High salinity is a major environmental stressor for crops. To understand the regulatory mechanisms underlying salt tolerance, we conducted a comparative transcriptome analysis between salt-tolerant and salt-sensitive jute (Corchorus spp.) genotypes in leaf and root tissues under salt stress and control conditions. In total, 68,961 unigenes were identified. Additionally, 11,100 unigenes (including 385 transcription factors (TFs)) exhibited significant differential expression in salt-tolerant or salt-sensitive genotypes. Numerous common and unique differentially expressed unigenes (DEGs) between the two genotypes were discovered. Fewer DEGs were observed in salt-tolerant jute genotypes whether in root or leaf tissues. These DEGs were involved in various pathways, such as ABA signaling, amino acid metabolism, etc. Among the enriched pathways, plant hormone signal transduction (ko04075) and cysteine/methionine metabolism (ko00270) were the most notable. Eight common DEGs across both tissues and genotypes with similar expression profiles were part of the PYL-ABA-PP2C (pyrabactin resistant-like/regulatory components of ABA receptors-abscisic acid-protein phosphatase 2C). The methionine metabolism pathway was only enriched in salt-tolerant jute root tissue. Twenty-three DEGs were involved in methionine metabolism. Overall, numerous common and unique salt-stress response DEGs and pathways between salt-tolerant and salt-sensitive jute have been discovered, which will provide valuable information regarding salt-stress response mechanisms and help improve salt-resistance molecular breeding in jute.

Cadmium (Cd) is a dangerous environmental contaminant. Jute (Corchorus sp.) is an important natural fiber crop with strong absorption and excellent adaptability to metal-stressed environments, used in the phytoextraction of heavy metals. Understanding the genetic and molecular mechanisms underlying Cd tolerance and accumulation in plants is essential for efficient phytoremediation strategies and breeding novel Cd-tolerant cultivars. Here, machine learning (ML) and hyperspectral imaging (HSI) combining genome-wide association studies (GWAS) and RNA-seq reveal the genetic basis of Cd resistance and absorption in jute. ML needs a small number of plant phenotypes for training and can complete the plant phenotyping of large-scale populations with efficiency and accuracy greater than 90%. In particular, a candidate gene for Cd resistance (COS02g_02406) and a candidate gene (COS06g_03984) associated with Cd absorption are identified in isoflavonoid biosynthesis and ethylene response signaling pathways. COS02g_02406 may enable plants to cope with metal stress by regulating isoflavonoid biosynthesis involved in antioxidant defense and metal chelation. COS06g_03984 promotes the binding of Cd²⁺ to ETR/ERS, resulting in Cd absorption and tolerance. The results confirm the feasibility of high-throughput phenotyping for studying plant Cd tolerance by combining HSI and ML approaches, facilitating future molecular breeding.

Cannabis sativa L., a dioecious plant, exhibits sex-specific medicinal active ingredients. However, their causes remain unexplored. In this study, C. sativa flowers exhibited significant intersexual morphological differences, particularly in glandular trichomes. 1676 DEGs and 700 DAMs were identified. Among 149 genes related to sexual differentiation, 77 encode hormone-related products presumably involved in dioecy. Female flowers had cannabinoid levels 16.88 times those of males. Metabolomic sequencing identified 28 distinct terpenoids. We identified CsDXPS1, CsLOX2, CsLOX1.5, CsAAE18, CsAAE6-1, CsAAE6-2, CsGGR, and the metabolite mevalonate-5P; all except AAE6 were highly expressed in female flowers, regulating terpene and cannabinoid production. Seven glandular-trichome-related DEGs showed significant positive correlation with cannabinoid and terpene abundance; female-enriched CsMYC4 (TPS activator) and CsMYB49 (secretion enhancer) emerged as pivotal transcriptional regulators. These results provide a theoretical basis for the directional selection of female and male strains with high production and cultivation value.