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The price of rice rose by more than 3 percent.
Literal
Rice's price [subject-が] 3 percent or-more rose.
３パーセント以上 is 'more than 3 percent' — 以上 means 'or more/above,' so the actual increase is at least 3%. The kana spelling あがった is a variant of 上がった ('rose'), giving a slightly softer or more colloquial feel. ~以上 paired with numbers is a common idiom in news, statistics, and reporting.