Related Experiment Video
Updated: Jul 13, 2026
09:09
Protocol for Assessing the Relative Effects of Environment and Genetics on Antler and Body Growth for a Long-lived Cervid
Published on: August 8, 2017
Genotype by environment interaction for production traits while accounting for heteroscedasticity
A G Fahey1, M M Schutz, D L Lofgren
1Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA. agfahey@purdue.edu
Journal of Dairy Science
|July 20, 2007
Summary
Heteroscedasticity in dairy herd data can bias genetic evaluations. This study found that addressing this data issue had minimal impact on genetic parameter estimates and genotype-by-environment interaction in grazing versus confinement systems.
Area of Science:
- Animal Genetics
- Dairy Science
- Quantitative Genetics
Background:
- Grazing (G) offers an alternative dairy production system to confinement (C).
- Heteroscedasticity (HV), or unequal variances, in yield data can bias genetic correlation estimates, potentially masking genotype-by-environment interactions (GxE).
- Accurate genetic evaluation requires understanding how HV affects heritabilities and genetic correlations between management systems.
Purpose of the Study:
- To investigate the impact of HV on heritability and genetic correlation estimates for milk, protein, and fat yield, and somatic cell scores.
- To determine if HV influences the accuracy of sire's predicted transmitting ability (PTA) in predicting daughter performance in G and C herds.
- To assess the presence of GxE between G and C systems under varying levels of HV.
Main Methods:
- Utilized large datasets from 366 G herds and 373 C herds, comprising 72,489 and 117,629 records, respectively.
- Divided herds into variance quartiles (Q(V)1-Q(V)4) based on milk yield.
- Applied a transformation to reduce HV by standardizing within-herd standard deviations, similar to USDA-DHIA methods.
- Analyzed daughter yield regressions on sire PTA and estimated heritabilities and genetic correlations between G and C systems.
Main Results:
- PTA overestimated daughter production in most variance quartiles for both G and C herds, with varying degrees by trait.
- Reducing HV had minimal effect on G herds but improved PTA accuracy in lower variance quartiles of C herds.
- Heritabilities for milk, protein, and fat yields were similar across G and C herds (approx. 0.16-0.21).
- Genetic correlations between C and G systems did not indicate significant GxE, except for a possible interaction in the lowest variance quartile.
Conclusions:
- Heteroscedasticity in dairy production data has a limited impact on heritability and genetic correlation estimates between grazing and confinement systems.
- The evidence for genotype-by-environment interaction between these systems is modest and does not appear to stem solely from heteroscedasticity.
- While PTA accuracy can be affected by HV, particularly in confinement herds, the overall genetic architecture of yield traits is consistent across management systems.
Related Concept Videos
02:27Background and Environment Affect Phenotype
Although the genetic makeup of an organism plays a major role in determining the phenotype, there are also several environmental factors, such as temperature, oxygen availability, presence of mutagens, that can alter an organism’s phenotype.
An example of how genetic background affects phenotype can be seen in horses. The Extension gene in horses is responsible for their coat color. A wild-type gene (EE) produces black pigment in the coat, while a mutant gene (ee) produces red pigment. A...
An example of how genetic background affects phenotype can be seen in horses. The Extension gene in horses is responsible for their coat color. A wild-type gene (EE) produces black pigment in the coat, while a mutant gene (ee) produces red pigment. A...
01:20Gene-Environment Interactions
Gene expression is a dynamic process that is significantly influenced by environmental factors. This interaction underlies the complex nature of biological development and the phenotypic differences observed among individuals, even among those with identical genetic makeups. Factors such as radiation, temperature, behavior, nutrition, and stress play pivotal roles in determining how genes are expressed. The concept of the reaction range is central to understanding this interaction. It posits...
01:06Heritability
Heritability is a statistical concept that measures the degree to which genetic differences among individuals contribute to trait variations within a population. It is a fundamental idea in genetics, often prone to misinterpretation. Heritability is expressed as a percentage, reflecting the proportion of variation in a specific trait across a population that can be linked to genetic differences. However, it's important to understand that heritability does not determine how "genetic" a trait is,...
01:09Epistasis Analysis
Although Mendel chose seven unrelated traits in peas to study gene segregation, most traits involve multiple gene interactions that create a spectrum of phenotypes. When the interaction of various genes or alleles at different locations influences a phenotype, this is called epistasis. Epistasis often involves one gene masking or interfering with the expression of another (antagonistic epistasis). Epistasis often occurs when different genes are part of the same biochemical pathway. The...
01:49Multiple Allele Traits
The Concept of Multiple Allelism
01:49Multiple Allele Traits
The Concept of Multiple Allelism