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Related Concept Videos

Trihybrid Crosses02:27

Trihybrid Crosses

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Trihybrid Crosses
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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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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Updated: Jun 12, 2025

Microsatellite DNA Genotyping and Flow Cytometry Ploidy Analyses of Formalin-fixed Paraffin-embedded Hydatidiform Molar Tissues
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GenoTriplo: A SNP genotype calling method for triploids.

Julien Roche1,2, Mathieu Besson2, François Allal3

  • 1Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France.

Plos Computational Biology
|September 24, 2024
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Summary

A new R package, GenoTriplo, offers an efficient method for genotyping triploids using SNP arrays. This robust tool improves accuracy and reduces errors, aiding genetic research and breeding in aquaculture and plants.

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Area of Science:

  • Genetics and Genomics
  • Aquaculture and Plant Breeding
  • Bioinformatics and Computational Biology

Background:

  • Triploidy is valuable in aquaculture and cultivated plants for enhanced growth, product quality, and preventing wild population contamination.
  • Accurate genetic information from triploids is crucial for academic research and breeding programs.
  • Existing methods for triploid SNP genotyping are limited, necessitating a more robust and efficient solution.

Purpose of the Study:

  • To develop an efficient and robust method for genotype calling from SNP arrays specifically for triploid organisms.
  • To implement this method into an accessible R package named GenoTriplo.
  • To evaluate the performance of GenoTriplo against existing methods for triploid SNP genotyping.

Main Methods:

  • Developed a novel genotype calling method for SNP arrays that does not require prior cluster position information and is resilient to luminescence signal shifts.
  • Implemented the method in the R package GenoTriplo, utilizing an initial overestimation of genotype groups followed by merging.
  • Compared GenoTriplo's performance with fitPoly using a dataset of 1232 triploid rainbow trout and 38,033 SNPs, assessing genotype concordance and error rates.

Main Results:

  • GenoTriplo demonstrated high robustness and fewer genotyping errors compared to fitPoly.
  • The methods showed 89% genotype consistency, but GenoTriplo identified discrepancies in genotype numbers for 26% of SNPs where it performed better.
  • GenoTriplo achieved >95% concordance with fitPoly when fitPoly was accurate, but fitPoly showed <50% concordance when GenoTriplo outperformed it, indicating GenoTriplo's superior accuracy.
  • GenoTriplo effectively identified low-frequency genotypes and showed high confidence in parentage assignment results.

Conclusions:

  • GenoTriplo provides a more accurate and robust solution for triploid SNP genotyping than existing methods.
  • The R package is versatile and can be adapted for genotyping diploids and higher ploidy individuals by adjusting parameters.
  • GenoTriplo facilitates reliable genetic analysis, supporting advancements in triploid breeding and research.