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Lipoxygenase 3 (<i>LOX3</i>) is a lipid peroxidase found in rice embryos that is known to affect seed quality. Interestingly, deletion of the <i>LOX3</i> gene has been shown to improve rice seed quality but decrease resistance to rice blast disease and drought. To investigate these opposing effects, we generated a <i>LOX3</i> knockout construct (Δ<i>Lox3</i>) in rice (<i>Oryza sativa</i> L.) plants. Blast resistance and transcription levels of rice genes in Δ<i>Lox3</i> rice plants and the effects of exogenous jasmonic acid (JA) on resistance and transcriptional levels of rice genes in <i>Magnaporthe oryzae-</i>infected Δ<i>Lox3</i> rice plants were further elucidated. The results showed that the Δ<i>Lox3</i> plants exhibited normal phenotypes, with high levels of methyl-linolenate and reactive oxygen species (ROS), and the genes involved in three Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways contributed to rice seed quality. <i>M. oryzae</i>-infected Δ<i>Lox3</i> plants exhibited serious blast symptoms with a reduced defense response but increased ROS-mediated cell death, and the genes involved in seven KEGG pathways contributed to rice seed quality. Exogenous JA treatment alleviated blast symptoms in infected Δ<i>Lox3</i> plants by hindering hyphal expansion, inhibiting ROS-mediated cell death, and increasing the defense response, and genes involved in 12 KEGG pathways contributed to rice seed quality. These findings demonstrate that <i>LOX3</i> plays an important role in rice growth and defense, and its knockout improves rice quality at the expense of disease resistance. Exogenous JA provides a means to compensate for the reduction in defense responses of <i>LOX3</i> knockout rice lines, suggesting potential applications in agricultural production.