Required properties for markers used to calculate unbiased estimates of the genetic correlation between populations.

Publisher: BioMed Central Country of Publication: France NLM ID: 9114088 Publication Model: Electronic Cited Medium: Internet ISSN: 1297-9686 (Electronic) Linking ISSN: 0999193X NLM ISO Abbreviation: Genet Sel Evol Subsets: MEDLINE

Publication: London : BioMed Central
Original Publication: Paris : Elsevier, c1989-

Genetic Markers/*genetics ; Genetics, Population/*methods ; Linkage Disequilibrium/*genetics; Alleles ; Bias ; Biomarkers ; Computer Simulation ; Gene Frequency/genetics ; Genetics, Population/statistics & numerical data ; Genotype ; Polymorphism, Single Nucleotide/genetics

Background: Generally, populations differ in terms of environmental and genetic factors, which can create differences in allele substitution effects between populations. Therefore, a single genotype may have different additive genetic values in different populations. The correlation between the two additive genetic values of a single genotype in two populations is known as the additive genetic correlation between populations and thus, can differ from 1. Our objective was to investigate whether differences in linkage disequilibrium (LD) and allele frequencies of markers and causal loci between populations affect the bias of the estimated genetic correlation. We simulated two populations that were separated by 50 generations and differed in LD pattern between markers and causal loci, as measured by the LD-statistic r. We used a high marker density to represent a high consistency of LD between populations, and lower marker densities to represent situations with a lower consistency of LD between populations. Markers and causal loci were selected to have either similar or different allele frequencies in the two populations.
Results: Our results show that genetic correlations were underestimated only slightly when the difference in allele frequencies between the two populations was similar for the markers and the causal loci. A lower marker density, representing a lower consistency of LD between populations, had only a minor effect on the underestimation of the genetic correlation. When the difference in allele frequencies between the two populations was not similar for markers and causal loci, genetic correlations were severely underestimated. This bias occurred because the markers did not predict accurately the relationships at causal loci.
Conclusions: For an unbiased estimation of the genetic correlation between populations, the markers should accurately predict the relationships at the causal loci. To achieve this, it is essential that the difference in allele frequencies between populations is similar for markers and causal loci. Our results show that differences in LD phase between causal loci and markers across populations have little effect on the estimated genetic correlation.

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Project Number: 14291 NWO-TTW and the Breed4Food partners Cobb Europe, CRV, Hendrix Genetics and Topigs Norsvin

0 (Biomarkers)
0 (Genetic Markers)

Date Created: 20181215 Date Completed: 20190304 Latest Revision: 20231005

20231215

PMC6295113

10.1186/s12711-018-0434-6

30547748