Journal Of Applied Genetics[JOURNAL]
Sun
200 papers
Genome-wide identification and expression profiling of the MYC gene family in Triticum monococcum L. subsp. aegilopoides with a focus on the red glume mutant.
Liu X, Zhao J, Zhao X … +3 more , Shen M, Zhang M, Zhang L
J Appl Genet · 2025 Sep · PMID 40983861 · Publisher ↗
MYC transcription factors, belonging to the basic helix-loop-helix (bHLH) superfamily, are widely recognized for their critical involvement in controlling various aspects of plant growth, developmental processes, and res...
MYC transcription factors, belonging to the basic helix-loop-helix (bHLH) superfamily, are widely recognized for their critical involvement in controlling various aspects of plant growth, developmental processes, and responses to environmental stresses. Triticum monococcum L. subsp. aegilopoides, a wild diploid wheat species, provides valuable Genetic resources for improving stress tolerance and nutritional traits. In this study, 18 TbMYC genes were identified in T. monococcum L. subsp. aegilopoides, characterized by diverse gene structures, conserved motifs, and distinct tissue-specific expression patterns. Phylogenetic analysis grouped these genes into six groups, revealing unique structural features and motifs that suggest functional diversification. Promoter analysis uncovered numerous cis-regulatory elements linked to light response, stress adaptation, and hormonal regulation, with TbMYC8 notably enriched in ABA-responsive elements, highlighting its potential involvement in abscisic acid-mediated stress responses. Synteny analysis demonstrated conserved TbMYCs across Triticeae species, underscoring their evolutionary significance. RNA-seq analysis identified five TbMYCs significantly implicated in the anthocyanin biosynthetic pathway, particularly in regulating pigment accumulation in a red-glume mutant. These findings underscore the critical roles of TbMYCs in stress adaptation and secondary metabolism, providing valuable insights for wheat improvement and functional genomics.
Revolutionizing neonatal health: India's journey from assays to advanced genetics.
Bisht A, Hasija Y
J Appl Genet · 2025 Sep · PMID 40983860 · Publisher ↗
According to UNICEF India, an estimated 67,385 neonates are born daily in India, each striving to survive the initial 28 days of life, which are pivotal in determining their future health prognosis. A significant number...
According to UNICEF India, an estimated 67,385 neonates are born daily in India, each striving to survive the initial 28 days of life, which are pivotal in determining their future health prognosis. A significant number of these neonates succumb to inborn errors of metabolism (IEM), resulting in a spectrum of either manageable or severe clinical consequences. The evolution of techniques from basics to next-generation sequencing (NGS) and cutting-edge bioinformatics has enabled the prompt and precise identification of metabolic defects during the early stages of life. But the limited awareness, facilities, and access to the screening program necessitate the urgent need for establishing a state-of-the-art screening initiative all over India. The program holds the potential to substantially diminish infant mortality rates and alleviate the national health burden. This article delineates inborn errors of metabolism, investigates the advancements in diagnostic methodologies, outlines the NGS technique, underscores the role of computational biology, and advocates for the establishment of a centralized screening initiative in India specifically for treatable IEM. Furthermore, a few case studies have been included to showcase the notable discoveries of genes and associated disorders facilitated by NGS along with some studies highlighting the advantages of employing computational biology.
Genome-wide identification and characterization of GATA transcription factors in Avena sativa L. and expression profiling under salinity stress.
Bokolia M, Singh T, Goyal N … +3 more , Kumar A, Singh K, Singh B
J Appl Genet · 2025 Sep · PMID 40971059 · Publisher ↗
GATA transcription factors are a group of type IV zinc-finger proteins that play critical roles in regulating plant growth, development, and responses to abiotic stress. These genes are characterized by a conserved DNA-b...
GATA transcription factors are a group of type IV zinc-finger proteins that play critical roles in regulating plant growth, development, and responses to abiotic stress. These genes are characterized by a conserved DNA-binding domain with the consensus sequence (A/T)GATA(A/G) and a type IV zinc-finger motif containing the conserved sequence CX2CX18-20CX2C. In this study, 27 GATA genes (designated AsGATA) were identified in Avena sativa using the GrainGenes genome database. Comprehensive analyses were performed to examine their conserved motifs, physicochemical properties, chromosomal localization, gene structures, phylogenetic relationships, and cis-acting regulatory elements. Based on the classification of GATA family members in Arabidopsis thaliana, the AsGATA genes were categorized into four subfamilies. Gene structure analysis revealed that members of the same subfamily generally exhibited similar structural features. Subcellular localization predictions indicated that most AsGATA proteins are Likely to function in the nucleus. Chromosomal mapping demonstrated the random distribution of the 27 AsGATA genes across the 21 chromosomes of Avena sativa. Expression profiling, based on RNA-Seq data from the NCBI SRA database, identified six AsGATA genes that are responsive to salt stress. These genes represent promising candidates for functional studies and could be leveraged in breeding programs to develop salt-tolerant Avena sativa varieties.
Genome-wide association study bridging genomics-phenomics gap in natural plant populations.
Roy S, Gadri HS, Sharma V … +3 more , Chowdhary MA, Dwivedi R, Bhardwaj P
J Appl Genet · 2026 Feb · PMID 40965825 · Publisher ↗
The planet hosts half a million plant species exhibiting a spectacular diversity of plant forms with genomes driving phenotypic variations. The genome information exists for less than 1% of species, limiting quantitative...
The planet hosts half a million plant species exhibiting a spectacular diversity of plant forms with genomes driving phenotypic variations. The genome information exists for less than 1% of species, limiting quantitative genomic studies in natural populations. This review explores how recent advances in cutting-edge genomic and phenomic techniques extended genome-wide association studies (GWAS) to wild, non-model species and other natural populations. We also discuss the incorporation of diverse bioinformatic tools into comprehensive in-silico pipelines and recommend implementing machine learning algorithms to address methodological challenges. The critical literature synthesis highlights several scopes of GWAS, bringing natural populations into the spotlight of genomic research. Thus, the study presents GWAS as a cornerstone for advancing quantitative genomics in natural populations. This shift holds great promise for understanding adaptation, trait evolution, and conservation genetics across diverse plant germplasm.
Shifting genetic structure of Polish sea trout populations: a contemporary perspective.
Bernaś R, Wąs-Barcz A, Horbacz T … +2 more , Szymański R, Lejk AM
J Appl Genet · 2026 Feb · PMID 40952578 · Full text
The genetic structure and variability of sea trout populations in the southern Baltic Sea were shaped during the last glaciation, in parallel with the evolution of the Baltic Sea. However, human activities-particularly h...
The genetic structure and variability of sea trout populations in the southern Baltic Sea were shaped during the last glaciation, in parallel with the evolution of the Baltic Sea. However, human activities-particularly hydrotechnical development and the introduction of non-local genetic lines-have altered and partially reduced the original genetic diversity. In the present study, the authors describe the historical changes that have occurred and present the current level of genetic variability within Polish sea trout populations. A total of 575 sea trout from nine river populations and three hatchery broodstocks were genotyped at 13 microsatellite loci. The global F obtained via AMOVA was moderate, at 0.041. The highest pairwise F values were observed between the Rutki and Aquamar broodstocks and all other populations. The lowest and statistically non-significant pairwise differences were detected between the Rega and Ina river populations, as well as between the Słupia and Łupawa. Genetic structure analysis revealed geographic differentiation, identifying either four or seven distinct clusters. Additionally, neighbour-joining clustering showed that the examined populations and stocks were divided into two main subgroups: one consisting of samples related to the Vistula origin, and the other comprising clearly separated Pomeranian populations. This paper discusses the emergence of new genetic variability driven by microevolutionary processes and presents a revised approach for sea trout population management.
Development and application of duplex and triplex assays for simultaneous detection of resistance genes to leaf rust, Fusarium head blight, powdery mildew, Septoria tritici blotch, eyspot, stem rust and yellow rust in wheat.
Bobrowska R, Moskalik J, Noweiska A … +3 more , Spychała J, Tomkowiak A, Kwiatek MT
J Appl Genet · 2026 Feb · PMID 40940614 · Full text
Resistance breeding is a widely promoted strategy for minimizing yield losses in wheat caused by various fungal diseases, including leaf rust (Puccinia triticina; Lr genes), Fusarium head blight (Fusarium spp.; Fhb), pow...
Resistance breeding is a widely promoted strategy for minimizing yield losses in wheat caused by various fungal diseases, including leaf rust (Puccinia triticina; Lr genes), Fusarium head blight (Fusarium spp.; Fhb), powdery mildew (Blumeria graminis; Pm), Septoria tritici blotch (Septoria tritici; Stb), eyespot (Oculimacula spp.; Pch-previously known as Pseudocercosporella herpotrichoides), stem rust (Puccinia graminis f. sp. tritici; Sr) and yellow rust (Puccinia striiformis; Yr). Understanding the prevalence of resistance genes in currently cultivated European varieties is crucial for their effective utilization in breeding programs. In this study, we developed 11 duplex and 13 triplex PCR assays for the simultaneous identification of diverse allelic combinations of disease resistance genes. Selected assays were used to analyze 70 European wheat varieties for the presence of 15 molecular markers associated with 12 resistance genes. The analyses identified diverse resistance gene combinations. The optimized multiplex PCR methods significantly reduce cost and time of analysis, making them valuable tools for marker-assisted selection (MAS) in wheat breeding programs.
Strigolactones modulate jasmonate-dependent transcriptional reprogramming during wound signalling in Arabidopsis.
Marzec M
J Appl Genet · 2025 Dec · PMID 40924357 · Full text
Mechanical wounding triggers rapid transcriptional and hormonal reprogramming in plants, primarily driven by jasmonate (JA) signalling. While the role of JA, ethylene, and salicylic acid in wound responses is well charac...
Mechanical wounding triggers rapid transcriptional and hormonal reprogramming in plants, primarily driven by jasmonate (JA) signalling. While the role of JA, ethylene, and salicylic acid in wound responses is well characterised, the contribution of strigolactones (SLs) remains largely unexplored. Here, for the first time, it was shown that SLs modulate wound-induced transcriptional dynamics in Arabidopsis thaliana. Using transcriptome profiling of wild-type (Columbia-0) and the SL biosynthesis mutant more axillary growth3 (max3), a discrete cohort of genes whose wound induction is SL-dependent was identified. These genes include core JA biosynthetic genes and several JA-responsive transcriptional repressors, indicating that SLs potentiate early JA signalling. Promoter motif and protein-protein interaction analyses revealed that SLs regulate a transcriptional module composed of AP2/ERF, WRKY, and C2H2 zinc-finger factors, which integrate JA signalling, ROS homeostasis, and tissue regeneration. Notably, many of these factors are misregulated in max3 even prior to wounding, suggesting a primed but hypo-responsive state. Presented findings suggest a model in which SLs act upstream of the JA burst, coordinating transcriptional readiness and post-injury activation. This expands the functional scope of SLs in stress response and positions them as potential modulators of hormone crosstalk during wound responses.
Association of the BoLA-DRB3*12:01 allele with resistance to bovine leukosis virus infection in Crioula Lageana cattle.
Fonteque GV, da Silva Casa M, Ribeiro GSN … +7 more , da Silva Z, Vogel CIG, Fonteque JH, da Costa UM, Giovambattista G, Takeshima SN, Miletti LC
J Appl Genet · 2026 Feb · PMID 40858974 · Publisher ↗
Enzootic bovine leukosis (EBL) caused by the bovine leukosis virus (BLV) disturbs the immune response in bovines, leading to severe economic losses, with a possible impact on public health. EBL has no treatment or vaccin...
Enzootic bovine leukosis (EBL) caused by the bovine leukosis virus (BLV) disturbs the immune response in bovines, leading to severe economic losses, with a possible impact on public health. EBL has no treatment or vaccine available, making the identification of genetic polymorphisms related to BLV resistance in locally adapted breeds like Crioula Lageana cattle valuable perspectives. This study aims to determine the presence of the BoLA-DRB3 alleles associated with susceptibility or resistance to BLV in Crioula Lageana cattle. For that, 208 Crioula Lageana bovines, spanning various ages, categories, and sexes, were subjected to blood sampling for DNA extraction for genetic characterization. The PCR targeted the 440-bp fragment of the env gene of the BLV and 284-bp for the alleles of the BoLA-DRB3 gene. The alleles were identified using Sanger sequencing, and the allele amount and frequency were determined by direct counting. For the determination of resistance or susceptibility, firstly the association between each allele and infection by BLV was determined using the chi-square test (p < 0.05), and then it was followed by an odds ratio analysis. The occurrence of BLV was 38.46% (80/208). The DRB3*12:01 allele was associated with resistance to BLV infection (p = 0.035, O.R. = 0.000. The presence of alleles linked to resistance to disease incidence highlights the potential to enhance genetic approaches in formulating management and control strategies for EBL in diverse cattle populations, with potential implications for livestock production, food safety, and public health.
Ataxia and oculomotor apraxia caused by a large-scale deletion in the senataxin gene.
Rusecka JM, Kierdaszuk B, Stępniak I … +14 more , Rydzanicz M, Stawiński P, Gambin T, Loska D, Kacprzak MM, Kaliszewska M, Piekutowska-Abramczuk D, Kamińska AM, Pronicka E, Bartnik E, Kostera-Pruszczyk A, Płoski R, Sobczyńska-Tomaszewska A, Tońska K
J Appl Genet · 2025 Aug · PMID 40830689 · Publisher ↗
Senataxin, an RNA/DNA helicase, is a key protein providing genome stability and one of the best characterized R-loop-binding factors playing an important role in transcription and DNA repair processes. Pathogenic SETX ge...
Senataxin, an RNA/DNA helicase, is a key protein providing genome stability and one of the best characterized R-loop-binding factors playing an important role in transcription and DNA repair processes. Pathogenic SETX gene variants cause autosomal recessive spinocerebellar ataxia with axonal neuropathy (AOA2, MIM #606002) and autosomal dominant juvenile amyotrophic lateral sclerosis (ALS4, MIM #602433), rare neurodegenerative disorders characterized by juvenile onset of progressive cerebellar ataxia, axonal sensorimotor peripheral neuropathy, combined upper and lower motor neuron symptoms, and increased serum alpha-fetoprotein (AFP; specific for AOA2). We report two cases of adult patients presenting with cerebellar syndrome, scanned speech, and exercise intolerance which started in the second/third decade of life and were followed by muscle weakness and impaired gait coordination. Whole exome sequencing (WES) was performed to analyze single nucleotide and copy number variants. A decreased coverage of a genomic region of around 16 kb on chromosome 9 (chr9:132,295,852-132,311,876), suggesting a deletion encompassing 5 exons of the SETX gene (exons 11-15, NM_015046.7) was observed. This homozygous SETX (9q34.13) deletion leads to a frame shift and consequently truncation of the helicase domain in the protein. Loss-of-function variants in the SETX gene are known to be pathogenic. Statistical analysis of NGS data from the Polish population identified a few heterozygous carriers, suggesting its region-specific origin.
Somatic and germinal mosaicism of a canonical splicing variant causing limb-girdle muscular dystrophy type 1B.
Wang G, Wang Y, Zhao D … +2 more , Yan C, Lin P
J Appl Genet · 2025 Aug · PMID 40818008 · Publisher ↗
Limb-girdle muscular dystrophy type 1B is one of several muscular dystrophies caused by pathogenic variants in the LMNA gene. In this study, we investigated the clinical, pathological, and genetic findings of an LGMD1B f...
Limb-girdle muscular dystrophy type 1B is one of several muscular dystrophies caused by pathogenic variants in the LMNA gene. In this study, we investigated the clinical, pathological, and genetic findings of an LGMD1B family. Genetic sequencing identified the proband and her younger brother both carried the canonical splicing c.513 + 1G > A variant in the LMNA gene. The variant was absent in the proband's mother, and a certain percentage of the LMNA variant was identified in the venous blood, urine, and semen sample of the proband's father by pyrophosphate sequencing. Further cDNA analysis demonstrated that the canonical splicing c.513 + 1G > A variant in intron 2 induced retention of the first 45 bp of intron 2, resulting in an in-frame insertion of 15 amino acids. Our study directly confirmed the presence of somatic and germinal mosaicism in the LGMD1B family and the pathogenicity of the canonical splicing variant in the LMNA gene.
Prevalence of intronic repeat expansions in the RFC1 gene in Polish patients with cerebellar syndrome.
Filip T, Karolina ZJ, Natalia D … +8 more , Henry H, Andrea C, Karolina R, Agnieszka P, Rafal P, Piotr J, Ewelina ED, Anna S
J Appl Genet · 2025 Aug · PMID 40802152 · Publisher ↗
Cerebellar ataxia with neuropathy and vestibular areflexia syndrome (CANVAS) is a recessively inherited neurodegenerative ataxic disorder, which has been associated with intronic biallelic repeat expansions in the RFC1 g...
Cerebellar ataxia with neuropathy and vestibular areflexia syndrome (CANVAS) is a recessively inherited neurodegenerative ataxic disorder, which has been associated with intronic biallelic repeat expansions in the RFC1 gene. Our objective was to assess retrospectively the prevalence of CANVAS in Polish population. We screened 2523 Polish patients in whom other repeat expansions were excluded. To determine the repeat expansions in the RFC1 gene in patients, we performed RFC1-flanking PCR and repeat primed PCR (RP-PCR) and to measure the size of the expansion we used Southern blotting and optical genome mapping to compare the results. We have observed the biallelic pathogenic motif/unit AAGGG expansions in 4.6% and expansions of non-pathogenic motifs AAAAG, AAAGG in 25% patients of our studied population. This is the first large-scale cohort study that confirms the relatively frequent occurrence of the CANVAS in Polish population. To increase the current diagnostics of late-onset ataxias within an unexplained molecular background, we suggest involving the RFC1 repeat expansions analysis to the routine diagnostic workflow.
NGS sequencing reveals the cause of hearing loss in a group of Polish patients with an isolated, non-DFNB1 hearing loss.
Niepokój K, Rygiel AM, Wertheim-Tysarowska K … +18 more , Sawicka J, Dorożko B, Grabarczyk A, Obersztyn E, Kutkowska-Kaźmierczak A, Klapecki J, Barczyk A, Własienko P, Jurczak P, Lebiedzińska A, Śmigiel R, Jakubiak A, Wierzba J, Kaczorowska E, Pietrzyk A, Sorbaj-Sucharska G, Limon J, Bal J
J Appl Genet · 2025 Aug · PMID 40796707 · Publisher ↗
The etiology of hearing loss (HL) is heterogeneous. It is estimated that 50-60% of the cases have a genetic background, with the other part being environmental. Isolated HL is responsible for nearly two-thirds of congeni...
The etiology of hearing loss (HL) is heterogeneous. It is estimated that 50-60% of the cases have a genetic background, with the other part being environmental. Isolated HL is responsible for nearly two-thirds of congenital cases, and the remaining part accounts for syndromic forms (SHL). The study aim was to examine the molecular basis of HL in 48 Polish patients with isolated, non-DFNB1 hearing loss using the targeted next-generation sequencing technique (NGS). The molecular cause of the HL was defined in 39.6% (19/48) of patients. In thirteen genes, we identified causative variants, including six novel ones: p.Gly1326Val (STRC), p.Pro104ThrfsTer2 (MYO6), p.Tyr186Ter (GATA3), p.Ile1584SerfsTer12 (MYO15A), p.Pro559Leu, and p.Glu542del (CDH23). The pathogenic status of novel variants was assessed by using bioinformatic tools and the ACMG recommendations. The most frequent genetic variants were the STRC gene deletions and point variants in Usher syndrome genes. For 36.8% of patients, the molecular diagnosis suggested SHL (Deafness-Infertility Syndrome (DIS), Hypoparathyroidism, Sensorineural Deafness and Renal Disease (HDR), Usher, Perrault and Waardenburg syndromes). The obtained results confirmed the heterogeneity of the molecular basis of HL in Polish patients and the usefulness of the NGS technique as a diagnostic tool.
Genome-wide association study uncovers the genetic loci for yield-related traits in waxy rice.
Fei Y, Mo Z
J Appl Genet · 2025 Aug · PMID 40784927 · Publisher ↗
Improving yield potential is a critical goal for breeders; however, yield-related loci are still less understood in waxy rice, which seriously limited the precise development of high-yield cultivars. Here, we investigate...
Improving yield potential is a critical goal for breeders; however, yield-related loci are still less understood in waxy rice, which seriously limited the precise development of high-yield cultivars. Here, we investigated six yield-related traits in a collection of 109 cultivated waxy rice accessions over two seasons and perform genome-wide association study using 1.81 million single nucleotide polymorphisms (SNPs) to elucidate the genetic basis underlying grain yield. Our analysis identified a total of 28 significant quantitative trait loci (QTLs), explaining 0.71-38.46% of phenotype variance. Of these, 17 was previously reported or contained genes known to govern the associated traits, while the remaining 11 appear to be novel alleles. Within the 28 QTLs, 379 residing genes were identified, and candidate yield-related genes in close proximity to the significant SNPs were extracted for haplotype analysis. The results showed that the genetic variations in Os09g0375700, Os09g0396300, and Os03g0609500 were highly associated with variations in thousand grain weight or panicle number. Our results dissected the possible genetic determinants of waxy rice yield and will be conducive to breed new cultivars with high yield in the future.
An updated molecular toolkit for genomics-assisted breeding of waxy sorghum [Sorghum bicolor (L.) Moench].
Yerka MK, Liu Z, Bean S … +8 more , Nigam D, Hayes C, Druetto D, Krishnamoorthy G, Meiwes S, Cucit G, Patil GB, Jiao Y
J Appl Genet · 2026 May · PMID 40784926 · Publisher ↗
Several mutations of the sorghum [Sorghum bicolor (L.) Moench] GRANULE-BOUND STARCH SYNTHASE (GBSS) gene [Sobic.010G022600; commonly known as Waxy (Wx)] result in a low amylose:amylopectin starch ratio. Recessive waxy (w...
Several mutations of the sorghum [Sorghum bicolor (L.) Moench] GRANULE-BOUND STARCH SYNTHASE (GBSS) gene [Sobic.010G022600; commonly known as Waxy (Wx)] result in a low amylose:amylopectin starch ratio. Recessive waxy (wx) alleles improve starch digestibility in ethanol production, human foods and beverages, and animal feed. However, breeding waxy sorghum is challenging due to reliance on traditional PCR markers for genotyping, which are not amenable to next-generation sequencing (NGS). Most commercial breeding programs use high-throughput genotyping and genomic selection in large, segregating populations prior to flowering. This study provides the first published NGS markers for the two most commonly used waxy (wx) alleles of sorghum and is the first to fully sequence the large insertion that is causal of the wx allele. In the absence of a pangenome including wx genotypes, we constructed an in silico B.Tx623 wx genome assembly from the B.Tx623 reference genome (v3.1.1) including the insertion, a ~ 5-kb-long terminal repeat (LTR) retrotransposon of the copia superfamily. The in silico wx assembly improved read mapping at Sobic.010G022600 in wx individuals, identified 78 new uniquely mapped reads, and made it possible to distinguish different Waxy genotypes using short-read sequencing data. Functional PACE-PCR markers, suitable for marker-assisted selection and multiplexed, low-to-mid-density genomic selection, were developed for Wx, wx, and wx alleles. The PACE markers were validated in segregating populations of three public and private breeding programs. These new molecular breeding resources comprise a toolkit that will improve the efficiency of developing commercial waxy sorghum hybrids using genomics-assisted approaches.
Genetic background of Richter transformation of atypical chronic lymphocytic leukemia to diffuse large B-cell lymphoma - a case study.
Przybysz S, Łojko-Dankowska A, Rakoczy M … +5 more , Marcinkowska-Swojak M, Zeńczak M, Gwóźdź-Bąk K, Handschuh L, Lewandowski K
J Appl Genet · 2025 Aug · PMID 40782136 · Publisher ↗
Atypical chronic lymphocytic leukemia (aCLL) is an indolent lymphoproliferative neoplasm derived from CD19-positive and CD5 or CD23-negative B cells. This paper presents the results of whole genome sequencing (WGS) of ly...
Atypical chronic lymphocytic leukemia (aCLL) is an indolent lymphoproliferative neoplasm derived from CD19-positive and CD5 or CD23-negative B cells. This paper presents the results of whole genome sequencing (WGS) of lymphoma cells collected from a 29-year-old woman initially diagnosed with aCLL and successfully treated with fludarabine, cyclophosphamide, and rituximab. Eight years later, due to disease progression, she was treated with ibrutinib. After 5 months, her status suddenly deteriorated. PET-CT results suggested Richter transformation (RT). Histopathological examination of nodal lesions confirmed the diagnosis of Diffuse Large B Cell Lymphoma (DLBCL). Finally, the patient was successfully treated with DHAP-R and alloHSCT. WGS of lymphoma cells revealed the presence of pathogenic (COL11A1, MGME1) and likely pathogenic variants (ZMYM3, ALG6, UBA5, and ATG7). Out of these genes, only ZMYM3 is recurrently mutated in B-cell chronic lymphocytic leukemia (B-CLL). The presence of the other lesions requires further studies and indicates the complex molecular background of aCLL transformation to DLBCL. Therefore, the whole-genome variant assessment is worth considering for introduction into a routine procedure at the time of B-CLL diagnosis, especially when RT is suspected.
Multi-trait stability index in the selection of high-yielding and stable barley genotypes.
Pour-Aboughadareh A, Jamshidi B, Jadidi O … +2 more , Bocianowski J, Niemann J
J Appl Genet · 2026 May · PMID 40770158 · Full text
The analysis of genotype-by-environment interaction (GEI) in multi-environmental trials (METs) represents a crucial component of breeding programs prior to the release of new commercial cultivars tailored for specific re...
The analysis of genotype-by-environment interaction (GEI) in multi-environmental trials (METs) represents a crucial component of breeding programs prior to the release of new commercial cultivars tailored for specific regions or diverse environmental conditions. Moreover, emphasizing individual traits during selection can yield misleading conclusions. Consequently, the implementation of robust selection models is essential for identifying superior genotypes based on multiple traits. The present dataset demonstrates the utility of the multi-trait stability index (MTSI) in identifying high-yielding and stable barley genotypes across ten diverse environments. The evaluated phenological and agronomic traits included days to heading, days to physiological maturity, grain-filling period, plant height, thousand-kernel weight, and grain yield. A combined analysis of variance (ANOVA) revealed significant effects attributable to environments (E), genotypes (G), and their interaction (GEI) across all assessed traits. Correlation analysis further indicated positive associations between all measured traits and grain yield. In the MTSI model, three first factors accounted for 75% of the total phenotypic variation observed across the test environments. The highest selection gain percentages were recorded for thousand-kernel weight and grain yield. Among the genotypes evaluated, G3, G10, and G14, characterized by the lowest values of the MTSI index, were identified as superior in terms of grain yield, stability, and desirable agronomic attributes. In conclusion, the findings highlight the efficacy of the MTSI in reliably identifying superior genotypes in METs. The results demonstrate that the MTSI index not only enhances the efficiency of the selection process but also improves the accuracy of genotype evaluation and ranking across heterogeneous environmental conditions. This underscores the potential of the MTSI index to support informed breeding decisions, ultimately facilitating the development of high-performing plant varieties that exhibit both yield stability and adaptability across diverse environments.
Cellular and molecular changes in mucopolysaccharidosis-plus syndrome caused by a homozygous c.599G > C (p.Arg200Pro) variant of the VPS33A gene.
Cyske Z, Rintz E, Narajczyk M … +4 more , Świątek N, Gaffke L, Pierzynowska K, Węgrzyn G
J Appl Genet · 2025 Aug · PMID 40758165 · Publisher ↗
Mucopolysaccharidosis-plus syndrome (MPSPS) is an ultrarare inherited metabolic disease (a few dozen patients diagnosed to date) which is characterised by accumulation of undegraded glycosaminoglycans (GAGs). Despite GAG...
Mucopolysaccharidosis-plus syndrome (MPSPS) is an ultrarare inherited metabolic disease (a few dozen patients diagnosed to date) which is characterised by accumulation of undegraded glycosaminoglycans (GAGs). Despite GAG storage occurs also in the groups of diseases classified as mucopolysaccharidoses (MPS), contrary to MPS, no dysfunctions of lysosomal enzymes is detected in MPSPS which is caused by mutations in the VPS33A gene. The c.1492C > T (p.Arg498Trp) variant, associated with a severe course of the disease, was found in most MPSPS patients. There are only two patients described to date with a homozygous c.599G > C (p.Arg200Pro) variant and a milder (juvenile) form. Until now, the molecular mechanism of MPSPS remained largely unknown, especially for the juvenile form. Here, a battery of cellular and molecular assays, performed using fibroblasts derived from a patient bearing the c.599G > C (p.Arg200Pro) variant of the VPS33A gene, indicated specific changes in cellular vacuoles, elevated levels of the EEA1 protein (required at the stages of the fusions of early and late endosomes, and early endosome sorting), changes in Golgi apparatus morphology, decreased levels of F-actin, and increased levels of α- and β-tubulins, as well as elevated levels of the LC3-II and p62 proteins (autophagy markers). Results of experiments presented here might suggest that severely decreased levels the p.Arg200Pro variant of VSP33A could cause defective endosomal trafficking, possibly resulting in inefficient delivery of GAGs to lysosomes, and their subsequent accumulation in cells. This might induce a cascade of secondary and tertiary disorders, finally expressing as the disease symptoms.
Identification of colorectal cancer molecular subtypes and prognostic features based on basement membrane-related genes.
Yang L, Ji Z, Ren Y … +5 more , Fang C, Han J, Luo D, Zhang R, Zhou S
J Appl Genet · 2025 Aug · PMID 40751879 · Publisher ↗
Recent evidence suggests that the basement membrane (BM) plays an important role in the progression of colorectal cancer (CRC). Here, we investigate the prognostic value of CRC based on BM-associated genes. BM-related di...
Recent evidence suggests that the basement membrane (BM) plays an important role in the progression of colorectal cancer (CRC). Here, we investigate the prognostic value of CRC based on BM-associated genes. BM-related differentially expressed genes (DEGs) in CRC were obtained through analysis of The Cancer Genome Atlas public database and literature. The DEGs were used to cluster tumor samples and perform survival analysis. A prognostic model was constructed based on the DEGs in CRC through regression analysis, and its predictive effect was evaluated and validated using the GEO dataset. The correlation between riskscore and tumor progression was evaluated, and Cox regression was used to verify the independence of riskscore by combining it with different clinical factors. A nomogram was drawn to predict the prognosis of CRC individuals. The differences in immune microenvironment between high-risk (H) and low-risk (L) groups were analyzed by ssGSEA and ESTIMATE. The tumor mutation burden (TMB) was calculated for the two groups. Drug sensitivity prediction was performed for the two groups. Finally, the expression levels of prognostic feature genes were validated through qPCR. Based on BM-related DEGs, CRC samples were classified into 2 clusters, with cluster 1 having significantly lower survival rates. A prognostic model was developed based on 7 genes (AGRN, TIMP1, UNC5A, SPARCL1, ADAMTS6, MMP1, and UNC5C). The model exhibited high predictive accuracy and demonstrated the potential to serve as an independent prognostic factor for predicting the prognosis of CRC individuals. A higher riskscore indicated a higher degree of tumor progression. Group H demonstrated higher levels of immune infiltration and TMB, suggesting that individuals in this group might be more suitable for immune therapy. Two first-line anti-tumor drugs, Gemcitabine and Cisplatin, with higher sensitivity to individuals in group L were obtained. The q-PCR results of the feature genes were consistent with the results of gene expression in the database. This study established a 7-gene BM-related prognostic model that could be used to analyze the immune landscape of CRC individuals and predict their sensitivity to immunotherapy and chemotherapy. This research provided a reference for the prognosis prediction and immunotherapy of CRC individuals.
Are head and neck versus abdominal paragangliomas driven by different single nucleotide events?
Kotlarz K, Ziemnicka K, Budny B … +10 more , Mielczarek M, Liu J, Wrotkowska E, Kaznowski J, Suchocki T, Kałużny J, Wierzbicka M, Dobosz P, Ruchała M, Szyda J
J Appl Genet · 2025 Jul · PMID 40728629 · Publisher ↗
Paragangliomas (PGLs) are a heterogeneous group of tumours of the nonepithelial neuroendocrine type, with a significant percentage being genetically determined. They can develop from cells of the parasympathetic as well...
Paragangliomas (PGLs) are a heterogeneous group of tumours of the nonepithelial neuroendocrine type, with a significant percentage being genetically determined. They can develop from cells of the parasympathetic as well as the sympathetic nervous system. Tumours located in the head and neck usually have a parasympathetic origin, whereas those in the abdomen have a sympathetic origin. The aim of this study was to determine whether the development of PGLs at both locations is associated with specific variants of genes with proven relevance for the formation of these tumours. Thirty-one patients with abdominal PGL and 16 with head and neck PGLs were analysed at 12 genes whose defects are among the most common genetic determinants of PGLs. The impact of SNPs (single nucleotide polymorphisms) on differentiation between both tumour types was assessed by fitting a decision tree and quantifying genotype effects of SNPs by the Shapley Additive Explanation metric. The study demonstrated that SNPs rs3748576 within the KIF1B gene and rs10060259 within the SDHA gene increase the probability of abdominal tumour locations, while heterozygous GA genotypes of rs2435351 located within the RET gene increase the probability of head and neck locations. The SNPs marked genes involved in the formation and functioning of the nervous system, but are located in introns, and thus themselves do not contribute to protein diversity. Still, intronic SNPs can indirectly affect the transcriptome by influencing alternative splicing, mRNA stability, or overlap with non-coding genes and other regulatory elements that affect transcription. Given this, it seems important to consider variants from non-coding regions in genetic analyses.
Different mRNAs encoding identical proteins: how and why?
Duan Y, Cao Q
J Appl Genet · 2026 Feb · PMID 40715649 · Publisher ↗
Alternative splicing (AS) produces various forms of mRNAs and protein isoforms and contributes to biodiversity. However, different mRNAs might have identical CDS and encode the same protein sequence. It is unclear why or...
Alternative splicing (AS) produces various forms of mRNAs and protein isoforms and contributes to biodiversity. However, different mRNAs might have identical CDS and encode the same protein sequence. It is unclear why organisms need these distinct mRNAs if they encode the same protein? We propose two complementary hypotheses, namely adaptive hypothesis and error hypothesis, and tested these ideas using genomes of four representative organisms, human, mouse, fruitfly, and Arabidopsis. We found that only the fruitfly meets most predictions made by the adaptive hypothesis, while the other species generally align with the error hypothesis. Fruitfly exhibits a surprisingly high fraction (> 70%) of protein-coding genes (PCGs) having multiple mRNAs encoding identical proteins. These mRNAs have long CDS, variable UTR lengths, and highly conserved protein sequences. In contrast, opposite or insignificant trends are observed in human, mouse, and Arabidopsis. While molecular errors are common in cell systems, in species like the fruitfly with large effective population size, the strong natural selection might maintain those mRNAs with potentially adaptive regulatory roles. Although encoding identical proteins, different mRNAs can be regulated in a condition-specific manner, facilitating adaptive evolution. Our work provides novel perspectives in genomics and evolutionary biology.
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