentiated cell can still give rise to a whole organism (as in plant tissue culture and animal cloning).
Mutations, lethal or developmental, are abnormal changes and are not the basis of normal differentiation.
So differentiation is associated with the differential expression of genes.