Comparative transcriptome analysis reveals key cadmium transport-related genes in roots of two pak choi (Brassica rapa L. ssp. chinensis) cultivars

BACKGROUND: Cadmium translocation from roots to shoots is a complex biological process that is controlled by gene regulatory networks. Pak choi exhibits wide cultivar variations in Cd accumulation. However, the molecular mechanism involved in cadmium translocation and accumulation is still unclear. To isolate differentially expressed genes (DEGs) involved in transporter-mediated regulatory mechanisms of Cd translocation in two contrasting pak choi cultivars, Baiyewuyueman (B, high Cd accumulator) and Kuishan’aijiaoheiye (K, low Cd accumulator), eight cDNA libraries from the roots of two cultivars were constructed and sequenced by RNA-sequencing. RESULTS: A total of 244,190 unigenes were obtained. Of them, 6827 DEGs, including BCd(10) vs. BCd(0) (690), KCd(10) vs. KCd(0) (2733), KCd(0) vs. BCd(0) (2919), and KCd(10) vs. BCd(10) (3455), were identified. Regulatory roles of these DEGs were annotated and clarified through GO and KEEG enrichment analysis. Interestingly, 135 DEGs encoding ion transport (i.e. ZIPs, P(1B)-type ATPase and MTPs) related proteins were identified. The expression patterns of ten critical genes were validated using RT-qPCR analysis. Furthermore, a putative model of cadmium translocation regulatory network in pak choi was proposed. CONCLUSIONS: High Cd cultivar (Baiyewuyueman) showed higher expression levels in plasma membrane-localized transport genes (i.e., ZIP2, ZIP3, IRT1, HMA2 and HMA4) and tonoplast-localized transport genes (i.e., CAX4, HMA3, MRP7, MTP3 and COPT5) than low Cd cultivar (Kuishan’aijiaoheiye). These genes, therefore, might be involved in root-to-shoot Cd translocation in pak choi. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-017-3973-2) contains supplementary material, which is available to authorized users.