You can use the MatteBorder to specify the dimensions of the border in each side. The constructor of MatteBorder is:
public MatteBorder(int top,
int left,
int bottom,
int right,
Color matteColor)
So if you want to have a border only on the bottom and right sides of your JPanel, you could write something like this:
JPanel panel = new JPanel();
panel.setBorder(BorderFactory.createMatteBorder(0, 0, 1, 1, Color.BLACK));