Search Results (392)

Background/Objectives: Precision nutrition informed by genetic profiling has been proposed to improve public health outcomes; however, long-term, community-based evidence remains limited. This study evaluated the long-term health and economic impacts of the Sakado Folate Project. Methods: Since 2006, residents participating in the Sakado Folate Project received gene-guided nutritional counseling focused on folate intake and related lifestyle factors. Target genes included methylenetetrahydrofolate reductase (MTHFR), angiotensinogen (AGT), adrenoreceptor B3 (ADRB3), and uncoupling protein 1 (UCP1); Δ5-fatty acid desaturase (FADS1) was incorporated later. Biochemical markers, genetic polymorphisms, and health indicators were monitored longitudinally. Population-level health outcomes and per-capita medical expenditure data were compared with regional and national statistics. Results: In program participants (n = 888), folate status and biochemical indicators improved: 76.1% achieved the serum folate target (≥9.5 ng/mL) and 55.3% achieved the serum total homocysteine target (≤7 μmol/L). Healthier lifestyle behaviors were observed across 99,565 Sakado residents, with the city recording the highest proportion of individuals actively attempting lifestyle improvement (31%) of all districts in the region. Disease prevalence was lower in Sakado City than in Saitama Prefecture overall, at standardized prevalence ratios of 52% for stroke and 86% for cerebral infarction. Per-capita medical expenditure was also lower in Sakado City (¥337,800) than the national average (¥392,044) in 2021. Conclusions: Long-term implementation of a community-based, gene-guided nutritional intervention may improve population health outcomes and reduce healthcare expenditures. Integrating nutrigenomics into public health strategies alongside community education and food environment improvements may contribute to sustainable healthcare systems in aging societies. Full article

This study demonstrated the effects of dietary supplementation with 1% raspberry (RO) or 1% strawberry (SO) seed oil from 5 to 12 weeks of age (n = 6/group) on folliculogenesis, hormonal parameters, the ovarian fatty acid profile, and the expression of related genes in juvenile rabbits. After slaughter, ovaries and blood were collected. Ovaries were used for histology, fatty acid profiling, and gene expression analysis, while plasma was used to measure progesterone (P4), testosterone (T), estradiol-17β (E2), follicle-stimulating hormone (FSH), and anti-Müllerian hormone (AMH) concentrations. Both RO and SO reduced the number of primary follicles (p = 0.04), whereas RO increased the number of antral follicles (p = 0.04) compared with the control. In both supplemented groups, FSH (p = 0.04 and p = 0.035) and AMH (p = 0.04) concentrations were higher. RO increased P4 and E2 (p = 0.03 and p = 0.013) concentrations, while SO only increased P4 (p = 0.02) levels. SO altered the ovarian fatty acid profile, increasing selected monounsaturated fatty acids and reducing polyunsaturated fatty acids, likely by increasing the expression of the converting enzyme, stearoyl-CoA desaturase 5 (p = 0.038). Overall, both oils influenced folliculogenesis through hormonal changes, and SO modified ovarian fatty acid composition, which may affect ovarian function in juvenile rabbits. Full article

Physalis grisea is an orphan crop with significant economic and medicinal potential. Although initial genome editing applications have recently emerged for Physalis species, the development and optimization of highly efficient, visually traceable Agrobacterium-mediated editing platforms remain crucial for advancing its functional genomics. This study uses the phytoene desaturase (PDS) gene—a key enzyme in the carotenoid biosynthetic pathway—as a visual reporter to develop a CRISPR/Cas9-mediated genome editing platform in P. grisea. A dual-target guide RNA (sgRNA) expression vector was constructed, and transgenic plants were successfully generated via Agrobacterium-mediated transformation of hypocotyl explants. Strikingly, phenotypic observations revealed that the regenerated mutants exhibited characteristic complete albino or green-white chimeric phenotypes, accompanied by distinct developmental retardation and dwarfing. Physiological quantitative analysis showed that total chlorophyll and carotenoid contents in the mutant leaves were significantly reduced by over 70% and 78%, respectively. Targeted sequencing further confirmed that the CRISPR/Cas9 system efficiently induced various mutations at the PgPDS locus (derived from Physalis grisea)—including fragment deletions, 1–4 bp insertions, and 2–3 bp substitutions—revealing a specific preference for non-homologous end joining (NHEJ) repair. In summary, this study not only validates the suitability of PgPDS as a reporter gene but also successfully establishes a robust genome editing technical system for P. grisea, providing a solid foundation for future functional genomics research and molecular breeding in this crop. Full article

Omega-3 fatty acid desaturases (FAD3, FAD7, and FAD8) are key enzymes responsible for the production of α-linolenic acid (ALA), which is an essential polyunsaturated fatty acid regulating membrane stability and serves as a precursor for jasmonic acid. In this study, we performed a comprehensive genome-wide molecular characterization of omega-3 fatty acid desaturase genes across seven plant species. Phylogenetic analysis placed FAD3 and FAD7/FAD8 proteins in distinct clades, indicating functional divergence despite strong sequence conservation. Gene structure analysis revealed conserved exon–intron formation with a few unique features. Multiple sequence alignment and motif analysis revealed high sequence similarity with three histidine-rich boxes responsible for catalytic activity. Cis-regulatory elements revealed the abundance of light-responsive and ABA-responsive elements such as Box4 and ABRE, suggesting environmentally induced responses of omega-3 fatty acid desaturase genes. Moreover, q-RT PCR analysis revealed that the combined stresses of temperature and salt strongly influence the transcript levels of omega-3 fatty acid desaturase (FAD3, FAD7, and FAD8) in Arabidopsis thaliana; among them, the FAD8 gene displayed significantly higher expression levels under salt stress conditions, especially at 22 °C temperature, indicating its possible leading role in stress adaptation. Furthermore, comparative promoter analysis revealed enrichment of stress-responsive motifs in the promoter regions of AtFAD7 and AtFAD8, whereas AtFAD3 contained more ABA-responsive elements. In addition, Pearson correlation analysis revealed a temperature-dependent relationship between promoter motifs and gene expression under salt stress at 31 °C in Arabidopsis thaliana. Overall, these findings suggest that omega-3 fatty acid desaturases are highly conserved yet transcriptionally dynamic under environmental conditions. This study provides a foundation for future genetic and functional studies of omega-3 fatty acid desaturase genes aimed at enhancing stress adaptation by targeting and regulating fatty acid metabolism. Full article

Docosahexaenoic acid (DHA) is an essential ω-3 polyunsaturated fatty acid (PUFA) with high nutritional and pharmaceutical value. The marine protist Aurantiochytrium is a promising industrial DHA producer; however, its DHA biosynthesis via the PUFA synthase pathway co-produces ω-6 docosapentaenoic acid (DPA), limiting DHA purity. Here, we introduced an ω-3 desaturase from Phytophthora infestans (Pin-O3D) into Aurantiochytrium sp. SD116. Functional validation in an Escherichia coli system co-expressing the native PUFA synthase confirmed that Pin-O3D converts DPA to DHA, shifting the DHA/DPA ratio from 1:1 to 2:1. Pin-O3D was then integrated into the fatty acid synthase (FAS) locus, simultaneously attenuating FAS activity and enabling heterologous gene expression. The engineered strain ΔFAS-Pin-O3D exhibited significantly (p < 0.0001 in t-test) increased DHA content (55.2% of total fatty acids) and DHA/DPA ratio (5.91) in shake flasks, with no negative impact on biomass or lipid accumulation. Fed-batch fermentation confirmed the scalability of this strategy, achieving a >20% increase in DHA/DPA ratio. This study demonstrates that combining heterologous ω-3 desaturase expression with FAS attenuation is an effective approach for optimizing PUFA profiles in Aurantiochytrium. Full article

This study explored the physiological responses and gene expression profiles of the Manila clam (Ruditapes philippinarum) and the hard clam (Mercenaria mercenaria) under heat and hyposaline stress. Experimental conditions involved increasing the temperature from 25 °C to 35 °C and decreasing salinity from 25 ppt to 15 ppt over a 6 h acclimation period, followed by 72 h exposure. Key physiological and immune indicators, including filtration rate, oxygen consumption rate, ammonia excretion rate, and the expression of related genes, were measured. Under heat stress, R. philippinarum exhibited higher filtration, oxygen consumption, and ammonia excretion rates than M. mercenaria at most sampling time points. The expression of fatty acid desaturase (Δ6FAD) and heat shock protein (HSP70) genes increased and then decreased for both species, whereas superoxide dismutase (Cu/Zn SOD) gene expression gradually decreased over time. Furthermore, the expression levels of all three genes were generally significantly higher in M. mercenaria compared to R. philippinarum. Under hyposaline stress, R. philippinarum exhibited significantly higher filtration, oxygen consumption, and ammonia excretion rates than M. mercenaria between 24 h and 72 h. Expression levels of the Na⁺-K⁺-ATPase (NKAα), HSP70, and Cu/Zn SOD genes remained higher in M. mercenaria compared to R. philippinarum. Overall, the present study indicates that M. mercenaria maintains relative stability and R. philippinarum exhibits greater physiological fluctuation under both heat and hyposaline stress. This study highlights bivalve species-specific responses to environmental stressors and provides valuable insights for aquaculture planning and ecological management in different environmental regions, particularly in the context of global climate change. Full article

Milk fat synthesis in dairy cows is a complex process affected by ruminal fermentation, systemic metabolism, and mammary gland activity. To explore the metabolic interplay across these systems, a multi-tissue metabolomics approach (rumen fluid, plasma, and milk) using ultra-high-performance liquid chromatography–mass spectrometry was used to identify metabolic differences between Chinese Holstein cows with high (H-MF, 5.82 ± 0.41%) and low (L-MF, 3.60 ± 0.12%) milk fat content under the same diet. The bovine mammary epithelial cells (BMECs) were also cultured to evaluate the impact of a key metabolite, malic acid (MA), on lipid metabolism. Our findings reveal distinct metabolic profiles across rumen fluid, plasma, and milk, with 96, 109, and 79 differential metabolites, respectively, between the L-MF and H-MF groups. In rumen fluid, H-MF cows showed higher levels of lauric acid and succinic acid, linked to fatty acid biosynthesis, while the L-MF cows had elevated citraconic and orotic acids, associated with amino acid metabolism and liver stress. Plasma from the H-MF cows contained higher β-hydroxybutyric acid, methionine sulfoxide, and phosphatidylcholine, supporting lipogenesis, whereas L-MF plasma showed increased 3-hydroxy-L-proline, indicating tissue catabolism. In milk, the L-MF cows had higher MA, while the H-MF cows exhibited elevated L-carnitine, linked to fatty acid β-oxidation. Metabolite trend analysis during rumen fluid–plasma–milk showed that 211 metabolites were classified into 8 profiles. Profile 1 had the largest number of metabolites whose levels were down-regulated from rumen to plasma and enriched in lipid metabolism. Profile 3 (mainly related to amino acid metabolism) and profile 4 (mainly related to energy metabolism) exhibited opposite trends from plasma to milk. In vitro, 200 μM of MA reduced the triglyceride content in BMECs and down-regulated lipogenic genes and their protein expression levels (fatty acid synthase, stearoyl-CoA desaturase and sterol regulatory element binding protein 1). These results highlight how rumen fluid, plasma, and milk metabolites collectively influence milk fat synthesis, with MA acting as a key regulator of lipid metabolism in mammary epithelial cells. Full article

Oleaginous microorganisms usually accumulate large amounts of lipids under nitrogen limitation and in a carbon-abundant environment. However, how cells sense changes in nitrogen and carbon levels in the culture medium remains a research hotspot. Previous studies have found that the target of rapamycin complex 1 (TORC1) plays a core role in lipid accumulation in oleaginous microorganisms. The results of the Kog1 (the member proteins of TORC1) knockout strain constructed earlier by our group showed that the Kog1 negatively regulated lipid accumulation in the oleaginous fungus Mucor circinelloides. In this study, transcriptomic analysis of the knockout and control strains under nitrogen-limited and nitrogen-sufficient culture was carried out to investigate significant differences in lipid accumulation. Kog1 knockout led to a significant decrease in cell dry weight and an increase in lipid content in M. circinelloides. The transcriptomic results showed that genes encoding the glyoxylic acid cycle and genes encoding acetyl-CoA carboxylase (ACC), fatty acid synthase (FAS), and Δ9 desaturase in lipid synthesis were upregulated to varying degrees under both conditions, indicating enhanced lipid metabolism that ultimately led to increased lipid accumulation. The knockout of the Kog1 gene also activated the pyruvate–acetaldehyde–acetate metabolic axis and significantly modified the branched-chain amino acid metabolic network, suggesting that Kog1 knockout reprograms the pathway of branched-chain amino acid synthesis and degradation, shifting the carbon flux from amino acid metabolism to acetyl-CoA accumulation. In addition, the gene encoding the SSK1p transcription factor, which participates in the nutrient stress response, was upregulated 41.9- and 51.9-fold in the Kog1 knockout strain compared with the control strain under nitrogen-limited and nitrogen-sufficient conditions, respectively. Full article

This experiment investigated the effects of dietary Artemisia ordosica Krasch. (AOK) supplementation on the n3-polyunsaturated fatty acid (n3-PUFA) profile of subcutaneous adipose tissue (SADT) in Arbas cashmere goats and explored the underlying transcriptional mechanisms. Forty healthy, weaned kids (120 ± 10 days of age; similar body weight) were randomly allocated to two groups (n = 20): a control group (CON, basal diet) and an AOK group (AOK, basal diet with 3% of the roughage replaced by AOK). The feeding trial spanned 104 days, consisting of a 14-day adaptation period and 90 days of data acquisition. Compared with the CON group, AOK significantly reduced the content of saturated fatty acids (SFAs) and n6-polyunsaturated fatty acids (n6-PUFAs)/n3-PUFAs (n6/n3). In contrast, the levels of n3-PUFAs in the SADT of cashmere goats increased markedly (p < 0.05). Compared with the CON group, AOK exhibited significantly higher activities of hormone-sensitive lipase (HSL) (p = 0.027), adenylyl cyclase 2 (ADCY2) (p = 0.010), adenylyl cyclase 5 (ADCY5) (p = 0.046), cluster of differentiation 36 (CD36) (p = 0.013), solute carrier family 27 member 4 (SLC27A4) (p = 0.021), and fatty acid binding protein 4 (FABP4) (p = 0.040), along with significantly lower activities of fatty acid synthase (FAS) (p = 0.002), lipoprotein lipase (LPL) (p = 0.048), and stearoyl-coa desaturase (SCD) (p = 0.026) in SADT. Compared with the CON group, the activities of superoxide dismutase (SOD) (p = 0.032), catalase (CAT) (p = 0.010), glutathione peroxidase (GSH-PX) (p = 0.029), and total antioxidant capacity (T-AOC) (p = 0.002) were significantly increased in the AOK group. Transcriptomic profiling revealed that AOK supplementation downregulated mRNA levels of ADCY2, ADCY5, LPL, FAS, SCD, stearoyl-CoA desaturase 1 (SCD1), stearoyl-CoA desaturase 2 (SCD2), glycogen synthase 1 (GYS1), acyl-CoA oxidase 1 (ACOX1), acetyl-CoA carboxylase (ACC), diacylglycerol acyltransferase 1 (DGAT1), fatty acid desaturase 1 (FADS1), solute carrier family 27 member 2 (SLC27A2), erythroblastic leukemia viral oncogene homolog 4 (ERBB4), and carnitine palmitoyltransferase 1B (CPT1B) (p < 0.05). It also markedly induced acyl-CoA synthetase long-chain family member 4 (ACSL4) (p < 0.01) in SADT. Genes significantly enriched in the adenosine-monophosphate-activated protein kinase (AMPK) signaling pathway included LPL, SCD1, CPT1B, and GYS1 (p = 0.010). Genes significantly enriched in the phosphatidylinositol 3-kinase-akt (PI3K-Akt) signaling pathway included GYS1 and ERBB4 (p = 0.015). CPT1B, ADCY2, and GYS1 were identified as the genes significantly enriched in the insulin resistance signaling pathway (p = 0.048). LPL was the only gene significantly enriched in the cholesterol metabolism pathway (p = 0.049). Genes showing a tendency toward significant enrichment in the peroxisome-proliferator-activated receptor (PPAR) signaling pathway included ACSL4, CPT1B, SCD1, and LPL (p = 0.051). These interconnected cascades improve insulin sensitivity, stimulate triglyceride (TG) hydrolysis, and modulate n3-PUFA levels. Supplementation with AOK enhances n3-PUFA content by accelerating TG breakdown while simultaneously restraining FA oxidation in SADT. Consequently, AOK supplementation can be effectively used to enhance the nutritional value of cashmere goat meat through improved n3-PUFA deposition in SADT. Full article

Sunflower is a globally important oilseed crop. Improving its fatty acid composition is crucial for enhancing oil quality and nutritional value. To dissect the genetic basis of quality traits, we performed genome resequencing on 203 sunflower inbred lines and conducted a genome-wide association study (GWAS) for five traits—oil content, stearic acid, palmitic acid, oleic acid, and linoleic acid—across three environments. We identified 103 significant single-nucleotide polymorphisms (SNPs) and 154 candidate genes. Notably, several associated loci were co-localized for multiple traits, suggesting pleiotropic effects or close genetic linkages. Integration with transcriptome data from developing seeds revealed that 66 candidate genes were expressed within 30 days after pollination, of which 12 showed significant differential expression between high- and low-oleic acid varieties. Functional characterization of a selected candidate, the ω-6 fatty acid desaturase gene (LOC110938218, designated HaDES8.11), demonstrated that the HaDES8.11-eGFP fusion protein localizes to the endoplasmic reticulum. Heterologous expression of HaDES8.11 in Arabidopsis thaliana significantly increased seed linoleic acid content while decreasing oleic acid content, confirming its role in fatty acid desaturation. Our study provides novel genetic insights and valuable candidate genes for the molecular breeding of sunflower with optimized oil quality. Full article

The accumulation dynamics and regulatory mechanisms of the alkylamides, the key pungent compounds in the fruits of Sichuan peppers, remain poorly understood. Using fruits of the Zanthoxylum planispinum var. dintanensis (Dintan) harvested at five key developmental stages, we comprehensively mapped the accumulation of numbering compounds and their underlying molecular drivers by integrating HPLC-based metabolite profiling and de novo transcriptomics. Total alkylamide content increased during development, with hydroxyl-α-sanshool (HαSS) being predominant. The contributions of hydroxyl-β-sanshool (HβSS) and hydroxyl-ε-sanshool (HεSS) increased in later stages. Cluster and correlation analyses identified 51 candidate genes strongly correlated (|r| ≥ 0.6) with HαSS accumulation, predominantly enriched in fatty acid and branched-chain amino acid metabolism pathways. The expression patterns of five stearoyl-CoA desaturase (SCD) genes, one long-chain acyl-CoA synthetase (ACSL/fadD), and one S-(hydroxymethyl)glutathione dehydrogenase/alcohol dehydrogenase (frmA) gene closely mirrored HαSS accumulation. In contrast, 3-oxoacyl-[acyl-carrier-protein] synthase II (fabF) and one β-ketoacyl-CoA synthase (KCS) gene exhibited a negative correlation. Accordingly, a positive regulatory network was constructed for HαSS accumulation. These findings revealed key candidate targets for deciphering the molecular basis of its unique flavor and for breeding high-pungency cultivars. Full article

The prevalence of metabolic dysfunction-associated steatohepatitis (MASH) is rising worldwide. hFGF1^ΔHBS, a variant of human fibroblast growth factor 1 with three substitutions in its heparin-binding sites, was previously shown by our group to ameliorate fatty liver. However, hFGF1^ΔHBS also significantly modulates systemic metabolism, making it unclear whether its hepatic benefits arise from direct liver-specific actions. Additionally, its poor pharmacokinetic profile underscores the need for alternative delivery strategies. Here, we employed adeno-associated virus serotype 8 under the thyroxine-binding globulin promoter (AAV8-TBG) to achieve sustained, hepatocyte-specific expression of hFGF1^ΔHBS. In high-fat-, high-cholesterol-diet-fed apolipoprotein E knockout mice, liver-directed hFGF1^ΔHBS expression markedly reduced hepatic steatosis, inflammation, and fibrosis, independent of changes in body weight, blood glucose, insulin sensitivity, body composition, or circulating triglyceride and cholesterol levels. Mechanistically, hFGF1^ΔHBS gene transfer normalized fatty acid synthesis and suppressed fatty acid uptake by downregulation of stearoyl-CoA desaturase-1 and cluster of differentiation 36. Importantly, these therapeutic effects were achieved without inducing hepatic hyperproliferation, as evidenced by unchanged expression of proliferating cell nuclear antigen and antigen Kiel 67. Collectively, our findings demonstrate that hFGF1^ΔHBS exerts direct hepatoprotective effects and that AAV8-TBG-mediated liver-directed hFGF1^ΔHBS delivery represents a safe and effective strategy for treating MASH. Full article

The high-oleic acid content of the safflower (Carthamus tinctorius L.) oil, regulated by the fatty acid desaturase 2-1 (CtFAD2-1) gene, provides superior oxidative stability for applications. To explore alternative genetic sources for this trait, we employed induced mutagenesis with gamma irradiation and ethyl methane sulfonate (EMS) for two safflower cultivars, AKS 207 and PKV Pink. Screening of M₂ populations identified several mutants with significantly higher oleic acid content, reaching up to 36.86%. The mutagenized populations also exhibited a wide spectrum of variation for other agronomically important traits, including increased oil content (up to 35.19%), enhanced seed protein (up to 22.51%), and seed size and weight. Correlation and principal component analyses confirmed the antagonistic relationship between oleic and polyunsaturated fatty acids and the positive association among seed size parameters. Molecular profiling using an allele-specific PCR assay targeting the CtFAD2-1 locus revealed that high-oleic mutants did not carry known mutations, suggesting the involvement of alternative alleles, micro-mutations, or other genes regulating oleic acid accumulation. This study provides valuable pre-breeding germplasm with improved agronomic and quality traits and identifies novel genetic sources for high-oleic acid in safflower. These mutants form a new genetic basis for understanding fatty acid biosynthesis and developing next-generation high-stability oil cultivars. Full article

DNA-protecting proteins (Dps) are crucial for safeguarding chromosomal DNA in starved cells during the stationary phase under stressful conditions. In previous research, the two Dps proteins in Deinococcus geothermalis, Dgeo_0257 (Dps3) and Dgeo_0281 (Dps1), were found to complement each other in protecting DNA from oxidative damage. This study investigates the physiological changes and transposition of insertion sequences (ISs) in a double-knockout (DK) mutant lacking both dps genes. Comparisons between the wild-type and mutant strains revealed significant phenotypic differences in viability under oxidative stress conditions induced by hydrogen peroxide and ferrous ions, particularly during the stationary phase. Notably, oxidative stress triggered the transposition of the IS families IS701 and IS5, with IS66 being transposed exclusively in the DK mutant into a gene encoding phytoene desaturase. Transcriptomic analysis using RNA-seq revealed substantial fold changes in gene expression across the genome. For example, the dgeo_1459–1460 gene cluster, which encodes a DUF421 domain-containing protein and a hypothetical protein, was highly upregulated under both oxidative and non-oxidative conditions. Interestingly, catalase, encoded by a single gene in D. geothermalis, was upregulated in the DK mutant during the stationary phase, with expression levels exceeding those observed in the single dps gene-deficient mutants. Conversely, a prominent downregulation of the Fur family regulator was detected. These findings highlight the growth phase-dependent physiological adaptation of the dps-DK mutant and reveal a novel IS transposition event of the ISBst12 group involving the IS66 family. Therefore, this study provides new observations into the influence of DNA-protective protein deficiency on oxidative stress responses and IS transposition in D. geothermalis, as well as the regulatory mechanisms of the catalase induction pathway, raising the need for further investigation into the role of OxyR. Full article

Background: The phytoene desaturase gene is a classical visual marker for validating CRISPR/Cas9 genome editing in plants, as its loss of function produces a readily scorable albino phenotype. While the biochemical basis of pigment loss is well established, it remains unclear whether pds knockout elicits transcriptomic changes extending beyond carotenoid biosynthesis. Resolving this question is essential for correctly interpreting pds-based editing outcomes and for assessing the robustness of phenotype-only screening approaches. Methods: A CRISPR/Cas9 editing platform targeting pds was established in diploid potato. Albino, non-albino edited, and wild-type tissues were subjected to RNA-seq profiling. Differential expression, functional enrichment, and weighted gene co-expression network analysis were integrated to resolve phenotype-associated transcriptional modules, and hierarchical regulatory layers underlying albinism. Results: CRISPR/Cas9-mediated disruption of pds in potato-generated stable albino phenotypes and revealed extensive transcriptomic reprogramming that was not limited to pigment loss. Albino tissues exhibited more than 9700 differentially expressed genes relative to both wild-type and non-albino edited tissues, whereas non-albino edits showed substantially fewer changes. Functional enrichment demonstrated pervasive suppression of photosynthesis and carbon metabolism alongside activation of secondary metabolism, stress responses, hormone signaling, and cell wall remodeling. WGCNA and cross-validation resolved these changes into distinct, phenotype-associated regulatory layers: MEorangered4 captured coordinated repression of starch and sucrose metabolism (r = −0.998), MEdarkgreen marked albino-linked activation of secondary metabolism and barrier biogenesis (r = 0.855; overlap with Albino Core set, OR = 23.65), while MEblack and MEgrey60 reflected downregulation of stress signaling, proteostasis, and hormone-integrative control and were enriched in transgenic–background-associated gene sets. Conclusions: pds knockout in potato is accompanied by broad transcriptomic changes beyond pigment biosynthesis, suggesting that albinism involves coordinated regulatory and metabolic adjustment under plastid dysfunction rather than pigment loss alone. These results refine the use of pds as a visual editing marker and provide a framework for linking localized genome edits to coordinated network-level transcriptional responses in plants. Full article