If you have SSN and are treated as resident alien, you have a choice to file Married Filing Jointly or Married Filing Separately. If you elect to file jointly with your wife, you will need to apply for an ITIN for her and you will also need to report all of her income. By filing jointly with her you will be making an election to treat her as a resident alien for tax purposes (just for tax, this doesn't actually make her a resident alien).
