Phenolic acids are known allelopathic compounds that may serve as the primary cause of continuous cropping obstacles in Coix lacryma-jobi L. (Coix). However, the concentrations, types, and specific stress responses of Coix to these phenolic acids still require further investigation. In this study, the cultivar ‘Wanyi 2′ was used to examine the effects of different phenolic acids and their concentrations on the growth of Coix. Four concentrations (0 mg/L, 10 mg/L, 100 mg/L, and 1000 mg/L) and four phenolic acid types (p-hydroxybenzoic acid, salicylic acid, cinnamic acid, and ferulic acid) were used to assess their influences on plant growth, leaf physiological parameters, and metabolic pathways under greenhouse conditions. In this greenhouse pot experiment, the effects of the four phenolic acids showed a similar tendency: a low concentration (10 mg/L) tended to promote the growth and root development of Coix seedlings, whereas high concentrations (100 and 1000 mg/L) generally showed inhibitory effects. Among these phenolic acids, ferulic acid exhibited the strongest inhibitory effect at the highest concentration (1000 mg/L), while salicylic acid showed the most pronounced growth-promoting effect at low concentrations (10 mg/L). In addition, high levels of phenolic acids markedly increased antioxidant enzyme activities and oxidative stress-related substances in Coix leaves, while reducing soluble sugar (SS) and soluble protein (SP) contents. Our data suggest that under phenolic acid stress, Coix leaves exhibited changes in the metabolism of phenolic acids (e.g., 4-methoxysalicylic acid, gallic acid) and amino acids (e.g., glutathione, proline), which may be associated with the adaptive response to allelochemical-induced stress. Overall, this study provides insights that may support strategies to optimize plant growth regulators and mitigate continuous cropping barriers in Coix.

HD-Zip (homeodomain-leucine zipper) transcription factors play a crucial role in plant growth, development, and stress response; however, the HD-Zip gene family of Coix lacryma-jobi L. has not been identified. In this study, a total of 40 HD-Zip gene family members were identified in the genome of Coix. According to phylogenetic analysis, the Coix HD-Zip gene was divided into four subfamilies (I–IV), of which the HD-Zip I subfamily can be further divided into five branches. Moreover, HD-Zip members of the same subfamily usually share similar gene structures and conserved motifs. The transcription factor binding site enrichment analysis showed that there are many motifs for binding with transcription factors such as ERF (Ethylene responsive factor), MYB (v-myb avian myeloblastosis viral oncogene homolog), and ARF (Auxin Response Factor) in the promoter region of the ClHDZ genes. The results of qPCR (Quantitative Polymerase Chain Reaction) and expression profile analysis showed that ClHD-Zip I genes showed different levels of expression under different stress treatments. Among them, ClHDZ4 was located in the nucleus, and its expression pattern was significantly upregulated under salt, drought, and high-temperature stress. In addition, ectopic expression of ClHDZ4 enhanced the growth of yeast strains under drought, salt, or high-temperature treatment. In summary, these results laid a foundation for further research on the resistance function of the Coix HD-Zip gene.