A wide range of morphological and physiological traits have been changed between cultivated rice Oryza sativa and wild rice Oryza rufipogon under domestication. Here we report the cloning of An-2 gene, encoding a Lonely Guy Like protein 6 (OsLOGL6), which catalyzes the final step of cytokinin synthesis in O.rufipogon. The near-isogenic line harboring a wild allele An-2 in the genetic background of the awnless indica Guangluai 4 shows that An-2 promote awn elongation by enhancing cell division, but decreases grain production by reducing grains per panicle and tillers per plant. We reveal that a genetic variation in the An-2 locus has a large impact on reducing awn length and increasing tiller and grain numbers in domesticated rice. Expressional analysis demonstrates that An-1 regulates the formation of awn primordial, and An-2 promotes awn elongation. Nucleotide diversity of An-2 locus in cultivated rice was found to be significantly reduced compared to that of wild rice, suggesting that An-2 locus was subjected to artificial selection. We therefore proposed that the selection of the genetic variation in An-2 was due to reduced awn length and increased grain yield in cultivated rice.