Chr1    mak   gene    120221  120946  .       +       .       ID=spa-h0003.02;Name=spa-h0003.02
Chr1    mak   mRNA    120221  120946  .       +       .       ID=spa-cap_Chr1_00M;Parent=spa-h0003.02;Name=spa-cap_Chr1_00M
Chr1    mak   exon    120221  120946  .       +       .       Parent=spa-cap_Chr1_00M
Chr1    mak   gene    18546165        18546939        .       +       .       ID=spa-h0004.02;Name=spa-h0004.02
Chr1    mak   mRNA    18546165        18546939        .       +       .       ID=spa-cap_Chr1_18;Parent=spa-h0004.02;Name=spa-cap_Chr1_18
Chr1    mak   exon    18546165        18546504        .       +       .       Parent=spa-cap_Chr1_18
Chr1    mak   exon    18546791        18546939        .       +       .       Parent=spa-cap_Chr1_18

spa-h0003.02  spa-cap_Chr1_00M
spa-h0004.02  spa-cap_Chr1_18

cat file | awk '$3 == "gene" && $9 == "spa-" {$9 = "XX"} {print}'

while read n k; do sed -i 's/$n/$k/g' file1; done < fileA