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Current knowledge and future directions in disease resistance breeding of Andean and Mesoamerican common bean gene pools: A review.

Future breeding efforts and the resilience of common bean production are constrained by the absence of a comprehensive synthesis of resistance sources, breeding strategies, and molecular tools across the Andean and Mesoamerican gene pools. This review consolidates current knowledge on disease resistance breeding in common bean, focusing on major resistance genes and quantitative trait loci (QTLs) associated with key diseases including anthracnose, angular leaf spot, halo blight, common bacterial blight, rust, and viral infections. The Andean gene pool predominantly contributes race-specific re…

Converging QTL mapping with MutMap identifies novel genomic regions associated with strong culm in rice (Oryza sativa L.).

This study characterizes wild-type and mutants of rice for culm strength at morphological, histological, and molecular levels, identifying key genes and genomic regions that govern the strong culm trait. Strong culm trait in rice has gained importance for sustainability in the realm of climate change. The mutants having economic important traits have become a potential source for the identification of genomic regions. The present study aimed to characterize rice mutants having strong culms and to identify genomic regions through conventional as well as NGS-based mapping approaches. Morphologic

Мультиомикальное восприятие окисляющих генов и нейродегенеративных заболеваний: от эпигенетического регулирования до патогенных патогенных патологий.

Окисляющий стресс (ОС) в значительной степени связан с возникновением и развитием нейродегенеративных заболеваний (НДД), однако его генетические детерминанты остаются недостаточно ясными. Цель этого исследования заключается в определении предполагаемой причинно-следственной связи между генами, связанными с ОСН (ОСРГ), и НДО наряду с потенциальными регулирующими и патогенными механизмами. С целью изучения предполагаемой причинно-следственной связи 936 ОСРГ с НИЗ была проведена работа по обобщению данных общегеномических исследований ассоциаций (ГВАС) и данных количественного выражения loci (eQT

Совпадение в аннотации оригинала
Oxidative stress (OS) is critically implicated in the onset and progression of neurodegenerative diseases (NDDs), yet its genetic determinan … ions of 936 OSRGs with NDDs, integrating genome-wide association studies (GWAS) data and expression quantitative trait loci (eQTL) data, using a multi-cohort design with blood eQTLs for discovery and replication, followed by brain eQTL validation. Subsequently, colocalization analysis was used to verify putative causal inferences in SMR. In addition, DNA methylation regu …

Identification of Novel Genetic Loci Involved in Testis Traits of the Jiangxi Local Breed Based on GWAS Analyses.

BACKGROUND: The testis, a critical reproductive organ in male animals, is responsible for sperm production and androgen secretion. Testis weight often correlates with reproductive performance, yet the genetic factors influencing testicular traits in chickens remain unclear. METHODS: Previous genome-wide association studies (GWAS) have identified key genes affecting testicular traits in Kangle Yellow chickens, along with the associated regulatory pathways and Gene Ontology (GO) terms, through bioinformatic analyses. In this study, we utilized the existing literature, full-length transcriptome

Causal Associations of Cardiovascular Proteins and Diabetic Nephropathy Revealed by Mediation and Phenome-Wide Mendelian Randomization.

Cardiovascular factors play a critical role in the progression of diabetic nephropathy (DN). This study utilized Mendelian randomization analysis to explore the causal relationships among cardiovascular proteins, risk factors, and DN. Using cis-protein quantitative trait loci (cis-pQTL) data for 90 cardiovascular proteins, we identified C-X3-C motif chemokine ligand 1 (CX3CL1) and colony-stimulating factor-1 (CSF-1) as potential therapeutic targets for DN. CX3CL1 was found to increase DN risk through mechanisms involving body mass index, fasting insulin, and hypertension. Conversely, CSF-1 app…

QTL identification and characterization of the recombination landscape of the mountain pine beetle (Dendroctonus ponderosae).

Insect pests can rapidly accumulate in number and thrive in diverse environments, making them valuable models for studying phenotypic plasticity and the genetic basis of local adaptation. The mountain pine beetle (Dendroctonus ponderosae) is a major forest pest, and adult body size and generation time are 2 traits that vary among populations and directly influence reproductive success and outbreak dynamics. To identify regions of the genome linked to these 2 traits, we generated double-digest RAD sequencing data from an F2 intercross, using populations from 2 Y haplogroups with phenotypic and

Association Analysis of the Circulating Proteome With Sarcopenia-Related Traits Reveals Potential Drug Targets for Sarcopenia.

BACKGROUND: Sarcopenia severely affects the physical health of the elderly. Currently, there is no specific drug available for sarcopenia. T … and nine sarcopenia-related traits were utilized as outcomes. IVs were classified into cis-protein quantitative trait loci (pQTLs) and trans-pQTLs based on their positions. We conducted cis-only MRSC analyses and cis + trans MRSC analyses using cis-pQTLs and cis + trans pQTLs as IVs, respectively. Post-MRSC analyses were conducted on the prioritized findings of MRSC, in …

Decoding eQTLs: unraveling their role in spondyloarthropathies pathogenesis and potential therapeutics.

Expression quantitative trait loci (eQTLs) represent genetic variants that influence gene expression, providing insights into the mechanisms linking genetic predisposition to complex diseases, including spondyloarthropathies (SpAs). SpAs, encompassing ankylosing spondylitis, psoriatic arthritis, reactive arthritis, and enteropathic arthritis, are related heterogeneous conditions with strong genetic components, particularly in HLA-B27 and non-HLA loci, but phenotypically distinct disorders. Recent advances in genome-wide association studies (GWAS) and transcriptomic studies have shown the poten…

3D chromatin-based variant-to-gene maps across 57 human cell types reveal the cellular and genetic architecture of autoimmune disease susceptibility.

BACKGROUND: Insight into the genetic basis for many common autoimmune disorders has been uncovered by genome-wide association studies (GWAS), but this alone does not reveal causal variants, effector genes, or the cell types impacted by disease-associated variation. RESULTS: Here, we generate 3D genomic datasets consisting of promoter-focused Capture-C, Hi-C, ATAC-seq, and RNA-seq and integrate this data with GWAS of 16 autoimmune traits to physically map disease-associated variants to the effector genes they likely regulate in 57 human cell types. The majority of variants implicated by these c

Интегрированное многоомикальное исследование молекулярных сетей окислительного стресса, вызывающее множественный склероз.

Окисляющий стресс (ОС) является ключевым патофизиологическим механизмом при множественном склерозе (MS). Однако основные механизмы, с помощью которых ОС сработала НР, остаются неизвестными. Для выявления потенциальных причинно-следственных целей в 1216 генах, связанных с ОС, был применен метод, основанный на обобщенных данных, на менделийской случайности (МСР). Учитывая, что гены могут выполнять свои биологические функции с помощью различных уровней ОМИК, использовались мультимики SMR, интегрирующие выражение, метилацию и белковую количественную loci (eQTL, mQTL и PQTL) связанных с OS генов из

Совпадение в аннотации оригинала
Oxidative stress (OS) is a key pathophysiological mechanism in multiple sclerosis (MS). However, the underlying mechanisms by which OS trigg … hrough different omics levels, the multi-omics SMR integrating expression, methylation, and protein quantitative trait loci (eQTL, mQTL, and pQTL) of OS-related genes from blood and brain tissues was utilized. Bayesian colocalization test was conducted to examine potential regulatory mechanisms of QTL risk variation in MS. To verify the robustness of our results, we vali …

Investigating the genetic determination of duration-of-fertility trait in breeding hens.

The duration-of-fertility (DF), which was defined as the number of days when breeding hens lay fertile eggs following copulation or artificial insemination (AI), is an important economic trait in chick production when it has strong effects on fertile egg output and production costs. Little is known about the underlying genes and molecular markers related to DF trait to date. Here, we measured the DF of 701 Chinese Jinghong hens and 408 Jingfen hens. The DF showed high individual variability and potential for genetic improvement. Then, 192 Jinghong breeding hens were provided for a genome-wide

Atlas of the plasma proteome in health and disease in 53,026 adults.

Large-scale proteomics studies can refine our understanding of health and disease and enable precision medicine. Here, we provide a detailed atlas of 2,920 plasma proteins linking to diseases (406 prevalent and 660 incident) and 986 health-related traits in 53,026 individuals (median follow-up: 14.8 years) from the UK Biobank, representing the most comprehensive proteome profiles to date. This atlas revealed 168,100 protein-disease associations and 554,488 protein-trait associations. Over 650 proteins were shared among at least 50 diseases, and over 1,000 showed sex and age heterogeneity. Furt

Genetic insights into therapeutic targets for gout: evidence from a multi-omics mendelian randomization study.

BACKGROUND: Considering that the treatment of gout is poor, we performed a Mendelian randomization (MR) study to identify candidate biomarkers and therapeutic targets for gout. METHODS: A drug-targeted MR study was performed for gout by integrating the gout genome-wide association studies (GWAS) summary data and cis expression quantitative trait loci of 2,633 druggable genes from multiple cohorts. Summary data-based Mendelian randomization (SMR) analyses based on transcript and protein levels were further implemented to validate the reliability of the identified potential therapeutic targets …

Variation in CD8 T cell IFNγ differentiation to strains of Toxoplasma gondii is characterized by small effect QTLs with contribution from ROP16.

INTRODUCTION: Toxoplasma gondii induces a strong CD8 T cell response characterized by the secretion of IFNγ that promotes host survival duri … response to T. gondii infected macrophages. RESULTS: Genetic mapping returned four non-interacting quantitative trait loci (QTL) with small effect on T. gondii chromosomes (chr) VIIb-VIII, X and XII. These loci encompass multiple gene candidates highlighted by ROP16 (chrVIIb-VIII), GRA35 (chrX), TgNSM (chrX), and a pair of uncharacterized NTPases (chrXII), whose locus w …

Systemic interindividual epigenetic variation in humans is associated with transposable elements and under strong genetic control.

BACKGROUND: Genetic variants can modulate phenotypic outcomes via epigenetic intermediates, for example at methylation quantitative trait loci (mQTL). We present the first large-scale assessment of mQTL at human genomic regions selected for interindividual variation in CpG methylation, which we call correlated regions of systemic interindividual variation (CoRSIVs). These can be assayed in blood DNA and do not reflect interindividual variation in cellular composition. RESULTS: We use target-capture bisulfite sequencing to assess DNA methylation at 4086 CoRSIVs in multiple tissues from each of…

Review: Genetic mutations affecting bull fertility.

Cattle are a well-suited "model organism" to study the genetic underpinnings of variation in male reproductive performance. The adoption of … sociation studies with quantitative measurements of semen quality and insemination success revealed quantitative trait loci for male fertility, but the underlying causal variants remain largely unknown. Moreover, these loci explain only a small part of the heritability of male fertility. Integrating genome-wide association studies with gene expression and other omics dat …

Integration of genetic colocalizations with physiological and pharmacological perturbations identifies cardiometabolic disease genes.

BACKGROUND: Identification of causal genes for polygenic human diseases has been extremely challenging, and our understanding of how physiol … gh-density lipoprotein, body mass index, and waist-hip ratio) combined with expression and splicing quantitative trait loci (eQTLs and sQTLs) from five metabolically relevant human tissues (subcutaneous and visceral adipose, skeletal muscle, liver, and pancreas). To elucidate the upstream regulators and functional mechanisms for these genes, we integrate their transcript …

Sex-heterogeneous SNPs disproportionately influence gene expression and health.

Phenotypic differences across sexes are pervasive, but the genetic architecture of sex differences within and across phenotypes is mostly un … , empP < 0.05). Interestingly, we found that sex-het SNPs significantly map to predicted expression quantitative trait loci (Pr-eQTLs) across brain and other tissues, methylation quantitative trait loci (meQTLs) during development, and transcription start sites, compared to sex-homogeneous SNPs. Finally, we verified that the sex-het disease/trait enrichment was not expla …

Risk Allele Frequency Analysis of Single-Nucleotide Polymorphisms for Vitamin D Concentrations in Different Ethnic Group.

The prevalence of vitamin D deficiency varies from 20.8% to 61.6% among populations of different ethnicities, suggesting the existence of a genetic component. The purpose of this study was to provide insights into the genetic causes of vitamin D concentration differences among individuals of diverse ancestry. We collected 320 single-nucleotide polymorphisms (SNPs) associated with vitamin D concentrations from a genome-wide association studies catalog. Their population-level allele frequencies were derived based on the 1000 Genomes Project and Korean Reference Genome Database. We used Fisher's

Understanding the role of corneal biomechanics-associated genetic variants by bioinformatic analyses.

PURPOSE: To analyze functions of corneal biomechanical properties (CBP)-related variants as corneal resistance factor (CRF) and corneal hysteresis (CH). METHODS: Related single nucleotide polymorphisms (SNPs) and genes were identified from NHGRI-EBI GWAS catalog, GWASdb v2 and possible data in published studies. HaploReg v4.1 was used to find linkage SNPs. Functional annotations were performed by GWAVA, CADD and RegulomeDB. GTEx Portal database was used to find out expression quantitative trait locus (eQTL) association. Enrichr was used to annotate the function of GWAS gene and the associated