BACKGROUND: The biological pathways related to Arabidopsis seed development have been well studied and functional genes involved in it have been discovered. However, functional studies about maize seed development were more limited compared to Arabidopsis.OBJECTIVE: Therefore, transferring knowledge from Arabidopsis into maize would facilitate functional studies about maize seed development.METHOD: In this study, public transcriptome data of the two species related to seed development were obtained. Co-expression network in each species was compared by integrating orthology information.RESULTS: This conserved co-functional network contained 4510 maize and 4808 Arabidopsis genes, respectively. Most of these genes were expressed in throughout embryo, early or later endosperm/seed. These conserved co-functional genes were significantly enriched for members of PPR protein family, which was consistent with that PPR proteins play an important role in maize seed development. Spatial-temporally co-functional genes were discovered in the seed coat and embryo. Furthermore, 66 well-studied genes involved in Arabidopsis seed development were co-functional with 319 maize genes and one maize gene (GRMZM2G036050) was further confirmed using an EMS-induced seed defective mutant by bulked segregating RNA sequencing (BSR) analysis.CONCLUSIONS: Altogether, these results showed the potential of this approach to support functional studies in maize seed development by transferring knowledge from Arabidopsis.