G3: Genes|Genomes|Genetics最新文献

{"title":"Duplication-based genetic dissection of the Down syndrome critical region reveals its complex functional organization.","authors":"Xiaoling Jiang, Chunhong Liu, Zhuo Xing, Yichen Li, Avrium Douglas, Lingqiu Gao, Annie Pao, Jill Silverman, Y Eugene Yu","doi":"10.1093/g3journal/jkag173","DOIUrl":"10.1093/g3journal/jkag173","url":null,"abstract":"<p><p>Down syndrome (DS), associated with trisomy 21, is the most common genetic cause of developmental delay and intellectual disability, yet the specific dosage-sensitive genes and the associated genetic mechanisms underlying these phenotypes remain incompletely defined. Here, we applied an additive genetic strategy to dissect the Down syndrome critical region (DSCR) by generating 2 complementary mouse models using Cre/loxP-mediated chromosome engineering that together span the entire DSCR on mouse chromosome 16: Dp(16)5Yey, duplicating the Setd4-Kcnj6 interval, and Dp(16)6Yey, duplicating the Kcnj15-Mx2 interval. In addition, we engineered a third duplication model, Dp(16)7Yey, carrying a selective duplication of the Dyrk1a-Kcnj6 interval containing only these 2 genes. Building upon our previously reported results, cognitive behavioral analyses of these 3 models reveal a complex functional genetic architecture of the DSCR, including dosage-sensitive genetic elements, interactions among these elements, and their contributions to DS-associated cognitive deficits. Together, these findings highlight the complexity of dosage-dependent genetic interactions, which provide important insights into DSCR functional organization and have major implications for the development of effective therapeutic strategies for DS-associated cognitive deficits. In addition, these duplication mouse models represent valuable resources for further genetic dissection of DS phenotypes beyond cognition.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13535499/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148360180","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomes of the ex-type strains of Elsinoë mangiferae and E. perseae, the causal agents of scab on mango and avocado.","authors":"Priscila Chaverri, Efraín Escudero-Leyva, Pepijn W Kooij, Cambly Morales-Lemus, Catalina Salgado-Salazar","doi":"10.1093/g3journal/jkag177","DOIUrl":"10.1093/g3journal/jkag177","url":null,"abstract":"<p><p>Elsinoë species are slow-growing, hemibiotrophic to necrotrophic fungi that cause scab diseases on economically important fruit crops. Genome resources for many host-specific species remain limited. We report high-quality draft genome assemblies for the ex-type strains of Elsinoë mangiferae (CBS 226.50) and E. perseae (CBS 406.34), causal agents of mango and avocado scab, respectively. Among 5 approaches tested, a Nanopore-only NextDenovo assembly produced the most contiguous genomes, yielding 24.5 Mb (E. mangiferae) and 25.1 Mb (E. perseae) assemblies with 13 and 18 contigs, respectively, BUSCO completeness scores of ∼94%, and multiple putative telomere-to-telomere chromosomes. Gene prediction identified 9,134 and 9,243 genes, respectively. Functional annotation revealed enrichment of metabolic and regulatory pathways, including those involved in posttranslational modification, protein transport, and secondary metabolism. Carbohydrate-active enzyme repertoires were small but conserved, consistent with stealth pathogenicity strategies and low plant cell wall degradation. Both genomes encoded large secretomes (>850 proteins), diverse protease repertoires (>300 proteins), Ecp2-like effector proteins, and multiple biosynthetic gene clusters, including clusters with similarity to those associated with elsinochrome and ACT-toxin II biosynthesis, some of which may contribute to host-pathogen interactions and disease development. A large fraction of genes lacked functional characterization, suggesting incomplete databases and/or the presence of lineage-specific genes potentially involved in virulence or host adaptation. These genome resources fill critical gaps for underrepresented Elsinoë species and provide taxonomically anchored references essential for diagnostics, comparative genomics, and research into the molecular basis of host specificity and pathogenicity in scab-causing fungi.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13535502/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148375209","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide SNP-based genomic diversity and population structure analysis in alpaca populations from Europe and Peru.","authors":"Kirsty Tan, Olusegun Olaniyi Adeniyi, Anna Letko, Eberhard Manz, Henrik Werner Wagner, Patrik Zanolari, Manuel More, Gustavo A Gutierrez-Reynoso, Cord Drögemüller, Gesine Lühken","doi":"10.1093/g3journal/jkag157","DOIUrl":"10.1093/g3journal/jkag157","url":null,"abstract":"<p><p>This study aimed to analyze the genetic diversity and population structure of alpacas in Germany, Switzerland, and Austria (German-speaking regions, GSR) and to compare with that of the country of origin of the species (Peru). A total of 179 animals from GSR and 151 from Peru were genotyped with a species-specific 76k SNP array. The observed and expected heterozygosity was 0.305 and 0.311 for GSR and 0.310 and 0.312 for Peru. The mean FROH values were 0.029 for GSR and 0.023 for Peru. In general, results show that breeders in both analyzed regions efficiently maintain genetic diversity. Principal component analysis identified the GSR and Peru populations as separate from each other, but the relative proximity of both clusters indicates the shared genetic heritage. FST and XPEHH methods identified genomic regions under selection for traits such as coat color and adaptation. Genome-wide association studies comparing black and brown with white or gray alpacas identified associated genome regions containing the ASIP and KIT genes, respectively. The association of a recently identified keratin locus on chromosome 16 with differences in fleece type in alpacas was confirmed, while the putative causality of a TRPV3 variant was rejected.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13535496/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148293920","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Spargel/dPGC-1 influences cell growth through the E2F1-mediated endocycle pathway.","authors":"Md Shah Jalal, Atanu Duttaroy","doi":"10.1093/g3journal/jkag180","DOIUrl":"10.1093/g3journal/jkag180","url":null,"abstract":"<p><p>The endocycle is a specialized variant of the eukaryotic cell cycle program observed in various tissues across diverse organisms ranging from insects to mammals. The endocycle promotes cellular growth by oscillating between the synthesis (S) and gap (G) phases, completely bypassing mitosis (M phase). E2F1 serves as a master regulator of the endocycle in Drosophila salivary glands, whereas the target of rapamycin (TOR) signaling pathway controls the levels of the E2F1 protein post-transcriptionally. Cellular growth in tissues that undergo the endocycle is also dependent on nutrient availability. Drosophila Spargel (dPGC-1) is orthologous to the PGC-1 family of transcriptional coactivators in vertebrates. In flies, Spargel influences cell growth through the insulin signaling pathway via TOR. However, the mechanisms by which Spargel regulates endocycle-mediated growth have yet to be established. Here, we report an essential role for Spargel in the Drosophila larval salivary gland that influences E2F1-mediated cellular growth. To elucidate the role of Spargel in cellular growth, we performed flippase (FLP)/FLP recombination target (FRT)-mediated mitotic clonal analysis in the salivary gland. The clonal analysis revealed that a cell-specific, complete loss of Spargel results in smaller nuclei with reduced DNA content due to inadequate DNA replication. Furthermore, the selective absence of Spargel abrogates the expression of a key DNA replication factor, E2F1, which promotes the G1 → S transition in the endocycle. Thus, mechanistically, Spargel plays a key role in cell growth by positively influencing the endocycle process through the E2F1 pathway.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13535446/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148389829","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A translocation within the Ogataea species complex alters local subtelomeric chromatin while maintaining overall genome organization.","authors":"Tiffany J Lundberg, Nickolas M Lande, Daniel Tourevski, Riley Figueroa, Sara J Hanson, Andrew D Klocko","doi":"10.1093/g3journal/jkag197","DOIUrl":"10.1093/g3journal/jkag197","url":null,"abstract":"<p><p>Eukaryotic genomic DNA is packaged in the nucleus as chromatin-a DNA-protein aggregate regulating genome function, including transcription. Chromatin is classified as either active euchromatin or silent heterochromatin, with each marked by distinct histone post-translational modifications (PTMs). Chromatin composition also mediates genome organization, including how heterochromatin aggregates at the nuclear periphery while euchromatin localizes to the nucleus center. In fungi, heterochromatic loci cluster, including independent centromere and telomere clusters that form the Rabl chromosome conformation. However, it is unknown if chromatin composition and genome organization are conserved in closely related fungi, and how these features are impacted by large-scale chromosomal rearrangements. Here, we examined differences in histone PTM deposition, gene expression, and genome organization in 2 yeast species from the order Pichiales, which diverged from the common ancestor shared with Saccharomyces cerevisiae more than 200 million years ago. We focused on Ogataea polymorpha, which is used for industrial protein production, and Ogataea haglerorum, an isolate of which harbors a translocation between chromosomes 1 and 6. We show that the enrichment of 3 activating PTMs-the trimethylation of lysine 4 of histone H3 (H3K4me3) and the acetylation of lysine 9 of histone H3 (H3K9ac) or lysine 16 of histone H4 (H4K16ac)-are similar genome-wide, yet gene orthologs have distinct chromatin and expression patterns. While both Ogataea genomes organize into a Rabl conformation, the O. haglerorum translocation alters subtelomeric chromatin composition and expression of genes affected by the translocation. Our work highlights the genome function differences that occur on a microevolutionary scale.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13535384/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148469857","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteome analyses reveal endoplasmic reticulum stress-induced changes in protein abundance associated with Ube2j2 deficiency in human cell culture.","authors":"Caroline L Dahlberg, Matthew Zinkgraf, Sophie Heiden Laugesen, Cecile Lützen Søltoft, Queralt Ginebra, Eric Paul Bennett, Rasmus Hartmann-Petersen, Lars Ellgaard","doi":"10.1093/g3journal/jkag172","DOIUrl":"10.1093/g3journal/jkag172","url":null,"abstract":"<p><p>The unfolded protein response (UPR) helps reinstate cellular proteostasis upon an accumulation of misfolded proteins in the endoplasmic reticulum (ER), in part through ER-associated degradation (ERAD). Ube2j2 is an ER-localized E2 ubiquitin-conjugating enzyme that participates in ERAD. We used mass spectrometry analysis of cultured U2OS cells to investigate how the loss of Ube2j2 affects the cellular proteome in response to tunicamycin-induced ER stress. We constructed a network of twelve statistically distinct modules of protein abundance profiles across conditions. We describe the gene ontology annotations for each module along with the \"hub gene\" proteins whose abundance levels most closely adhere to each module's protein abundance profile. Our analysis identifies known Ube2j2-associated pathways (eg the UPR and ERAD) and cellular functions that were previously unassociated with Ube2j2 (eg RNA metabolism, ER-Golgi transport, and cell-cycle progression). These data are available via ProteomeXchange with identifier PXD076153 and provide avenues for further investigation into the cellular functions of Ube2j2 under basal and ER-stressed conditions.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13535379/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148548476","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diploids derived from polyploids: genetic characteristics of four novel interspecific Sorghum populations.","authors":"Wenqian Kong, Pheonah Nabukalu, Stan Cox, Jaxk Reeves, Andrew H Paterson","doi":"10.1093/g3journal/jkag165","DOIUrl":"10.1093/g3journal/jkag165","url":null,"abstract":"<p><p>Polyploidy has repeatedly shaped grass evolution, yet direct observations of how polyploid-derived chromosomes behave when returned to diploidy remain rare. Interspecific crosses between diploid Sorghum bicolor and tetraploid hybrids derived from Sorghum halepense generate mixed-ploidy progeny, providing an opportunity to examine chromosome transmission during the early stages of diploidization. Using genome-wide SNP markers, we characterized chromosomal inheritance patterns in 2 diploid and 2 tetraploid families derived from these crosses. Genotype-dosage profiles alone distinguished diploids from tetraploids with complete accuracy, reflecting strong ploidy-dependent differences in dosage-class distributions. Although diploid progeny retained much of the halepense-derived genomic background, several genomic intervals exhibited extended, nonrandom runs of S. bicolor homozygosity that remained polymorphic in corresponding tetraploid populations. These patterns, together with recurrent segregation distortion across independent families, suggest that the transition from tetraploidy to diploidy can expose allelic combinations that differ in transmission or viability. Analyses of flowering time further indicated that diploid and tetraploid derivatives possess distinct genomic architectures, with major association peaks occurring in different chromosomal regions across ploidy levels. Collectively, these results indicate that early diploidization involves nonrandom retention and loss of parental haplotypes shaped by both selective and structural constraints. The diploid extractions characterized here provide a rare empirical system for investigating the early stages of diploidization and a practical framework for studying and eventually mobilizing polyploid-derived variation for sorghum germplasm development. However, broader integration into elite breeding programs will require additional evaluation of cross-fertility, meiotic behavior, and chromosomal stability across diverse breeding backgrounds.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13535381/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148404179","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A marine-derived fungal genome of Annulohypoxylon annulatoides reveals AT-rich isochores with putative regulatory functions.","authors":"Che-Yu Thiat-Ut Kuo, Yu-Ching Liu, Cheng-Ju Yang, Chieh-Ping Lin, Hung-Wei Chen, Huei-Mei Hsieh, Yu-Ming Ju, Tsui-Hua Liu, Yi-Chien Lee, Isheng Jason Tsai","doi":"10.1093/g3journal/jkag192","DOIUrl":"10.1093/g3journal/jkag192","url":null,"abstract":"<p><p>Marine and coastal fungi experience intense environmental variability, yet the genomic features associated with tolerance to such conditions remain unclear. From 56 fungal isolates collected along the Lailai rocky shore in northern Taiwan, we selected the coastal isolate Annulohypoxylon annulatoides RYS0019 for phenotypic and genomic investigation because of its prevalence and distinctive stress-response profile. Compared with 5 bark-derived conspecific strains, RYS0019 showed distinct growth and recovery dynamics under salinity, temperature, and UV-associated stress treatments. We generated a high-quality 41.8 Mb de novo genome assembly with 11,523 predicted proteins and compared it with 15 other Hypoxylaceae genomes. Across Annulohypoxylon genomes, we identified variably sized and dispersed AT-rich isochores that are repeat-enriched and gene-poor. Despite variation in AT content, core gene content and Pfam domain profiles remained broadly conserved. Most AT-rich isochores were embedded within syntenically conserved regions and showed limited positional conservation across species, supporting recurrent, lineage-specific formation or expansion after species divergence. These regions also exhibit several sequence and structural features consistent with scaffold/matrix attachment regions, raising the possibility that they influence higher-order genome organization or context-dependent regulation. Together, our findings identify repeat-rich genome architecture as a dynamic feature of Annulohypoxylon genome evolution and provide a framework for testing how such regions may contribute to fungal environmental flexibility.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13535480/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148435888","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The complete sequence of the silkworm W chromosome uncovers its rapid evolution by large-scale duplications/deletions and translocation of W-linked genes.","authors":"Wanshun Li, Hiroaki Abe, Yue Chen, Jianqiu Liu, Yanjue Wang, Masahiro Ajimura, Shenglong Li, Yingdan Xiao, Huizhen Guo, Jiaqi Wu, Yajing Xu, Xue Yang, XiaoXue Yang, Shaopeng Hao, Qihue He, Tsuguru Fujii, Ken Sahara, Atsuo Yoshido, Yusuke Takehana, Kiyoshi Naruse, Kallare P Arunkumar, Marian R Goldsmith, Guy Smagghe, František Marec, Qingyou Xia, Kazuei Mita","doi":"10.1093/g3journal/jkag170","DOIUrl":"10.1093/g3journal/jkag170","url":null,"abstract":"<p><p>The complete sequence of the W chromosome, which carries feminization activity in the silkworm, is crucial for understanding the sex-determination system in Lepidoptera. However, extensive accumulation of transposons due to lack of recombination, the very rare protein-coding genes and almost no information about molecular markers has hindered full W sequencing. We report the first complete silkworm W sequence (T2T_W, 11683305 bp) obtained by combining sequencing-assembly technologies and newly developed error detection methods, evaluated with genetically mapped W-RAPD markers, W-mutants, and W-derived BAC clones. The T2T_W sequence showed that the W is composed of a massive 92% accumulation of transposons and repeat sequences, among which the main constituents are intact LTR/LINE retrotransposons indicating recent expansions. In addition to Fem clusters producing Fem piRNA (Feminizer-derived PIWI-interacting RNA), we found 26 protein-coding genes in the W sequence. These include four gene pairs encoding zinc-finger motifs designated z1:z20 and a gene encoding serine/arginine repetitive matrix protein 1-like (SRRM1-like). To identify candidate genes for female sex-determination and differentiation we also sequenced the shortest W (3.8 Mb) from a translocation mutant with feminizing activity, which harbored four conventional genes: a Fem cluster, a pair of z1:z20 isoforms, z20-S, and a SRRM1-like gene. Phylogenetic analysis revealed that z1:z20 originated from a copy of an autosomal zinc-finger gene pair, z2:z21, translocated onto the W around 2.43 Mya and subsequently amplified to yield 4 W-linked zinc-finger gene pairs. The complete W sequence revealed that large-scale deletions and amplifications played a significant role in W chromosome evolution.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13535481/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148351462","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Using deep learning models as a genetic architecture for the simulation of breeding schemes.","authors":"Olumide Onabanjo, Theo Meuwissen, Hans Magnus Gjøen, Emre Karaman, Thinh T Chu, Peer Berg","doi":"10.1093/g3journal/jkag187","DOIUrl":"10.1093/g3journal/jkag187","url":null,"abstract":"<p><p>In several simulation studies, long-term selection led to the rapid depletion of genetic variance. These outcomes differ from real-life observations that we aim to replicate, thereby highlighting a fundamental limitation of current classical quantitative genetic simulation models. Deep learning (DL) models have demonstrated promising results in capturing complex interactions essential for maintaining genetic variance; thus, we hypothesize that DL-based genetic simulation models may preserve more genetic variance than classical models, because the biological pathways underlying complex traits exhibit interactions that classical models ignore. The primary objective of this study was to introduce alternative DL-based genetic simulation models and compare them with classical genetic simulation models in terms of their retention of additive genetic variance under truncation selection in a simulated full-sib pig breeding scheme using real haplotypes as founders. After 20 generations of directional truncation selection, the classical models (A, ADAA, and ADAAADDD) retained between 55% and 64% of their initial additive genetic variance. In contrast, while the DL_simple model lost all its additive variance, the DL medium retained 92% to 98% of its additive variance, and the DL_complex model's initial additive variance increased by 296% to 314%. This paper introduces DL-based genetic simulation models and concludes that their ability to retain additive genetic variance depends on the models' architectural complexity. When sufficiently complex, DL-based models exhibit greater retention of additive genetic variance because they intrinsically capture epistatic interactions that are converted into additive variance, as selection progresses, thus, affirming the role of non-additive genetic effects in maintaining long-term genetic variation.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13535453/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148410964","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}