Journal of Applied Genetics最新文献

{"title":"From cytogenetics to cytogenomics: a new era in the diagnosis of chromosomal abnormalities in domestic animals.","authors":"M Switonski, I Szczerbal, J Nowacka-Woszuk","doi":"10.1007/s13353-025-00943-x","DOIUrl":"https://doi.org/10.1007/s13353-025-00943-x","url":null,"abstract":"<p><p>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).</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143046139","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic etiology of Perrault syndrome in Iranian families: first report from Iran and literature review.","authors":"Ebrahim Shokouhian, Kimia Kahrizi, Hossein Najmabadi, Mojgan Babanejad","doi":"10.1007/s13353-025-00940-0","DOIUrl":"https://doi.org/10.1007/s13353-025-00940-0","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143023442","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Novel and recurrent genetic variants associated with male and female infertility.","authors":"Katarzyna K Jankowska, Anna Kutkowska-Kazmierczak, Klaudia Ślusarczyk, Alicja Domaszewicz, Katarzyna Duk, Jan Karol Wolski, Katarzyna Kozioł, Justyna Sawicka, Jakub Klapecki, Piotr Laudański, Katarzyna Wertheim-Tysarowska, Agnieszka Magdalena Rygiel","doi":"10.1007/s13353-024-00935-3","DOIUrl":"https://doi.org/10.1007/s13353-024-00935-3","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142983667","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genotype by year interaction and additive and epistasis gene effects for Fusarium stalk rot resistance in doubled haploid lines of maize (Zea mays L.).","authors":"Jan Bocianowski, Kamila Nowosad, Dariusz Zalewski, Agata Kaczmarek-Pieńczewska","doi":"10.1007/s13353-025-00938-8","DOIUrl":"https://doi.org/10.1007/s13353-025-00938-8","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142978576","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Oligogenic risk score for Gilles de la Tourette syndrome reveals a genetic continuum of tic disorders.","authors":"Malgorzata Borczyk, Jakub P Fichna, Marcin Piechota, Sławomir Gołda, Mateusz Zięba, Dzesika Hoinkis, Paweł Cięszczyk, Michal Korostynski, Piotr Janik, Cezary Żekanowski","doi":"10.1007/s13353-024-00930-8","DOIUrl":"https://doi.org/10.1007/s13353-024-00930-8","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142949138","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Complementarity of biomarker screening and genetic analyses based on the case of an attenuated multiple sulfatase deficiency.","authors":"Patryk Lipiński, Agnieszka Ługowska, Agnieszka Pollak, Rafał Płoski, Anna Tylki-Szymańska","doi":"10.1007/s13353-024-00936-2","DOIUrl":"https://doi.org/10.1007/s13353-024-00936-2","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142949128","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A 280 bp SINE insertion within the pig PLA2G16 could potentially modify gene expression through integration with its transcript.","authors":"Cai Chen, Mengli Wang, Yao Zheng, Ziyan Liu, Phiri Azele, Ahmed A Saleh, Xiaoyan Wang, Chengyi Song","doi":"10.1007/s13353-024-00933-5","DOIUrl":"https://doi.org/10.1007/s13353-024-00933-5","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142914852","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development and longitudinal neurocognitive functioning in mucopolysaccharidosis type IIIC: a case study.","authors":"Paulina Anikiej-Wiczenbach, Monika Limanówka, Maria Mazurkiewicz-Bełdzińska, Karolina Pierzynowska, Grzegorz Węgrzyn, Jolanta Wierzba, Katarzyna Milska-Musa, Arkadiusz Mański","doi":"10.1007/s13353-024-00934-4","DOIUrl":"https://doi.org/10.1007/s13353-024-00934-4","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142909563","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effect of miR-10a on the proliferation and differentiation of yak adipocyte precursors.","authors":"Quyangangmao Su, Zhanhong Gao, Fengshuo Zhang, Zhenling Wu, Qiurong Ji, Kaina Zhu, Linsheng Gui","doi":"10.1007/s13353-024-00932-6","DOIUrl":"https://doi.org/10.1007/s13353-024-00932-6","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142882101","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of quantitative trait loci for in vitro plant regeneration from leaf microexplants in cucumber (Cucumis sativus L.).","authors":"Renata Słomnicka, Magdalena Cieplak, Magda Antosiewicz, Alicja Sadłos, Aleksandra Galczak, Karolina Kaźmińska, Grzegorz Bartoszewski","doi":"10.1007/s13353-024-00927-3","DOIUrl":"https://doi.org/10.1007/s13353-024-00927-3","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142876733","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}