Identification of candidate genes related to aroma in rice by analyzing the microarray data of highly aromatic and nonaromatic recombinant inbred line bulks

Aroma is an important factor affecting the rice quality. However, the breeding strategies for improving aroma, the molecular basis of the aroma formation, and aroma-related genes are yet to be investigated. In this study, microarray analysis was performed followed by gene ontology (GO) enrichment analysis and protein–protein interaction (PPI) network analysis for discovering the differentially expressed genes in the bulks of an aromatic and a nonaromatic recombinant inbred line (RIL) derived from a cross between a basmati rice variety, Pusa 1121, and a nonaromatic rice variety, Pusa 1342. GO enrichment analysis categorized a total of 2577 differentially expressed genes into 24 functional groups. The metabolic process was the most highly overrepresented category enriched by the differentially expressed genes. One of the most paramount minor subcategories in the metabolic process category was “cellular aromatic compound metabolic process (GO: 0006725)” with 21 genes that may serve as novel candidates for genes involved in aroma formation. According to the network analysis, six downregulated genes, as well as two upregulated genes, were identified as critical in the PPI network. These results will provide a perspective for unveiling the key components of the mechanisms behind the aroma formation in rice and give the required information on client-oriented breeding.