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It is never clearly explained. In the novel there is a reference to a time Sam accidentally threw a bucket of urine all over Joe Bob and leaving the money was a way of making amends, although that seems far fetched. Some have speculated that perhaps Sam, who had a history of drinking and having affairs with married women after the deaths of his sons, was in fact Joe Bob's biological father and left the money as a result, but this is purely speculation.
The movie never fully explains what lies at the heart of the Poppers' marriage problems, but McMurtry's novel reveals that Coach Popper is probably a homosexual, and has interfered with male students. He gives Ruth no affection, and the little sexual contact they have is hasty and perfunctory. He appears very misogynistic, and disgusted by intimacy with Ruth.
Though the novel is set in the fictional Texas town of Thalia, it was renamed Anarene in the screenplay. Both were based on the real Texas town of Archer City, where McMurtry grew up. The movie was made on location there.
Billy was no relation to Sam the Lion. Sam simply took Billy under his wing, as he had a natural fatherly tendency towards the boys in the town. (It is important to note that no impropriety is hinted at in the book or film.)
In both the film and the novel, Joe Bob does not rape the girl. She pulls her underpants down in exchange for an ice cream. It is assumed that very little else took place. The novel offers a lengthy explanation for Joe Bob's behavior: he is sexually repressed, tormented for his entire adolescence by his desire to masturbate, but suffering under the weight of guilt.
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