Selecting sequence variants to improve genomic predictions for dairy cattle
Paul M VanRaden1, Melvin E Tooker2, Jeffrey R O'Connell3
1Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, USA. Paul.VanRaden@ars.usda.gov.
Genetics, Selection, Evolution : GSE
|March 9, 2017
Summary
Selecting specific genetic variants from sequencing data significantly improves genomic prediction accuracy in cattle. This study demonstrates that strategic selection of high-impact variants enhances reliability more than using all available sequence data.
Area of Science:
- Animal Genetics
- Genomic Prediction
- Bioinformatics
Background:
- Population-scale sequencing projects have identified millions of genetic variants.
- Subsets of these variants are crucial for routine genomic predictions and genotyping arrays.
- Effective methods for selecting sequence variants are needed.
Purpose of the Study:
- To compare methods for selecting sequence variants for genomic predictions.
- To evaluate the impact of sequence variants on prediction reliability in Holstein cattle.
- To assess computational strategies for efficiently handling large-scale genomic data.
Main Methods:
- Compared two tests using simulated and real data from the 1000 Bull Genomes Project.
- Combined candidate sequence variants with high-density (HD) imputed genotypes.
- Assessed imputation quality and tested predictions for 33 traits in validation bulls.
Main Results:
- Average imputation accuracy was over 97% for both tests.
- Adding sequence single nucleotide polymorphisms (SNPs) and insertions-deletions (InDels) to HD SNPs yielded modest reliability gains (0.4-0.6%).
- Selecting the top 16,648 candidate SNPs with the largest estimated effects improved reliability by 2.7 percentage points.
Conclusions:
- Selected sequence variants improve genomic prediction reliabilities, with gains larger than those from adding HD SNPs.
- Efficient computing strategies are necessary to balance costs and maximize accuracy when using millions of variants.
- Strategic selection of high-impact variants is key for enhancing genomic predictions in large populations.
More Related Videos
08:04Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons
Published on: June 6, 2025
1.7K
05:53Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
Published on: June 21, 2018
10.8K
Related Concept Videos
02:26Comparing Copy Number Variations and SNPs
18.9K
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%...
18.9K
02:51Multi-species Conserved Sequences
4.9K
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...
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
4.9K
01:29Pharmacogenomics: Identification of New Drug Targets
55
Advances in genomics have profoundly influenced drug discovery by increasing both the speed and accuracy of pharmaceutical development. Pharmacogenomics, which examines how genetic variation influences drug response, facilitates the identification of novel therapeutic targets and enables patient stratification for personalized treatment. These strategies contribute to improved drug efficacy, minimized adverse effects, and more efficient clinical trial design.Mapping genetic differences...
55
01:25Genetic Variation
1.5K
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,...
Genes exist in different versions called alleles,...
1.5K
01:27Principles of Pharmacogenetics: Types of Genetic Variants
65
The human genome is over 99.9% identical between individuals, yet genetic differences exist at millions of bases. The human genome contains approximately 3 million variant positions per individual, many of which are heterozygous, contributing to genetic diversity and individual traits. Genetic variations include single-nucleotide polymorphisms (SNPs), insertions, deletions, and copy number variations (CNVs).SNPs, the most common variation, involve single-base changes in DNA. These can be...
65
01:05Single Nucleotide Polymorphisms-SNPs
19.1K
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,...
19.1K