How are neural networks encoded in the DNA?
Here's at least one paper describing some of what is known about development of neural network in Caenorhabditis elegans

http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1001044

It mentions at least one relevant gene

" There is evidence showing that several guidance molecules like Netrin and Nerfin-1 are expressed in the early stages of development. Netrin is a protein involved in axonal guidance in vertebrates as well as in invertebrates [21], [22], [23] and is specifically known to influence early path-finding events [23], [24], [25]. Nerfin-1 belonging to a highly conserved family of Zn-finger proteins, is found transiently expressed in neuron precursors and plays a role in early path finding. Studies involving pioneering neurons in the central nervous system of Drosophila melanogaster have shown that Nerfin-1, whose expression is spatially and temporally regulated [25], is essential in early axonal guidance. "

You can also have a lot at the Wikipedia article called  "Development_of_the_nervous_system_in_humans"

One interesting fact is that C. elegans has 20 000 genes, 302 neurons and about 5000 chemical synapses, 2000 neuromuscular junctions and some 500 gap junctions. In humans there are an estimated 20 000-25 000 genes in humans, about 85 billion neurons and 100 trillion synapses.

This excerpt from http://www.tandfonline.com/doi/full/10.3109/0954898X.2011.638968 explains this seeming paradox though

"studies in a range of species suggest that fundamental similarities, in spatial and topological features as well as in developmental mechanisms for network formation, are retained across evolution. ‘Small-world’ topology and highly connected regions (hubs) are prevalent across the evolutionary scale, ensuring efficient processing and resilience to internal (e.g. lesions) and external (e.g. environment) changes. Furthermore, in most species, even the establishment of hubs, long-range connections linking distant components, and a modular organization, relies on similar mechanisms."