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BackgroundZinc (Zn) malnutrition has been linked to serious health concerns in humans. Targeting genetic biofortification of rice grain Zn can efficiently improve the global Zn nutritional status. To genetically enhance rice grain Zn content, the genetic and molecular mechanisms of Zn deficiency response need to be elucidated. Here, Differential Gene Expression Analysis (DGEA) and Weighted Gene Coexpression Analysis (WGCNA) were established to identify modules of coexpressed genes, the most preserved genes and molecular pathways regulating Zn deficiency response in rice varieties. ResultsTwelve modules of coexpressed genes were obtained by WGCNA using 1649 differentially expressed genes (DEGs) from our DGEA and 2121 Zn genes from earlier studies. Three modules (TTA-M, TRA-M and CA-M) were judged the most relevant for Zn deficiency based on their richness in the well-recognized Zn deficiency responsive (ZDR) genes and molecular pathways. 96 (17%), 188 (47.6%) and 96 (24%) genes from TTA-M, TRA-M and CA-M modules respectively, were significantly expressed in the DGEA. These coexpressed DEGs (CoDEGs) were considered as the most preserved Zn deficiency responsive genes. Of the well-known ZDR genes, only OsZIP8, OsZIP10, OsMT1a and OsNAAT1 were preserved. Functional annotations for all CoDEGs from the identified ZDR modules showed that glutathione metabolism and biosynthesis of secondary metabolites were the most quickly upregulated molecular pathways. Lastly, a biology-informed gene-gene interaction network analysis (GGIN) indicated that CoDEGs including OsLSI3, OsWOX11, OsNRT1.1B, OsPSK5, OsSWN6 and OsMID1 strongly interact with the recognized ZDR genes in the ZDR modules. Curiously, these CoDEGs were previously validated for other economic traits in rice. ConclusionFindings from this study provide comprehensive insights into the molecular mechanisms of Zn deficiency response in rice and may facilitate gene and pathway prioritization, to enhance Zn use efficiency (ZUE) and Zn biofortification in rice.