Journal Article

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

Xia, Shenglan, Li, Dan, Liu, Caifeng, Yu, Rugang, Shi, Gangrong, Du, Xueling

2017

Overview

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.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Accumulation / Accumulators / Adenosine triphosphatase / Analysis / Animal Genetics and Genomics / Annotations / Biological activity / Biological Transport - genetics / Biomedical and Life Sciences / Brassica / Brassica rapa - genetics / Brassica rapa - metabolism / Brassica rapa chinensis / Cadmium / Cadmium - metabolism / Cd stress / Chinese cabbage / Cultivars / Gene expression / Gene Expression Profiling / Gene sequencing / Genes / Genetic aspects / Genetic transcription / Genomics / Ion transport / Life Sciences / Metabolism / Microarrays / Microbial Genetics and Genomics / Molecular Sequence Annotation / Pak choi / Physiological aspects / Plant Genetics and Genomics / Plant Proteins - genetics / Plant Proteins - metabolism / Plant Roots - genetics / Proteins / Proteomics / Regulatory mechanisms (biology) / Research Article / Ribonucleic acid / RNA / RNA sequencing / Root / Roots / Signal transduction / Soil contamination / Transcriptome / Transcriptomic methods / Translocation / Transport