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

Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

16.6K
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...
16.6K
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

19.2K
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%...
19.2K
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

7.2K
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...
7.2K
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

19.7K
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,...
19.7K

You might also read

Related Articles

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

Sort by
Same author

Guiding eQTL mapping and genomic prediction of gene expression in three pig breeds with tissue-specific epigenetic annotations from early development.

Genomics·2025
Same author

Patient preoperative positioning for THA affects postoperative acetabular cup angle and leg length discrepancy: a prospective case series.

Scientific reports·2025
Same author

Genomic evaluation for juvenile mortality including causal variants in French Holstein and Montbéliarde cattle breeds.

Journal of dairy science·2025
Same author

Erosion of estimated genomic breeding values with generations is due to long distance associations between markers and QTL.

Genetics, selection, evolution : GSE·2025
Same author

Differential Gene Expression Analysis of Whole Blood Transcriptome Between Young and Old Border Collie Dogs.

Veterinary sciences·2025
Same author

Dog Domestication Strongly Relied on Translation Regulation According to Differential Gene Expression Analysis.

Animals : an open access journal from MDPI·2024
Same journal

Invited review: Manufacturing Whey Protein Colloidal Particles via Liquid Antisolvent Precipitation Method: Particle Formation Mechanism and Ingredient Functionality Aspects.

Journal of dairy science·2026
Same journal

Colostrum programs early t lymphocyte-mediated immunity in neonatal dairy calves: effects of deprivation and preservation method on passive transfer and antigen-specific responses.

Journal of dairy science·2026
Same journal

Functional Characterization and Application of Autochthonous Lactic Acid Bacteria from Chinese Kefir for Improved Fermented Milk Quality.

Journal of dairy science·2026
Same journal

Distinct contributions of the Agr and LuxS quorum-sensing systems to stress tolerance, biofilm formation, and persistence of Staphylococcus aureus in dairy-processing environments.

Journal of dairy science·2026
Same journal

Integrating automated body condition scores and lactation data via optimization algorithms for maximized milk revenue and minimized cost of delayed conception in dairy cows.

Journal of dairy science·2026
Same journal

Assessing genotype by feed interactions for milk production traits in dairy cattle.

Journal of dairy science·2026
See all related articles

Related Experiment Video

Updated: Mar 24, 2026

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

10.8K

Alternative haplotype construction methods for genomic evaluation.

Dávid Jónás1, Vincent Ducrocq2, Marie-Noëlle Fouilloux3

  • 1INRA, UMR1313 Génétique animale et biologie intégrative, 78350 Jouy-en-Josas, France; AgroParisTech, 16 rue Claude Bernard, 75231 Paris 05, France; ALLICE, 149 rue de Bercy, 75012 Paris, France.

Journal of Dairy Science
|March 21, 2016
PubMed
Summary
This summary is machine-generated.

Researchers developed a method to select optimal haplotypes for genomic evaluation, improving prediction accuracy in dairy cattle. Combining single nucleotide polymorphisms (SNPs) into haplotypes enhances genomic prediction by increasing linkage disequilibrium with quantitative trait loci (QTL).

Keywords:
dairy cattlegenomic evaluationhaplotypesingle nucleotide polymorphism

More Related Videos

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

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

Published on: December 7, 2021

2.9K
An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
10:17

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

Published on: November 3, 2010

23.4K

Related Experiment Videos

Last Updated: Mar 24, 2026

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

10.8K
Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

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

Published on: December 7, 2021

2.9K
An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
10:17

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

Published on: November 3, 2010

23.4K

Area of Science:

  • Animal Genetics
  • Quantitative Genetics
  • Genomic Prediction

Background:

  • Current genomic evaluation methods primarily use single nucleotide polymorphisms (SNPs) as genomic markers.
  • SNPs can be combined into multiallelic haplotypes to potentially improve genomic prediction accuracy.
  • Haplotypes leverage higher linkage disequilibrium with quantitative trait loci (QTL) compared to individual SNPs.

Purpose of the Study:

  • To develop a method for identifying superior haplotypes for genomic evaluation.
  • To compare the effectiveness of selected haplotypes against individual SNPs and other haplotype combinations.
  • To enhance genomic prediction accuracy in dairy cattle production traits.

Main Methods:

  • Identified quantitative trait loci (QTL)-SNPs with the largest effects on traits from a bovine 50K SNP chip.
  • Selected haplotypes of 3, 4, or 5 SNPs from genomic windows surrounding QTL-SNPs.
  • Developed and tested two methods for selecting optimal haplotypes based on allele frequency assumptions.
  • Validated methods using a dairy cattle population (2,235 bulls) and daughter yield deviations (DYD).

Main Results:

  • Combining SNPs into haplotypes increased the correlation between DYD and genomic breeding values by an average of 2% compared to using individual SNPs.
  • Proposed haplotype selection methods reduced under- and over-represented alleles, decreasing frequencies <1% by 17.4% and >40% by 43.4%.
  • Selected haplotypes improved correlations by 0.7–0.9 percentage points compared to haplotypes constructed from QTL-SNPs and flanking markers.
  • One method was implemented in French dairy cattle genomic evaluation in April 2015.

Conclusions:

  • Haplotype-based genomic evaluation can improve prediction efficiency without additional costs through strategic marker selection.
  • The developed methods effectively identify optimal haplotypes for enhanced genomic prediction in dairy cattle.
  • This approach offers a cost-effective way to boost the accuracy of genomic breeding value estimation.