Related Experiment Video
Updated: May 25, 2026
04:52
Following the Dynamics of Structural Variants in Experimentally Evolved Populations
Published on: February 3, 2023
Long-term response to genomic selection: effects of estimation method and reference population structure for
John W M Bastiaansen1, Albart Coster, Mario P L Calus
1Animal Breeding and Genomics Centre, Wageningen University, Wageningen, the Netherlands. john.bastiaansen@wur.nl
Genetics, Selection, Evolution : GSE
|January 26, 2012
Summary
Genomic selection methods show minor long-term response differences. GBLUP (Genomic Best Linear Unbiased Prediction) minimizes inbreeding and genetic variance reduction, outperforming other methods when marker effects aren't updated.
Area of Science:
- Animal and Plant Breeding
- Quantitative Genetics
- Genomics
Background:
- Genomic selection is crucial for genetic improvement in animals and plants.
- Investigating breeding value estimation, reference population structure, and genetic architecture impacts on genomic selection response is essential.
Purpose of the Study:
- To evaluate the long-term response to genomic selection under varying conditions.
- To compare breeding value estimation methods (GBLUP, Bayesian, PLSR) and reference population structures (shallow vs. deep).
Main Methods:
- Genomic breeding values estimated using GBLUP, Bayesian, and PLSR methods.
- Shallow (1 generation) and deep (5 generations) reference populations were utilized.
- Selection simulated for ten generations under four genetic architectures.
Main Results:
- Long-term selection response differences were minimal across methods and architectures.
- GBLUP (deep reference) and PLSR (shallow reference) showed advantages for architectures with 30-300 QTL.
- GBLUP reduced inbreeding and genetic variance more effectively than PLSR and Bayesian methods.
Conclusions:
- GBLUP offers advantages in reducing inbreeding and genetic variance during selection.
- Reference population structure had limited impact on long-term accuracy and response.
- Shallow reference populations provided early benefits, but deep populations did not improve long-term accuracy when marker effects were not updated.
Related Concept Videos
01:25What is Population Genetics?
A population is composed of members of the same species that simultaneously live and interact in the same area. When individuals in a population breed, they pass down their genes to their offspring. Many of these genes are polymorphic, meaning that they occur in multiple variants. Such variations of a gene are referred to as alleles. The collective set of all the alleles within a population is known as the gene pool.
01:12Analysis of Population Pharmacokinetic Data
Analysis of population pharmacokinetic data involves studying the behavior of drugs within diverse populations to understand their pharmacokinetic parameters. Traditional pharmacokinetic methods typically involve collecting samples from a few individuals and estimating these parameters. While these methods are commonly used, they have limitations in capturing the variability in drug response among individuals or heterogeneous populations. Population pharmacokinetics is employed to address these...
01:29Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving
Mechanistic models play a crucial role in algorithms for numerical problem-solving, particularly in nonlinear mixed effects modeling (NMEM). These models aim to minimize specific objective functions by evaluating various parameter estimates, leading to the development of systematic algorithms. In some cases, linearization techniques approximate the model using linear equations.
In individual population analyses, different algorithms are employed, such as Cauchy's method, which uses a...
In individual population analyses, different algorithms are employed, such as Cauchy's method, which uses a...
02:05Gene Evolution - Fast or Slow?
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
In contrast, regions which code...
01:23Mechanistic Models: Compartment Models in Individual and Population Analysis
Mechanistic models are utilized in individual analysis using single-source data, but imperfections arise due to data collection errors, preventing perfect prediction of observed data. The mathematical equation involves known values (Xi), observed concentrations (Ci), measurement errors (εi), model parameters (ϕj), and the related function (ƒi) for i number of values. Different least-squares metrics quantify differences between predicted and observed values. The ordinary least squares (OLS)...
03:33Genetic Drift
Natural selection—probably the most well-known evolutionary mechanism—increases the prevalence of traits that enhance survival and reproduction. However, evolution does not merely propagate favorable traits, nor does it always benefit populations.