Yes. You can file married filing separately and each of you can open a 529 plan for your daughter. However, the total contributions per beneficiary is $2000 per year so between both of your accounts, the contributions cant be greater than $2000. For example, if one of you contributes $1000 during the year, the other spouse can only contribute $1000 during that same year.
Additionally, for each of you to make contributions to a 529 plan, the individual adjusted gross income for each of you, for the year, has to be less than $110,000. Please refer to page 46 of pub 970 under the heading, "coverdell education savings account" for additional information. https://www.irs.gov/pub/irs-pdf/p970.pdf