Journal Of Applied Genetics[JOURNAL]
Sun
200 papers
Genome-wide identification and characterization of NAC transcription factor-derived microsatellites in wheat (Triticum aestivum L.).
Singh P, Sharma H, Das D … +5 more , Fandade V, Goyal M, Sharma V, Bhandawat A, Roy J
J Appl Genet · 2026 Feb · PMID 40327279 · Publisher ↗
Bread wheat (Triticum aestivum L.) is one of the widely consumed staple foods, providing 20% of the total protein and calories in human nutrition. Seeing its importance in the global food supply, the enrichment of functi...
Bread wheat (Triticum aestivum L.) is one of the widely consumed staple foods, providing 20% of the total protein and calories in human nutrition. Seeing its importance in the global food supply, the enrichment of functional genomic resources is vital for meeting future demands and ensuring sustainable production. In addition to the presence of functional domains, the presence of microsatellites within transcription factors makes them valuable candidates for enriching functional marker resources. The NAC transcription factor family regulates a variety of physiological processes in cereal crops. Hence, the present study aims to develop and characterize Triticum aestivum NAC MicroSatellites (TaNACMS) to enrich functional marker resources for genetic diversity analysis, marker-assisted selection, and evolutionary studies. In total, 520 SSRs were identified from 451 TaNAC sequences, and a set of 66 TaNACMS was used for cross-transferability in wild/related wheat species. The cross-transferability rate of 90.22% revealed high locus conservation. Further, 16 TaNACMS were utilized for the characterization of genetic diversity in Indian wheat varieties. These TaNACMS produced 40 alleles (2.5 alleles per locus) with an average observed heterozygosity (H), expected heterozygosity (H), and polymorphic information content (PIC) of 0.392, 0.417, and 0.380, respectively. The genetic analysis of wheat genotypes, using principal coordinates analysis (PCoA), neighbor-joining (NJ) clustering, and Bayesian-based STRUCTURE, has revealed three distinct genetic clusters. Two of these clusters consist of Indian wheat varieties, while the third cluster comprises wild/related wheat species. In conclusion, the high rate of transferability of TaNACMS can be effectively utilized for gene flow both within and between species, highlighting evolutionary connections between cultivated wheat and related species. Additionally, these SSRs will aid the marker repository and benefit the wheat improvement programs through marker-assisted selection (MAS).
Identification of non-synonymous SNPs affecting structure and function of MLH1 and NBN proteins: a computational approach.
Gund V, Sharma S, Chandan S … +2 more , Garg S, Singh S
J Appl Genet · 2026 May · PMID 40312597 · Publisher ↗
The genes NBN and MLH1 are critical for DNA repair, and this study aimed to detect and predict the effects of pathogenic single nucleotide polymorphisms (SNPs) in their mRNA and protein sequences. An in silico analysis a...
The genes NBN and MLH1 are critical for DNA repair, and this study aimed to detect and predict the effects of pathogenic single nucleotide polymorphisms (SNPs) in their mRNA and protein sequences. An in silico analysis assessed the impact of SNPs on the physicochemical properties, structure, stability, and function of MLH1 and NBN proteins. Results revealed that some SNPs significantly alter protein stability, structure, and binding interactions, potentially impairing DNA repair. Molecular docking studies further indicated disruptions in protein-protein interactions due to specific SNPs. These findings underscore the importance of using in silico methods to predict the functional effects of genetic variations, providing insights that could guide personalized treatments and improve cancer detection.
Transcriptomic analysis of inhibitory effects of isothiazolone antimicrobial agents on Aspergillus amstelodami ZR.
Tang J, Liang Q, Zhang R … +1 more , Huang X
J Appl Genet · 2025 Sep · PMID 40304973 · Publisher ↗
The preservation of marine specimens requires effective methods to ensure research accuracy and ecological sustainability. However, conventional preservatives (e.g., formaldehyde) pose environmental and health risks due...
The preservation of marine specimens requires effective methods to ensure research accuracy and ecological sustainability. However, conventional preservatives (e.g., formaldehyde) pose environmental and health risks due to their toxicity. In this study, we isolated Aspergillus amstelodami from the surface of Oreochromis mossambicus specimens and evaluated the antifungal potential of 1,2-benzoisothiazolin-3-one and Kathon. Both agents exhibited strong inhibitory effects on fungal growth, as evidenced by clear inhibition zones. Transcriptomic analysis revealed: (1) upregulation of detoxification-related genes, including cytochrome P450-mediated xenobiotic/drug metabolism, ABC transporters, and two-component systems, and (2) downregulation of ribosome biogenesis genes, impairing protein synthesis in Aspergillus amstelodami. In conclusion, this study provides novel insights into the molecular antifungal mechanisms of isothiazolone antimicrobial agents in combating contamination of marine biological specimens caused by Aspergillus amstelodami.
Melatonin in crop plants: from biosynthesis through pleiotropic effects to enhanced stress resilience.
Michałek M, Ogrodowicz P, Kempa M … +2 more , Kuczyńska A, Mikołajczak K
J Appl Genet · 2025 Sep · PMID 40304972 · Full text
Melatonin plays a crucial role in enhancing plant resilience to environmental stresses by regulating physiological and biochemical responses. This review provides an overview of melatonin biosynthesis, signaling pathways...
Melatonin plays a crucial role in enhancing plant resilience to environmental stresses by regulating physiological and biochemical responses. This review provides an overview of melatonin biosynthesis, signaling pathways, and its interactions with phytohormones, highlighting its multifunctional roles across various crop species. We summarize recent discoveries regarding the biosynthetic pathways of melatonin and its crucial metabolites, emphasizing the importance of tryptophan and serotonin in this process. Furthermore, we discuss the intricate crosstalk between melatonin and phytohormones, particularly auxins, cytokinins, and brassinosteroids, which collectively influence root development, growth, and stress tolerance, among other traits. The antioxidant activity of melatonin and its derivatives, along with their impact on photosynthesis, has also been thoroughly discussed. Notably, melatonin's regulatory actions promote root growth, thereby improving water and nutrient absorption under stress conditions. The identification of candidate genes and a putative receptor provides a foundation for future studies aimed at elucidating the molecular mechanisms underlying melatonin signaling in crop species. Ultimately, this review underscores the potential of harnessing melatonin in crop improvement strategies to enhance resilience to abiotic stresses while promoting sustainable agricultural practices.
Spinocerebellar ataxia 27B (SCA27B)-a systematic review and a case report of a Polish family.
Hirschfeld AS, Misiorek JO, Dabrowska M … +10 more , Muszynski J, Gerhart BJ, Zenczak M, Rakoczy M, Rolle K, Switonski PM, Napierala JS, Handschuh L, Napierala M, Badura-Stronka M
J Appl Genet · 2025 Dec · PMID 40299270 · Full text
Dominantly inherited GAA repeat expansions in the FGF14 gene have recently been identified as the cause of spinocerebellar ataxia 27B (SCA27B). Our study focused on a Polish patient case along with asymptomatic family me...
Dominantly inherited GAA repeat expansions in the FGF14 gene have recently been identified as the cause of spinocerebellar ataxia 27B (SCA27B). Our study focused on a Polish patient case along with asymptomatic family members. Moreover, we systematically reviewed available case reports to better understand the SCA27B phenotype. Genetic tests for SCA27B were performed on genomic DNA isolated from blood. Long-range polymerase chain reaction (LR-PCR) followed by Nanopore sequencing was conducted to establish the number of GAA repeats. The available literature was systematically reviewed per the recommendations of the Preferred Reporting Items for Systematic Reviews and Meta-analyses. The patient's genetic studies identified pure expansions of (GAA) 420/94 repeats in FGF14, confirming the SCA27B diagnosis. A systematic review of 815 cases provides further insight into the typical clinical presentation, with gait ataxia (95.96%) being the most prevalent symptom, followed by abnormal saccadic pursuits (80.69%), nystagmus (71.15%), diplopia (54.05%), and dysarthria (51.22%). Notably, 41.87% of cases exhibited episodic symptoms. The correlation between GAA repeat expansions and the pathogenesis of SCA27B requires further studies. The unique course of the disease with episodic symptoms may cause diagnostic difficulties. Due to its high prevalence in the European population, SCA27B should be considered when diagnosing the causes of late-onset cerebellar ataxia.
In silico approach on structural and functional characterization of heat shock protein from Sulfobacillus acidophilus.
Mitra P, Chatterjee S
J Appl Genet · 2025 Sep · PMID 40232564 · Publisher ↗
The 70 kDa heat shock proteins (Hsp70 s) are highly conserved and ubiquitous molecular chaperones. Hsp70 proteins are intimately involved in different biological activities including maintaining protein homeostasis and r...
The 70 kDa heat shock proteins (Hsp70 s) are highly conserved and ubiquitous molecular chaperones. Hsp70 proteins are intimately involved in different biological activities including maintaining protein homeostasis and resisting environmental stress for survival. Characterizations of eukaryotic Hsp70 s with diverse functions are well established but investigations needed for prokaryotes. For better understanding, the sequences of Sulfobacillus acidophilus were retrieved from UniProt. Retrieved stress proteins were renamed as SaHsp70 s and performed an in silico analysis to identify sequential, structural properties and functional attributes. The in silico characterization of these proteins revealed that they are acidic, mostly thermostable globular protein with NAD(P)-binding Rossmann-folding. Molecular mass of SaHsp70 s ranged from 31.9 to 68.5 kDa and mainly localized in the cytoplasm. Phylogeny revealed the evolutionary distance and relationship among retrieved proteins. Domain analyzed only SaHsp70 - 1, SaHsp70 - 3, and SaHsp70 - 14 have actual conserved domain for Hsp70 and share the same clade on phylogenetic tree. Major part of each protein was abundant with α-helix and random coil which make it thermally stable and suitable for interacting with other proteins. SAVES and ProSA server proves the reliability, stability, and consistency tertiary structure of SaHsp70 s. Functional analysis was done in terms of membrane protein topology, PPI network generation, active and proteolytic cleavage sites prediction, conserved motif and domain detection. CastP predicted Gly, Lys, Thr, Glu, Pro, Gln, Arg and Val act as catalytic residue, are important for metal ions binding. Intramolecular interaction analysis suggested Lys67, Thr12, Thr170, Gly 168, Gly 169, and Glu 141 of SaHsp70 - 14 proteins could play central role in various complex cellular functions like stress mitigation, thermal stability, and related developmental processes.
Fibrodysplasia ossificans progressiva: genetic and clinical characterization in a cohort of Polish patients and review of potential therapies.
Szoszkiewicz A, Szczepanek M, Bukowska-Olech E … +3 more , Sowińska-Seidler A, Socha M, Jamsheer A
J Appl Genet · 2026 Feb · PMID 40220125 · Full text
Fibrodysplasia ossificans progressiva (FOP; OMIM #135100) is a rare genetic disorder characterized by congenital malformation of the great toes and progressive heterotopic ossification of soft tissues. To date, the disea...
Fibrodysplasia ossificans progressiva (FOP; OMIM #135100) is a rare genetic disorder characterized by congenital malformation of the great toes and progressive heterotopic ossification of soft tissues. To date, the disease has been linked to 15 pathogenic variants in the ACVR1 gene, which encodes a type I receptor for bone morphogenetic proteins. Most patients with FOP carry a recurrent single-nucleotide substitution (c.617G>A; p.Arg206His) in the ACVR1 gene. The genotype-phenotype correlations for atypical pathogenic variants of ACVR1 are poorly understood. In this study, we report the largest population of Polish patients affected by FOP and analyze their phenotypes and genotypes. We screened the whole ACVR1 coding sequence of 16 patients affected by FOP to confirm the presence of pathogenic variants. Thirteen individuals carried the classic pathogenic variant (p.Arg206His) and had a classic or FOP-plus phenotype. In agreement with the findings of previous studies, one patient with a p.Gly356Asp pathogenic variant had a variant FOP phenotype. We point to an unusual phenomenon in two patients who carried atypical pathogenic variants (p.Gly356Asp and p.Arg258Ser) and displayed a classic FOP phenotype. Our study extends the understanding of FOP's genotype-phenotype correlation, suggesting that classic FOP phenotypes are associated with non-classic pathogenic variants. We also summarize the recent advances in drug development for this condition. Therefore, the study may be valuable for clinicians consulting patients with FOP.
Genetic nexus of assisted reproduction technique efficacy in infertile women: insights from a comprehensive retrospective study.
Li F, Ye B, Chen M … +5 more , Zhou X, Yu L, Xiang J, Ren X, Zhang J
J Appl Genet · 2026 Feb · PMID 40178765 · Full text
Infertility presents a substantial challenge for women of reproductive age, exerting profound effects on both individual well-being and healthcare systems. Despite its critical role in folate and homocysteine pathways, t...
Infertility presents a substantial challenge for women of reproductive age, exerting profound effects on both individual well-being and healthcare systems. Despite its critical role in folate and homocysteine pathways, the influence of methylenetetrahydrofolate reductase (MTHFR) on the success of assisted reproductive techniques (ART) remains insufficiently understood. This knowledge gap impedes the development of personalized therapeutic strategies. Our study seeks to elucidate the relationship between MTHFR and ART outcomes, exploring potential mediators to enhance treatment efficacy. A cohort of 311 women with infertility was recruited for our study. Multivariate linear models were utilized to evaluate the relationship between the MTHFR 677T allele (a missense mutation resulting in an alanine to valine substitution) and the efficacy of ART, including both treatment outcomes and the number of ART cycles required. Sequential mediation analysis was conducted to elucidate the potential mediators influencing ART efficacy. The MTHFR 677T allele carried by infertile women was associated with a 17-51% reduction in ART efficacy (P < 0.05). This encompassed poorer overall ART outcomes, such as clinical pregnancy and live birth rates, as well as an increased number of ART cycles. Sequential mediation analysis suggested that anti-Müllerian hormone (AMH) and age may act as mediators modulating the impact of the MTHFR 677T allele on ART treatment efficacy. This study has unveiled the intricate connection between MTHFR 677T allele and ART treatment efficacy in infertile women, shedding light on the mediating role of AMH and age.
Gene therapy as an innovative approach to the treatment of hemophilia B-a review.
Wróblewska K, Bieszczad D, Popławska M … +3 more , Ziętara KJ, Zajączkowska M, Filip A
J Appl Genet · 2025 Sep · PMID 40178764 · Full text
Hemophilia B is a disease that affects the human coagulation system, causing the absence or deficiency of coagulation factor IX, which may manifest itself in uncontrolled bleeding that is life-threatening to patients. Du...
Hemophilia B is a disease that affects the human coagulation system, causing the absence or deficiency of coagulation factor IX, which may manifest itself in uncontrolled bleeding that is life-threatening to patients. Due to its inheritance, the disease more often affects men, and the severity of symptoms directly correlates with the concentration of the missing factor IX; hence, the aim of therapy is to maintain it at a level that allows for sufficient hemostasis. The basic model of treatment offered to patients is based on primary prevention with coagulation factor IX with a prolonged half-life, which, however, does not solve the numerous problems faced by patients. An innovative proposal that, despite initial concerns, is becoming more and more popular every day is the recently approved genetic therapy in Europe, which uses viral vectors to transfer the correct gene that encodes coagulation factor IX. The introduction of a recombinant gene in place of its defective counterpart seems to be a promising solution and the beginning of a new era in which genetic therapies have a chance to develop their full potential and replace existing therapeutic regimens.
Genome-wide analysis of the phosphate transporter gene family in oats: insights into phosphorus and water deficiency responses.
Li J, Yang Y, Huang H … +4 more , Yu J, Zhou Q, Jia Z, Chen S
J Appl Genet · 2026 Feb · PMID 40164903 · Publisher ↗
Phosphorus (P) and water are essential for plant growth and development, exerting a significant influence on global crop production. The phosphate transporter (PHT) gene family plays a pivotal role in phosphate (Pi) upta...
Phosphorus (P) and water are essential for plant growth and development, exerting a significant influence on global crop production. The phosphate transporter (PHT) gene family plays a pivotal role in phosphate (Pi) uptake, transport, and homeostasis under diverse environmental conditions. In this study, we conducted a comprehensive genome-wide identification and characterization of the PHT gene family in Avena sativa. A total of 32 non-redundant AsPHT genes were identified in the OT3098 genome, classified into two subfamilies: AsPHT1 (21 genes) and AsPHO (11 genes). AsPHT1 proteins were predominantly hydrophobic with one or two exons, whereas AsPHO proteins were hydrophilic, exhibiting a more complex structure with 13-15 exons. Cis-regulatory element analysis revealed an abundance of hormone- and stress-responsive elements in the promoters of AsPHT genes, indicating their potential roles in adaptive responses to Pi and water deficiency. Gene expression profiling under low Pi and drought conditions demonstrated differential expression of 22 AsPHT genes in roots and leaves at the seedling stage, with distinct responses to the two stresses, highlighting the functional diversity of the AsPHT gene family. These findings provide valuable insights into the molecular mechanisms underlying Pi and water acquisition in oats and offer potential applications for developing varieties with enhanced Pi use efficiency and drought tolerance.
Evaluation of the taxonomic classification tools and visualizers for metagenomic analysis using the Oxford nanopore sequence database.
Bebawy AS, Saad BT, Saad MT … +4 more , Mosaad GS, Gomaa FAM, Alshahrani MY, Aboshanab KM
J Appl Genet · 2025 Sep · PMID 40155586 · Publisher ↗
Microbial metagenomic identification is generally attributed to the specificity and type of the bioinformatic tools, including classifiers and visualizers. In this study, the performance of two major classifiers, Centrif...
Microbial metagenomic identification is generally attributed to the specificity and type of the bioinformatic tools, including classifiers and visualizers. In this study, the performance of two major classifiers, Centrifuge and Kraken2, and two visualizers (Recentrifuge and Krona) has been thoroughly investigated for their efficiency in the identification of the microorganisms using the Whole-Genome Sequence (WGS) database and four targeted databases including NCBI, Silva, Greengenes, and Ribosomal Database Project (RDP). Two standard DNA metagenomic library replicates, Zymo and Zymo-1, were used as quality control. Results showed that Centrifuge gave a higher percentage of Pseudomonas aeruginosa, Escherichia coli, and Salmonella enterica identification than Kraken2. Compared to Recentrifuge, Kraken2 was more accurate in identifying Staphylococcus aureus, Listeria monocytogenes, Bacillus subtilis, and Cryptococcus neoformans. The results of the rest of the detected microorganisms were generally consistent with the two classifiers. Regarding visualizers, both Recentrifuge and Krona provided similar results regarding the abundance of each microbial species regardless of the classifier used. The differences in results between the two mentioned classifiers may be attributed to the specific algorithms each method uses and the sequencing depth. Centrifuge uses a read mapping approach, while Kraken2 uses a k-mer-based system to classify the sequencing reads into taxonomic groups. In conclusion, both Centrifuge and Kraken2 are effective tools for microbial classification. However, the choice of classifier can influence the accuracy of microbial classification and, therefore, should be made carefully, depending on the desired application, even when the same reference database is used.
Identification of lncRNA expression profiles associated with ovarian development and ageing process in mice.
Chen S, Zhou Z, Mo J … +6 more , Yang X, Pan Y, Liu R, Jallow MB, Zhang F, Wu Y
J Appl Genet · 2025 Dec · PMID 40133750 · Publisher ↗
Long non-coding RNA (lncRNA) participates in various biological processes, however, neither the expression profile nor the biological role of lncRNAs in mammalian ovaries has been fully studied. In this work, the lncRNA...
Long non-coding RNA (lncRNA) participates in various biological processes, however, neither the expression profile nor the biological role of lncRNAs in mammalian ovaries has been fully studied. In this work, the lncRNA transcriptomic analysis of postnatal mice ovaries was performed by using bulk RNA sequencing in C57BL/6 mice. A total of 5302 lncRNAs were found in mouse ovaries, and 1836 lncRNAs were differentially expressed during the development and ageing process, of which targets were enriched in the developmental process, reproduction, etc. Developmental stage specific lncRNAs showed functions in system development, inflammatory response, myeloid leukocyte activation, etc. Moreover, a co-expression network analysis based on reproduction-related genes reveals lncRNAs that may regulate multiple mRNA targets in ovaries, including Neat1, Gm11613 and Gm43915. Two cis-acting lncRNAs, Ptgs2os and Gm14705, showed correlated expression pattern with their potential targets Ptgs2 and Aff2 respectively, and these lncRNA-mRNA pairs were conserved in mice and humans. WGCNA further identified 10 co-expressed modules with distinct expression patterns associated with ovarian development and ageing. Taken together, our results reveal a transcriptomic profile of mouse ovaries over the reproductive lifespan, providing insights into the molecular mechanisms of ovarian development and ageing.
Rare T-box variants in adult pulmonary arterial hypertension with congenital heart disease.
Li L, Chen G, Qiao N … +4 more , Li J, Wang Z, Lyu Y, Guo Y
J Appl Genet · 2026 May · PMID 40126773 · Publisher ↗
We report the clinical and genetic features of three adult patients with congenital heart disease-associated pulmonary arterial hypertension (CHD-PAH) carrying rare T-box variants. All three patients had weakness and cya...
We report the clinical and genetic features of three adult patients with congenital heart disease-associated pulmonary arterial hypertension (CHD-PAH) carrying rare T-box variants. All three patients had weakness and cyanosis. Two patients had chest tightness, dry cough, and hemoptysis, and one patient had lower limb edema. Besides meeting the diagnostic criteria of CHD-PAH, three patients respectively presented the clinical features of specific syndromes. Specifically, patient 1 presented with clinical features consistent with tetralogy of Fallot, patient 2 presented with characteristics associated with small patella syndrome, and the patient 3 exhibited features consistent with Holt-Oram syndrome. Exome sequencing revealed that the TBX1 (c.820 T > C) variant was identified in patient 1, the TBX4 (c.251del) variant was detected in patient 2 and the TBX5 (c.486del) variant was found in patient 3. Our study for the first time found that CHD-PAH patients carry T-box gene variants, which has added new clues to understanding the pathogenesis of CHD-PAH and is expected to provide new targets and ideas for the diagnosis and treatment of CHD-PAH.
A homozygous LAMB3 frameshift variant in junctional epidermolysis bullosa-affected Bleu du Maine sheep.
Letko A, Harkema L, Peterson K … +2 more , Dijkman R, Drögemüller C
J Appl Genet · 2025 Sep · PMID 40100311 · Full text
Epidermolysis bullosa (EB) is a group of inherited skin disorders characterized by skin fragility and blistering. Here, four Bleu du Maine lambs, sired by one ram, were diagnosed with EB very early in life. Due to the se...
Epidermolysis bullosa (EB) is a group of inherited skin disorders characterized by skin fragility and blistering. Here, four Bleu du Maine lambs, sired by one ram, were diagnosed with EB very early in life. Due to the severity of the clinical signs, the lambs had to be euthanized. The affected lambs exhibited hoof sloughing and multiple ulcerations on the head, oral cavity, skin over the joints, and the ruminal pillars. Histopathology showed abrupt subepidermal clefts, epidermal detachment directly above the basal membrane, and ulcerations consistent with junctional EB (JEB). Two cases underwent whole-genome sequencing (WGS) to identify the genetic cause. Genomic analyses with the hypothesis of autosomal recessive inheritance identified the most likely pathogenic homozygous 1-bp deletion in the LAMB3 gene (NC_056065.1:g.73166198delG). Recessive forms of JEB in humans and dogs are caused by variants in LAMB3 gene, which encodes β3 subunit of laminin 332, a critical component of the epidermal basal membrane. The ovine frameshift variant putatively introduces a premature stop codon and disrupts the donor splice site of exon 20. The variant allele was homozygous in both sequenced cases and heterozygous in three unaffected close relatives and was absent in 1075 unrelated control sheep of various other breeds. This study highlights the importance of genetic investigation in veterinary diagnostics of and represents the first report of a LAMB3-related recessive EB in sheep. The findings enable genetic testing to inform breeding strategies and provide a second spontaneous large animal model for LAMB3-related JEB in humans.
Functional analysis of HvSNAC1 in stomatal dynamics and drought adaptation.
Kurowska M, Janiak A, Sitko K … +10 more , Potocka I, Gajecka M, Sybilska E, Płociniczak T, Lip S, Rynkiewicz M, Wiecha K, Nawrot M, Daszkowska-Golec A, Szarejko I
J Appl Genet · 2025 Dec · PMID 40100310 · Full text
Drought stress can damage crop growth and lead to a decline in yield, thereby affecting food security, especially in regions vulnerable to climate change. SNAC1 (stress-responsive NAC1), the NAC transcription factor fami...
Drought stress can damage crop growth and lead to a decline in yield, thereby affecting food security, especially in regions vulnerable to climate change. SNAC1 (stress-responsive NAC1), the NAC transcription factor family member, plays a crucial role in stomatal movement regulation. Effective regulation of stomatal movement is essential for protecting plants from water loss during adverse conditions. Our hypothesis revolves around altering HvSNAC1 activity by introducing a point mutation in its encoding gene, thereby influencing stomatal dynamics in barley. Two TILLING mutants, each harboring missense mutations in the NAC domain, exhibited higher stomatal density after drought stress compared to the parent cultivar 'Sebastian'. These mutants also demonstrated distinct patterns of ABA-induced stomatal movement compared to the wild-type (WT). To delve deeper, we conducted a comprehensive analysis of the transcriptomes of these mutants and the parent cultivar 'Sebastian' under both optimal watering conditions and 10 days of drought stress treatment. We identified differentially expressed genes (DEGs) between the mutants and WT plants under control and drought conditions. Furthermore, we pinpointed DEGs specifically expressed in both mutants under drought conditions. Our experiments revealed that the cis-regulatory motif CACG, previously identified in Arabidopsis and rice, is recognized by HvSNAC1 in vitro. Enrichment analysis led to the identification of the cell wall organization category and potential target genes, such as HvEXPA8 (expansin 8), HvXTH (xyloglucan endotransglucosylase/hydrolase), and HvPAE9 (pectin acetylesterase 9), suggesting their regulation by HvSNAC1. These findings suggest that HvSNAC1 may play a role in regulating genes associated with stomatal density, size and reopening.
Is it possible to select body weight without compromising carcass traits and reproductive efficiency in Caracu cattle?
Ligori VA, Malheiros JM, Carrara ER … +5 more , Dominguez-Castaño P, da Silva Neto JB, Dos Santos Gonçalves Cyrillo JN, Mercadante MEZ, Zadra LEF
J Appl Genet · 2025 Dec · PMID 40095401 · Publisher ↗
The Caracu is a taurine breed adapted to Brazil's climatic conditions and has been selected for 40 + years for Body Weight (BW), maintaining performance records across multiple generations in its database. However, selec...
The Caracu is a taurine breed adapted to Brazil's climatic conditions and has been selected for 40 + years for Body Weight (BW), maintaining performance records across multiple generations in its database. However, selecting young animals for BW can result in excessive growth, potentially impacting carcass and reproductive traits. This study aimed to estimate genetic correlations and, based on these estimates, evaluate how selection for BW (adjusted to 378 and 550 days of age for males and females, respectively) has influenced carcass traits and reproductive efficiency in this breed. The dataset contained records for BW (kg), Ribeye area (REA, cm), Height-to-width ratio of the Longissimus dorsi muscle (HWR), Backfat thickness (BFT, mm), Rump fat thickness (RFT, mm), Yearly scrotal circumference (SC, cm), and Days to calving (DC, days) from animals born between 1966 and 2022. (Co)variance components were estimated by Bayesian inference using two-trait animal models. Analyses were conducted to estimate genetic parameters for pairs of traits, including BW with carcass traits (BW × REA, BW × HWR, BW × BFT, and BW × RFT) and BW with reproductive traits (BW × DC and BW × SC). Additionally, analyses were performed for pairwise combinations among carcass traits (REA × HWR, REA × BFT, REA × RFT, HWR × BFT, HWR × RFT, and RFT × BFT) and between reproductive traits (DC × SC). The relationship matrix included 4,783 animals, of which 829 were genotyped with the GGP Bovine 100 K SNP panel. Favorable genetic correlations (r) were observed between BW and REA (0.51 ± 0.11), HWR (0.45 ± 0.17), SC (0.24 ± 0.13), and RFT (0.15 ± 0.21), with the latter being favorable but low. On the other hand, unfavorable genetic correlations were observed between BW and BFT (-0.07 ± 0.21), which was unfavorable but close to zero relationship, and between BW and DC (0.48 ± 0.15). The significance of carcass and reproductive traits is underscored by the favorable, r between BW and the carcass traits REA (BW × REA) and HWR (BW × HWR), while a high, unfavorable r was observed between BW and DC cows. These findings emphasize the importance of carefully balancing genetic selection to optimize growth, carcass quality, and adequate reproduction in Caracu cattle.
Calcium-sensing receptor genetic variants and their association with CKD-MBD in South Indian Tamils.
Priyadarshini G, Dhinesh A, Parameswaran S … +3 more , Sahoo J, Selvarajan S, Rajappa M
J Appl Genet · 2026 May · PMID 40085338 · Publisher ↗
The progressive degradation of the renal parenchyma and reduction of functional nephrons characterise chronic kidney disease (CKD). Disorders of bone mineral metabolism is one of the leading causes of morbidity and morta...
The progressive degradation of the renal parenchyma and reduction of functional nephrons characterise chronic kidney disease (CKD). Disorders of bone mineral metabolism is one of the leading causes of morbidity and mortality in CKD. Calcium-sensing receptor (CASR) allows cells to detect changes in blood calcium levels and regulate its concentration. Hence, we aim to study the relationship between genetic variants of CASR and CKD and their relation with mineral bone disease (MBD). A total of 180 CKD patients and 180 controls were recruited. Bone mineral density of the lumbar spine, hip, and forearm was measured using a dual X-ray absorptiometry (DEXA) scan. Circulating levels of parathyroid hormone (PTH) were measured by ELISA. Genotyping was done by real-time quantitative PCR. A significant difference in the distribution of the GAG haplotype (rs7652589, rs1501899, rs1801725) was observed between CKD patients and controls. Participants with the GT genotype of rs1801725 had lower BMD in the forearm. The TT genotype of rs1801725 was associated with decreased serum calcium levels. A regression model indicated that the GT genotype of rs1801725 and AG and GG genotypes of rs7652589 were significant predictors of forearm BMD. GAG haplotype of CASR SNPs is linked to CKD risk in South Indian Tamils. GT genotype of rs1801725 and AG and GG genotype of rs7652589 are independent predictors of MBD in patients with CKD.
Pivotal role of biallelic frequency analysis in identifying copy number alterations using genome-wide methods in tumors with a high level of aneuploidy.
Rymuza J, Woroniecka R, Grygalewicz B … +1 more , Bujko M
J Appl Genet · 2026 Feb · PMID 40036001 · Publisher ↗
Chromosome number abnormalities is one of the hallmarks of cancer. DNA copy number alterations (CNA) are studied using various genome-wide methods. In our study, we investigated CNA in human pituitary tumors using three...
Chromosome number abnormalities is one of the hallmarks of cancer. DNA copy number alterations (CNA) are studied using various genome-wide methods. In our study, we investigated CNA in human pituitary tumors using three platforms CytoSNP-850 K microarrays, low-pass whole-genome sequencing (average × 7 coverage, LPWGS), and Infinium Methylation EPIC array. Virtual karyotypes based on each dataset were generated using open-source software packages for each sample. Concordant CNA profiles were found for most of tumor. Surprisingly, substantial discrepancies between results from SNP arrays and LPWGS/EPIC arrays were identified in 20% of tumors, for which discrimination of true karyotype was required. B-allelic frequency data from SNP arrays was crucial to adjust normal ploidy level as ultimately verified with FISH. The discrepancy between virtual karyotypes was more pronounced the more CNAs were found. When CNAs covered around half of genome, the level of normal/diploid copy number was incorrectly set with methods, based solely on signal intensity/read-counts coverage. To conclude, CNA analyses with methods such as LPWGS and methylation arrays in highly aneuploid tumors are prone to a bias from improper normal ploidy level setting. These methods are commonly used therefore, we aimed to aware the scientific community about this underestimated methodological problem.
MiRNA signature analysis in LSCC gene expression profiles indicates hsa-miR-299-5p as a new tumor suppressor.
Janiszewska J, Paczkowska J, Kostrzewska-Poczekaj M … +8 more , Schreiber AM, Kiwerska K, Bednarek K, Kowal-Wiśniewska E, Drozdowska Z, Wierzbicka M, Jarmuż-Szymczak M, Giefing M
J Appl Genet · 2026 Feb · PMID 40025000 · Publisher ↗
Given the importance of epigenetic mechanisms in the downregulation of tumor suppressor genes and the activation of oncogenes, herein we focused on microRNA silencing as a cause of oncogene activation in laryngeal squamo...
Given the importance of epigenetic mechanisms in the downregulation of tumor suppressor genes and the activation of oncogenes, herein we focused on microRNA silencing as a cause of oncogene activation in laryngeal squamous cell carcinoma (LSCC). In our study, we aimed at identifying regulatory microRNA signatures in LSCC mRNA profiles from our previous analysis. By this approach, we identified 14 overexpressed genes that shared a common regulatory hsa-miR-299-5p signature in LSCC samples. Subsequent RT-qPCR analysis confirmed the downregulation of hsa-miR-299-5p as well as the overexpression of 3 out of 14 genes: PATZ1, PURB, and TFAM in both LSCC cell lines and tumor samples compared to non-cancerous controls. Further, we have demonstrated a direct interaction between hsa-miR-299-5p and TFAM 3'UTR using dual luciferase assay. Importantly, we have shown decreased TFAM protein level after mimicry of hsa-miR-299-5p expression in three LSCC cell lines. Moreover, cell lines with restored activity of hsa-miR-299-5p demonstrated reduced viability compared to cell lines treated with the negative control. In conclusion, we point to hsa-miR-299-5p as a tumor-suppressive microRNA with the potential to regulate TFAM and consequently influence cell viability.
Identification of SNP markers associated with yield in winter oilseed rape (Brassica napus L.) hybrids.
Bocianowski J, Nowosad K, Kozak B … +1 more , Martofel J
J Appl Genet · 2026 Feb · PMID 39985735 · Publisher ↗
Winter oilseed rape (Brassica napus), a crucial crop in temperate regions, is a key contributor to global vegetable oil production and an essential component of crop rotations due to its ability to improve soil structure...
Winter oilseed rape (Brassica napus), a crucial crop in temperate regions, is a key contributor to global vegetable oil production and an essential component of crop rotations due to its ability to improve soil structure and fertility. Enhancing its yield is vital for meeting the increasing demand for sustainable oil production, supporting food security, and optimizing biofuel production, while also ensuring the economic viability of agricultural systems in colder climates. The aim of the research was to determine association between SNP molecular markers and rapeseed yield. The plant material for this study consisted of 276 oilseed rape hybrids. The experiment was conducted in four localities: Borowo, Kończewice, Małyszyn, and Strzelce. The mean yield values ranged from 0.07 kg (for hybrid EH_20212 in Małyszyn) to 9.10 kg (for hybrid EH_20410 in Kończewice). The genotype matrix for 276 hybrids was constructed using marker data from the parental genotypes of inbred individuals (maternal and paternal lines). The matrix was coded as {- 1, 0, 1}, assuming an additive effect of the alleles. A total of 13,116 SNP markers were identified. For association mapping, 12,581 polymorphic markers were used. The results of the observation of the yield and sequencing were used for association mapping, which ultimately resulted in the selection of twenty-six molecular markers important (LOD > 5.0) simultaneously in all four localities.
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