Identification of heavy metal transport-related genes and microRNAs in response to cadmium toxicity and micronutrient deficiency in barley roots

Abstract

Plants have evolved specialized transport systems to regulate heavy metal accumulation. However, the transcriptional regulation and evolutionary aspects of heavy metal-related transporters remain largely unexplored. In this study, cross-homeostasis among divalent metal ions including cadmium (Cd^{2 +}), iron (Fe²⁺), manganese (Mn²⁺), zinc (Zn²⁺), and copper (Cu²⁺) was investigated in barley (Hordeum vulgare L.) roots under conditions of cadmium excess and micronutrient deficiency. Through comparative genomics analysis across six plant species, we systematically identified 532 heavy metal-associated transporter genes, including those from the ABC, CAX and MFS families. Integrated genome-transcriptome analyses revealed distinct accumulation mechanisms in hyperaccumulator species and uncovered competitive interactions among metal transporters. Weighted gene co-expression network analysis of 666 transcriptome samples identified 35 candidate transcription factors (including bHLH, NAC, and WRKY family members) within eight co-expressed modules potentially governing metal homeostasis. Furthermore, integrated small RNA sequencing with miRNA-target correlation analysis uncovered 29 miRNA-transporter regulatory pairs, suggesting post-transcriptional control mechanisms. Our findings propose evolutionary perspectives on heavy metal-related transporters and delineate a transcriptional regulatory network activated under metal stress, offering new insights for gene manipulation strategies aimed at reducing Cd accumulation and improving micronutrient balance in crops.

Keywords: Comparative genomics; Heavy metals; MicroRNAs; Transcriptional regulation; Transporter.