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

Modern Molecular Taxonomy

Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...

Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

You might also read

Related Articles

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

Sort by

Same author

Cell-based crop phenotyping for future climates.

The New phytologist·2026

Same author

Multi-indicator water-quality prediction in mining areas using a feature-tokenizer transformer with spatiotemporal features.

Environmental research·2026

Same author

Machine learning to predict genotypes and genotype-environment interaction associated with complex traits for genomic selection.

Plant phenomics (Washington, D.C.)·2026

Same author

Wild Barley Exhibits Higher Phosphorus-Use Efficiency and Greater Rhizosheath Carboxylates Than Cultivated Barley Under Low-Phosphorus Conditions.

Physiologia plantarum·2026

Same author

HICnet: A two-stage framework based on region partitioning for predicting HIC values from car point clouds.

Accident; analysis and prevention·2026

Same author

Nonlinear biogeographic responses and threshold patterns in vegetative versus reproductive traits across China's ecosystems.

Journal of environmental management·2026

Search research articles

Related Experiment Video

Updated: Dec 20, 2025

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Identifying barley pan-genome sequence anchors using genetic mapping and machine learning.

Shang Gao^1,2, Jinran Wu³, Jiri Stiller¹

¹Agriculture and Food, CSIRO, St Lucia, QLD, 4067, Australia.

TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik

|May 26, 2020

Summary

This summary is machine-generated.

Researchers identified 1.844 million barley pan-genome sequence anchors from over 12,000 genotypes using genetic mapping and machine learning. This advances comprehensive pan-genome construction for barley genetic research and breeding.

More Related Videos

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens

Published on: June 28, 2018

Related Experiment Videos

Last Updated: Dec 20, 2025

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens

Published on: June 28, 2018

Area of Science:

Genomics
Plant Science
Bioinformatics

Background:

Crop pan-genomes are crucial for genetic research and breeding, as single genotypes do not encompass all species' genes.
Developing large-scale pan-genomes for complex, repetitive genomes like barley using deep sequencing is currently impractical.

Purpose of the Study:

To identify barley pan-genome sequence anchors from large genotype-by-sequencing (GBS) datasets.
To combine genetic mapping and machine learning for efficient pan-genome construction in barley.

Main Methods:

Utilized genotype-by-sequencing (GBS) data from 11,166 domesticated and 1140 wild barley genotypes.
Employed genetic mapping and machine learning algorithms to identify pan-genome sequence anchors.
Validated identified presence/absence variation (PAV) tags against the hulless barley reference genome.

Main Results:

Identified 1.844 million barley pan-genome sequence anchors.
Discovered 532,253 presence/absence variation (PAV) tags, with 83.6% validation in domesticated and 88.6% in wild barley.
Association analyses indicated varying importance of PAV and non-PAV tags for traits like flowering time, plant height, and kernel size.

Conclusions:

Barley pan-genome sequence anchors derived from GBS data facilitate comprehensive pan-genome construction.
These anchors significantly aid genetic studies, including structural variation identification, genetic mapping, and breeding in barley.
The approach offers a practical method for building large-scale pan-genomes in species with complex genomes.