Integrated Transcriptomic and Phenotypic Analyses Reveal Tissue-Specific Nitrogen Responses and Candidate Genes for Low-Nitrogen Tolerance in Sorghum

Multi-tissue transcriptomics reveals candidate co-expression and metabolic networks associated with low-nitrogen adaptation in oat

Integrated physiological, transcriptomic and metabolomic analysis reveals differential cold response in wheat seedlings across varieties

Background Cold stress is a major environmental constraint limiting wheat productivity worldwide. Although numerous cold-responsive pathways have been identified, the molecular basis of differential cold tolerance among genetically related wheat lines remains poorly understood. In this study, two wheat sibling lines derived from a single progeny plant of the same parental cross, Luyan951 (cold-tolerant) and Luyan955 (cold-sensitive), were employed to investigate the regulatory mechanisms of cold adaptation through integrated physiological, transcriptomic, and metabolomic analyses. Results Physiological assays revealed that Luyan951 exhibited markedly enhanced cold tolerance, with a survival rate of 52.67% following cold treatment compared with 20.67% in Luyan955. This enhanced tolerance was accompanied by 1.90–2.41-fold greater increases in antioxidant enzyme activities (SOD, CAT, and POD) and 1.84–4.50-fold greater accumulation of proline and soluble sugars relative to Luyan955, along with substantially lower MDA accumulation. Transcriptomic and metabolomic analyses identified phenylpropanoid biosynthesis and jasmonic acid (JA) signaling as key pathways associated with cold adaptation. Compared with Luyan955, cultivar Luyan951 exhibited stronger activation of these pathways under cold stress. Key genes involved in phenylpropanoid biosynthesis (CAD, and 4CL) and JA signaling (JAZ, MYC2) were significantly upregulated in Luyan951, as confirmed by qRT-PCR. Bioinformatic analyses further suggested that AP2/ERF transcription factors may act as upstream regulators of these pathways. Furthermore, subcellular localization and transcriptional activation experiments confirmed the nuclear localization and transactivation function of three AP2/ERF genes (TraesCS5D02G318400, TraesCS6A02G381000, TraesCS6D02G366100). Conclusions Our findings indicate that the phenylpropanoid biosynthesis pathway plays a significant role in the cold tolerance of wheat, and together with the jasmonic acid signaling pathway, it forms a crucial regulatory network. This network promotes the scavenging of reactive oxygen species, maintains osmotic homeostasis, and stabilizes metabolism under low-temperature stress. Integrated analyses further suggest that this network may be coordinated by upstream ERF transcription factors. These findings provide comprehensive insights into the molecular mechanisms of wheat cold adaptation and offer valuable candidate genes and pathways for the genetic improvement of cold tolerance in wheat.

Comprehensive RNA-Seq analysis revealed molecular pathways and genes associated with drought tolerance in Morus alba cv. Yunsang-2.

Drought stress driven by global climate change critically restricts mulberry growth. The identification of drought-responsive genes in the Yunnan-adapted Yunsang cultivar is essential for mitigating environmental constraints on sericulture. In this study, seedlings of the mulberry cultivar Yunsang-2 were subjected to drought stress under greenhouse conditions. Leaf samples were collected for physiological analysis (proline content and CAT and POD activities) and transcriptome profiling via RNA-Seq. The results revealed that compared with the plants in the CK group, the drought-stressed plants had significantly increased CAT and POD activities by 7 days post-stress (DPS) and accumulated markedly greater amounts of proline at 9 and 12 DPS. Transcriptomic analysis revealed that drought resistance involves key genes enriched in the abscisic acid (ABA), gibberellin (GA), and brassinosteroid (BR) signaling pathways, such as PYR, ABF, PIF3, and BSK. Furthermore, we identified 156 TFs as potential regulatory hubs. Among these genes, MnERF21 was tentatively identified as a candidate positive regulator of drought resistance. Our findings systematically elucidate the molecular mechanisms underlying drought tolerance in mulberry and provide novel insights into the drought resistance strategies of Yunnan-adapted germplasms.

StuPPO9 Enhances Drought Tolerance in Potato (Solanum tuberosum) by Coordinating Photosynthetic Stability and Secondary Metabolism Reprogramming

It is suggested that StuPPO9 confers drought resilience through a multi-layered network involving optimized carbon allocation, reinforced cell wall integrity, and enhanced ROS scavenging capacity.

Genome-wide analysis of amino acid transporter genes reveals their potential roles in drought stress and drought-associated disease responses in peanut (Arachis hypogaea)

A genome-wide characterization and expression analysis of the peanut AAT gene family and identifies candidate genes for future functional studies on stress-associated amino acid transport and metabolic adjustment in peanut roots are provided.

Genome‑wide analysis of the maize CK1 family and functional characterization of ZmCK1-8 in modulating root architecture and nitrate‑responsive physiological traits under low‑nitrogen conditions

A novel component of the maize nitrogen-signaling network is uncovered and provide a candidate gene for further functional studies on low-nitrogen adaptation in maize.