Journal Of Applied Genetics[JOURNAL]
Sun
200 papers
Endometrial factors and pregnancy loss frequency in recurrent pregnancy loss patients: comparing RT-PCR microbiology, microbial cultures, and immunohistochemistry of endometrium biopsy.
Klimaszyk K, Wirstlein P, Bednarek-Rajewska K … +4 more , Jankowski M, Svarre Nielsen H, Wender Ożegowska E, Kędzia M
J Appl Genet · 2025 May · PMID 39976842 · Full text
The objective of this study is to investigate the presence of bacteria in endometrial samples from patients with recurrent pregnancy loss (RPL) and explore potential correlations between bacterial presence, chronic endom...
The objective of this study is to investigate the presence of bacteria in endometrial samples from patients with recurrent pregnancy loss (RPL) and explore potential correlations between bacterial presence, chronic endometritis, and previous pregnancy loss history. Endometrial samples from 90 RPL patients were analysed using RT-PCR to detect 10 specific bacterial species. A subgroup of 65 patients underwent additional microbial culture and immunohistochemistry for plasma cell identification. Correlations between bacterial presence, chronic endometritis, and the number of previous pregnancy losses were evaluated. We detected at least one out of 10 chosen bacteria DNA by RT-PCR in 24.4% (22/90) of endometrial samples. Patients with PCR-identified bacteria had a significantly higher number of previous pregnancy losses (median 3 vs 2, p = 0.01). No correlation was observed between bacterial presence and chronic endometritis diagnosis. A significant correlation was found between bacterial detection by PCR and microbial culture (p = 0.03), though culture methods detected fewer positive cases. In RPL patients, detecting DNA from at least one of 10 selected bacterial species by RT-PCR correlates with a higher number of previous pregnancy losses. However, this bacterial presence does not correlate with chronic endometritis diagnosis based on the CD138 immunohistochemistry-identified plasma cell count. These findings suggest a potential role of endometrial bacteria in RPL that may be independent of the classical inflammatory response associated with chronic endometritis.
Identification of novel biallelic mutations in CFAP53 associated with fetal situs inversus totalis and literature review.
Guo Z, Tan M, Zhu H … +8 more , Lou G, Xia X, Yang W, Lv Y, Huang J, Wang R, Hao B, Liao S
J Appl Genet · 2026 May · PMID 39969775 · Publisher ↗
Visceral heterotaxy is a congenital malformation characterized by the abnormal arrangement of left-right axis of visceral organs. To date, several genes implicated in the regulation of laterality patterning have been ide...
Visceral heterotaxy is a congenital malformation characterized by the abnormal arrangement of left-right axis of visceral organs. To date, several genes implicated in the regulation of laterality patterning have been identified. Notably, CFAP53, also referred to as CCDC11, is involved in the regulation of ciliary motility, and mutations in this gene have been linked to a rare condition of heterotaxy. In this study, whole-exome sequencing (WES) was utilized to analyze the genetic causes of a fetus in a Chinese family, presenting with situs inversus totalis. In silico predictions and functional studies were performed to evaluate the pathogenicity of the identified candidate gene variants. WES revealed two novel compound heterozygous mutations, c.777G > T and c.1013A > T, in the CFAP53 gene. Minigene experiments demonstrated that c.777G > T may result in splicing aberrations, thus leading to the production of truncated CFAP53 proteins. Additionally, in silico analyses indicate that c.1013A > T could disrupt the interaction between CFAP53 and its target protein, TTC25. We report the second documented case of fetus with situs inversus totalis due to biallelic loss-of-function variants in CFAP53. According to literature review, our findings provide a basis for the prenatal diagnosis and genetic counseling of CFAP53 mutation-associated visceral heterotaxy.
CALR-mutant myeloproliferative neoplasms: insights from next-generation sequencing.
Mroczkowska-Bękarciak A, Szeremet A, Chyrko O … +1 more , Wróbel T
J Appl Genet · 2026 Feb · PMID 39960584 · Full text
Essential thrombocythemia and primary myelofibrosis belong to the group of BCR::ABL1-negative myeloproliferative neoplasms. The presence of mutations in the JAK2, CALR, and MPL genes is essential for the diagnosis of mye...
Essential thrombocythemia and primary myelofibrosis belong to the group of BCR::ABL1-negative myeloproliferative neoplasms. The presence of mutations in the JAK2, CALR, and MPL genes is essential for the diagnosis of myeloproliferative neoplasms. These mutations are called "driver" mutations. However, not only leading mutations have been identified in patients with MPN, but also more than half of individuals with essential thrombocythemia and more than 80% of patients with myelofibrosis have additional mutations. One technique that makes it possible to find prognostic, predictive, and diagnostic indicators is next-generation sequencing. Coexisting mutations are associated with reduced response to therapy, shortened overall survival, and a higher risk of transformation to acute myeloid leukemia or myelofibrosis. The study group consisted of 42 patients with the diagnosis of BCR::ABL1-negative MPN and the presence of a mutation in the CALR gene. The research material was archival, and DNA was obtained from patients' peripheral blood. Forty genes (17 genes, 23 hotspots) were sequenced using the commercial kit AmpliSeq for Illumina Myeloid Panel applying the targeted next-generation sequencing approach. For the study, the Illumina MiniSeq platform was used. The analysis of the obtained genetic results was carried out using bioinformatics tools and genetic databases. We studied 42 CALR-positive ET (n = 28) and MF (n = 14) patients with NGS panel testing. The median age at diagnosis of the entire patient series was 58 years. Additional mutations were detected in 48% of patients in the whole cohort. The most frequently mutated genes in the study population were ASXL1, TET2, and DNMT3A, which are largely associated with epigenetic regulatory mechanisms. NGS panel studies represent a breakthrough in the diagnostic and prognostic evaluation of MPNs with CALR mutations. The ability to perform such a comprehensive study provides valuable information on the biology of the disease and the selection of the appropriate treatment regimen. The use of new technologies shows that not only driver mutations have clinical significance for the patient. NGS has the potential to increase the precision and effectiveness of diagnosis and prognosis.
Utilization of doubled haploid breeding approach in introgression of QTL/gene(s) for parental line improvement of hybrid rice.
Bhuyan SS, Barik DP, Dash B … +10 more , Rout P, Chandravani M, Baral S, Mishra A, Verma RL, Katara JL, Chidambaranathan P, Devanna BN, Prabhukarthikeyan SR, Samantaray S
J Appl Genet · 2025 Dec · PMID 39960583 · Publisher ↗
This study aimed to improve the restorer line IR 42266-29-3R (A42) for multiple stress tolerance using integrated marker-assisted backcross breeding (MABB) and the doubled haploid (DH) approach. The primary objective was...
This study aimed to improve the restorer line IR 42266-29-3R (A42) for multiple stress tolerance using integrated marker-assisted backcross breeding (MABB) and the doubled haploid (DH) approach. The primary objective was to introduce the abiotic stress tolerant QTL (qDTY1.1 and qHTSF4.1) into the background IR 42266-29-3R, which already harbors three bacterial blight (BB) resistance genes (xa5, xa13, and Xa21). The BCF population was derived from crosses between IR 42266-29-3R and N22, leading to the development of 113 true DHs. Efficient callus induction (29.64%) was achieved using N6 medium supplemented with 2.0 mg/l 2,4-D, 0.5 mg/l BAP, and 3% maltose. Green plant regeneration rates were notably high on the MS medium supplemented with 0.5 mg/l NAA, 0.5 mg/l Kn, 2.0 mg/l BAP, and 3% sucrose, reaching 68.6% and 61.9% on the 2nd and 7th days, respectively. From the 113 DHs, 24 were selected based on superior morpho-agronomic traits and maximum gene combinations. These DHs underwent phenotypic evaluation during the reproductive stage for drought and heat stress responses, alongside assessment for BB resistance. Among them, CS65 showed a genetic profile encompassing xa13, Xa21, qDTY1.1, and qHTSF4.1, while six others exhibited xa5, Xa21, qDTY1.1, and qHTSF4.1. Notably, CS1, CS3, CS37, CS64, and CS65 demonstrated low susceptibility to heat and drought stresses, coupled with yields comparable to the recurrent parent and moderate to high resistance against bacterial blight. CS65 emerged as the most promising genotype due to its robust tolerance to multiple stresses and improved yield potential. Moreover, eight out of the 24 DHs tested positive for both Rf3 and Rf4 genes, displaying spikelet fertility rates exceeding 75%. These selected restorer lines will serve as foundational material for developing superior hybrid rice lines, while the non-restorer lines will contribute to the broader pool of rice varieties in future breeding programs.
Genetic analysis of autosomal dominant polycystic kidney disease in Iranian families: a combined Sanger and next-generation sequencing study.
Rafiee M, Razipour M, Keramatipour M … +2 more , Roozbeh J, Entezam M
J Appl Genet · 2026 May · PMID 39951171 · Publisher ↗
Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited renal disorder, primarily caused by mutations in the PKD1 and PKD2. Genetic testing is valuable for the diagnosis, prognosis, and clinical...
Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited renal disorder, primarily caused by mutations in the PKD1 and PKD2. Genetic testing is valuable for the diagnosis, prognosis, and clinical management of ADPKD. Next-generation sequencing (NGS) techniques can overcome the limitations of traditional Sanger sequencing for the genetic diagnosis of ADPKD. This study included 18 Iranian ADPKD families. Long-range PCR and Sanger sequencing were used to analyze PKD1 and PKD2. Subsequently, NGS-based gene panel testing and whole-exome sequencing (WES) were also performed in selected families. Pathogenic/likely pathogenic variants were identified in 13/18 families (72.2%), including 9 in PKD1 and 4 in PKD2. Five novel variants were discovered (c.10016C > A, c.2096_2097 + 4del, c.12138 + 5G > C in PKD1; c.2359-8_2373del, c.180_181delGC in PKD2). Additionally, WES revealed a pathogenic PKD1 frameshift deletion (c.11376delG) in one genetically unresolved family, likely missed by initial Sanger sequencing due to allelic dropout. This study expands the mutational spectrum of PKD1/PKD2 with five novel variants. The findings demonstrate the advantages of NGS over conventional Sanger sequencing methods. The genetically unresolved cases suggest the potential involvement of variants within non-coding regions, large copy number variations, or novel genes in ADPKD pathogenesis. Whole-genome sequencing is warranted to investigate these unresolved cases further.
Hfq influences ciprofloxacin accumulation in Escherichia coli independently of ompC and ompF post-transcriptional regulation.
Turbant F, Lewandowska N, Bloch S … +4 more , Wien F, Chauvet H, Węgrzyn G, Arluison V
J Appl Genet · 2025 May · PMID 39920540 · Publisher ↗
The antibiotic resistance of pathogenic bacteria is currently one of the major problems in medicine, and finding novel antibacterial agents is one of the most difficult tasks in the field of biomedical sciences. Studies...
The antibiotic resistance of pathogenic bacteria is currently one of the major problems in medicine, and finding novel antibacterial agents is one of the most difficult tasks in the field of biomedical sciences. Studies on such tasks can be successful only if genetic and molecular mechanisms leading to antibiotic resistance/sensitivity are understood. Previous reports indicated that the bacterial protein Hfq, discovered as an RNA chaperone but subsequently demonstrated to play also other functions in cells, is involved in the mechanisms of the response of bacterial cells to antibiotics. Recently, it was found that Hfq dysfunction resulted in more effective accumulation of an antibiotic ciprofloxacin in Escherichia coli cells irrespective of the presence or absence of the AcrB efflux pump. However, small RNA-mediated impairment of expression of the ompF gene, which encodes a porin involved in antibiotics influx, reversed the effects of the absence of Hfq on the antibiotic accumulation. This led to the hypothesis that Hfq might influence ciprofloxacin accumulation in the manner independent on its RNA chaperone function, as this protein might also influence cellular membrane structure and functions. Here, we demonstrate that in ompC and ompF mutants of E. coli, accumulation of ciprofloxacin is significantly impaired in the absence of Hfq or its C-terminal domain. These results corroborate the above-mentioned hypothesis on a sRNA-independent mechanism of Hfq-mediated modulation of the antibiotic transmembrane transport. Since fluoroquinolones use both protein- and lipid-mediated pathways to cross the outer membrane, Hfq may influence both processes. This possibility will be discussed herein.
Scope for a threshold animal model for genetic evaluation for hip dysplasia.
de Andrade FM, Jardim LPCR, Tyska DU … +2 more , Nunes RL, Cobuci JA
J Appl Genet · 2025 Sep · PMID 39913054 · Publisher ↗
Hip dysplasia (HD) is a major welfare problem, and in the present work, we investigated a sample of Bernese Mountain Dog breed bred in Brazil to estimate the genetic parameters for HD and to determine the best model for...
Hip dysplasia (HD) is a major welfare problem, and in the present work, we investigated a sample of Bernese Mountain Dog breed bred in Brazil to estimate the genetic parameters for HD and to determine the best model for the estimation of breeding values (EBV) of dogs. The pedigree database consisted of 2218 dogs, of which 1202 had the hip phenotype available, corresponding to the X-ray (XR) classification according to the Fédération Cynologique Intenationale. Comparisons were made between seven different threshold models considering the HD phenotype with five classifications (reports from A to E) according to the XR (PHD1) and the binary phenotype with joints considered normal (report A) and abnormal (reports B to E) (PHD2). The threshold animal model was used to estimate the variance components and predict the genetic values. Fourteen models were evaluated, seven using variable PHD1 and another seven considering variable PHD2. Evaluated fixed effects were sex, birth year, or country of birth, which differed between models. The best fit model for the PHD1 phenotype estimated a heritability value of 0.30, while the best fit model for PHD2 estimated a value of 0.36. EBVs ranged from - 0.736 to 1.040 for PHD1 and from - 1.050 to 1.459 for PHD2, showing a wide diversity in the genetic merit of dogs. Approximately 40% of the animals had an EBV accuracy value greater than 50%. Considering the best two fit models for the tested phenotypes, we opted for the indication and use of the model working with PHD1, because of the direct correspondence of the PHD1 phenotype with the five possibilities of hip XR reports, once this facilitates understanding by both veterinarians and breeders. This model is used as the only fixed effect of the birth year. The present study is one of the first on canine genetic improvement approach in Brazil, and our results indicate the importance and potential of the use of EBV in the selection of sires for the improvement of HD in the national breeding of the breed.
QTL mapping of Fusarium ear rot resistance using genotyping by target sequencing (GBTS) in maize.
Meng B, Wang S, Li WX … +2 more , Guo Z, Tang J
J Appl Genet · 2025 Dec · PMID 39907963 · Publisher ↗
Fusarium ear rot (FER) is a global disease caused by the fungal pathogen Fusarium verticillioides. Maize FER resistance is a quantitative trait controlled by polygenes. In this study, a doubled haploid (DH) population in...
Fusarium ear rot (FER) is a global disease caused by the fungal pathogen Fusarium verticillioides. Maize FER resistance is a quantitative trait controlled by polygenes. In this study, a doubled haploid (DH) population involving 159 lines, developed from the inbred lines B73 (susceptible) and CXS161 (highly resistant), was inoculated with Fusarium verticillioides across 4-year-location environment combinations in China during 2021 and 2022. The lines were genotyped using target sequencing with a 10 K SNP array. The results showed that the estimated broad-sense heritability (H) in each environment ranged from 0.659 to 0.871, with an overall H of 0.805. The average genetic length between adjacent markers in the genetic map constructed using multiple single-nucleotide polymorphisms (mSNP) was smaller than that constructed using SNP, whereas the maximal genetic length was almost the same. Using a genetic map constructed with a SNP, two quantitative trait loci (QTL) were identified on chromosomes 2 and 5, which explained 7.65% and 9.58% of the phenotypic variation, respectively. Using the genetic map constructed by mSNP, four QTL were identified, explaining 6.04-12.60% of the phenotypic variation. Moreover, two kompetitive allele-specific PCR (KASP) markers were developed using single-marker analysis methods, with one KASP marker validated across a backcross population that can be effectively used to identify FER resistance. In conclusion, using mSNP for genetic map construction does not confer advantages when the population size is limited and the marker density is high. However, the mSNP-constructed map identified more minor-effect QTL despite possessing a lower likelihood of the odds (LOD) values.
HIF1A, EPAS1, and VEGFA: angiogenesis and hypoxia-related gene expression in endometrium and endometrial epithelial tumors.
Englert-Golon M, Tokłowicz M, Żbikowska A … +5 more , Sajdak S, Kotwicka M, Jagodziński P, Pławski A, Andrusiewicz M
J Appl Genet · 2026 Feb · PMID 39888575 · Full text
Endometrial cancer (EC) is the second most frequent gynecological malignancy and the sixth most common women's cancer worldwide. EC incidence rate is increasing rapidly. Apart from the classical, we should consider angio...
Endometrial cancer (EC) is the second most frequent gynecological malignancy and the sixth most common women's cancer worldwide. EC incidence rate is increasing rapidly. Apart from the classical, we should consider angiogenesis and hypoxia-related genes as a reason for EC manifestation and progression. We compared the patterns of HIF1A, EPAS1, and VEGFA (genes of interest - GOIs) mRNA expression in 92 cases. HIF1A and VEGFA levels were higher in EC patients than in controls. VEGFA differed significantly between controls and both tumor grades G2 and G3, and we observed a positive correlation for HIF1A and VEGFA with EC grading. VEGFA levels were significantly higher in post-menopausal compared to pre-menopausal patients. All GOIs demonstrated strong correlations in pre-menopausal cases and weak correlations in post-menopausal cases. A positive correlation was observed in pre-menopausal controls for all GOIs and in post-menopausal patients for only EPAS1 and VEGFA. HIF1A and EPAS1 positively correlated with VEGFA in post-menopausal EC cases. Multiple linear regression analyses revealed that menopause, body mass index (BMI), and HIF1A expression are significant stimulating factors for EC occurrence. HIF1A levels were higher in EC patients after BMI and comorbidity number adjustment. The gene-to-gene relation could be seen as either a diagnostic or a therapeutic target in EC. Physicians should inform patients about modifiable risk factors such as BMI. Second, more attention should be paid to diagnosing patients with comorbidities in older age and after menopause. These factors should be considered in designing angiogenesis and hypoxia-related gene-targeting therapies.
Genetic diversity and selection signatures in sheep breeds.
Rodrigues JL, Braga LG, Watanabe RN … +4 more , Schenkel FS, Berry DP, Buzanskas ME, Munari DP
J Appl Genet · 2025 Sep · PMID 39883377 · Full text
Natural and artificial selection in domesticated animals can cause specific changes in genomic regions known as selection signatures. Our study used the integrated haplotype score (iHS) and Tajima's D tests within non-ov...
Natural and artificial selection in domesticated animals can cause specific changes in genomic regions known as selection signatures. Our study used the integrated haplotype score (iHS) and Tajima's D tests within non-overlapping windows of 100 kb to identify selection signatures, in addition to genetic diversity and linkage disequilibrium estimates in 9498 sheep from breeds in Ireland (Belclare, Charollais, Suffolk, Texel, and Vendeen). The mean observed and expected heterozygosity for all the sheep breeds were 0.353 and 0.355, respectively. Suffolk had the least genetic variation and, along with Texel, had slower linkage disequilibrium decay. iHS and Tajima's D detected selection signatures for all breeds, with some regions overlapping, thus forming longer segments of selection signatures. Common selection signatures were identified across iHS and Tajima's D methods for all breeds, with Belclare and Texel having several common regions under positive selection. Several genes were detected within the selection signature regions, including ITGA4, TLR3, and TGFB2 related to the immune system against endoparasites; DLG1, ROBO2, MXI1, MTMR2, CEP57, and FAM78B related to reproductive traits; WDR70 related to milk traits; SCHM1 and MYH15 related to meat traits; and TAS2R4, TAS2R39, and TAS2R40 related to adaptive traits. In conclusion, our results demonstrated moderate genetic diversity in the sheep breeds and detected and characterized selection signatures harboring genes associated with reproductive traits, milk production, meat production, and adaptive traits such as endoparasite resistance.
From cytogenetics to cytogenomics: a new era in the diagnosis of chromosomal abnormalities in domestic animals.
Switonski M, Szczerbal I, Nowacka-Woszuk J
J Appl Genet · 2025 Sep · PMID 39869248 · Publisher ↗
Identification of chromosomal abnormalities is an important issue in animal breeding and veterinary medicine. Routine cytogenetic diagnosis of domestic animals began in the 1960s with the aim of identifying carriers of c...
Identification of chromosomal abnormalities is an important issue in animal breeding and veterinary medicine. Routine cytogenetic diagnosis of domestic animals began in the 1960s with the aim of identifying carriers of centric fusion between chromosome 1 and 29 in cattle. In the 1970s, chromosome banding techniques were introduced, and in the 1980s, the first cytogenomic techniques, based on the development of locus- and chromosome-specific probes, were used. Since the beginning of the twenty-first century, molecular techniques (such as polymorphism of microsatellite markers, droplet digital PCR, SNP microarrays, and whole genome sequencing) have begun to be widely used in animal breeding. This review is focused on the cytogenomic diagnosis of chromosome abnormalities in cattle, horses, pigs, dogs, and cats. We show that these approaches are very useful in large-population screening studies of the prevalence of aneuploidies (mainly of sex chromosomes) and structural rearrangements (centric fusions and reciprocal translocations).
Genetic etiology of Perrault syndrome in Iranian families: first report from Iran and literature review.
Shokouhian E, Kahrizi K, Najmabadi H … +1 more , Babanejad M
J Appl Genet · 2026 Feb · PMID 39847269 · Publisher ↗
Perrault syndrome (PS) is an extremely rare autosomal recessive condition characterized primarily by bilateral sensorineural hearing loss in both genders and primary or secondary ovarian failure in females. Neurological...
Perrault syndrome (PS) is an extremely rare autosomal recessive condition characterized primarily by bilateral sensorineural hearing loss in both genders and primary or secondary ovarian failure in females. Neurological features such as cerebral ataxia, peripheral neuropathy, epilepsy, and intellectual disability are frequent manifestations of PS. To date, six genes have been reported to cause PS, and nearly 100 families have been identified worldwide with this syndrome. Exome sequencing was performed on two unrelated Iranian families presenting with Perrault syndrome. Family A included three offspring affected with bilateral severe to profound congenital hearing loss, cerebral ataxia, epilepsy, and intellectual disability. Family B included a female affected with bilateral moderate to severe hearing loss and peripheral neuropathy. In Family A, a compound heterozygous mutation (c.21delA and a novel missense mutation c.512C > G) in the CLPP gene was identified. In Family B, a homozygous mutation c.874C > A in the TWNK gene was found in the affected female. These findings represent the first report of genetic variations in the CLPP and TWNK genes in Iranian families with Perrault syndrome. The study expands the genetic landscape of Perrault syndrome by identifying novel mutations in the CLPP and TWNK genes. It also highlights the utility of exome sequencing as a cost-effective and powerful tool for diagnosing rare and complex genetic disorders like Perrault syndrome.
Novel and recurrent genetic variants associated with male and female infertility.
Jankowska KK, Kutkowska-Kazmierczak A, Ślusarczyk K … +9 more , Domaszewicz A, Duk K, Wolski JK, Kozioł K, Sawicka J, Klapecki J, Laudański P, Wertheim-Tysarowska K, Rygiel AM
J Appl Genet · 2025 Dec · PMID 39809967 · Publisher ↗
Recently, the knowledge of the genetic basis of fertility disorders has expanded enormously, mainly thanks to the use of next-generation sequencing (NGS). However, the genetic cause of infertility, in the majority of pat...
Recently, the knowledge of the genetic basis of fertility disorders has expanded enormously, mainly thanks to the use of next-generation sequencing (NGS). However, the genetic cause of infertility, in the majority of patients, is still undefined. The aim was to identify novel and recurrent pathogenic/likely pathogenic variants in patients with isolated infertility or puberty delay using a targeted NGS technique. We have enrolled 41 patients (36 males and 5 females) with infertility problems or delayed puberty. We included the patients with hypogonadotropic hypogonadism (n = 12), hypergonadotropic hypogonadism (n = 15), abnormal sperm parameters (n = 10), androgen insensitivity syndrome (n = 3) and 46,XY gonadal dysgenesis (n = 1). Genetic tests were performed using targeted NGS panel of 35 genes implicated in fertility. Pathogenic or likely pathogenic variants potentially explaining the clinical phenotype were identified in 12 of 41 patients (29%). These included 9 of 12 patients (75%) with hypogonadotropic hypogonadism, 2 of 3 patients (66%) with androgen insensitivity syndrome, and the single patient with 46,XY gonadal dysgenesis. Among the 18 identified variants, 4 were novel (FGF8:p.Ala147Thr; SEMA3A:p.Arg544Cys; FGFR1:p.Thr141IlefsTer10; NSMF: p.Tyr242Cys), while 14 were recurrent. Our study expands the knowledge of the genetic basis of the infertility disorders and highlights the importance of genetic testing for proper diagnosis making and genetic counselling.
Genotype by year interaction and additive and epistasis gene effects for Fusarium stalk rot resistance in doubled haploid lines of maize (Zea mays L.).
Bocianowski J, Nowosad K, Zalewski D … +1 more , Kaczmarek-Pieńczewska A
J Appl Genet · 2025 Dec · PMID 39808252 · Publisher ↗
Fusarium stalk rot is the main factor reducing the quality of maize grain and leads to significant yield losses, which that ranges from 20 to 100%, depending on the degree of infection and weather conditions. Understandi...
Fusarium stalk rot is the main factor reducing the quality of maize grain and leads to significant yield losses, which that ranges from 20 to 100%, depending on the degree of infection and weather conditions. Understanding its genetic mechanism is key to improving grain quality and ultimate yield. An experiment with 26 doubled haploid (DH) lines of maize was conducted in the northern part of the Lower Silesia Province in Poland over a ten-year period (2013-2022). The study assessed resistance to Fusarium stalk rot. The objectives were to evaluate genotype-year interactions for resistance to Fusarium stalk rot in maize DH lines using the additive main effects and multiplicative interaction (AMMI) model, to select DH lines that are stable across all years of testing and specific to particular environmental conditions, and to estimate additive and epistatic effects. AMMI results demonstrated a significant effect of genotype, year, and their interaction on Fusarium stalk rot resistance. The KN16 line is recommended for inclusion in further research within the breeding program due to its excellent stability and high average resistance to Fusarium stalk rot. Estimates of additive gene action effects were statistically significant in each year of the study. Estimates of epistasis (total additive by additive interaction) effects for Fusarium stalk rot resistance were also statistically significant in all ten years of the study. Only in 2013 was the epistasis effect positive (0.168). These results indicate that achieving biological advances in resistance to Fusarium stalk rot should be an important focus of ongoing maize breeding programs.
Oligogenic risk score for Gilles de la Tourette syndrome reveals a genetic continuum of tic disorders.
Borczyk M, Fichna JP, Piechota M … +7 more , Gołda S, Zięba M, Hoinkis D, Cięszczyk P, Korostynski M, Janik P, Żekanowski C
J Appl Genet · 2025 Dec · PMID 39792217 · Publisher ↗
Gilles de la Tourette syndrome (GTS) and other tic disorders (TDs) have a substantial genetic component with their heritability estimated at between 60 and 80%. Here we propose an oligogenic risk score of TDs using whole...
Gilles de la Tourette syndrome (GTS) and other tic disorders (TDs) have a substantial genetic component with their heritability estimated at between 60 and 80%. Here we propose an oligogenic risk score of TDs using whole-genome sequencing (WGS) data from a group of Polish GTS patients, their families, and control samples (n = 278). In this study, we first reviewed the literature to obtain a preliminary list of 84 GTS/TD candidate genes. From this list, 10 final risk score genes were selected based on single-gene burden tests (SKAT p < 0.05) between unrelated GTS cases (n = 37) and synthetic control samples based on a database of local allele frequencies. These 10 genes were CHADL, DRD2, MAOA, PCDH10, HTR2A, SLITRK5, SORCS3, KCNQ5, CDH9, and CHD8. Variants in and in the vicinity (± 20 kbp) of the ten risk genes (n = 7654) with a median minor allele frequency in the non-Finnish European population of 0.02 were integrated into an additive classifier. This risk score was then applied to healthy and GTS-affected individuals from 23 families and 100 unrelated healthy samples from the Polish population (AUC-ROC = 0.62, p = 0.02). Application of the algorithm to a group of patients with other tic disorders revealed a continuous increase of the oligogenic score with healthy individuals with the lowest mean, then patients with other tic disorders, then GTS patients, and finally with severe GTS cases with the highest oligogenic score. We have further compared our WGS results with the summary statistics of the Psychiatric Genomics Consortium genome-wide association study (PGC GWAS) of TDs and found no signal overlap except for the CHADL gene locus. Polygenic risk scores from common variants of GTS GWAS show no difference between patient and control groups, except for the comparison between patients with non-GTS TDs and patients with severe GTS. Overall, we leveraged WGS data to construct a GTS/TD risk score based on variants that may cooperatively contribute to the aetiology of these disorders. This study provides evidence that typical and severe adult GTS as well as other tic disorders may exist on a single spectrum in terms of their genetic background.
Complementarity of biomarker screening and genetic analyses based on the case of an attenuated multiple sulfatase deficiency.
Lipiński P, Ługowska A, Pollak A … +2 more , Płoski R, Tylki-Szymańska A
J Appl Genet · 2025 Sep · PMID 39776369 · Publisher ↗
Multiple sulfatase deficiency (MSD) is an ultra-rare lysosomal disease caused by defective activation of cellular sulfatases comprising clinical features of mucopolysaccharidoses, sphingolipidoses, and other sulfatase de...
Multiple sulfatase deficiency (MSD) is an ultra-rare lysosomal disease caused by defective activation of cellular sulfatases comprising clinical features of mucopolysaccharidoses, sphingolipidoses, and other sulfatase deficiencies. We present a case of an infant with feeding difficulties related to autism spectrum disorder (ASD) who was diagnosed at 10 months of age with MSD by next-generation sequencing (NGS). Biochemical results obtained in dried blood spot (DBS) samples were inconsistent and not suggesting MSD in the light of identified pathogenic SUMF1 variants. However, follow-up analyses at 20 months of age revealed an increased concentration of sulfatides in DBS. It should be noted that biochemical tests, routinely used as screening methods, have a risk of false negative results, especially regarding mild/attenuated phenotypes, as presented in our report.
A 280 bp SINE insertion within the pig PLA2G16 could potentially modify gene expression through integration with its transcript.
Chen C, Wang M, Zheng Y … +5 more , Liu Z, Azele P, Saleh AA, Wang X, Song C
J Appl Genet · 2025 Sep · PMID 39745593 · Publisher ↗
In our previous study, we identified a Short Interspersed Nuclear Element Retrotransposon Insertion Polymorphism (SINE-RIP) within the 3' untranslated region (3'UTR) of the Phospholipase A2 Group XVI (PLA2G16) gene, whic...
In our previous study, we identified a Short Interspersed Nuclear Element Retrotransposon Insertion Polymorphism (SINE-RIP) within the 3' untranslated region (3'UTR) of the Phospholipase A2 Group XVI (PLA2G16) gene, which is essential in lipid metabolism. In this study, we confirmed the presence of this 280 bp SINE insertion and examined its distribution across ten distinct pig breeds using PCR and sequencing. Subsequently, RT-PCR was employed to determine its potential for co-transcription. Finally, qPCR analysis was performed to evaluate the insertion's effect on PLA2G16 expression. The results indicated significant polymorphism at this site among different breeds. The SINE insertion can co-transcribe with PLA2G16 and shows a tissue-specific relationship with its expression in backfat and liver. Specifically, in Sujiang and Mi pigs, individuals homozygous for the SINE insertion (SINE) demonstrated significantly lower PLA2G16 expression (p < 0.01) in backfat compared to those without the insertion (SINE). Conversely, in Sujiang pigs, SINE individuals exhibited significantly higher expression (p < 0.05) in the liver compared to SINE counterparts. These findings suggest that the SINE insertion in the 3'UTR of PLA2G16 can fuse with the target gene, forming a new transcript that may affect gene expression levels in a tissue-specific manner.
Development and longitudinal neurocognitive functioning in mucopolysaccharidosis type IIIC: a case study.
Anikiej-Wiczenbach P, Limanówka M, Mazurkiewicz-Bełdzińska M … +5 more , Pierzynowska K, Węgrzyn G, Wierzba J, Milska-Musa K, Mański A
J Appl Genet · 2025 Sep · PMID 39739235 · Publisher ↗
This case study presents a comprehensive analysis of the neurocognitive, medical, and developmental functioning of a 9-year-old girl diagnosed with mucopolysaccharidosis type IIIC (MPS IIIC). Genetic testing revealed a h...
This case study presents a comprehensive analysis of the neurocognitive, medical, and developmental functioning of a 9-year-old girl diagnosed with mucopolysaccharidosis type IIIC (MPS IIIC). Genetic testing revealed a homozygous pathogenic variant of the HGSNAT gene (c.1872C > A), typically associated with severe neurodegeneration. However, her clinical presentation has been milder compared to the expected progression based on her genetic profile and residual enzyme levels. The child's current overall intellectual functioning was at the level of moderate intellectual disability; however, her developmental age has remained at the level of 5;3 for the last 3 years. The neuropsychological assessment showed some moderate difficulties in the patient's functioning, and brain magnetic resonance imaging showed no abnormalities. The results revealed that the child maintains the majority of her cognitive skills at a stable level, except for a marked decline in working memory. The study highlights the complexity and variability in the progression of MPS IIIC, emphasizing the need for early diagnosis, regular monitoring, and a multidisciplinary approach. This case highlights the need to consider individual variability in MPS IIIC progression, even when genetic and biochemical markers suggest a more severe course.
Effect of miR-10a on the proliferation and differentiation of yak adipocyte precursors.
Su Q, Gao Z, Zhang F … +4 more , Wu Z, Ji Q, Zhu K, Gui L
J Appl Genet · 2025 May · PMID 39715988 · Publisher ↗
The fat content of yak meat is significantly correlated with the meat quality, and an appropriate fat content helps to improve the texture of the meat. The involvement of miR-10a in regulating the differentiation and pro...
The fat content of yak meat is significantly correlated with the meat quality, and an appropriate fat content helps to improve the texture of the meat. The involvement of miR-10a in regulating the differentiation and proliferation of various cell types has been reported. Therefore, in this study, the effects of miR-10a on lipid droplet accumulation were investigated by transfection of yak adipocyte precursors with an miR-10a inhibitor, followed by Oil Red O, BODIPY, EdU staining, and cell cycle analysis of the transfected and control cells. The relative expression of lipogenic marker genes was determined by RT-qPCR to clarify the effect of miR-10a on the differentiation and proliferation of yak adipocyte precursors. Mature adipocytes were collected for transcriptome analysis to identify differentially expressed target genes and the association of these genes with adipogenic pathways was investigated by GO and KEGG enrichment analyses. In addition, the phylogeny and expression profiles of miR-10a were analyzed in various yak tissues. The results showed that miR-10a could inhibit the differentiation and promote the proliferation of yak adipocyte precursors. Analysis of the RNA-Seq results showed that miR-10a inhibitor and inhibitor NC had six differentially expressed genes: FABP4, AKR1B7, IGF2, ROCK1, IFNB1, and PLA2G3. These genes were found to be involved in the regulation of adipogenesis, with IGF2 and IFNB1 being upregulated in the PI3K-Akt signaling pathway, which is activated upon stimulation by IGF2 and IFNB1 and inhibits the differentiation and promotes the proliferation of yak adipocytes precursor, which in turn affected adipogenesis. Moreover, phylogenetic analysis indicated that miR-10a evolved relatively recently in yak and sheep, while tissue expression profiles showed that miR-10a was highly expressed in yak lung tissues.
Identification of quantitative trait loci for in vitro plant regeneration from leaf microexplants in cucumber (Cucumis sativus L.).
Słomnicka R, Cieplak M, Antosiewicz M … +4 more , Sadłos A, Galczak A, Kaźmińska K, Bartoszewski G
J Appl Genet · 2025 Sep · PMID 39710817 · Full text
Plant regeneration in tissue cultures is crucial for the application of biotechnological methods to plant breeding. However, the genetic basis of in vitro plant regeneration is not fully understood. For cucumber, regener...
Plant regeneration in tissue cultures is crucial for the application of biotechnological methods to plant breeding. However, the genetic basis of in vitro plant regeneration is not fully understood. For cucumber, regeneration protocols from different types of explants have been reported, but thus far, the molecular basis of regeneration from cotyledon explants has only been studied. The aim of this work was to identify quantitative trait loci (QTLs) for in vitro plant regeneration from cucumber leaf microexplants. Plant regeneration was evaluated using a population of recombinant inbred lines (RILs) developed from a cross between line B10, characterized by high regeneration efficiency, and the low regeneration efficiency line Gy14. All RILs were scored for frequency of callus formation, organogenesis, and shoot regeneration. RILs with regeneration efficiencies higher than that of line B10 have been observed. QTLs for the frequency of organogenesis and shoot regeneration were identified. All the QTLs were mapped on cucumber chromosome 6, explaining 11.9 to 20% of the phenotypic variance. The major-effect QTL for organogenesis or6.1 was located on the upper arm of chromosome 6. The QTLs for shoot regeneration frequency, sr6.1A and sr6.1B, were located on the lower arm of chromosome 6. Analysis of the genomic region corresponding to these QTLs combined with gene expression profiling revealed that CsARF6 and CsWOX9 are gene candidates underlying these QTLs. This study is a step toward identifying the genes controlling the ability of cucumber plant regeneration from leaf explants.
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