IF 5.1 3区生物学

Genetics Pub Date : 2025-10-08 DOI: 10.1093/genetics/iyaf146

Nisha D Kamath, Kenneth A Matreyek

{"title":"Comprehensive mutational characterization of the calcium-sensing STIM1 EF-hand reveals residues essential for structure and function.","authors":"Nisha D Kamath, Kenneth A Matreyek","doi":"10.1093/genetics/iyaf146","DOIUrl":"10.1093/genetics/iyaf146","url":null,"abstract":"Calcium signaling is a fundamental molecular means of cellular regulation. Store operated calcium entry (SOCE) is a major intracellular signaling module, wherein calcium release from the endoplasmic reticulum (ER) triggers transmembrane STIM1 proteins to conformationally shift and oligomerize to prompt calcium influx from the extracellular environment. STIM1 senses ER calcium concentrations with its canonical EF-hand domain, and missense variants can dysregulate SOCE and cause Tubular Aggregate Myopathy, Stormorken Syndrome, or immunodeficiency. Few STIM1 EF-hand variants are characterized, obscuring how STIM1 sequence controls its function, and hampering clinical interpretation of STIM1 variants observed in patients. We leveraged fitness costs caused by overexpression of STIM1 variants in cultured human cells to functionally characterize 706 of the 720 possible single amino acid variants of the STIM1 canonical EF-hand. The calcium-coordinating EF-hand residues exhibited varying mutational patterns. The trailing helix possessed a core of immutable residues, even depleting during library propagation in bacteria, implicating residues normally restraining STIM1 aggregation. The leading helix only exhibited toxicity in cells with endogenous STIM1, implicating a multimerization-dependent STIM1 regulatory module. No cytotoxic STIM1 variants were observed in healthy human populations. Some disease-associated variants had low scores, but most pathogenic variants were not overtly cytotoxic in our assay. We demonstrate that orthogonal measurements for STIM1 oligomerization, cytoplasmic calcium influx, and cellular stress complement the cytotoxicity phenotypes to enhance variant understanding. Collectively, these data reveal the complex molecular roles embedded in the STIM1 canonical EF-hand sequence for its function in promoting calcium signaling through SOCE.","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":5.1,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12505291/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144754906","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}

引用次数: 0

Echoes of eugenics: confronting its effects in indigenous genomics. 优生学的回响：面对其在本土基因组学中的影响。

IF 5.1 3区生物学

Genetics Pub Date : 2025-10-08 DOI: 10.1093/genetics/iyaf127

Carissa A Sherman, Shirin Nataneli, Katrina G Claw, Jazlyn A Mooney

{"title":"Echoes of eugenics: confronting its effects in indigenous genomics.","authors":"Carissa A Sherman, Shirin Nataneli, Katrina G Claw, Jazlyn A Mooney","doi":"10.1093/genetics/iyaf127","DOIUrl":"10.1093/genetics/iyaf127","url":null,"abstract":"In this perspective piece, we review the history of eugenics and its impacts on Indigenous peoples of North America. The perspective outlines historical policies, such as forced sterilization and immigration efforts targeting Indigenous populations. We explore how science is intertwined with eugenics and how eugenic ideologies continue to negatively impact Indigenous communities and science today. The work investigates the legacy of eugenics in shaping genetic studies, including genetic counseling and large-scale initiatives like the Human Genome Diversity Project. Additionally, we consider how institutions and biomedical research settings have committed inexcusable and unethical science that contributed to Indigenous peoples' attitudes toward genetic and biomedical research. The work addresses the challenges genetic testing, including direct-to-consumer testing, poses to Indigenous people's identities, culture, and sovereignty. Acknowledging this devastating history is essential to understanding its continued impact on Indigenous communities today. We conclude by highlighting ongoing efforts and strategies to effectively engage with Indigenous peoples in genetic research, emphasizing the responsibilities of modern researchers to build trust, ensure ethical practices, and contribute to inclusive and respectful science.","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":5.1,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12505307/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144838349","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}

引用次数: 0

Targeted loss of heterozygosity in Candida albicans using CRISPR-Cas9 reveals the functional impact of allelic variation. 利用CRISPR-Cas9靶向丢失白色念珠菌杂合性揭示等位基因变异对功能的影响。

IF 5.1 3区生物学

Genetics Pub Date : 2025-10-08 DOI: 10.1093/genetics/iyaf154

Philippe C Després, Nicholas C Gervais, Meea Fogal, Ruby K J Rogers, Christina A Cuomo, Rebecca S Shapiro

{"title":"Targeted loss of heterozygosity in Candida albicans using CRISPR-Cas9 reveals the functional impact of allelic variation.","authors":"Philippe C Després, Nicholas C Gervais, Meea Fogal, Ruby K J Rogers, Christina A Cuomo, Rebecca S Shapiro","doi":"10.1093/genetics/iyaf154","DOIUrl":"10.1093/genetics/iyaf154","url":null,"abstract":"The diploid genome of the fungal pathogen Candida albicans is highly heterozygous, with most allele pairs diverging at either the coding or regulatory level. When faced with selection pressure like antifungal exposure, this hidden genetic diversity can provide a reservoir of adaptive mutations through loss of heterozygosity (LOH) events. Validating the potential phenotypic impact of LOH events observed in clinical or experimentally evolved strains can be difficult due to the challenge of precisely targeting one allele over the other. Here, we show that a CRISPR-Cas9 system can be used to overcome this challenge. By designing allele-specific guide RNA sequences, we can induce targeted, directed LOH events, which we validate by whole-genome long-read sequencing. Using this approach, we efficiently recapitulate a recently described LOH event that increases resistance to the antifungal fluconazole. Additionally, we find that the recombination tracts of these induced LOH events have similar lengths to those observed naturally. To facilitate future use of this method, we provide a database of allele-specific sgRNA sequences for Cas9 that provide near genome-wide coverage of heterozygous sites through either direct or indirect targeting. This approach will be useful in probing the adaptive role of LOH events in this important human pathogen.","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":5.1,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12505295/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144838355","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}

引用次数: 0

Dark side of the honeymoon: reconstructing the Asian × European rose breeding history through the lens of genomics. 蜜月的阴暗面：通过基因组学的镜头重建亚洲和欧洲的玫瑰育种历史。

IF 5.1 3区生物学

Genetics Pub Date : 2025-10-08 DOI: 10.1093/genetics/iyaf163

Thibault Leroy, Elise Albert, Tatiana Thouroude, Sylvie Baudino, Jean-Claude Caissard, Annie Chastellier, Jérôme Chameau, Julien Jeauffre, Thérèse Loubert, Saretta Nindya Paramita, Alix Pernet, Vanessa Soufflet-Freslon, Cristiana Oghina-Pavie, Fabrice Foucher, Laurence Hibrand-Saint Oyant, Jérémy Clotault

{"title":"Dark side of the honeymoon: reconstructing the Asian × European rose breeding history through the lens of genomics.","authors":"Thibault Leroy, Elise Albert, Tatiana Thouroude, Sylvie Baudino, Jean-Claude Caissard, Annie Chastellier, Jérôme Chameau, Julien Jeauffre, Thérèse Loubert, Saretta Nindya Paramita, Alix Pernet, Vanessa Soufflet-Freslon, Cristiana Oghina-Pavie, Fabrice Foucher, Laurence Hibrand-Saint Oyant, Jérémy Clotault","doi":"10.1093/genetics/iyaf163","DOIUrl":"10.1093/genetics/iyaf163","url":null,"abstract":"Roses hold significant symbolic value in Western cultural heritage, often serving as a symbol of love and romance. Despite their ancient cultivation, the appreciation for the phenotypic diversity of roses emerged relatively recently, notably during the 19th century. This period is characterized by a remarkable expansion in the number of varieties, from around 100 to over 8,000, representing a golden age for roses. To trace the history of rose breeding in Europe and unveil genetic changes during this period, we gathered phenotypic and genetic data from 204 accessions. These included botanical roses and varieties cultivated between 1,800 and 1,910. Whole-genome sequences from 32 accessions were also included. Our analysis revealed a temporal shift in the genetic makeup, transitioning from a historical European to a near-Asian genetic background within a few generations. This shift was accompanied by a notable reduction in genetic diversity, attributed to the backcrossing with the less diverse Asian genepool, plus some genomic signatures of selection. We have generated the largest GWAS catalog for rose to date, offering a valuable resource for future breeding initiatives. We emphasize the critical importance of preserving ancient rose collections to safeguard diversity and ensure a sustainable breeding for the long-term.","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":5.1,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144838347","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}

引用次数: 0

Trade-off between antibacterial immune defense and oogenesis progression in female Drosophila melanogaster. 雌性黑腹果蝇抗菌免疫防御与卵子发生进程的权衡。

IF 5.1 3区生物学

Genetics Pub Date : 2025-10-08 DOI: 10.1093/genetics/iyaf151

Kathleen E Gordon, Shravasti Ray, Jeremy M Marcin, Patrick M Gonzales, Mona L Li, Crystal Liang, Mariana F Wolfner, Brian P Lazzaro

{"title":"Trade-off between antibacterial immune defense and oogenesis progression in female Drosophila melanogaster.","authors":"Kathleen E Gordon, Shravasti Ray, Jeremy M Marcin, Patrick M Gonzales, Mona L Li, Crystal Liang, Mariana F Wolfner, Brian P Lazzaro","doi":"10.1093/genetics/iyaf151","DOIUrl":"10.1093/genetics/iyaf151","url":null,"abstract":"Trade-offs between reproduction and immunity are common in animals, potentially due to preferential allocation of limiting resources. In Drosophila melanogaster, mating stimulates egg production but also triggers a rapid and persistent decrease in female immune defense. Proteins essential for both processes are produced in fat body tissue, which may result in competition for cellular resources that could drive a functional trade-off between reproduction and immune defense. We predicted that arrest of oogenesis prior to egg provisioning would alleviate postmating immune suppression because cellular stress would be relieved, but that postmating immune suppression would be observed in genotypes that fully provision eggs even if fertility is compromised. In the present study, we test these predictions by evaluating postmating immune competence in mated D. melanogaster mutants that arrest oogenesis either prior to, or subsequent to, vitellogenesis. Consistent with our prediction, we find that mated female immune defense is maintained when egg development is arrested prior to vitellogenesis. We find that progression through the vitellogenic stages of oogenesis results in postmating immune suppression, except in the case of a mutant with an egg-retention phenotype, where we infer that the failure to lay eggs results in feedback that inhibits subsequent egg development. We additionally show that elimination of yolk protein synthesis in the fat body and follicle cells of the ovary partially restores female immune capacity. Nevertheless, females that lack yolk protein genes still experience partially reduced immune capacity after mating, suggesting that other reproductive demands also suppress immune defense.","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":5.1,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12505294/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144762064","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}

引用次数: 0

On ARGs, pedigrees, and genetic relatedness matrices. 关于arg，系谱和遗传亲缘矩阵。

IF 5.1 3区生物学

Genetics Pub Date : 2025-10-08 DOI: 10.1093/genetics/iyaf219

Brieuc Lehmann, Hanbin Lee, Luke Anderson-Trocmé, Jerome Kelleher, Gregor Gorjanc, Peter L Ralph

{"title":"On ARGs, pedigrees, and genetic relatedness matrices.","authors":"Brieuc Lehmann, Hanbin Lee, Luke Anderson-Trocmé, Jerome Kelleher, Gregor Gorjanc, Peter L Ralph","doi":"10.1093/genetics/iyaf219","DOIUrl":"https://doi.org/10.1093/genetics/iyaf219","url":null,"abstract":"Genetic relatedness is a central concept in genetics, underpinning studies of population and quantitative genetics in human, animal, and plant settings. It is typically stored as a genetic relatedness matrix (GRM), whose elements are pairwise relatedness values between individuals. This relatedness has been defined in various contexts based on pedigree, genotype, phylogeny, coalescent times, and, recently, ancestral recombination graph (ARG). For some downstream applications, including association studies, using ARG-based GRMs has led to better performance relative to the genotype GRM. However, they present computational challenges due to their inherent quadratic time and space complexity. Here, we first discuss the different definitions of relatedness in a unifying context, making use of the additive model of a quantitative trait to provide a definition of ``branch relatedness'' and the corresponding ``branch GRM''. We explore the relationship between branch relatedness and pedigree relatedness (i.e., kinship) through a case study of French-Canadian individuals that have a known pedigree. Through the tree sequence encoding of an ARG, we then derive an efficient algorithm for computing products between the branch GRM and a general vector, without explicitly forming the branch GRM. This algorithm leverages the sparse encoding of genomes with the tree sequence and hence enables large-scale computations with the branch GRM. We demonstrate the power of this algorithm by developing a randomized principal components algorithm for tree sequences that easily scales to millions of genomes. All algorithms are implemented in the open source tskit Python package. Taken together, this work consolidates the different notions of relatedness as branch relatedness and by leveraging the tree sequence encoding of an ARG it provides efficient algorithms that enable computations with the branch GRM that scale to mega-scale genomic datasets.","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":5.1,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145253359","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}

引用次数: 0

A theoretical framework linking the effective number of breeders to demographic stochasticity in iteroparous species. 将育种者有效数量与种群随机性联系起来的理论框架。

IF 5.1 3区生物学

Genetics Pub Date : 2025-10-08 DOI: 10.1093/genetics/iyaf152

Tetsuya Akita

{"title":"A theoretical framework linking the effective number of breeders to demographic stochasticity in iteroparous species.","authors":"Tetsuya Akita","doi":"10.1093/genetics/iyaf152","DOIUrl":"10.1093/genetics/iyaf152","url":null,"abstract":"The effective number of breeders (Nb) is widely used as a genetic summary statistic, yet its role in shaping demographic variability has remained underexplored. Here, we present a theoretical framework for iteroparous species that integrates Nb into the stochastic recruitment process of the number of adults (N) by modeling individual-level relationships between adult females and their offspring. We partition recruitment variation into parental, non-parental, and environmental components, and show that demographic stochasticity arising from non-Poisson reproduction, summarized by Nb, can amplify environmental variance. Assuming an equal sex ratio and no sex-specific variation, we derive an approximation linking Nb to this amplification when Nb/N<0.1. For instance, Nb<42 can increase recruitment variance by more than 5%. A key advantage of this approach is that Nb can be estimated from genetic data collected from a single cohort, making it applicable in data-limited or conservation-priority systems. We applied the framework to six single-cohort data sets from three published studies (crayfish, salamander, and brook trout), confirming that non-Poisson amplification remains detectable whenever Nb<50, even when Nb/N > 0.1. Our framework highlights a distinct causal pathway by which increased reproductive variance contributes to demographic variability and extinction risk, especially in species where both Nb and Nb/N are small. These findings provide new theoretical justification for using Nb as a life-history-independent metric to quantify demographic stochasticity and connect genetic monitoring with population viability analysis.","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":5.1,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144785736","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}

引用次数: 0

Genetic analysis of JNK MAPK signaling in stress-induced avoidance behavior in C. elegans. 秀丽隐杆线虫应激诱导回避行为中JNK - MAPK信号的遗传分析

IF 5.1 3区生物学

Genetics Pub Date : 2025-10-08 DOI: 10.1093/genetics/iyaf143

Pei-Shu Jao, Chun-Liang Pan

{"title":"Genetic analysis of JNK MAPK signaling in stress-induced avoidance behavior in C. elegans.","authors":"Pei-Shu Jao, Chun-Liang Pan","doi":"10.1093/genetics/iyaf143","DOIUrl":"10.1093/genetics/iyaf143","url":null,"abstract":"Mitogen-activated protein kinase (MAPK) signaling is a conserved signal transduction pathway broadly implicated in cellular growth, development, and stress responses. While prior studies suggest that it is involved in certain forms of stress-induced learning, whether this role is acute during adult learning or represents early developmental effects on adult behaviors remains unclear. Here, we show that the c-Jun N-terminal kinase (JNK) MAPK pathway in Caenorhabditis elegans, consisting of mlk-1/MAPKKK, mek-1/MAPKK, and kgb-1/MAPK, acts in the nervous system to promote learned bacterial avoidance under mitochondrial stress, with the MAPK phosphatase VHP-1 counteracting it. Mutants of mlk-1, mek-1, and kgb-1 display moderate sensorimotor defects, and KGB-1 depletion throughout the entire larval to young adult stage, but not solely in adulthood or at any specific larval stage, recapitulates learning defects of the kgb-1 mutant. Transient kgb-1 expression in early development rescues the deficits of adult aversive learning, while adult expression fails to restore the behavioral functions. These data suggest that the role of JNK MAPK signaling in stress-induced avoidance behavior is primarily indirect, presumably via regulation of early neural development. Our work calls for a more rigorous examination of the temporal and tissue requirement of gene functions involved in learning and behavior.","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":5.1,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144734523","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}

引用次数: 0

The role of environmental stress in promoting mutators through evolutionary rescue: quantitative predictions. 通过进化救援，环境压力在促进突变体中的作用：定量预测。

IF 5.1 3区生物学

Genetics Pub Date : 2025-10-08 DOI: 10.1093/genetics/iyaf157

Marwa Z Tuffaha, Lindi M Wahl

{"title":"The role of environmental stress in promoting mutators through evolutionary rescue: quantitative predictions.","authors":"Marwa Z Tuffaha, Lindi M Wahl","doi":"10.1093/genetics/iyaf157","DOIUrl":"10.1093/genetics/iyaf157","url":null,"abstract":"The role of mutation rate in evolutionary rescue has been extensively explored, but little work has investigated how evolutionary rescue can promote mutators, lineages with higher mutation rates. Under complete linkage, we investigate the likelihood of evolutionary rescue on a mutator background that either emerges de novo or pre-exists in the population prior to a severe environmental change. If such an evolutionary rescue event occurs, the mutator lineage sweeps into the population, and thus the environmental stress has promoted mutators. Our findings indicate that mutation rate evolution can substantially boost rescue probabilities, but stronger mutators are most effective when the wildtype has a low mutation rate, while their advantage diminishes for higher wildtype mutation rates. Interestingly, at intermediate wildtype mutation rates, emerging mutators can be almost equally likely to sweep no matter how slowly or quickly the environment changes. However, at low wildtype mutation rates, mutators are only likely to sweep for very slow environmental changes due to the sequential nature of necessary mutations for such sweeps to occur. Finally, we show that pre-existing mutators can be significantly more likely to rescue the population compared with the wildtype, provided the wildtype's mutation rate is relatively low. This research opens new avenues for investigating mutator dynamics in response to environmental stress.","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":5.1,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144838356","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}

引用次数: 0

Global epistasis in budding yeast driven by many natural variants whose effects scale with fitness. 芽殖酵母的全局上位是由许多自然变异驱动的，其影响与适应度有关。

IF 5.1 3区生物学

Genetics Pub Date : 2025-10-08 DOI: 10.1093/genetics/iyaf136

Ilan Goldstein, Joseph J Hale, Ian M Ehrenreich

{"title":"Global epistasis in budding yeast driven by many natural variants whose effects scale with fitness.","authors":"Ilan Goldstein, Joseph J Hale, Ian M Ehrenreich","doi":"10.1093/genetics/iyaf136","DOIUrl":"10.1093/genetics/iyaf136","url":null,"abstract":"Global epistasis is a phenomenon in which the effects of genetic perturbations depend on the fitness of the individuals in which they occur. In populations with natural genetic variation, global epistasis arises from interactions between perturbations and polymorphic loci that are mediated by fitness. To investigate the prevalence and characteristics of loci involved in these interactions in the budding yeast Saccharomyces cerevisiae, we used combinatorial DNA barcode sequencing to measure the fitness of 169 cross progeny (segregants) subjected to 8,126 CRISPRi perturbations across 2 environments. Global epistasis was evident in these data, with more fit segregants within each environment exhibiting greater sensitivity to genetic perturbations than less fit segregants. We dissected the genetic basis of this global epistasis by scanning the genome for loci whose effects covary with CRISPRi-induced reductions in population fitness. This approach identified 58 loci that interact with fitness, most of which exhibited larger effects in the absence of genetic perturbations. In aggregate, these loci explained the observed global epistasis in each environment and demonstrated that the loci contributing to global epistasis largely overlap with those influencing fitness in unperturbed conditions.","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":5.1,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12505298/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144660859","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}

引用次数: 0

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