G3: Genes|Genomes|Genetics最新文献

Signatures of natural selection may indicate a genetic basis for the beneficial effects of oily fish intake in indigenous people from coastal Ecuador. 自然选择的迹象可能表明，厄瓜多尔沿海土著居民摄入油性鱼类的益处是有遗传基础的。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-01-28 DOI: 10.1093/g3journal/jkaf014

Débora Y C Brandt, Oscar H Del Brutto, Rasmus Nielsen

{"title":"Signatures of natural selection may indicate a genetic basis for the beneficial effects of oily fish intake in indigenous people from coastal Ecuador.","authors":"Débora Y C Brandt, Oscar H Del Brutto, Rasmus Nielsen","doi":"10.1093/g3journal/jkaf014","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf014","url":null,"abstract":"Atahualpa is a rural village located in coastal Ecuador, a region that has been inhabited by people as early as 10,000 years ago. The traditional diet of their indigenous inhabitants is rich in oily fish and they have, therefore, served as a model for investigating the beneficial effects of such a diet. However, the genetic background of this population has not been studied. In this study, we sequenced the genomes of Atahualpa residents to look for variants under natural selection, which could mediate the effects of oily fish intake. DNA was extracted from 50 blood samples from randomly selected individuals recruited in the Atahualpa Project Cohort. After applying various filters, we calculated genome-wide genotype likelihoods from 33 samples, and combined data from those samples with data from other populations to investigate how the Atahualpa population is genetically related to these populations. Using selection scans, we identified signals of natural selection that may explain the above-mentioned dietary effects. The genetic ancestry in Atahualpa residents is 94.1% of indigenous American origin, but is substantially diverged from other indigenous populations in neighboring countries. Significant signatures of natural selection were found in the Atahualpa population, including a broad selection signal around the SUFU gene, which is a repressor of Hedgehog pathway signaling and associated with lipid metabolism, and another signal in the upstream region of LRP1B which encodes low-density lipoprotein (LDL) receptor related protein 1B. Our selection study reveals genes under selection in the Atahualpa population, which could mediate the beneficial effects of oily fish intake in this population.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143052017","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

Draft genome sequence of the glasshouse-potato aphid Aulacorthum solani.

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-01-24 DOI: 10.1093/g3journal/jkaf013

Joseph Torres, Paula Rozo-Lopez, William Brewer, Omid Saleh Ziabari, Benjamin J Parker

引用次数: 0

Genetic differentiation in the MAT-proximal region is not sufficient for suppressing recombination in Podospora anserina.

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-01-24 DOI: 10.1093/g3journal/jkaf015

Pierre Grognet, Robert Debuchy, Tatiana Giraud

{"title":"Genetic differentiation in the MAT-proximal region is not sufficient for suppressing recombination in Podospora anserina.","authors":"Pierre Grognet, Robert Debuchy, Tatiana Giraud","doi":"10.1093/g3journal/jkaf015","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf015","url":null,"abstract":"Recombination is advantageous over the long-term, as it allows efficient selection and purging deleterious mutations. Nevertheless, recombination suppression has repeatedly evolved in sex and mating-type chromosomes. The evolutionary causes for recombination suppression and the proximal mechanisms preventing crossing overs are poorly understood. Several hypotheses have recently been suggested based on theoretical models, and in particular that divergence could accumulate neutrally around a sex-determining region and reduce recombination rates, a self-reinforcing process that could foster progressive extension of recombination suppression. We used the ascomycete fungus Podospora anserina for investigating these questions: a 0.8 Mbp region around its mating-type locus is non-recombining, despite being collinear between the two mating types. This fungus is mostly selfing, resulting in highly homozygous individuals, except in the non-recombining region around the mating-type locus that displays differentiation between mating types. Here, we test the hypothesis that sequence divergence alone is responsible for recombination cessation. We replaced the mat- idiomorph by the sequence of the mat+ idiomorph, to obtain a strain that is sexually compatible with the mat- reference strain and isogenic to this strain in the MAT-proximal region. Crosses showed that recombination was still suppressed in the MAT-proximal region in the mutant strains, indicating that other proximal mechanisms than inversions or mere sequence divergence are responsible for recombination suppression in this fungus. This finding suggests that selective mechanisms likely acted for suppressing recombination, or the spread of epigenetic marks, as the neutral model based on mere nucleotide divergence does not seem to hold in P. anserina.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143028447","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 diversity and environmental adaptation in Ethiopian tef.

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-01-24 DOI: 10.1093/g3journal/jkae303

Kirsten Hein, Dejene Girma, John McKay

{"title":"Genetic diversity and environmental adaptation in Ethiopian tef.","authors":"Kirsten Hein, Dejene Girma, John McKay","doi":"10.1093/g3journal/jkae303","DOIUrl":"https://doi.org/10.1093/g3journal/jkae303","url":null,"abstract":"Orphan crops serve as essential resources for both nutrition and income in local communities and offer potential solutions to the challenges of food security and climate vulnerability. Tef [Eragrostis tef (Zucc.)], a small-grained allotetraploid, C4 cereal mainly cultivated in Ethiopia, stands out for its adaptability to marginal conditions and high nutritional value, which holds both local and global promise. Despite its significance, tef is considered an orphan crop due to limited genetic improvement efforts, reliance on subsistence farming, and its nutritional, economic, and cultural importance. Although pre-Semitic inhabitants of Ethiopia have cultivated tef for millennia (4000-1000 BCE), the genetic and environmental drivers of local adaptation remain poorly understood. To address this, we resequenced a diverse collection of traditional tef varieties to investigate their genetic structure and identify genomic regions under environmental selection using redundancy analysis, complemented by differentiation-based methods. We identified 145 loci associated with abiotic environmental factors, with minimal geographic influence observed in the genetic structure of the sample population. Overall, this work contributes to the broader understanding of local adaptation and its genetic basis in tef, providing insights that support efforts to develop elite germplasms with improved environmental resilience.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143032807","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

Multiple regulators constrain the abundance of C. elegans DLK-1 in ciliated sensory neurons.

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-01-24 DOI: 10.1093/g3journal/jkaf004

Yue Sun, Junxiang Zhou, Arunima Debnath, Bokun Xie, Zhiping Wang, Yishi Jin

{"title":"Multiple regulators constrain the abundance of C. elegans DLK-1 in ciliated sensory neurons.","authors":"Yue Sun, Junxiang Zhou, Arunima Debnath, Bokun Xie, Zhiping Wang, Yishi Jin","doi":"10.1093/g3journal/jkaf004","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf004","url":null,"abstract":"The conserved MAP3K DLKs are widely known for their functions in synapse formation, axonal regeneration and degeneration, and neuronal survival, notably under traumatic injury and chronic disease conditions. In contrast, their roles in other neuronal compartments are much less explored. Through an unbiased forward genetic screening in C. elegans for altered patterns of GFP-tagged DLK-1 expressed from the endogenous locus, we have recently uncovered a mechanism by which the abundance of DLK-1 is tightly regulated by intraflagellar transport in ciliated sensory neurons. Here, we report additional mutants identified from the genetic screen. Most mutants exhibit increased accumulation of GFP::DLK-1 in sensory endings, and the levels of misaccumulated GFP::DLK-1 are exacerbated by loss of function in cebp-1, the b-Zip transcription factor acting downstream of DLK-1. We identify several new mutations in genes encoding proteins functioning in intraflagellar transport and cilia assembly, in components of BBSome, MAPK-15 and DYF-5 kinases. We report a novel mutation in the chaperone HSP90 that causes misaccumulation of GFP::DLK-1 and up-regulation of CEBP-1 selectively in ciliated sensory neurons. We also find that the guanylate cyclase ODR-1 constrains GFP::DLK-1 abundance throughout cilia and dendrites of AWC neurons. Moreover, in odr-1 mutants, AWC cilia display distorted morphology, which is ameliorated by loss of function in dlk-1 or cebp-1. These data expand the landscape of DLK-1 signaling in ciliated sensory neurons and underscore a high degree of cell- and neurite- specific regulation.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143032811","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

Optimized genetic tools for neuroanatomical and functional mapping of the Aedes aegypti olfactory system.

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-01-24 DOI: 10.1093/g3journal/jkae307

Shruti Shankar, Diego Giraldo, Genevieve M Tauxe, Emma D Spikol, Ming Li, Omar S Akbari, Margot P Wohl, Conor J McMeniman

{"title":"Optimized genetic tools for neuroanatomical and functional mapping of the Aedes aegypti olfactory system.","authors":"Shruti Shankar, Diego Giraldo, Genevieve M Tauxe, Emma D Spikol, Ming Li, Omar S Akbari, Margot P Wohl, Conor J McMeniman","doi":"10.1093/g3journal/jkae307","DOIUrl":"https://doi.org/10.1093/g3journal/jkae307","url":null,"abstract":"The mosquito Aedes aegypti is an emerging model insect for invertebrate neurobiology. We detail the application of a dual transgenesis marker system that reports the nature of transgene integration with circular donor template for CRISPR-Cas9-mediated homology-directed repair at target mosquito chemoreceptor genes. Employing this approach, we demonstrate the establishment of cell-type-specific T2A-QF2 driver lines for the A. aegypti olfactory co-receptor genes Ir8a and orco via canonical homology-directed repair and the CO2 receptor complex gene Gr1 via noncanonical homology-directed repair involving duplication of the intended T2A-QF2 integration cassette separated by intervening donor plasmid sequence. Using Gr1+ olfactory sensory neurons as an example, we show that introgression of such T2A-QF2 driver and QUAS responder transgenes into a yellow cuticular pigmentation mutant strain facilitates transcuticular calcium imaging of CO2-evoked neural activity on the maxillary palps with enhanced sensitivity relative to wild-type mosquitoes enveloped by dark melanized cuticle. We further apply Cre-loxP excision to derive marker-free T2A-QF2 in-frame fusions to clearly map axonal projection patterns from olfactory sensory neurons expressing these 3 chemoreceptors into the A. aegypti antennal lobe devoid of background interference from 3xP3-based fluorescent transgenesis markers. The marker-free Gr1 T2A-QF2 driver facilitates clear recording of CO2-evoked responses in this central brain region using the genetically encoded calcium indicators GCaMP6s and CaMPARI2. Systematic application of these optimized methods to different chemoreceptors stands to enable mapping A. aegypti olfactory circuits at peripheral and central levels of olfactory coding at high resolution.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143032815","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

De-novo Genome Assembly of the Edwardsiid Anthozoan Edwardsia elegans.

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-01-24 DOI: 10.1093/g3journal/jkaf011

Auston I Rutlekowski, Vengamanaidu Modepalli, Remi Ketchum, Yehu Moran, Adam M Reitzel

{"title":"De-novo Genome Assembly of the Edwardsiid Anthozoan Edwardsia elegans.","authors":"Auston I Rutlekowski, Vengamanaidu Modepalli, Remi Ketchum, Yehu Moran, Adam M Reitzel","doi":"10.1093/g3journal/jkaf011","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf011","url":null,"abstract":"Cnidarians (sea anemones, corals, hydroids, and jellyfish) are a key outgroup for comparisons with bilaterial animals to trace the evolution of genomic complexity and diversity within the animal kingdom, as they separated from most other animals 100s of millions of years ago. Cnidarians have extensive diversity, yet the paucity of genomic resources limits our ability to compare genomic variation between cnidarian clades and species. Here we report the genome for Edwardsia elegans, a sea anemone in the most specious genus of the family Edwardsiidae, a phylogenetically important family of sea anemones that contains the model anemone Nematostella vectensis. The E. elegans genome is 396 Mb in length and predicted to encode approximately 49,000 proteins. We annotated large conservation of macrosynteny between E. elegans and other Edwardsiidae anemones as well as conservation of both microRNAs and ultra conserved noncoding elements previously reported in other cnidarians species. We also highlight microsyntenic variation of clustered developmental genes and ancient gene clusters that vary between species of sea anemones, despite previous research showing conservation between cnidarians and bilaterians. Overall, our analysis of the E. elegans genome highlights the importance of using multiple species to represent a taxonomic group for genomic comparisons, where genomic variation can be missed for large and diverse clades.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143028442","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 haplotype-resolved chromosome-level genome assembly of Urochloa decumbens cv. Basilisk resolves its allopolyploid ancestry and composition.

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-01-24 DOI: 10.1093/g3journal/jkaf005

Camilla Ryan, Fiona Fraser, Naomi Irish, Tom Barker, Vanda Knitlhoffer, Alex Durrant, Gillian Reynolds, Gemy Kaithakottil, David Swarbreck, Jose J De Vega

{"title":"A haplotype-resolved chromosome-level genome assembly of Urochloa decumbens cv. Basilisk resolves its allopolyploid ancestry and composition.","authors":"Camilla Ryan, Fiona Fraser, Naomi Irish, Tom Barker, Vanda Knitlhoffer, Alex Durrant, Gillian Reynolds, Gemy Kaithakottil, David Swarbreck, Jose J De Vega","doi":"10.1093/g3journal/jkaf005","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf005","url":null,"abstract":"Haplotyped-resolved phased assemblies aim to capture the full allelic diversity in heterozygous and polyploid species to enable accurate genetic analyses. However, building non-collapsed references still presents a challenge. Here, we used long-range interaction Hi-C reads (high-throughput chromatin conformation capture) and HiFi PacBio reads to assemble the genome of the apomictic cultivar Basilisks from Urochloa decumbens (2n = 4x = 36), an outcrossed tetraploid Paniceae grass widely cropped to feed livestock in the tropics. We identified and removed Hi-C reads between homologous unitigs to facilitate their scaffolding and employed methods for the manual curation of rearrangements and misassemblies. Our final phased assembly included the four haplotypes in 36 chromosomes. We found that 18 chromosomes originated from diploid U. brizantha and the other 18 from either U. ruziziensis or diploid U. decumbens. We also identified a chromosomal translocation between chromosomes 5 and 32, as well as evidence of pairing exclusively within subgenomes, except for a homoeologous exchange in chromosome 21. Our results demonstrate that haplotype-aware assemblies accurately capture the allelic diversity in heterozygous species, making them the preferred option over collapsed-haplotype assemblies.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143032790","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 Sox2 Enhancer Cluster Regulates Region-Specific Neural Fates from Mouse Embryonic Stem Cells.

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-01-24 DOI: 10.1093/g3journal/jkaf012

Ian C Tobias, Sakthi D Moorthy, Virlana M Shchuka, Lida Langroudi, Mariia Cherednychenko, Zoe E Gillespie, Andrew G Duncan, Ruxiao Tian, Natalia A Gajewska, Raphaël B Di Roberto, Jennifer A Mitchell

{"title":"A Sox2 Enhancer Cluster Regulates Region-Specific Neural Fates from Mouse Embryonic Stem Cells.","authors":"Ian C Tobias, Sakthi D Moorthy, Virlana M Shchuka, Lida Langroudi, Mariia Cherednychenko, Zoe E Gillespie, Andrew G Duncan, Ruxiao Tian, Natalia A Gajewska, Raphaël B Di Roberto, Jennifer A Mitchell","doi":"10.1093/g3journal/jkaf012","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf012","url":null,"abstract":"Sex-determining region Y box 2 (Sox2) is a critical transcription factor for embryogenesis and neural stem and progenitor cell (NSPC) maintenance. While distal enhancers control Sox2 in embryonic stem cells (ESCs), enhancers closer to the gene are implicated in Sox2 transcriptional regulation in neural development. We hypothesize that a downstream enhancer cluster, termed Sox2 regulatory regions 2-18 (SRR2-18), regulates Sox2 transcription in neural stem cells and we investigate this in NSPCs derived from mouse ESCs. Using functional genomics and CRISPR-Cas9 mediated deletion analyses we investigate the role of SRR2-18 in Sox2 regulation during neural differentiation. Transcriptome analyses demonstrate that loss of even one copy of SRR2-18 disrupts the region-specific identity of NSPCs, reducing the expression of genes associated with more anterior regions of the embryonic nervous system. Homozygous deletion of this Sox2 neural enhancer cluster causes reduced SOX2 protein, less frequent interaction with transcriptional machinery, and leads to perturbed chromatin accessibility genome-wide further affecting the expression of neurodevelopmental and anterior-posterior regionalization genes. Furthermore, homozygous NSPC deletants exhibit self-renewal defects and impaired differentiation into cell types found in the brain. Altogether, our data define a cis-regulatory enhancer cluster controlling Sox2 transcription in NSPCs and highlight the sensitivity of neural differentiation processes to decreased Sox2 transcription, which causes differentiation into posterior neural fates, specifically the caudal neural tube. This study highlights the importance of precise Sox2 regulation by SRR2-18 in neural differentiation.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143028439","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

Using feedback in pooled experiments augmented with imputation for high genotyping accuracy at reduced cost.

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-01-23 DOI: 10.1093/g3journal/jkaf010

Camille Clouard, Carl Nettelblad

{"title":"Using feedback in pooled experiments augmented with imputation for high genotyping accuracy at reduced cost.","authors":"Camille Clouard, Carl Nettelblad","doi":"10.1093/g3journal/jkaf010","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf010","url":null,"abstract":"Conducting genomic selection in plant breeding programs can substantially speed up the development of new varieties. Genomic selection provides more reliable insights when it is based on dense marker data, in which the rare variants can be particularly informative. Despite the availability of new technologies, the cost of large-scale genotyping remains a major limitation to the implementation of genomic selection. We suggest to combine pooled genotyping with population-based imputation as a cost-effective computational strategy for genotyping SNPs. Pooling saves genotyping tests and has proven to accurately capture the rare variants that are usually missed by imputation. In this study, we investigate adding iterative coupling to a joint model of pooling and imputation that we have previously proposed. In each iteration, the imputed genotype probabilities serve as feedback input for adjusting the per-sample prior genotype probabilities, before running a new imputation based on these adjusted data. This flexible setup indirectly imposes consistency between the imputed genotypes and the pooled observations. We demonstrate that repeated cycles of feedback can take advantage of the strengths in both pooling and imputation when an appropriate set of reference haplotypes is available for imputation. The iterations improve greatly upon the initial genotype predictions, achieving very high genotype accuracy for both low and high frequency variants. We enhance the average concordance from 94.5% to 98.4% at limited computational cost and without requiring any additional genotype testing.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143028450","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