Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

6.5K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
6.5K
Survival Tree01:19

Survival Tree

183
Survival trees are a non-parametric method used in survival analysis to model the relationship between a set of covariates and the time until an event of interest occurs, often referred to as the "time-to-event" or "survival time." This method is particularly useful when dealing with censored data, where the event has not occurred for some individuals by the end of the study period, or when the exact time of the event is unknown.
 Building a Survival Tree
Constructing a...
183
Phylogenetic Trees03:21

Phylogenetic Trees

48.2K
Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.
48.2K
Applications of Molecular Taxonomy01:20

Applications of Molecular Taxonomy

211
Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...
211
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

4.4K
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
4.4K
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

18.1K
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%...
18.1K

You might also read

Related Articles

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

Sort by
Same author

Discovery and Validation of SVEP1 and Other Novel Cardiovascular Biomarkers For Patients with Kidney Failure On Maintenance Hemodialysis.

medRxiv : the preprint server for health sciences·2026
Same author

Multiomic analysis of ART-interruption cohorts identifies cell-extrinsic and -intrinsic mechanisms driving lymphocyte-mediated control of HIV rebound.

Immunity·2026
Same author

Differential transcriptomic and circadian regulation across giant kelp blades based on relative tissue age.

Journal of phycology·2026
Same author

Risk factors for mortality in patients with kidney failure on hemodialysis identified by proteomic analysis of CRIC and PACE studies.

Nature communications·2025
Same author

Haplotype-Resolved Chromatin Conformation Data Reveals Relationship Between Transposable Elements and Chromosomal Pairing.

Genome biology and evolution·2025
Same author

Comparative Genomics of Sex-Determination-Related Genes Reveals Shared Evolutionary Patterns Between Bivalves and Mammals, but Not Fruit Flies.

Molecular ecology·2025
Same journal

Potential role of the <i>Trpv4 c.1491+1G>A</i> mutation in pulmonary fibrosis in a gene-edited mouse model.

Frontiers in genetics·2026
Same journal

Utilization of whole exome sequencing to identify hereditary mutations in Palestinian families with hereditary cancers.

Frontiers in genetics·2026
Same journal

Research of N-acetyl-L-cysteine on CD40-CD40L pathway in pulmonary fibrosis induced by silicon dioxide.

Frontiers in genetics·2026
Same journal

Novel variants in LSS related hypotrichosis simplex 14.

Frontiers in genetics·2026
Same journal

Network-based analysis identifies shared mechanisms between ischemic stroke and myocardial infarction and therapeutic ingredients of Buyang Huanwu Decoction.

Frontiers in genetics·2026
Same journal

GWAS analysis of a depression cohort defined by an EHR-phenotyping algorithm reveals the role of immune regulations in depression risk.

Frontiers in genetics·2026
See all related articles

Related Experiment Video

Updated: Oct 19, 2025

Comparative Lesions Analysis Through a Targeted Sequencing Approach
08:16

Comparative Lesions Analysis Through a Targeted Sequencing Approach

Published on: November 5, 2019

6.9K

Interspecific Sample Prioritization Can Improve QTL Detection With Tree-Based Predictive Models.

Min-Gyoung Shin1, Sergey V Nuzhdin1

  • 1Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States.

Frontiers in Genetics
|September 23, 2021
PubMed
Summary
This summary is machine-generated.

Combining wild and hybrid crop data improves the discovery of genetic markers for enhanced crop traits. This approach is particularly effective for identifying predictive quantitative trait loci (QTLs) under complex regulatory conditions.

Keywords:
QTLchickpeagradient boostinginterspecificmachine learningrandom forestsample prioritization

More Related Videos

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
10:23

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

Published on: July 11, 2025

318
Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
05:53

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Published on: June 21, 2018

10.3K

Related Experiment Videos

Last Updated: Oct 19, 2025

Comparative Lesions Analysis Through a Targeted Sequencing Approach
08:16

Comparative Lesions Analysis Through a Targeted Sequencing Approach

Published on: November 5, 2019

6.9K
A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
10:23

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

Published on: July 11, 2025

318
Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
05:53

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Published on: June 21, 2018

10.3K

Area of Science:

  • Plant genetics and breeding
  • Agricultural science
  • Bioinformatics

Background:

  • Increasing demand for advanced crop cultivars necessitates improved stress and disease resistance.
  • Wild crop relatives offer valuable genetic resources for trait improvement.
  • Current methods often analyze wild and hybrid materials separately, potentially missing synergistic discoveries.

Purpose of the Study:

  • To investigate the efficiency of combining wild and interspecific hybrid crop data for quantitative trait locus (QTL) discovery.
  • To develop a method for identifying predictive QTLs, especially under complex genetic regulation like trans-regulatory mechanisms.
  • To enhance the detection of genetic signals that might be lost when analyzing datasets independently.

Main Methods:

  • A simulation study was designed to model scenarios with trans-regulatory mechanisms suppressing causal marker expression.
  • A probabilistic sampling approach was employed to prioritize consistent genotypic and phenotypic patterns across combined datasets.
  • Machine learning algorithms, specifically random forest and gradient boosting, were utilized to apply the prioritization scheme.

Main Results:

  • Combining data from wild and interspecific hybrid materials proved more efficient for identifying predictive QTLs compared to separate analyses.
  • The probabilistic sampling and machine learning approach successfully facilitated the investigation of predictive causal markers.
  • This integrated method was particularly beneficial in scenarios involving suppressed gene expression due to trans-regulation, preserving valuable genetic signals.

Conclusions:

  • Integrating data from diverse crop genetic resources (wild and hybrid) offers a powerful strategy for QTL discovery.
  • The developed methodology enhances the identification of key genetic markers for crop improvement, especially under complex regulatory networks.
  • This approach holds significant potential for accelerating the development of advanced crop cultivars with superior stress and disease resistance.