Abstract
Soil cadmium (Cd) pollution threatens food safety. This study aimed to identify genes related to Cd accumulation in rice. Low- (Shennong 315, short for S315) and high- (Shendao 47, short for S47) Cd-accumulative rice cultivars were incubated with CdCl2·2.5H2O. RNA-seq and weighted gene co-expression network analysis (WGCNA) were performed to identify the modules and genes associated with Cd-accumulative traits of rice. After Cd stress treatment, the Cd content in various tissues of S315 was significantly higher than that of S47. In the stem nodes, the Cd distribution results of the two varieties indicated that the unelongated nodes near the root (short for node A) had a stronger ability to block Cd transfer upwards than the panicle node (short for node B). Cd stress induced huge changes in gene expression profiles. After analyzing the differentially expressed genes (DEGs) in significantly correlated WGCNA modules, we found that genes related to heavy metal transportation had higher expression levels in node A than that in node B, such as Copper transporter 6 (OS04G0415600), Zinc transporter 10 (OS06G0566300), and some heavy-metal associated proteins (OS11G0147500, OS03G0861400, and OS10G0506100). In the comparison results between S315 and S47, the expression of chitinase (OS03G0679700 and OS06G0726200) was increased by Cd treatment in S315. In addition, OsHSPs (OS05G0460000, OS08G0500700), OsHSFC2A (OS02G0232000), and OsDJA5 (OS03G0787300) were found differentially expressed after Cd treatment in S315, but changed less in S47. In summary, different rice varieties have different processes and intensities in response to Cd stress. The node A might function as the key tissue for blocking Cd upward transport into the panicle via vigorous processes, including of heavy metal transportation, response to stress, and cell wall.
Highlights
Because of the great difference between S315 and S47, most of the modules in WGCNA are not significant
Among the differentially expressed genes (DEGs) positively associated with the trait of the unelongated nodes near the root, we identified that Heavy metal transport/detoxification protein domain containing proteins (OS03G0383900, OS03G0861400, OS10G0506100, OS11G0147500), Copper transporter 6 (OS04G0415600) and Zinc transporters (OS04G0613000 and OS06G0566300) were significantly enriched in “metal ion transport” Gene Ontoloy (GO) term (GO:0030001), the expression patterns of which mediated these differences in Cd accumulation www.nature.com/scientificreports www.nature.com/scientificreports between the two types of nodes
After screening the co-expressed DEGs induced by Cd treatment, we found the expression patterns were quite different between S315 and S47 (Fig. 7a)
Summary
Because of the great difference between S315 and S47, most of the modules in WGCNA are not significant. We analyzed all co-expressed DEGs by GO and KEGG enrichment methods. After screening the co-expressed DEGs induced by Cd treatment, we found the expression patterns were quite different between S315 and S47 (Fig. 7a). Most DEGs enriched in these GO terms, including OS08G0500700 (OsHSP82A, Heat shock protein 82), OS02G0232000 (OsHSFC2A, Heat shock transcription factor 29), OS04G0444800 (OsFRO1, Ferric reductase-like transmembrane component family protein), OS07G0448100 (OsPIP2, Plasma membrane integral protein), showed higher expression in S315 than S47 in control, which decreased by Cd treatment in S315, but no significant changes in S47 (Fig. 7b–e). These findings showed that genes might have crucial roles in regulating Cd accumulation in rice
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