Genome-wide transcriptome and physiological analyses provide new insights into cadmium tolerance to tomato seedlings

Background: Cadmium (Cd) pollution in agricultural soils has become one of the main environmental problems in China. This study investigated the underlying molecular mechanism controlling the effects of auxin and lignin in response to Cd stress in tomato. Results Cadmium treatment significantly inhibited the root growth (by 43.46%) of tomato seedlings, and induced their antioxidant enzyme activities (POD and CAT). Cadmium treatment decreased their shoot dry weight and root dry weight at day 7, 40.42% and 60.40%, respectively. The content of malondialdehyde (MDA) increased and total chlorophyll contents were reduced during the treatment. A comparative transcriptome (RNA-Seq) was de novo assembled and differentially expressed genes (DEGs) with altered expression levels were investigated among wild type cultivars A57 with or without cadmium ion treatment for 24 h. A total of 18,883 unigenes were grouped into 51 Gene Ontology (GO) categories and 89 Kyoto Encyclopedia of Genes and Genomes terms (KEGG). A number of 1,563 differentially expressed genes (DEGs) were found in Cd-exposed tomato seedlings, including 559 down-regulated genes and 1157 up-regulated genes. Go term enrichment analysis indicated that various auxin signaling pathway-related GO terms were significantly enriched in DEGs. Most genes involved in lignin biosynthesis pathway were up-regulated, for instance, COMT and CCOMT. Conclusions The transcriptome expression profiles of tomato seedlings under Cd stresses obtained in this study provided a resource for identifying common mechanisms in the lignification formation and the inhibition of plant growth.