I assume you’re talking about the “Come-a cow cow” section?

This particular song is based on an older tune called “The Old Chisholm Trail.” Other than the nonsense syllables the lyrics are quite different but that was the source. In the older tune it seems to be based on typical herding commands and similar sorts of shouts. I’ve heard versions that have a “ya!” or a “yippee-ka-yay” as a part of those things. This song and those like it were common ones sung while the cowboys did their herding. The line was later modified by Lead Belly in his expansion of the original.

Such an expansion isn’t unusual for this type of song, either. While a standard set of lyrics may be used today, folk tunes like this tended to have many, many verses made up by whatever individuals were singing it at the time. Standardized versions came about when people made an effort to explore and notate this folk music, as musicians like Percy Grainger did with English music.

Other songs that use similar lyrical elements would include “Git Along Little Dogies,” which famously has the “whoppie-ti-yi-yo” in the chorus. You’ll find similar songs in this collection by musicologist John Lomax. Chisholm Trail sheet music is on page 61.