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Related Concept Videos

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Epistasis Analysis

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Although Mendel chose seven unrelated traits in peas to study gene segregation, most traits involve multiple gene interactions that create a spectrum of phenotypes. When the interaction of various genes or alleles at different locations influences a phenotype, this is called epistasis. Epistasis often involves one gene masking or interfering with the expression of another (antagonistic epistasis). Epistasis often occurs when different genes are part of the same biochemical pathway. The...
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In addition to multiple alleles at the same locus influencing traits, numerous genes or alleles at different locations may interact and influence phenotypes in a phenomenon called epistasis. For example, rabbit fur can be black or brown depending on whether the animal is homozygous dominant or heterozygous at a TYRP1 locus. However, if the rabbit is also homozygous recessive at a locus on the tyrosinase gene (TYR), it will have an unshaded coat that appears white, regardless of its TYRP1...
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Pleiotropy is the phenomenon in which a single gene impacts multiple, seemingly unrelated phenotypic traits. For example, defects in the SOX10 gene cause Waardenburg Syndrome Type 4, or WS4, which can cause defects in pigmentation, hearing impairments, and an absence of intestinal contractions necessary for elimination. This diversity of phenotypes results from the expression pattern of SOX10 in early embryonic and fetal development. SOX10 is found in neural crest cells that form melanocytes,...
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When more than one gene is responsible for a given phenotype, the trait is considered polygenic. Human height is a polygenic trait. Studies have uncovered hundreds of loci that influence height, and there are believed to be many more. Due to the high number of genes involved, as well as environmental and nutritional factors, height varies significantly within a given population. The distribution of height forms a bell-shaped curve, with relatively few individuals in the population at the...
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Some of Mendel’s crosses examined three pairs of contrasting characteristics. Such a cross is called a trihybrid cross. A trihybrid cross is a combination of three individual monohybrid crosses. For example, plant height (tall vs. short), seed shape (round vs. wrinkled), and seed color (yellow vs. green).
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Updated: Dec 3, 2025

Large-Scale Multi-Omics Genome-Wide Association Studies Mo-GWAS: Guidelines for Sample Preparation and Normalization
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simplePHENOTYPES: SIMulation of pleiotropic, linked and epistatic phenotypes.

Samuel B Fernandes1, Alexander E Lipka2

  • 1Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, 61801, USA.

BMC Bioinformatics
|November 1, 2020
PubMed
Summary

The simplePHENOTYPES R package simulates pleiotropy for multiple traits, aiding genomic analysis. This tool facilitates the validation of multivariate statistical approaches for genetic studies.

Keywords:
Computer simulationCorrelated traitsMultivariate dataQuantitative genetics

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Area of Science:

  • Genetics
  • Bioinformatics
  • Quantitative Genetics

Background:

  • Advances in genotyping and phenotyping generate large datasets.
  • Multivariate statistical analyses are crucial for identifying pleiotropy.
  • Optimal tools are needed to assess the performance of these analyses.

Purpose of the Study:

  • To develop an R/CRAN package for simulating pleiotropy.
  • To facilitate testing and validation of multivariate statistical approaches.
  • To support the assessment of genetic architectures including additive, dominance, and epistatic models.

Main Methods:

  • Development of the simplePHENOTYPES R/CRAN package.
  • Simulation of pleiotropy, partial pleiotropy, and spurious pleiotropy.
  • Integration with common marker data formats and quantitative genetics software.

Main Results:

  • simplePHENOTYPES can simulate thousands of phenotypes rapidly.
  • Vignettes demonstrate simulating correlated traits.
  • Demonstrated compatibility with standard GWAS software and equivalence with other packages.

Conclusions:

  • simplePHENOTYPES simulates multiple traits with varying pleiotropy.
  • Facilitates rigorous assessment of GWAS and genomic selection (GS) approaches.
  • Available on GitHub for broader accessibility.