Single-cell multiome reveals root hair-specific responses to salt stress

Soil salinization, exacerbated by environmental deterioration and improper cultivation, is a major challenge for sustainable agriculture. The root is the primary organ in plants to perceive and respond to salt stress. Utilizing single-cell sequencing, we have created the first single-cell transcriptional and chromatin accessibility landscape for normal and salt-stressed root tips in non-heading Chinese cabbage (NHCC). Our study reveals that salt stress disrupts the normal differentiation of root hairs, leaving many in an undifferentiated state and preventing stress response gene expression. Inter-species analyses show that both salt and osmotic stresses inhibit root hair differentiation and elongation similarly, resulting in fewer, malfunctioning root hairs. We found that high salinity affects root hair iron transport. Salt stress-responsive genes, cell type-specific transcriptional regulatory networks, and trajectory curves are linked to iron transport. Specifically, the expression of BcIRT2, a metal transporter gene, is influenced by salt stress. Silencing BcIRT2 causes chlorotic leaves and increases salt sensitivity, reducing iron content in NHCC roots. Our findings offer significant insights into plant salt stress responses and provide valuable information for breeding salt-tolerant NHCC and other crops.