Related Experiment Video
Updated: Jun 12, 2025
11:54
Microsatellite DNA Genotyping and Flow Cytometry Ploidy Analyses of Formalin-fixed Paraffin-embedded Hydatidiform Molar Tissues
Published on: October 20, 2019
9.1K
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
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.
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.
Related Concept Videos
02:27Trihybrid Crosses
23.2K
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).
The F1 generation plants of a trihybrid cross are heterozygous for all three traits and produce eight gametes. Upon self-fertilization, these gametes have an equal...
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).
The F1 generation plants of a trihybrid cross are heterozygous for all three traits and produce eight gametes. Upon self-fertilization, these gametes have an equal...
23.2K
01:05Single Nucleotide Polymorphisms-SNPs
14.8K
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,...
14.8K
02:26Comparing Copy Number Variations and SNPs
17.6K
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.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
17.6K