IF 3.3 3区生物学

Genetics Pub Date : 2025-06-20 DOI: 10.1093/genetics/iyaf119

Lucile Toniutti, Simon Rio, Camille Madec, Sébastien Ricci, Chantal Guiougou, Franck Marius, Claude Mina, Jean-Marie Eric Delos, Frédéric Lambert, Jean-Claude Efile, Angélique D'Hont, Guillaume Martin, Jean-Yves Hoarau, Frédéric Salmon

{"title":"Combining ability of banana triploid hybrid progenitors and genomic prediction of cross performance for agro-morphological traits.","authors":"Lucile Toniutti, Simon Rio, Camille Madec, Sébastien Ricci, Chantal Guiougou, Franck Marius, Claude Mina, Jean-Marie Eric Delos, Frédéric Lambert, Jean-Claude Efile, Angélique D'Hont, Guillaume Martin, Jean-Yves Hoarau, Frédéric Salmon","doi":"10.1093/genetics/iyaf119","DOIUrl":"https://doi.org/10.1093/genetics/iyaf119","url":null,"abstract":"Breeding disease-resistant cultivars that meet commercial criteria is essential to sustain banana production threatened by major diseases. Edible bananas are seedless triploid hybrids which represent end-breeding products. Hence, the crucial step in banana breeding is to improve and combine the parents. Currently, little information is available on parental combining abilities and on the inheritance of major traits to effectively guide banana breeding strategies. In this study, a breeding population of 2723 triploids individuals resulting from multiparental diploid-tetraploid crosses was characterized during three crop cycles for 23 traits relating to plant and fruit architecture and bunch yield components. The phenotypic variance was partitioned between non-genetic and genetic effects, the latter including the general combining ability of diploid and tetraploid parents, their specific combining ability and additional variance due to the within-cross genetic variability. Heritability was moderate to high depending on the trait and revealed the predominance of the tetraploid parent's contribution to hybrid performance for most traits. The use of parental genomic information enabled cross mean performance prediction through genomic relationship matrices of general and specific combining abilities, the latter being partitioned into dominance and across-population epistasis contributions. Predictive abilities often greater than 0.5 were obtained, particularly when the tetraploid parent was observed in other crosses and, for some traits, when neither parent was observed. Information on trait inheritance and genomic prediction of cross mean performance will help selecting and combining parents, facilitating the identification of promising hybrids.","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144334210","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

Efficient epistasis inference via higher-order covariance matrix factorization. 基于高阶协方差矩阵分解的上位推理。

IF 3.3 3区生物学

Genetics Pub Date : 2025-06-20 DOI: 10.1093/genetics/iyaf118

Kai S Shimagaki, John P Barton

引用次数: 0

Functional Analysis of Human EED Variants Using Drosophila. 果蝇对人类EED变异的功能分析。

IF 3.3 3区生物学

Genetics Pub Date : 2025-06-20 DOI: 10.1093/genetics/iyaf120

Sharri S Cyrus, Sònia Medina Giró, Tianshun Lian, Douglas W Allan, William T Gibson

引用次数: 0

Trans-regulatory loci shape natural variation of gene expression plasticity in Arabidopsis. 反调控位点塑造拟南芥基因表达可塑性的自然变异。

IF 3.3 3区生物学

Genetics Pub Date : 2025-06-19 DOI: 10.1093/genetics/iyaf116

Mariele Lensink, Grey Monroe, Dan Kliebenstein

{"title":"Trans-regulatory loci shape natural variation of gene expression plasticity in Arabidopsis.","authors":"Mariele Lensink, Grey Monroe, Dan Kliebenstein","doi":"10.1093/genetics/iyaf116","DOIUrl":"https://doi.org/10.1093/genetics/iyaf116","url":null,"abstract":"Organisms regulate gene expression in response to environmental cues, a process known as plasticity, to adjust to changing environments. Research into natural variation and the evolution of plasticity frequently studies cis-regulatory elements with theory suggesting they are more important evolutionarily than trans-regulatory elements. Genome-wide association studies have supported this idea, observing a predominance of cis-loci affecting plasticity. However, studies in structured populations provide a contrasting image, raising questions about the genetic architecture of natural variation in plasticity. To circumvent potential statistical difficulties present in genome-wide association studies, we mapped loci underlying transcriptomic plasticity in response to salicylic acid using recombinant inbred lines generated from two random Arabidopsis thaliana accessions. We detected extensive transgressive segregation in the salicylic acid response, suggesting that plasticity to salicylate in Arabidopsis is polygenic. Most loci (>75%) underlying this variation act in trans, especially for loci influencing plasticity. Trans-acting loci were enriched in genome hotspots, with predominantly small effect sizes distributed across many genes. This could potentially explain their under-discovery in genome-wide association studies. This work reveals a potentially important role for trans-acting loci in plastic expression responses, with implications for understanding plant adaptation to different environments.","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144327473","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

Evolution of GC-biased gene conversion by natural selection. 自然选择中gc偏向基因转化的进化。

IF 3.3 3区生物学

Genetics Pub Date : 2025-06-13 DOI: 10.1093/genetics/iyaf111

Augustin Clessin, Julien Joseph, Nicolas Lartillot

{"title":"Evolution of GC-biased gene conversion by natural selection.","authors":"Augustin Clessin, Julien Joseph, Nicolas Lartillot","doi":"10.1093/genetics/iyaf111","DOIUrl":"https://doi.org/10.1093/genetics/iyaf111","url":null,"abstract":"GC-biased gene conversion (gBGC) is a recombination-associated evolutionary process that biases the segregation ratio of AT:GC polymorphisms in the gametes of heterozygotes, in favour of GC alleles. This process is the major determinant of the variation in base composition across the human genome and can be the cause of a substantial burden of deleterious GC alleles. While the importance of GC-biased gene conversion in molecular evolution is increasingly recognised, the reasons for its existence and its variation in intensity between species remain largely unknown. Using simulations and semi-analytical approximations, we investigated the evolution of gBGC as a quantitative trait evolving by mutation, drift and natural selection. We show that in a finite population in which most mutations are deleterious, gBGC is under weak stabilising selection around a positive value that mainly depends on the intensity of the mutational bias and on the selective constraints exerted on the genome. Importantly, the levels of gBGC that evolve by natural selection do not minimize the load in the population and even increase it substantially in regions of high recombination rate. Therefore, even if they reduce the fitness of the population, the levels of gBGC currently observed in humans may in fact have been (weakly) positively selected.","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144286930","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

Learning evolutionary parameters from genealogies using allelic trees. 利用等位基因树从家谱中学习进化参数。

IF 3.3 3区生物学

Genetics Pub Date : 2025-06-12 DOI: 10.1093/genetics/iyaf112

Antoine Aragon, Amaury Lambert, Thierry Mora, Aleksandra M Walczak

引用次数: 0

Towards more sustainable research: reducing the environmental impact when working with Drosophila. 走向更可持续的研究：与果蝇合作时减少对环境的影响。

IF 3.3 3区生物学

Genetics Pub Date : 2025-06-12 DOI: 10.1093/genetics/iyaf114

Milo Challiner, Saroj Saurya, Sanjai Patel, Jordan W Raff, Maggy Fostier, Andreas Prokop

{"title":"Towards more sustainable research: reducing the environmental impact when working with Drosophila.","authors":"Milo Challiner, Saroj Saurya, Sanjai Patel, Jordan W Raff, Maggy Fostier, Andreas Prokop","doi":"10.1093/genetics/iyaf114","DOIUrl":"https://doi.org/10.1093/genetics/iyaf114","url":null,"abstract":"The ever-increasing amounts of plastic waste and greenhouse gas emissions worldwide threaten our environment. Biomedical laboratories across the world generate serious amounts of plastic waste often disposed of via high-emission strategies. Achieving sustainability is imperative but requires awareness and knowledge of the regulations, available options and their implications. To illustrate the thought processes involved we showcase the Manchester Fly Facility which supports work with the genetic model organism Drosophila and serves 13 research groups. In 2022, we estimated ∼4 tonnes of 'clinical' waste generation by the facility enriched with single-use polystyrene plastic containers, all frozen for 2 days and then incinerated. We calculate the resulting environmental and economic costs and compare them to practices reported to us from other fly facilities worldwide. We then discuss feasible management options, separately explaining alternative choices for (1) container materials, (2) the processing of genetically modified organisms, (3) re-use strategies and (4) waste management procedures. This information hopefully raises awareness and understanding to incentivise laboratories worldwide to adopt more sustainable choices, as is permitted by their local infrastructure and regulations. To illustrate what can be achieved, we extrapolate the Manchester data from 2022 to a period of 10 years and calculate the impact of different management strategies, indicating that up to 80% in greenhouse gas emissions and 76% in plastic waste can be saved. The resulting economic savings are of further benefit and could be re-invested to pay for additional workforce, which may otherwise pose an important barrier to re-use scenarios in many countries.","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144286932","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

Analysis of Combinatorial Cohesin Subunit Gene Deletions in Budding Yeast. 出芽酵母组合内聚蛋白亚基基因缺失分析。

IF 3.3 3区生物学

Genetics Pub Date : 2025-06-10 DOI: 10.1093/genetics/iyaf107

Grace Duke, Robert V Skibbens

{"title":"Analysis of Combinatorial Cohesin Subunit Gene Deletions in Budding Yeast.","authors":"Grace Duke, Robert V Skibbens","doi":"10.1093/genetics/iyaf107","DOIUrl":"https://doi.org/10.1093/genetics/iyaf107","url":null,"abstract":"Throughout the cell cycle, DNA molecules convert between hierarchical intramolecular (cis) and intermolecular (trans) associations. Cohesin ATPase complexes produce both types of DNA associations which collectively are required for sister chromatid segregation, chromatin condensation, genomic architecture, gene transcription, and DNA repair. The mechanisms that regulate cohesin cis- and trans-activities, however, remain controversial. A popular model is that a regulatory complex (Pds5, Irr1/Scc3, and Rad61) sits atop a core ring-like complex (Mcd1/Scc1, Smc1, and Smc3), the latter of which exhibits the inherent ATPase activities responsible for producing cis-and trans-DNA conformations. Additional proteins transiently interact with cohesins to promote cohesin deposition onto DNA (Scc2 and Scc4) or stabilize cohesin-DNA binding (Eco1/Ctf7). Of these nine components, only RAD61 is non-essential. Recent findings, however, identified pairs of suppressor mutations that support the viability of cells individually deleted for either PDS5 or ECO1/CTF7 (herein ECO1). Intriguingly, CLN2 deletion is common in both suppressor pairs, suggesting that combined suppressor mutations may support the viability of cells co-deleted for both ECO1 and PDS5. These results further suggest that the addition of other suppressor mutations (such as ELG1 and RAD61) may support the viability of cells deleted of all auxiliary subunits - including IRR1/SCC3 (herein SCC3). Here, we test these predictions and report on novel gene deletion combinations required for cell cycle progression and cell viability.","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144259131","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

Adaptive gene expression parallelism in the male reproductive tract of two Drosophila species. 两种果蝇雄性生殖道适应性基因表达的平行性。

IF 3.3 3区生物学

Genetics Pub Date : 2025-06-10 DOI: 10.1093/genetics/iyaf113

Tiezheng Fan, Julie M Cridland, David J Begun

{"title":"Adaptive gene expression parallelism in the male reproductive tract of two Drosophila species.","authors":"Tiezheng Fan, Julie M Cridland, David J Begun","doi":"10.1093/genetics/iyaf113","DOIUrl":"https://doi.org/10.1093/genetics/iyaf113","url":null,"abstract":"While stabilizing selection is likely an important process leading to conserved phylogenetic patterns of gene expression, the role of selection in driving expression divergence amongst populations and species is much less clear. One approach for identifying adaptation is to document parallel evolution, the independent evolution of similar phenotypes in multiple species in response to similar selective pressures. Latitudinal clines are a classic system for studying adaptation in many species, including Drosophila; multiple species exhibit clines for several phenotypes, such as body and wing size. However, the extent of latitudinal transcriptome variation and the degree to which such variation is shaped by selection remain unclear. Here, we investigate transcriptomes of North American D. melanogaster and D. simulans with a focus on the male reproductive tract. For both species we sampled accessory glands and testis from lines derived from two locations, one low latitude (Panama City, Panama), and one high latitude (Maine, USA). We observed a striking similarity between species in the directionality and magnitude of latitudinal expression variation in the accessory gland but not in the testis. This suggests that selection has fine-tuned accessory gland transcript abundance in a similar manner in response to latitudinal selection pressures in both species. In addition to gene level parallelism, these species exhibit correlated fluctuations of high vs. low latitude expression differences on a larger chromosomal scale. Analysis of whole male transcriptomes from the same population samples suggests that parallel latitudinal selection responses play an important role in expression adaptation for both species.","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144259214","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 regulatory architecture of gene expression variation in C. elegans revealed by multi-strain allele-specific analysis. 多菌株等位基因特异性分析揭示秀丽隐杆线虫基因表达变异的调控结构。

IF 3.3 3区生物学

Genetics Pub Date : 2025-06-10 DOI: 10.1093/genetics/iyaf110

Avery Davis Bell, Francisco Valencia, Annalise B Paaby

{"title":"The regulatory architecture of gene expression variation in C. elegans revealed by multi-strain allele-specific analysis.","authors":"Avery Davis Bell, Francisco Valencia, Annalise B Paaby","doi":"10.1093/genetics/iyaf110","DOIUrl":"https://doi.org/10.1093/genetics/iyaf110","url":null,"abstract":"An outstanding question in the evolution of gene expression is the composition of the underlying regulatory architecture and the processes that shape it. Mutations affecting a gene's expression may reside locally in cis or distally in trans; the accumulation of these changes, their interactions, and their modes of inheritance influence how traits are expressed and how they evolve. Here, we interrogated gene expression variation in C. elegans, including the first allele-specific expression analysis in this system, capturing effects in cis and in trans that govern gene expression differences between the reference strain N2 and seven wild strains. We observed extensive compensatory regulation, in which opposite effects in cis and trans at individual genes mitigate expression differences among strains, and that genes with expression differences exhibit strain specificity. As the genomic distance increased between N2 and each wild strain, the number of genes with expression differences also increased. We also report for the first time that expression-variable genes are lower expressed on average than genes without expression differences, a trend that may extend to humans and Drosophila melanogaster and may reflect the selection constraints that govern the universal anticorrelation between gene expression and rate of protein evolution. Together, these and other observed trends support the conclusion that many C. elegans genes are under stabilizing selection for expression level, but we also highlight outliers that may be biologically significant. To provide community access to our data, we introduce an easily accessible, interactive web application for gene-based queries: https://wildworm.biosci.gatech.edu/ase/.","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144259132","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

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