In reviewing the instructions for filing a Mississippi tax return I was unable to find any information preventing you from filing separately for MS when you have filed jointly on your federal return.
"..Separate returns (two returns) are filed when each spouse completes his/her own return. Each spouse reports his/her own income and deductions on a separate return. BOTH spouses must file returns even though one spouse may have little or no income. If one spouse elects to itemize deductions, both must itemize. Each spouse is entitled to only one-half of the total exemption authorized. Each spouse must list the other spouse on his/her return."
This link https://INDIVIDUAL INCOME TAX BUREAU has the complete instructions for filing Mississippi tax returns
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