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

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. 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 ). 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

Drought stress is a primary abiotic constraint limiting potato productivity. While polyphenol oxidase (PPO) is known to participate in stress responses, the specific role of StuPPO9 in drought tolerance remains poorly understood. In this study, we generated StuPPO9-overexpressing (OE) and CRISPR/Cas9-mediated knockout (C4) lines in the potato cultivar ‘Atlantic’. Under sustained drought stress, OE lines exhibited significantly superior growth phenotypes compared to wild-type (WT) and C4 plants, characterized by increased leaf and root relative water content, root number and enhanced photosynthetic efficiency (Pn and Gs). OE plants also maintained lower levels of MDA and ROS through elevated antioxidant enzyme activities. Notably, transcriptomic analysis revealed that StuPPO9 triggers a global reprogramming of metabolic pathways. Key drought-responsive genes associated with phenylpropanoid biosynthesis (e.g., anthocyanin acyltransferase), terpenoid metabolism, and hormone signaling (e.g., HPt protein) were significantly upregulated in OE plants. These findings suggest that StuPPO9 confers drought resilience through a multi-layered network involving optimized carbon allocation, reinforced cell wall integrity, and enhanced ROS scavenging capacity. This study provides a promising genetic target and theoretical foundation for breeding drought-resistant potato varieties.

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

Nitrogen deficiency is a major constraint of global maize production. Although CK1 family members have diverse regulatory functions in eukaryotes, the CK1 family in maize has not yet been systematically identified, and their roles in maize nitrogen metabolism remain poorly understood. In the current study, we sought to identify the ZmCK1 family members and investigate the physiological and molecular roles of ZmCK1s in maize growth under low-nitrogen conditions. We identified 20 maize ZmCK1 family members and characterized them through phylogenetic analysis, motif and domain prediction, gene structure analysis, promoter cis-element annotation, and nitrate-responsive transcriptome profiling. ZmCK1-8 , a nitrate-responsive gene, was selected for functional analysis. B73 and ZmCK1-8 mutants were hydroponically cultured under low-nitrogen conditions to assess root architecture, glutamine synthetase (GS), glutamate synthase (GOGAT), nitrate reductase (NR), and protein and nitrogen contents. The mutants exhibited enhanced root growth, suggesting that ZmCK1-8 plays a role in regulating root growth under low‑nitrogen condition and is associated with altered nitrogen‑related physiological traits. Transcriptomic analysis identified 256 and 660 genotype‑dependent nitrate‑responsive genes in ck1‑8‑1 and ck1‑8‑2 mutants, respectively, enriched in hormone signaling, stimulus responses, and transmembrane transporter activity. Loss of ZmCK1-8 was associated with upregulation of ZmGS1-5 , and altered nitrogen-related physiological traits. Yeast two-hybrid and BiFC assays confirmed that ZmCK1-8 physically interacts with the chromatin remodeler ZmCHB101. RT-qPCR analysis of ZmCHB101 RNAi line further suggested that ZmCK1-8 and ZmCHB101 share several downstream targets, including ZmGS1–5 , GOGAT , and ZmPTR11 . In contrast, other nitrate-responsive genes, such as ZmPTR12 , ZmNPF25 , and ZmNPF34 , showed distinct expression patterns between the two genetic backgrounds. Genome-wide analysis identified 20 ZmCK1 members, of which ZmCK1-8 was found to be associated with nitrate‑induced root growth. Loss of ZmCK1-8 function is associated with altered nitrogen-related physiological traits in roots, while ZmGS1-5 is identified as a candidate downstream responder. Furthermore, ZmCK1-8 physically interacts with ZmCHB101, though the mechanistic link between this interaction and target-gene regulation remains to be established. These results uncover a novel component of the maize nitrogen-signaling network and provide a candidate gene for further functional studies on low‑nitrogen adaptation in maize.