Journal Of Applied Genetics[JOURNAL]
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200 papers
Correction to: Unraveling the genetic basis of MODY: insights from next‑generation sequencing.
Eser M, Hekimoglu G, Dursun F
J Appl Genet · 2025 May · PMID 39420128 · Publisher ↗
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Profiling mRNA and miRNA expression variations associated with cyclin-dependent kinase pathway in the low-grade luminal early breast cancer.
Khamaneh AM, Mohajeri N, Naghili B … +1 more , Zarghami N
J Appl Genet · 2025 Sep · PMID 39373948 · Publisher ↗
Luminal A and B subtypes of breast tumors have fluctuated in proliferation rates, which arise from cell cycle dysregulation in cancer. Besides, microRNAs can regulate various cell processes through integration with mRNA....
Luminal A and B subtypes of breast tumors have fluctuated in proliferation rates, which arise from cell cycle dysregulation in cancer. Besides, microRNAs can regulate various cell processes through integration with mRNA. miRNAs that target the cell cycle are significant because of their prediction capability of prognosis. The objective of this study is to discover the integration between miRNA-mRNA and miRNA-miRNA related to cyclin-dependent kinase. Thirty-four pairs of human primary breast cancer and tumor margin samples from luminal breast cancer patients were investigated to assess the expression levels of CCND1, E2F1, miR-124, miR-503, miR-449a, and miR-449b. Afterward, the expression levels of mRNAs and miRNAs were investigated by real-time PCR. Statistical analysis was conducted to compare the expression levels between breast cancer and corresponding normal tissues. The protein expressions of E2F1 and CCND1 were verified by western blotting. Further, the correlation between mRNAs and miRNAs was calculated. E2F1 was significantly increased in both luminal A and B patients, while CCND1 was upregulated only in luminal B. Significant differences in all miRNAs were detected in both luminal A and B biopsy specimens (p < 0.0001). The correlation analysis revealed a positive strong correlation between miR-124 and E2F1 in luminal A patient. Moreover, the correlation test confirmed the ability of miR-449a to increase the CCND1 gene in luminal B subtypes. Also, miRNA correlation exhibited the miRNA-miRNA interaction in luminal breast cancer. This study demonstrated the novel miRNA-mRNA and miRNA-miRNA interactions, providing new insights into the molecular integration in luminal A and B patients. The authors propose that this research could contribute to introducing valuable biomarkers for luminal cancerous cells.
Unraveling the genetic basis of MODY: insights from next-generation sequencing.
Eser M, Hekimoglu G, Dursun F
J Appl Genet · 2025 May · PMID 39361122 · Publisher ↗
Maturity-onset diabetes of the young (MODY) is an uncommon kind of monogenic diabetes. The major characteristics of MODY include not having insulin resistance and the absence of autoimmunity, early onset, and a family hi...
Maturity-onset diabetes of the young (MODY) is an uncommon kind of monogenic diabetes. The major characteristics of MODY include not having insulin resistance and the absence of autoimmunity, early onset, and a family history suggesting autosomal-dominant inheritance. Nonetheless, genetic testing is necessary for diagnosis. The MODY-related genes CEL, ABCC8, PDX1, GCK, WFS1, HNF4A, HNF1A, and HNF1B were examined using Next Generation Sequencing (NGS) in this investigation. This study aimed to evaluate the genetic and clinical characteristics of patients referred with a preliminary diagnosis of MODY, retrospectively. A total of 30 patients (18 male and 12 female) participated, with ages ranging from 5 to 56. Eight distinct genetic variants were identified in 17 cases (57%). Pathogenic variants in the HNF1A gene have been identified. Likely pathogenic variants were found in CEL, ABCC8, GCK, and HNF4A. The genes APPL1, BLK, INS, KCNJ1, KLF11, NEUROD1, PAX4, RFX6, and ZFP57 were shown to be mutation-free. Four distinct pathogenic variants are found in this series. Unexpectedly high rates of pathogenic variants have been found in the HNF1A gene. In 27% of cases, there is a family history of vertically transmitted diabetes. The study highlights the importance of genetic testing for individuals with early-onset diabetes and a strong family history of the condition. Comprehensive genetic testing and increased public awareness are essential for MODY.
Comparative genome analysis of endophytic Bacillus amyloliquefaciens MR4: a potential biocontrol agent isolated from wild medicinal plant root tissue.
Yang K, Dai X, Maitikadir Z … +3 more , Zhang H, Hao H, Yan C
J Appl Genet · 2024 Dec · PMID 39348005 · Full text
In this investigation, 396 endophytic bacterial strains from six indigenous medicinal plant species within the Xinjiang Tumor Peak National Nature Reserve were subjected to screening. The strain MR4 emerged as a notewort...
In this investigation, 396 endophytic bacterial strains from six indigenous medicinal plant species within the Xinjiang Tumor Peak National Nature Reserve were subjected to screening. The strain MR4 emerged as a noteworthy contender, demonstrating pronounced biocontrol capabilities coupled with exceptional cold tolerance. Through morphological scrutiny and comprehensive genomic sequencing, MR4 was identified as Bacillus amyloliquefaciens. Antagonistic assays revealed MR4's efficacy in suppressing the causative agents of cotton wilt and verticillium wilt, achieving inhibition rates surpassing 50%. Analyses, underpinned by PCR methodologies, indicated MR4's capacity to biosynthesize a minimum of eight distinct antimicrobial agents. The whole-genome sequencing data indicated that B. amyloliquefaciens MR4 had the genome size and GC content of 4,017,872 bp and 47.14%, respectively, and 4191 coding genes were identified. The genome consists of a single chromosome and one plasmid. Moreover, it was augmented by annotations from various databases, including GO, KEGG, and COG. The pathogenicity of MR4 undergoes evaluation, while predictions concerning MR4's secondary metabolites have disclosed gene clusters for 13 varieties of these compounds, with particular emphasis on surfactins and fengycin. Comparative analyses with four paradigmatic strains shed light on MR4's genomic composition and its phylogenetic lineage within the Bacillus genus. The genomic data pertaining to MR4 have been duly submitted to the NCBI GenBank, bearing the accession numbers CP146236 (Chr1) and CP146237 (plas1). This study endeavors to furnish potent microbial resources for the biocontrol and enhancement of plant growth, thereby providing a theoretical groundwork for MR4's agronomic utilization.
QTL analysis of sorghum grain traits based on high-density genetic map.
Cao N, Ding Y, Xu J … +5 more , Cheng B, Gao X, Li W, Zou G, Zhang L
J Appl Genet · 2025 Sep · PMID 39305455 · Full text
Sorghum grain traits are important agronomic traits directly related to yield and are key factors affecting the brewing process of distill liquor. Exploring the genes controlling those traits is of great significance for...
Sorghum grain traits are important agronomic traits directly related to yield and are key factors affecting the brewing process of distill liquor. Exploring the genes controlling those traits is of great significance for understanding the genetic mechanism of sorghum grain development. In this study, we conducted genotyping using Super-GBS technology on a recombinant inbred lines (RILs) population derived from the cross between "BTx623" and "Hongyingzi," consisting of 205 lines. The grain-related traits of the RIL population were investigated in Guiyang, Anshun in Guizhou, and Ledong in Hainan in China. By inclusive composite interval mapping (ICIM) method, a total of 47 quantitative trait locus (QTL) related to four grain traits (thousand grain weight, grain length, grain width, and length-width ratio) were identified across 10 chromosomes. Among them, 20 important QTL were repeatedly detected in multiple traits or environments and distributed on chromosomes 1 (1), 2 (2), 3 (5), 4 (5), 5 (1), 6 (2), 7 (2), 8 (1), and 9 (1). Six candidate genes were identified within the confidence interval of these QTL, and they are homologous to genes controlling rice grain development (OsMADS1, RGG2, OsNST1, SMG1, OsGRF8, and OsAP2-39). The results provide a basis for further cloning and functional verification of these candidate genes.
Measurement of the effectiveness of Clonostachys rosea in reducing Fusarium biomass on wheat straw.
Kulik T, Treder K, Rochoń M … +6 more , Załuski D, Sulima P, Olszewski J, Bilska K, Elena G, Kowalski T
J Appl Genet · 2024 Dec · PMID 39276302 · Full text
The survival and growth of plant pathogens on crop residues are key factors facilitating the dynamics of crop diseases. Spores (e.g., perithecia, and chlamydospores) and mycelium of pathogenic fungi overwinter on harvest...
The survival and growth of plant pathogens on crop residues are key factors facilitating the dynamics of crop diseases. Spores (e.g., perithecia, and chlamydospores) and mycelium of pathogenic fungi overwinter on harvest residues, such as straw, and serve as initial inoculum infecting crops in the next growing season. Therefore, targeting overwintering fungi is essential to attaining effective disease control. Beneficial microorganisms offer advantages in controlling pathogens through their ability to colonize and exploit different environmental niches. In this study, we applied qPCR assays to explore the biocontrol performance of locally isolated strains of Clonostachys against various Fusarium pathogens. We proved that prior colonization of wheat straw by Fusarium spp. can be effectively reduced by Clonostachys rosea. We demonstrated that the efficiency of C. rosea to reduce Fusarium inoculum appears to remain at a similar level for most studied strains regardless of the target pathogen and the level of colonization of substrates by pathogens. Efficient performance of local C. rosea strains identifies possible targets for future strategies to control Fusarium diseases in cereals. Our study also highlights the challenge in sequence-based determination of C. rosea, which is crucial for the efficient selection of beneficial strains for biocontrol purposes.
Splice-altering variant of PJVK gene in a Mauritanian family with non-syndromic hearing impairment.
Salame M, Bonnet C, Singh-Estivalet A … +9 more , Brahim SM, Roux S, Boussaty EC, Hadrami M, Hamed CT, Sidi AM, Veten F, Petit C, Houmeida A
J Appl Genet · 2025 Dec · PMID 39230647 · Full text
PJVK gene was recently shown to create hypervulnerability to sound in humans and was the first human gene implicated in non-syndromic hearing impairment due to neural defect. Targeted next-generation sequencing of over 1...
PJVK gene was recently shown to create hypervulnerability to sound in humans and was the first human gene implicated in non-syndromic hearing impairment due to neural defect. Targeted next-generation sequencing of over 150 known deafness genes was performed in the proband. Sanger sequencing was used to validate the PJVK variant and confirm familial segregation of the disease. A minigene-based assay has been performed to assess the impact of the variant on splicing. We identified a novel c.550-6A > G acceptor splice-site variant in the PJVK gene in the homozygous state in a Mauritanian child with severe to profound congenital deafness. The substitution was located in intron 4. The effect of the variation was demonstrated by a minigene assay which showed that the variation, an insertion of an additional 5 bp, created a new splice site resulting in the appearance of a premature stop codon (p.Phe184Tyrfs*26) and likely a truncated protein. This result constitutes a new splice-site variant report in the PJVK gene leading to DFNB59 type associated with autosomal recessive non-syndromic hearing impairment (ARNSHI).
Association of ACE and AGTR1 variants with retinopathy of prematurity: a case-control study and meta-analysis.
Durska A, Szpecht D, Gotz-Więckowska A … +1 more , Strauss E
J Appl Genet · 2025 Dec · PMID 39186201 · Full text
Retinopathy of prematurity (ROP) is a major cause of childhood blindness worldwide, linked to gene variants in the renin-angiotensin-aldosterone system, including angiotensin-converting enzyme (ACE) and angiotensin II re...
Retinopathy of prematurity (ROP) is a major cause of childhood blindness worldwide, linked to gene variants in the renin-angiotensin-aldosterone system, including angiotensin-converting enzyme (ACE) and angiotensin II receptor type 1 (AGTR1). This study aims to evaluate the association between ACE insertion/deletion (I/D) and AGTR1 rs5186A > C variants with the occurrence and progression of ROP in a Polish cohort. A total of 377 premature infants were enrolled in the study. The ACE variant was evaluated using PCR, and AGTR1 was assessed using TaqMan probes. Clinical characteristics, including risk factors and comorbidities, were documented. A meta-analysis of the effects of the studied variants on ROP was also conducted. The AGTR1 rs5186C allele was significantly associated with both the progression of ROP and treatment outcomes. Homozygotes exhibited a 2.47-fold increased risk of developing proliferative ROP and a 4.82-fold increased risk of treatment failure. The impact of this allele increased at low birth weight. A meta-analysis, including 191 cases and 1661 controls, indicated an overall risk of 1.7 (95%CI 1.02-2.84) for the recessive effect of the rs5186C allele. The ACE variant did not show a significant association with ROP in our population; however, a meta-analysis of 996 cases and 2787 controls suggested a recessive effect of the insertion allele (an odds ratio of 1.21 (95%CI 1.00-1.60)). These results indicate that gain-of-function AGTR1 variants may play a crucial role in the development of ROP, potentially by promoting angiogenesis and pro-inflammatory effects. Screening for these variants could facilitate the development of personalized risk assessment and treatment strategies for ROP.
Deciphering early responsive signature genes in rice blast disease: an integrated temporal transcriptomic study.
Antony A, Veerappapillai S, Karuppasamy R
J Appl Genet · 2024 Dec · PMID 39180632 · Publisher ↗
Rice blast disease, caused by Magnaporthe oryzae, reigns as the top-most cereal killer, jeopardizing global food security. This necessitates the timely scouting of pathogen stress-responsive genes during the early infect...
Rice blast disease, caused by Magnaporthe oryzae, reigns as the top-most cereal killer, jeopardizing global food security. This necessitates the timely scouting of pathogen stress-responsive genes during the early infection stages. Thus, we integrated time-series microarray (GSE95394) and RNA-Seq (GSE131641) datasets to decipher rice transcriptome responses at 12- and 24-h post-infection (Hpi). Our analysis revealed 1580 differentially expressed genes (DEGs) overlapped between datasets. We constructed a protein-protein interaction (PPI) network for these DEGs and identified significant subnetworks using the MCODE plugin. Further analysis with CytoHubba highlighted eight plausible hub genes for pathogenesis: RPL8 (upregulated) and RPL27, OsPRPL3, RPL21, RPL9, RPS5, OsRPS9, and RPL17 (downregulated). We validated the expression levels of these hub genes in response to infection, finding that RPL8 exhibited significantly higher expression compared with other downregulated genes. Remarkably, RPL8 formed a distinct cluster in the co-expression network, whereas other hub genes were interconnected, with RPL9 playing a central role, indicating its pivotal role in coordinating gene expression during infection. Gene Ontology highlighted the enrichment of hub genes in the ribosome and protein translation processes. Prior studies suggested that plant immune defence activation diminishes the energy pool by suppressing ribosomes. Intriguingly, our study aligns with this phenomenon, as the identified ribosomal proteins (RPs) were suppressed, while RPL8 expression was activated. We anticipate that these RPs could be targeted to develop new stress-resistant rice varieties, beyond their housekeeping role. Overall, integrating transcriptomic data revealed more common DEGs, enhancing the reliability of our analysis and providing deeper insights into rice blast disease mechanisms.
Correction to: The analysis of transcriptomic signature of TNBC-searching for the potential RNA‑based predictive biomarkers to determine the chemotherapy sensitivity.
Supplitt S, Karpinski P, Sasiadek M … +8 more , Laczmanski L, Kujawa D, Matkowski R, Kasprzak P, Abrahamowska M, Maciejczyk A, Iwaneczko E, Laczmanska I
J Appl Genet · 2025 Feb · PMID 39179763 · Full text
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Expanding TBCE-related phenotype-novel variant causing rigid spine, eosinophilia, neutropenia, and nocturnal hypoxemia.
Badura-Stronka M, Hirschfeld AS, Globa E … +5 more , Winczewska-Wiktor A, Potulska-Chromik A, Kostera-Pruszczyk A, Wicher D, Krawczyński MR
J Appl Genet · 2025 May · PMID 39153170 · Full text
We report three patients with the novel variant c.100 + 1G > A of the TBCE gene and describe the presented clinical phenotype in detail. We also systematically reviewed the literature for clinical similarities and dissim...
We report three patients with the novel variant c.100 + 1G > A of the TBCE gene and describe the presented clinical phenotype in detail. We also systematically reviewed the literature for clinical similarities and dissimilarities among all known patients with pathogenic TBCE variants. The clinical phenotype observed in patients with pathogenic TBCE variants is broader than previously described. Homozygous carriers of the c.100 + 1G > A variant exhibit a markedly milder clinical course, with no deviations in the calcium-phosphate metabolism and central nervous system pathology in MRI studies. Additionally, two patients manifest highly specific symptoms such as a rigid spine, eosinophilia, neutropenia, and nocturnal hypoxemia. Furthermore, cryptorchidism was observed in male patients. The identification of the pathogenic c.100 + 1G > A variant has thus far been limited to patients of Central-Eastern European descent, suggesting a potential founder mutation in this population.
Urofacial (Ochoa) syndrome with a founder pathogenic variant in the HPSE2 gene: a case report and mutation origin.
Del Valle-Peréz M, Mejía-García A, Echeverri-López D … +7 more , Gallo-Bonilla K, Tejada-Moreno JA, Villegas-Lanau A, Chvatal-Medina M, Restrepo JE, Cuartas-Montoya G, Zapata-Builes W
J Appl Genet · 2025 Sep · PMID 39150614 · Full text
Urofacial syndrome or Ochoa syndrome (UFS or UFOS) is a rare disease characterized by inverted facial expression and bladder dysfunction that was described for the first time in Colombia. It is an autosomal recessive pat...
Urofacial syndrome or Ochoa syndrome (UFS or UFOS) is a rare disease characterized by inverted facial expression and bladder dysfunction that was described for the first time in Colombia. It is an autosomal recessive pathology with mutations in the HPSE2 and LRIG2 genes. However, 16% of patients do not have any mutations associated with the syndrome. Despite the importance of neurobiology in its pathophysiology, there are no neurological, neuropsychological, or psychological studies in these patients. A 30-year-old male from Medellín, Colombia, with a significant perinatal history, was diagnosed with grade 4 hydronephrosis on his first ultrasound test. At 4 months of age, symptoms such as hypomimia, lagophthalmos, and recurrent urinary tract infections started to manifest. Imaging studies revealed urinary tract dilatation, vesicoureteral reflux, and a double collector system on his left side, which led to the diagnosis of UFS. Multiple procedures, including vesicostomy, ureterostomy, and enterocystoplasty, were performed. At 20 years of age, he achieved urinary sphincter control. Genetic analysis revealed a founder pathogenic variant, c.1516C > T (p.Arg506Ter), in the HPSE2 gene, which produces a truncated protein that lacks 86 amino acids. This variant is classified as pathogenic according to the ClinVar database for UFS. The mutation age is approximately 260-360 years, and the two alleles share a 7.2-7.4 Mb IBD segment. Moreover, we detected European local ancestry in the IBD segment, which is consistent with a Spanish introduction. Neurological examination, neuropsychological assessment, and psychological testing revealed no abnormalities, except for high stress levels. Clinical analysis of this patient revealed distorted facial expression and detrusor-sphincter dyssynergia, which are typical of patients with UFS. Genetic analysis revealed a pathogenic variant in the HPSE2 gene of European origin and a mutation age of 260-360 years. From a neurological, neuropsychological, and psychological (emotional and personality) perspective, the patient showed no signs or symptoms of clinical interest.
Identification of genes involved in the tomato root response to Globodera rostochiensis parasitism under varied light conditions.
Matuszkiewicz M, Święcicka M, Koter MD … +1 more , Filipecki M
J Appl Genet · 2025 Feb · PMID 39143454 · Full text
Understanding the intricate interplay between abiotic and biotic stresses is crucial for deciphering plant responses and developing resilient cultivars. Here, we investigate the combined effects of elevated light intensi...
Understanding the intricate interplay between abiotic and biotic stresses is crucial for deciphering plant responses and developing resilient cultivars. Here, we investigate the combined effects of elevated light intensity and nematode infection on tomato seedlings. Chlorophyll fluorescence analysis revealed significant enhancements in PSII quantum yield and photochemical fluorescence quenching under high light conditions. qRT-PCR analysis of stress-related marker genes exhibited differential expression patterns in leaves and roots, indicating robust defense and antioxidant responses. Despite root protection from light, roots showed significant molecular changes, including downregulation of genes associated with oxidative stress and upregulation of genes involved in signaling pathways. Transcriptome analysis uncovered extensive gene expression alterations, with light exerting a dominant influence. Notably, light and nematode response synergistically induced more differentially expressed genes than individual stimuli. Functional categorization of differentially expressed genes upon double stimuli highlighted enrichment in metabolic pathways, biosynthesis of secondary metabolites, and amino acid metabolism, whereas the importance of specific pathogenesis-related pathways decreased. Overall, our study elucidates complex plant responses to combined stresses, emphasizing the importance of integrated approaches for developing stress-resilient crops in the face of changing environmental conditions.
Short communication: catechol-O-methyltransferase allelic variation in relation to psychological and hormonal indices of stress in children and adolescents with chromosome 22q11.2 deletion syndrome (22q11.2DS).
Beebe JL, Martin CR, Sanders AFP … +4 more , Guidry J, Faheem F, Atallah J, Beaton EA
J Appl Genet · 2025 May · PMID 39126435 · Full text
Chromosome 22q11.2 deletion syndrome (22q11.2DS) is a developmental disorder with high rates of anxiety and psychosis. Catechol-O-methyltransferase (COMT) regulates epinephrine (E), norepinephrine (NE), and dopamine (DA)...
Chromosome 22q11.2 deletion syndrome (22q11.2DS) is a developmental disorder with high rates of anxiety and psychosis. Catechol-O-methyltransferase (COMT) regulates epinephrine (E), norepinephrine (NE), and dopamine (DA) and is implicated in both anxiety and psychotic disorders. The aim of this study was to determine how COMT variation relates to psychological anxiety and associated stress physiology responsiveness to better understand symptom heterogeneity in people with 22q11.2DS. We examined COMT allelic variation in relation to anxiety and hypothalamic-pituitary-adrenocortical (HPA) and sympathetic-adrenomedullary (SAM) hormonal stress indicators in 30 children and adolescents with 22q11.2DS. Contrary to expectation, individuals with the higher activity COMTval allele had higher anxiety levels versus those with the low activity (COMTmet) allele (p = 0.021; Glass' Δ = 0.69). Anxiety was not correlated with salivary cortisol (CORT) or alpha-amylase (sAA) in either group. Groups did not differ in CORT levels (p = 0.58), but the COMTmet group had higher sAA (p = 0.026; Glass' Δ = 0.67, uncorrected) suggesting greater SAM reactivity but not HPA activity. This suggests that COMT allelic variation may contribute to differences in acute SAM but not slower HPA stress reactivity in those with 22q11.2DS.
Genotype-environment interaction for grain yield in maize (Zea mays L.) using the additive main effects and multiplicative interaction (AMMI) model.
Bocianowski J, Nowosad K, Rejek D
J Appl Genet · 2024 Dec · PMID 39115751 · Full text
Genotype-environment interaction consists of the different response of individual genotypes resulting from changing environmental conditions. Its significance is a phenomenon that makes the breeding process very difficul...
Genotype-environment interaction consists of the different response of individual genotypes resulting from changing environmental conditions. Its significance is a phenomenon that makes the breeding process very difficult. On the one hand, the breeder expects stable genotypes, i.e., yielding similarly regardless of environmental conditions. On the other hand, selecting the best genotypes for each region is one of the key challenges for breeders and farmers. The aim of this study was to evaluate genotype-by-environment interaction for grain yield in new maize hybrids developed by Plant Breeding Smolice Co. Ltd., utilizing the additive main effects and multiplicative interaction (AMMI) model. The investigation involved 69 maize (Zea mays L.) hybrids, tested across five locations in a randomized complete block design with three replications. Grain yield varied from 8.76 t ha (SMH_16417 in Smolice) to 16.89 t ha (SMH_16043 in Płaczkowo), with a mean yield of 13.16 t ha. AMMI analysis identified significant effects of genotype, environment, and their interaction on grain yield. Analysis of variance indicated that 25.12% of the total variation in grain yield was due to environment factor, 35.20% to genotypic differences, and 21.18% to genotype by environmental interactions. Hybrids SMH_1706 and SMH_1707 are recommended for further breeding programs due to their high stability and superior average grain yield.
GGE biplot analysis for cane yield and sugar yield in advanced clones of sugarcane (Saccharum sp. complex).
Chaudhary D, Jeena AS, Singh NK … +3 more , Pant U, Rohit R, Gaur S
J Appl Genet · 2025 May · PMID 39066953 · Publisher ↗
The present investigation was taken up to study the G × E interaction and stability in 14 sugarcane clones during 2020-2021 and 2021-2022 at four different locations namely Pantnagar, Kashipur, Dhanauri (Haridwar), and D...
The present investigation was taken up to study the G × E interaction and stability in 14 sugarcane clones during 2020-2021 and 2021-2022 at four different locations namely Pantnagar, Kashipur, Dhanauri (Haridwar), and Dhakrani (Dehradun) for cane yield (CY) and sugar yield (SY) at the 10-month and 12-month stages. The research aimed to identify stable, high-yielding sugarcane clones adaptable to diverse environmental conditions, enhancing productivity and profitability for farmers in Uttarakhand, India. The combined ANOVA revealed significant differences among the clones (22.20% to 29.54% variation), environments (35% to 39.62% variation), and their interactions (19.91% to 24.16% variation) for CY and SY at both stages. To analyze the stability of genotypes and G × E interactions, the GGE biplot method was employed. The first two PCs explained 77.94% for CY, 74.39% for SY at the 10-month stage, and 81.01% for SY at 12-month stage of the total variation of the GGE model. The GGE biplots revealed that for CY, the mega-environment exhibited CoPant 16222 and CoPant 16223 as the winning genotypes. For SY at the 10-month stage, CoPant 17221 and CoPant 16222 were the best clones in two different mega-environments, while at the 12-month stage, the mega-environment showed CoPant 16222 and CoPant 16223 as the winning genotypes. Dehradun (2020) and Kashipur (2020) were identified as the best test environments for selecting widely and specifically adapted genotypes, respectively, for CY and SY at the 10-month as well as 12-month stages. In a nutshell, GGE biplot analysis identified the best-performing sugarcane clones and best test environments in Uttarakhand, India. Clone CoPant 16222 showed high mean performance and stability for cane and sugar yield, making it suitable for recommendation to farmers.
Antibiotic resistance and its correlation with biofilm formation and virulence genes in Klebsiella pneumoniae isolated from wounds.
Allami M, Mohammed EJ, Alnaji Z … +1 more , A Jassim S
J Appl Genet · 2024 Dec · PMID 39031267 · Publisher ↗
Klebsiella pneumoniae is the most important species of the Klebsiella genus and often causes hospital infections. These bacteria have a high resistance to most of the available drugs, which has caused concern all over th...
Klebsiella pneumoniae is the most important species of the Klebsiella genus and often causes hospital infections. These bacteria have a high resistance to most of the available drugs, which has caused concern all over the world. In this study, we investigated the antibiotic resistance profile and the ability to produce extended-spectrum beta-lactamase (ESBL) among K. pneumoniae isolates, and then we investigated the relationship between these two factors with biofilm formation and the prevalence of different virulence genes. In this study, 130 isolates of K. pneumoniae isolated from wounds were investigated. The antibiotic resistance of the isolates was evaluated by the disk diffusion method. The microtiter plate method was used to measure biofilm formation. The prevalence of virulence genes was detected by multiplex PCR. Among the examined isolates, 85.3% showed multidrug resistance. 87.6% of the isolates were ESBL-positive. Imipenem, meropenem, and fosfomycin were the most effective drugs. The ability of the isolates to produce biofilm was strong (80%), moderate (12.3%), and weak (7.6%), respectively. fimH, mrKD, entB, and tolC virulence genes were observed in all isolates. High prevalence of antibiotic resistance (especially multidrug resistance), high prevalence of ESBL-producing isolates, the ability of all isolates to biofilm formation, and the presence of fimH, mrKD, entB, and tolC virulence genes in all isolates show the importance of these factors in the pathogenesis of K. pneumoniae isolates in Iraq.
Genetic diversity and population structure of Uganda cassava germplasm.
Sichalwe KL, Kayondo I, Edema R … +7 more , Dramadri IO, AAdjei E, Kulembeka H, Kimani W, Mgonja D, Rubahaiyo P, Kanju E
J Appl Genet · 2024 Dec · PMID 39012576 · Publisher ↗
Cassava (Manihot esculenta Crantz) holds significant economic importance globally. Evaluating a diverse range of germplasm based on molecular characteristics not only enhances its preservation but also supports its utili...
Cassava (Manihot esculenta Crantz) holds significant economic importance globally. Evaluating a diverse range of germplasm based on molecular characteristics not only enhances its preservation but also supports its utilization in breeding programs. In this study, we assessed genetic diversity and population structure among 155 cassava genotypes from Uganda using 5247 single nucleotide polymorphism (SNP) markers. Genotyping by sequencing (GBS) was employed for SNP discovery and to evaluate genetic diversity and population structure using the ADMIXTURE software. The cassava accessions comprised two populations: 49 accessions from Ugandan lines and 106 accessions resulting from crosses between South American and Ugandan lines. The average call rate of 96% was utilized to assess marker polymorphism. Polymorphic information content values of the markers ranged from 0.1 to 0.5 with an average of 0.4 which was moderately high. The principal component analysis (PCA) showed that the first two components captured ~ 24.2% of the genetic variation. The average genetic diversity was 0.3. The analysis of molecular variance (AMOVA) indicated that 66.02% and 33.98% of the total genetic variation occurred within accessions and between sub-populations, respectively. Five sub-populations were identified based on ADMIXTURE structure analysis (K = 5). Neighbor-joining tree and hierarchical clustering tree revealed the presence of three different groups which were primarily based on the source of the genotypes. The results suggested that there was considerable genetic variation among the cassava genotypes which is useful in cassava improvement and conservation efforts.
Modulation of gene expression in immune-related organs by in ovo stimulation with probiotics and prophybiotics in broiler chickens.
Wishna-Kadawarage RN, Połtowicz K, Hickey RM … +1 more , Siwek M
J Appl Genet · 2025 Feb · PMID 38987456 · Full text
In ovo stimulation has been studied intensively as an alternative to antibiotic use in poultry production. We investigated the potential use of a probiotic in combination with a phytobiotic as a prophybiotic for in ovo s...
In ovo stimulation has been studied intensively as an alternative to antibiotic use in poultry production. We investigated the potential use of a probiotic in combination with a phytobiotic as a prophybiotic for in ovo stimulation and reported its beneficial effects on the gut microbiome of broiler chickens. The current study further investigates the gene expression in the immune-related organs of these chickens to understand the tissue-specific immunomodulatory effects of the treatments. The selected prophybiotic (Leuconostoc mesenteroides with garlic aqueous extract) and its probiotic component alone were injected into ROSS308 chicken eggs on the 12th day of incubation, and gene expression in cecal tonsils, spleen, and liver at 35 days of age was determined using qPCR method. The relative expression of each treatment was compared to the positive control, chickens injected with physiological saline in ovo. The results displayed a downregulation of pro- and anti-inflammatory cytokines in the cecal tonsils of the probiotic group and the liver of the prophybiotic group. The spleen displayed upregulated AVBD1 in both groups and upregulated IL1-β in the probiotic group. The probiotic group displayed increased expression of genes related to metabolism of energy (COX16), protein (mTOR), and lipids (CYP46A1) whereas the prophybiotic group displayed reduced expression of genes related to cholesterol synthesis (SREBP1) and glucose transportation (SLC2A2) in the liver. In conclusion, Leuconostoc mesenteroides differentially modulated gene expression in chickens when administered in ovo in combination with garlic aqueous extract. Further in ovo studies with different prophybiotic combinations are required to optimize the benefits in broiler chickens.
Identifying key genes and functionally enriched pathways in acute myeloid leukemia by weighted gene co-expression network analysis.
Jian J, Yuan C, Hao H
J Appl Genet · 2025 May · PMID 38977582 · Publisher ↗
Acute myeloid leukemia (AML) is characterized by the uncontrolled proliferation of myeloid leukemia cells in the bone marrow and other hematopoietic tissues and is highly heterogeneous. While with the progress of sequenc...
Acute myeloid leukemia (AML) is characterized by the uncontrolled proliferation of myeloid leukemia cells in the bone marrow and other hematopoietic tissues and is highly heterogeneous. While with the progress of sequencing technology, understanding of the AML-related biomarkers is still incomplete. The purpose of this study is to identify potential biomarkers for prognosis of AML. Based on WGCNA analysis of gene mutation expression, methylation level distribution, mRNA expression, and AML-related genes in public databases were employed for investigating potential biomarkers for the prognosis of AML. This study screened a total of 6153 genes by analyzing various changes in 103 acute myeloid leukemia (AML) samples, including gene mutation expression, methylation level distribution, mRNA expression, and AML-related genes in public databases. Moreover, seven AML-related co-expression modules were mined by WGCNA analysis, and twelve biomarkers associated with the AML prognosis were identified from each top 10 genes of the seven co-expression modules. The AML samples were then classified into two subgroups, the prognosis of which is significantly different, based on the expression of these twelve genes. The differentially expressed 7 genes of two subgroups (HOXB-AS3, HOXB3, SLC9C2, CPNE8, MEG8, S1PR5, MIR196B) are mainly involved in glucose metabolism, glutathione biosynthesis, small G protein-mediated signal transduction, and the Rap1 signaling pathway. With the utilization of WGCNA mining, seven gene co-expression modules were identified from the TCGA database, and there are unreported genes that may be potential driver genes of AML and may be the direction to identify the possible molecular signatures to predict survival of AML patients and help guide experiments for potential clinical drug targets.
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