Identification of seed-quality related genes in rice (Oryza sativa L.)

Seed quality is a significant factor in rice production, because of its impact on farmer incomes and the economy. So, identifying candidate genes involved in the seed composition quality trait is essential for developing high-quality genotypes. To this end, forty-one genes associated with the seed composition quality trait were retrieved from Planteome (https://browser.planteome.org/amigo ). A gene network was predicted among the genes via the STRING v۱۱ database (https://string-db.org/). After that, the predicted network was automatically expanded by the STRING database, which resulted in the prediction of ۵ genes, namely OsJ_۱۰۲۲۶ (Vacuolar sorting protein ۹ domain containing protein, expressed), OsJ_۱۷۳۴۴ (Putative phosphatidylinositol ۳-kinase), BGLU۸ (Beta-glucosidase ۸), BGLU۴ (Beta-glucosidase ۴), and OS۰۳T۰۸۴۲۷۰۰-۰۳ (Putative Vacuolar sorting protein). Interactions of the predicted genes with the well-known genes involved in seed quality support their role in seed quality. Moreover, the predicted promoter sequences were checked for the presence of transcription factor binding sites using PlantCARE (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/). According to the promoter analysis of the predicted genes, important transcription factor binding sites related to zein metabolism regulation were identified, confirming the involvement of the predicted genes in the seed composition quality. To our knowledge, there is no detailed study about the role of these predicted candidate genes in seed composition quality. These findings provide a new avenue for functional analyses of novel predicted genes and give clues to engineering high-quality rice.

Keywords:

network analysis , rice , seed composition quality trait