On GitHub, you can use Fenced Block to have code block syntax-highlighted, for example:
var a=1;
Also it seems to be only way to have syntax highlighting. The indentation doesn't enable highlighting from what I see.

This will confuse Vim's syntax highlighter because that is not part of standard syntax of Markdown. Although, it is fairly coder-readable, you know it is a code block. I am not sure Markdown processors will do when they don't understand such syntax.

But that is not a major issue to me, the sort-of-incorrect syntax highlighting in Vim is. Not only Vim is confused, so am I. It is very hard to read the content while you are writing. (Note: I was using this mkd.vim)

I found a fix for it. The ideal way to have additional syntax is to add an after-syntax, normally they are stored in ~/.vim/after/syntax. So I added a file with the following content:
syn region markdownCode matchgroup=markdownCodeDelimiter start="``` \=" end=" \=```" keepend contains=markdownLineStart
I didn't use that fix, it seems to have slight glitch like default markdown syntax highlighting from Vim for fenced block. But maybe it is because I messed some stuff up while I was trying with that mkd.vim. Right now, I am only using highlighting from Vim.