Transposable element polymorphisms improve prediction of complex agronomic traits in rice DOI Creative Commons

Ioanna‐Theoni Vourlaki,

Raúl Castanera, Sebastián E. Ramos‐Onsins

и другие.

Theoretical and Applied Genetics, Год журнала: 2022, Номер 135(9), С. 3211 - 3222

Опубликована: Авг. 5, 2022

Transposon insertion polymorphisms can improve prediction of complex agronomic traits in rice compared to using SNPs only, especially when accessions be predicted are less related the training set. (TIPs) significant sources genetic variation. Previous work has shown that TIPs detection causative loci on rice. Here, we quantify fraction variance explained by single nucleotide (SNPs) TIPs, and explore whether only SNPs. We used eleven relevance from five different population groups (Aus, Indica, Aromatic, Japonica, Admixed), 738 total. assess applying data split validation two scenarios. In within-population scenario, performance improved Indica varieties rest accessions. across all Aromatic Admixed populations. each Bayes C a Bayesian reproducible kernel Hilbert space regression were compared. find explain an important total they also genomic prediction. outperformed nine out analyzed. some like leaf senescence or grain width, increased predictive correlation 30-50%. Our results evidence, for first time, genotyping rice,

Язык: Английский

Functional neurogenomics in autism spectrum disorders: A decade of progress DOI
Lucy Bicks, Daniel H. Geschwind

Current Opinion in Neurobiology, Год журнала: 2024, Номер 86, С. 102858 - 102858

Опубликована: Март 27, 2024

Язык: Английский

Процитировано

8
The systemic lupus erythematosus-associated NCF190H allele synergizes with viral infection to cause mouse lupus but also limits virus spread DOI Creative Commons
Yanpeng Li, Ana Coelho, Zhilei Li

и другие.

Nature Communications, Год журнала: 2025, Номер 16(1)

Опубликована: Фев. 13, 2025

Abstract Studying how single nucleotide polymorphisms (SNPs) crosstalk with non-autologous factors to cause complex autoimmune diseases is challenging. An amino acid replacement in the neutrophil cytosolic factor 1 ( NCF1 -339/ R90H ) leading lower reactive oxygen species induction has been reported as major SNP for systemic lupus erythematosus (SLE). Here we show that infection murine norovirus (MNV) contributes of Ncf1 90H mice. Mutant upregulates IFN-α/JAK1/STAT1 pathway macrophages and anti-MNV-antibody production. In parallel, MNV mice Toll-like receptor 7 macrophages, plasmacytoid dendritic cells B220 + splenocytes, thereby promoting germinal center formation lupus-associated autoantibodies These compounded effects lead protection against but also glomeruloneph ritis proteinuria arthritis absence chemical inducers such pristane. Our data thus suggest this SLE-associated SNP, , synergizes induce development mouse lupus.

Язык: Английский

Процитировано

1
An evolving understanding of multiple causal variants underlying genetic association signals DOI
Erping Long, Jacob Williams, Haoyu Zhang

и другие.

The American Journal of Human Genetics, Год журнала: 2025, Номер unknown

Опубликована: Фев. 1, 2025

Язык: Английский

Процитировано

1
Using genome‐wide associations and host‐by‐pathogen predictions to identify allelic interactions that control disease resistance DOI Creative Commons
Owen Hudson, Jeremy Brawner

The Plant Genome, Год журнала: 2025, Номер 18(1)

Опубликована: Фев. 24, 2025

Abstract Characterizing the molecular mechanisms underlying disease symptom expression has been used to improve human health and resistance in crops animal breeds. Quantitative trait loci genome‐wide association studies (GWAS) are widely identify genomic regions that involved progression. This study extends traditional GWAS significance tests of host pathogen marker main effects by utilizing dual‐genome reaction norm models evaluate importance host‐single nucleotide polymorphism (SNP) pathogen‐SNP interactions. Disease severity data from Fusarium ear rot (FER) on maize ( Zea mays L.) is demonstrate use both genomes selection for breeding identification interact across organisms impact FER development. Dual genome prediction improved heritability estimates, error variances, model accuracy while providing predictions host‐by‐pathogen interactions may be test SNP–SNP Independent populations identified significantly associated were using two different tests. Predictions dual with population structure or polygenic effects. As well, incorporating markers also included relationship matrices account structure. Subsequent evaluation protein–protein candidate genes near interacting SNPs provides a further silico method expedite genes.

Язык: Английский

Процитировано

1
The transition from genomics to phenomics in personalized population health DOI
James T. Yurkovich, Simon J. Evans, Noa Rappaport

и другие.

Nature Reviews Genetics, Год журнала: 2023, Номер 25(4), С. 286 - 302

Опубликована: Дек. 13, 2023

Язык: Английский

Процитировано

21
Genetic risk factors for ME/CFS identified using combinatorial analysis DOI Creative Commons
Sayoni Das,

Krystyna Taylor,

James Kozubek

и другие.

Journal of Translational Medicine, Год журнала: 2022, Номер 20(1)

Опубликована: Дек. 14, 2022

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a debilitating chronic disease that lacks known pathogenesis, distinctive diagnostic criteria, and effective treatment options. Understanding the genetic (and other) risk factors associated with would begin to help alleviate some of these issues for patients.

Язык: Английский

Процитировано

26
Patient-Derived In Vitro Models of Microglial Function and Synaptic Engulfment in Schizophrenia DOI Creative Commons
Steven D. Sheridan, Joy E. Horng, Roy H. Perlis

и другие.

Biological Psychiatry, Год журнала: 2022, Номер 92(6), С. 470 - 479

Опубликована: Янв. 19, 2022

Язык: Английский

Процитировано

24
From genetic variation to precision medicine DOI Creative Commons

Panagiotis I. Sergouniotis,

Tomas Fitzgerald, Ewan Birney

и другие.

Cambridge Prisms Precision Medicine, Год журнала: 2023, Номер 1

Опубликована: Янв. 1, 2023

Abstract Genetics has been an important tool for discovering new aspects of biology across life. In humans, there is growing momentum behind the application this knowledge to drive innovation in clinical care, most notably through developments precision medicine. Nowhere impact genetics on practice more striking than field rare disorders. For these conditions, individual disease susceptibility influenced by DNA sequence variation a single or small number genes. contrast, common disorders are multifactorial and caused complex interplay multiple genetic, environmental stochastic factors. The longstanding division human into components obscured continuum traits echoes century-old debate between Mendelian biometric views genetics. article, we discuss differences data concepts Opportunities unify two areas noted importance adopting holistic perspective that integrates diverse genetic factors discussed.

Язык: Английский

Процитировано

16
Single-nucleus genomics in outbred rats with divergent cocaine addiction-like behaviors reveals changes in amygdala GABAergic inhibition DOI Creative Commons
Jessica Zhou, Giordano de Guglielmo,

Aaron J. Ho

и другие.

Nature Neuroscience, Год журнала: 2023, Номер 26(11), С. 1868 - 1879

Опубликована: Окт. 5, 2023

Abstract The amygdala processes positive and negative valence contributes to addiction, but the cell-type-specific gene regulatory programs involved are unknown. We generated an atlas of single-nucleus expression chromatin accessibility in outbred rats with high low cocaine addiction-like behaviors following prolonged abstinence. Differentially expressed genes between groups were enriched for energy metabolism across cell types. Rats addiction index (AI) showed increased relapse-like GABAergic transmission amygdala. Both phenotypes reversed by pharmacological inhibition glyoxalase 1 enzyme, which metabolizes methylglyoxal—a GABA A receptor agonist produced glycolysis. Differences AI implicated pioneer transcription factors basic helix-loop-helix, FOX, SOX activator protein families. observed opposite regulation many Most notably, excitatory neurons had greater inhibitory rats.

Язык: Английский

Процитировано

16
XMAP: Cross-population fine-mapping by leveraging genetic diversity and accounting for confounding bias DOI Creative Commons
Mingxuan Cai, Zhiwei Wang,

Jiashun Xiao

и другие.

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Окт. 28, 2023

Fine-mapping prioritizes risk variants identified by genome-wide association studies (GWASs), serving as a critical step to uncover biological mechanisms underlying complex traits. However, several major challenges still remain for existing fine-mapping methods. First, the strong linkage disequilibrium among can limit statistical power and resolution of fine-mapping. Second, it is computationally expensive simultaneously search multiple causal variants. Third, confounding bias hidden in GWAS summary statistics produce spurious signals. To address these challenges, we develop method cross-population (XMAP) leveraging genetic diversity accounting bias. By using from global biobanks genomic consortia, show that XMAP achieve greater power, better control false positive rate, substantially higher computational efficiency identifying signals, compared Importantly, output be integrated with single-cell datasets, which greatly improves interpretation putative their cellular context at resolution.

Язык: Английский

Процитировано

14