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Results for “quantitative genetic variation”

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At least 37 records · Page 2Linked to original sources
PubMed2025

Genetic diversity, population structure in a historical panel of Brazilian soybean cultivars.

Soybean [Glycine max (L.) Merrill] is one of the most widely grown legumes in the world, with Brazil being its largest producer and exporter. Breeding programs in Brazil have resulted from multiple cycles of selection and recombination starting from a small number of USA cultivar ancestors in the 1950s and 1960s years. This process has led to the successful adaptation of this crop to tropical conditions, a phenomenon known as tropicalization. Many studies describe a narrow genetic background in Brazilian soybean cultivars. Various factors can affect the genetic diversity in species, especially in cultivated crops, such as the reproduction type, artificial selection, and the number and sources of variability in the breeding programs. In turns, the genetic diversity can affect the linkage disequilibrium blocks (LD) patterns and, consequently, molecular breeding strategies for selection of target loci for agronomic traits. We used high-throughput genotyping with SoySNP50K Illumina SNP markers to assess a collection of 370 Brazilian soybean accessions covering more than 60 years of soybean breeding in Brazil. Our goal was to investigate population structure and genetic diversity in the Brazilian germplasm, detect patterns of LD blocks, and identify regions presenting signals of selective swaps linked with quantitative trait loci (QTLs) of agronomic interest. Population structure analysis revealed two major groups among all genotypes, primarily differentiated by the year of release, separating old and new cultivars (before and after 2000´s years), and by growth habit (stem termination type-SST). The group I comprises about 75% of the panel and includes cultivars release before 2000`s years, including the oldest cultivars released in Brazil, most of which exhibit a determinate growth habit and maturity groups VI and VII. Group II includes only 83 materials, but shows higher levels of diversity than group I, representing most recent introductions in Brazilian germplasm. Further analysis of substructure within Group I, identified seven subgroups with no clear trend for segregation based on maturity group, STT or year of release. Instead, these subgroups were based on the contribution of key donors of disease resistance and adaptability, as soybean cultivation expanded from the South to Central region of Brazil. This finding is consistent with the history of soybean expansion in Brazil. We identified 123 genomic regions under selection among the groups of Brazilian cultivars associated with 440 quantitative trait loci (QTLs), revealing regions fixed across the breeding process associated with yield, disease resistance, water efficiency use, and others.

Glycine max↗
PubMed1979

Digital ridge counts and genetic fields.

Principal components analysis of quantitative digital dermatoglyphics in a large Oxfordshire sample, subdivided into male, female, urban, and rural subsamples, suggests several distinguishable components. These appear meaningful biologically in that they resemble factors of limb growth, as suggested by evidence from disturbances in limb extremity development. The components are consistent in all four subsamples and are very similar to those identified in a large sample of Berkshire data. It is suggested that digital quantitative dermatoglyphic variation may provide an example of genetic field theory.

Dermatoglyphics↗
PubMed2025

Gut fungi are associated with human genetic variation and disease risk.

Human genetic determinants of the gut mycobiome remain uninvestigated despite decades of research highlighting tripartite relationships between gut bacteria, genetic background, and disease. Here, we present the first genome-wide association study on the number and types of human genetic loci influencing gut fungi relative abundance. We detect 148 fungi-associated variants (FAVs) across 7 chromosomes that statistically associate with 9 fungal taxa. Of these FAVs, several occur in the protein-coding genes PTPRC, ANAPC10, NAV2, and CDH13. Additional FAVs link to tissue-specific gene expression as fungi-associated expression quantitative trait loci. Notably, the relative abundance of gut yeast Kazachstania associates with genetic variation in CDH13 encoding T-cadherin, a protein linked to cardiovascular disease. Kazachstania forms a causal relationship with cardiovascular disease risk in a mendelian two-sample randomization analysis. These findings establish previously unrecognized connections between human genetics, gut fungi, and chronic disease, broadening the paradigm of human-microbe interactions in the gut to the mycobiome.

Humans↗
PubMed2026

Mapping the regulatory architecture of circadian clock adaptation: A genome-wide eQTL analysis in Drosophila melanogaster.

The circadian clock enables organisms to align internal daily rhythms with environmental cues, with major consequences for survival and fitness. Although the molecular framework of this system in Drosophila melanogaster is well characterized through transcription translation feedback loops involving ten core clock genes, the genetic basis of natural variation in their expression remains poorly understood. Here, we used natural expression variation to identify expression quantitative trait loci (eQTLs) through genome-wide association mapping. Using the Drosophila Genetic Reference Panel, we measured relative expression of all core clock genes at a single time point two hours after light onset. We identified 109 significant SNPs and 28 indels associated with expression variation across the clock network. Expression levels varied widely, with Pdp1ε showing the greatest variation (an 86-fold difference between extreme lines) and cyc the least (11.3-fold). Only three significant SNPs were located within clock genes themselves, all in Clk, whereas most associations represented trans-eQTLs in genes with diverse molecular functions. Candidate regulators included transcription factors such as Abd-B, tai, and E5; RNA binding proteins including Pum, Bru-3, and Mbl; and several long noncoding and antisense RNAs. Variants were also detected in gbb and the BMP pathway transcription factor Mad. Consistent with this, Mad knockdown reduced vri expression. Together, these results reveal a complex regulatory architecture underlying natural variation in circadian gene expression.

Journal Article↗
PubMed2026

Complex genotype-phenotype relationships in neurodevelopmental disorders.

With the advent of sequencing technologies in recent years, hundreds of high-confidence risk genes have been implicated in neurodevelopmental disorders (NDDs). However, individuals carrying pathogenic variants in the same gene frequently exhibit diverse clinical presentations, including varied symptoms and diagnoses. We propose that this heterogeneity arises from different interacting factors that modulate the phenotypic outcomes of pathogenic variants, including variant-level features, modifying variation across the genome, prenatal and early-life environmental exposures, and developmental noise. Resolving these factors requires integrative approaches that combine population-scale genetics and functional genomics with environmental monitoring and quantitative assessments of stochastic developmental variation. Advancing our understanding of these factors is critical to elucidating the etiology of NDDs and improving diagnostic and personalized therapeutic strategies.

Humans↗
PubMed1978

[Intelligence : individual differences, genetic factors, environmental factors and interaction between the genotype and the environment (author's transl)].

The authors undertook a review of published work on the sources of variation in individual differences in intelligence. They should : 1) that methods of quantitative genetics concerning intelligence are not applicable to human populations ; 2) that the results of studies on adoptions and on twins do not permit one to estimate the respective roles of environment and heredity ; 3) that this division of variance had no heuristic value in the study of human intelligence.

Animals↗
PubMed1977

Isozyme and allozyme patterns in embryonic Drosophila cell culture lines.

Two independently derived embryonic Drosophila cell culture lines were examined for 19 gene-enzyme systems. At two loci, alpha-glycerophosphate dehydrogenase on chromosome 2, and isocitrate dehydrogenase on chromosome 3, allelic variation was detected. These can now serve as genetic markers to identify hybrid cell clones. Quantitative differences between cell lines were found for five enzymes.

Alleles↗
PubMed2025

Saturating the eQTL map in Drosophila: Genome-wide patterns of cis and trans regulation of transcriptional variation in outbred populations.

Most genetic polymorphisms associated with complex traits are found in non-coding regions of the genome. Characterizing their effect presents a formidable challenge, and expression quantitative trait locus (eQTLs) mapping has been a key approach to do so. As comprehensive eQTL maps are available only for a few species, here we developed the Drosophila outbred synthetic population (Dros-OSP) and used it to characterize the landscape of transcriptional regulation in Drosophila melanogaster. We collected head and body transcriptomes and genomes from 1,286 outbred flies and mapped local and distant eQTLs for 98% of the genes. We characterized the network organization of the transcriptome across tissues and described the properties of local and distal eQTLs in terms of genetic diversity, heritability, connectivity, and pleiotropy. These results provide new insights into the genetic basis of transcriptional regulation in the fruit fly and offer a new mapping resource that will expand the possibilities currently available for the Drosophila community.

Animals↗
PubMed1977

Developmental expression and biochemical characterization Nassarius obsoleta.

Electrophoretic analysis of catalase isozyme patterns of Nassarius obsoleta indicates that these isozymes are products of two separate loci. Five aminopeptidase isozymes have also been detected in N. obsoleta and the data suggest that at least two loci encode these aminopetidase isozymes. Experiments designed to test for the interconvertibility of the isozymes indicated that the two catalase isozymes and that two of the five aminopeptidase isozymes tested were not conformational artifacts but distinct genetic products. No change in catalase isozyme expression, but considerable quantitative variation in catalase specific activity was noted during early developmental stages of N. obsoleta. Both qualitative and quantitative changes were noted in aminopeptidase expression during early developmental stages. This paper also describes several physicochemical parameters for each of the two enzymes under study.

Age Factors↗
PubMed2026

Genotypic and phenotypic consequences of domestication in dogs.

Runs of homozygosity (ROH) are genomic regions that arise when identical haplotypes are inherited from a shared ancestor. In this study, we explored ROH across 556 whole-genome sequences from domesticated and non-domesticated dogs. Then, we leveraged ROH from 466 breed dogs, representing 13 breed groups and 13 phenotypic traits, to investigate associations between genetic diversity and non-disease phenotypes. We identified significant associations between the ROH-based inbreeding coefficient (FROH) and multiple phenotypes. These include three quantitative traits (height, weight, lifespan) and ten morphological and coat-related traits. After correcting for population structure, we identified more than 45 genes associated with quantitative traits that exceeded suggestive or genome-wide significance (GWS) thresholds. We also observed distinct patterns of inbreeding across dog populations, including elevated levels of long ROH in modern breed dogs relative to more ancient breeds, consistent with intensive breeding practices during Victorian-era breed formation. Together, our results demonstrate how domestication, demographic bottlenecks, and selective breeding have shaped patterns of homozygosity and contributed to the genetic architecture of complex traits in dogs, highlighting an important role for non-additive genetic variation and polygenicity.

Animals↗
PubMed2026

The genetic control of rapid genome content divergence in Arabidopsis thaliana.

Genome evolution in eukaryotes is predominantly driven by the dynamics of repetitive sequences, which vary widely in both copy number and sequence composition. Rates of repeat evolution differ between and within species and are likely modulated by both genetics and environment. To uncover factors shaping the rate of genome content evolution, we analyzed 1043 resequenced Arabidopsis thaliana genomes using a novel K-mer-based approach to characterize genome content variation and identify hypervariable regions underlying differences in repeat abundance. We next treated repeat abundance as a quantitative trait and performed genome-wide association analyses across more than 400 repeat families to identify the genetic basis of copy number variation. Integrating these results through a meta-GWAS approach revealed both cis-acting variants and more than 50 candidate trans-acting loci associated with repeat abundance genome-wide. Cis-acting variation was predominantly localized to pericentromeric and centromeric regions, whereas trans-acting loci were enriched for candidate genes involved in DNA replication, DNA repair, and DNA methylation regulation. The results are consistent with purifying selection acting against mutations that accelerate genome content divergence, favoring alleles that constrain repeat expansion. Together, these findings provide new insights into the genetic architecture and evolutionary forces shaping genome evolution in A. thaliana and establish a framework for investigating these processes in other plant species.

Arabidopsis↗
PubMed2026

The genetic control of rapid genome content divergence in Arabidopsis thaliana.

Genome evolution in eukaryotes is predominantly driven by the dynamics of repetitive sequences, which vary widely in both copy number and sequence composition. Rates of repeat evolution differ between and within species and are likely modulated by both genetics and environment. To uncover factors shaping the rate of genome content evolution, we analyzed 1,142 resequenced Arabidopsis thaliana genomes using a novel K-mer based approach to characterize genome content variation and identify hypervariable regions underlying differences in repeat abundance. We next treated repeat abundance as a quantitative trait and performed genome-wide association analyses across more than 400 repeat families to identify the genetic basis of copy number variation. Integrating these results through a meta-GWAS approach revealed both cis-acting variants and more than 50 trans-acting loci that regulate repeat abundance genome-wide. Cis-acting variation was predominantly localized to pericentromeric and centromeric regions, whereas trans-acting loci were enriched for candidate genes involved in DNA replication, DNA repair, DNA methylation regulation. Finally, we found evidence that purifying selection acts against mutations that accelerate genome content divergence, favoring alleles that constrain repeat expansion. Together, these findings provide new insights into the genetic architecture and evolutionary forces shaping genome evolution in A. thaliana and establish a framework for investigating these processes in other plant species.

Journal Article↗
PubMed2026

Analysis of deep-resequencing data of 984 soybean accessions reveals structural variations underlying agronomic traits.

Genomic structural variants (SVs) are major sources of genetic variation and have profound impacts on phenotypic traits. However, their functional effects remain largely unexplored in soybean. Here, we resequence 940 soybean accessions. Together with 44 publicly available datasets, we identify 602,281 SVs. Using a graph-based genome, we detect an additional 58,760 presence/absence variations (PAVs) that broadly affect gene expression. Population genomic analyses reveal that SVs serve as a core driving force for soybean domestication and improvement. Integrating SVs with QTLs for oil and protein content, and performing GWAS on 27 traits, we identify key functional SVs. These include transposable element insertions altering seed coat color, multiple insertions within a cytochrome P450 gene modifying flower and hypocotyl color, and a GmMATE1 deletion enhancing seed size. Together, our study establishes a comprehensive SV map of soybean, offering a valuable resource for dissecting the genetic basis of complex traits to accelerate molecular breeding.

Glycine max↗
PubMed1977

Detection of genetic variation with radioactive ligands. II. Genetic variants of vitamin D-labeled group-specific component (Gc) proteins.

A novel technique for detecting electrophoretic and quantitative variants of group-specific component (Gc) proteins is described. The technique, in vitro labeling with radioactive vitamin D followed by polyacrylamide gel electrophoresis and autoradiography (PAGE autoradiography), permits sensitive, high resolution detection of Gc variants by virtue of a physiologically significant property: the ability of Gc to bind vitamin D and 25-hydroxyvitamin D. Using this procedure, anodal Gc variants, with mobility similar to Gc Aborigine and Gc Eskimo, were observed in Chinese, Japanese, African Pygmies, and American Blacks. The gene frequency of these variants ranges from 2.6% to 15%; they were not previously known to be polymorphic in these populations. In addition to qualitative variants, individual variation in Gc band density ratios is documented and discussed. These studies not only illustrate the utility of PAGE autoradiography in screening Gc, but also confirm that a major functional role of Gc in man and other animals is the transport of vitamin D and vitamin D metabolites.

Adult↗
PubMed1975

Studies on the molecular defect in galactosemia.

The galactose metabolic pathway and some of the consequences of deficient galactokinase or gal-1-P uridyltransferase activity have been discussed. The existence of CRM in transferase deficiency galactosemia is presented as evidence that this disease is the result of a structural gene mutation. The finding of both quantitative and qualitative variation in transferase CRM among different galactosemic patients argues that genetic heterogeneity exists within this group. Data supporting a Ping-Pong mechanism of action for human transferase reaction is proposed.

Adenosine Triphosphate↗
PubMed1977

Quantitation of beta 1c/1A globulin (C3) in inbred mice: variation dependent upon strain, age, sex and environment.

The effect of age, sex, genetic backgrounds and environmental factors on mouse C3 level was studied. In general, C3 level increased as a mouse became older. Little difference in C3 level was observed between male and female of all ages. C3 level was found in a great variation from strain to strain, but we could not demonstrate any major role of H-2 in determining serum C3 level. Serum C3 level is not shown to be linked to the serum level of H-2 linked serum protein Ss (C4). On the other hand a close correlation between C3 level and C5 level was demonstrated. Serum C3 markedly increased, along with C5, when mice were injected with turpentine oil, suggesting both components are acute phase reactants. The degree of increase in C3 level in response to turpentine oil injection appeared to be controlled by a single or a very few genes probably not linked to H-2.

Age Factors↗
PubMed1978

Spontaneous murine lupus-like syndromes. Clinical and immunopathological manifestations in several strains.

MRL/1 and BXSB male mice have a systemic lupus erythematosus (SLE)-like disease similar to but more acute than that occurring in NZB X W mice. The common elements of lymphoid hyperplasia, B-cell hyperactivity, autoantibodies, circulating immune complex (IC), complement consumption, IC glomerulonephritis with gp70 deposition, and thymic atrophy were found in all three kinds of SLE mice. On the basis of these common elements, SLE seen in these mice can be considered a single disease in the same sense that human SLE is one disease. The differences in the SLE expressed in the different mice are no greater than those found in an unselected series of humans with SLE. However, the significant quantitative and qualitative variations in abnormal immunologic expression suggest that different constellations of factors, genetic and/or pathophysiologic, may operate in the three murine strains and that each constellation is capable of leading, via its particular abnormal immunologic consequences, to the activation of common immunopathologic effector mechanisms that cause quite similar SLE-like syndromes. From an experimental point of view, the availability of several inbred murine strains of commonplace histocompatibility types that express an SLE-like syndrome makes possible innumerable manipulations which should help to elucidate the nature and cause(s) of this disorder.

Animals↗