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This is a sentence from chapter 11 of Tobira:

日本人は季節や天候の変化を大変気にするが、これは日本人が米作りを非常に大事なことと考え、どうやって効率よく米を生産するかが、日本人の生活の仕方や考え方に強い影響を与えてきたことと関係があると言われている。

I think I was able to understand it well before I came upon the と関係がある part; now I can't seem to understand what the whole sentence means. What has a relation with what?

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This is a deeply nested sentence, but its basic structure is "AはBと関係があると言われている", or "A is said to be related to B". What's tricky about this sentence is that B itself is two very long clauses, one of which even contains an embedded question:

  • A: これ this
  • B: 日本人が米作りを非常に大事なことと考え、どうやって効率よく米を生産するかが、日本人の生活の仕方や考え方に強い影響を与えてきたこと
    the fact that the Japanese consider rice cultivation to be very important, and that how to produce rice efficiently has strongly influenced the way of life and thinking of the Japanese people

Note that これ is marked with は but the two subjects in the B part are marked with が (because it's in a こと-clause).

日本人は季節や天候の変化を大変気にするが、[これ]Aは[日本人が米作りを非常に大事なことと考え、どうやって効率よく米を生産するかが、日本人の生活の仕方や考え方に強い影響を与えてきたこと]Bと関係があると言われている。

Japanese people are very concerned about seasons and weather changes. [This]A is said to be realted to [the fact that the Japanese consider rice cultivation to be very important, and that how to produce rice efficiently has strongly influenced the way of life and thinking of the Japanese people]B.

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You can encapsulate the whole thing between これは and と関係がある. The structure is これはAと関係があるといわれている=It is said that this is related to (the fact that) A, where A is 日本人が米作りを....与えてきたこと.

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