create json from bash variable and associative array

Assuming that none of the keys or values in the "animals" array contains newline characters:

for i in "${!animals[@]}"do  printf "%s\n%s\n"  "${i}" "${animals[$i]}"done | jq -nR --arg oldMcD "$mcD" --arg eei "$eei" '  def to_o:    . as $in    | reduce range(0;length;2) as $i ({};         .[$in[$i]]= $in[$i+1]);  {$oldMcD,    $eei,   onthisfarm: [inputs] | to_o}'

Notice the trick whereby {$x} in effect expands to {(x): $x}

Using "\u0000" as the separator

If any of the keys or values contains a newline character, you could tweak the above so that "\u0000" is used as the separator:

for i in "${!animals[@]}"do    printf "%s\0%s\0"  "${i}"  "${animals[$i]}"done | jq -sR --arg oldMcD "$mcD" --arg eei "$eei" ' def to_o:   . as $in   | reduce range(0;length;2) as $i ({};       .[$in[$i]]= $in[$i+1]);  {$oldMcD,    $eei,   onthisfarm: split("\u0000") | to_o }'

Note: The above assumes jq version 1.5 or later.

You can reduce associative array with for loop and pipe it to jq:

for i in "${!animals[@]}"; do    echo "$i"    echo "${animals[$i]}"done |jq -n -R --arg mcD "$mcD" --arg eei "$eei" 'reduce inputs as $i ({onThisFarm: [], mcD: $mcD, eei: $eei}; .onThisFarm[0] += {($i): (input | tonumber ? // .)})'