The crossroads where Mr. Shimerda is buried can be understood as a metaphor for both Antonia's and Jim's futures. Both spend time as children on the prairie in the early years when a single stake marks the divisions between farms. They both leave the prairie on divergent roads, Antonia to work in nearby Black Hawk, and Jim to eventually earn a degree at Harvard. Later, "when all the fields (are) under fence", they meet again on the prairie, their "two roads...cross(ing)...on (that) corner" where Mr. Shimerda lies buried. With her husband and their large brood of children, Antonia has come back on the road she had taken so many years before, and Jim has met her at the crossroads to witness her fulfillment, their lives "dusty roads...like soft grey rivers flowing past" the old man's grave (Bk.I, Ch.XVI).
I think the metaphor can also represent the bond between Jim and Antonia. When Mr. Shimerda dies and is buried at the crossroads, Jim's and Antonia's time of idyllic friendship is at a crossroads as well. From that time, Antonia must put all her efforts into working on the farm, while Jim goes on with this education. They no longer have the opportunity to grow together in childlike exploration and wonder, and Antonia acknowledges this when she tearfully asks Jim, "sometime you will tell me all those nice things you learn at the school, won't you, Jimmy...you won't forget my father?" (Bk.I, Ch.XVII).