Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Comparing Copy Number Variations and SNPs

Comparing Copy Number Variations and SNPs

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%...

Genome-wide Association Studies-GWAS

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...

Prediction Intervals

Prediction Intervals

The interval estimate of any variable is known as the prediction interval. It helps decide if a point estimate is dependable.
However, the point estimate is most likely not the exact value of the population parameter, but close to it. After calculating point estimates, we construct interval estimates, called confidence intervals or prediction intervals. This prediction interval comprises a range of values unlike the point estimate and is a better predictor of the observed sample value, y.

End Point Prediction: Gran Plot

End Point Prediction: Gran Plot

A Gran plot is used to predict the equivalence volume or endpoint of a potentiometric or acid-base titration without reaching the endpoint. Typically, titration data is collected as a function of the titrant's volume up to a point less than the equivalence volume and then transformed into a linear format. The straight line is extended to the x-axis, indicating the necessary titrant volume to achieve the equivalence point.
For potentiometric titration, the Gran plot is created by plotting...

Genetic Variation

Genetic Variation

Genetic variation is the diversity in DNA sequences found among individuals of the same species. This diversity is crucial for a species' survival because it helps organisms adapt to environmental changes. Genetic variation begins with fertilization, where an egg and sperm cell merge. Each of these cells carries 23 chromosomes, up to 46 in the fertilized egg. Chromosomes are long DNA strands that contain genes, the basic units of heredity.
Genes exist in different versions called alleles,...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Limited Plasticity of Stomatal Development in Apple Trees Across Diverse European Climates.

Physiologia plantarum·2026

Same author

Integrative multi-environmental genomic prediction in apple.

Horticulture research·2025

Same author

Human longevity and Alzheimer's disease variants act via microglia and oligodendrocyte gene networks.

Brain : a journal of neurology·2025

Same author

Circulating blood circular RNA in Parkinson's Disease; from involvement in pathology to diagnostic tools in at-risk individuals.

NPJ Parkinson's disease·2024

Same author

Plasma acellular transcriptome contains Parkinson's disease signatures that can inform clinical diagnosis.

medRxiv : the preprint server for health sciences·2024

Same author

A phased genome of the highly heterozygous 'Texas' almond uncovers patterns of allele-specific expression linked to heterozygous structural variants.

Horticulture research·2024

Search research articles

Related Experiment Video

Updated: Jul 5, 2025

Author Spotlight: Advancing Alzheimer's Research – Exploring Early Detection and Multi-Omics Approaches

Author Spotlight: Advancing Alzheimer's Research – Exploring Early Detection and Multi-Omics Approaches

Published on: December 15, 2023

GenoDrawing: An Autoencoder Framework for Image Prediction from SNP Markers.

Federico Jurado-Ruiz¹, David Rousseau², Juan A Botía³

¹Center for Research in Agricultural Genomics (CRAG), 08193 Barcelona, Cerdanyola, Spain.

Plant Phenomics (Washington, D.C.)

|January 19, 2024

Summary

This summary is machine-generated.

GenoDrawing, a new autoencoder framework, predicts apple images from genomic data. This tool aids in understanding plant traits and benefits fruit tree breeding by analyzing single-nucleotide polymorphisms (SNPs).

More Related Videos

Author Spotlight: Impact of Intergenic Interactions on Disease-Identifying Dark Biomarkers

Author Spotlight: Impact of Intergenic Interactions on Disease-Identifying Dark Biomarkers

Published on: March 1, 2024

Pattern-based Search of Epigenomic Data Using GeNemo

Pattern-based Search of Epigenomic Data Using GeNemo

Published on: October 8, 2017

Related Experiment Videos

Last Updated: Jul 5, 2025

Author Spotlight: Advancing Alzheimer's Research – Exploring Early Detection and Multi-Omics Approaches

Author Spotlight: Advancing Alzheimer's Research – Exploring Early Detection and Multi-Omics Approaches

Published on: December 15, 2023

Author Spotlight: Impact of Intergenic Interactions on Disease-Identifying Dark Biomarkers

Author Spotlight: Impact of Intergenic Interactions on Disease-Identifying Dark Biomarkers

Published on: March 1, 2024

Pattern-based Search of Epigenomic Data Using GeNemo

Pattern-based Search of Epigenomic Data Using GeNemo

Published on: October 8, 2017

Area of Science:

Plant genomics and bioinformatics
Machine learning applications in agriculture
High-throughput phenotyping

Background:

Genome sequencing provides vast genotypic data for plant analysis.
Genomic selection and neural networks (NNs) predict complex traits.
Autoencoders are effective NN models for unsupervised feature extraction in plant phenotyping.

Purpose of the Study:

Introduce GenoDrawing, an autoencoder framework for predicting and retrieving apple images from single-nucleotide polymorphism (SNP) data.
Assess the utility of GenoDrawing for predicting traits that are difficult to define.
Explore the impact of SNP selection on image prediction accuracy.

Main Methods:

Developed a novel autoencoder framework named GenoDrawing.
Utilized a low-depth SNP array for apple image prediction.
Trained and evaluated the model on a dataset of shape-related SNPs.

Main Results:

GenoDrawing successfully predicted apple images from SNP data, demonstrating proficiency with a small dataset.
SNPs associated with visual traits significantly impacted generated image quality, aligning with biological expectations.
Performance degraded when unrelated SNPs were included in simpler NN architectures.

Conclusions:

GenoDrawing offers a practical framework for genomic prediction in fruit tree phenotyping, especially for smaller breeding companies.
The study highlights the importance of selecting relevant SNPs for accurate image prediction.
Further research should focus on advanced models and balanced datasets for improved outcomes in genomic-based image prediction.