Estimating genetic diversity across the neutral genome with the use of dense marker maps.
BACKGROUND
With the advent of high throughput DNA typing, dense marker maps have become available to investigate genetic diversity on specific regions of the genome. The aim of this paper was to compare two marker based estimates of the genetic diversity in specific genomic regions lying in between markers: IBD-based genetic diversity and heterozygosity.


METHODS
A computer simulated population was set up with individuals containing a single 1-Morgan chromosome and 1665 SNP markers and from this one, an additional population was produced with a lower marker density i.e. 166 SNP markers. For each marker interval based on adjacent markers, the genetic diversity was estimated either by IBD probabilities or heterozygosity. Estimates were compared to each other and to the true genetic diversity. The latter was calculated for a marker in the middle of each marker interval that was not used to estimate genetic diversity.


RESULTS
The simulated population had an average minor allele frequency of 0.28 and an LD (r(2)) of 0.26, comparable to those of real livestock populations. Genetic diversities estimated by IBD probabilities and by heterozygosity were positively correlated, and correlations with the true genetic diversity were quite similar for the simulated population with a high marker density, both for specific regions (r = 0.19-0.20) and large regions (r = 0.61-0.64) over the genome. For the population with a lower marker density, the correlation with the true genetic diversity turned out to be higher for the IBD-based genetic diversity.


CONCLUSIONS
Genetic diversities of ungenotyped regions of the genome (i.e. between markers) estimated by IBD-based methods and heterozygosity give similar results for the simulated population with a high marker density. However, for a population with a lower marker density, the IBD-based method gives a better prediction, since variation and recombination between markers are missed with heterozygosity.
Engelsma
Krista A
KA
Wageningen UR Livestock Research, Animal Breeding and Genomics Centre, PO Box 65, 8200 AB Lelystad, The Netherlands. krista.engelsma@wur.nl
Calus
Mario P L
MP
Bijma
Piter
P
Windig
Jack J
JJ
D000818:Animals; D015415:Biomarkers; D002417:Cattle / Q000235:genetics*; D005787:Gene Frequency; D014644:Genetic Variation; D016678:Genome; D006579:Heterozygote; D020641:Polymorphism, Single Nucleotide; D011336:Probability
D015415:Biomarkers
Genetics. 2008 Jan;178(1):553-61
18202394
Philos Trans R Soc Lond B Biol Sci. 2005 Jul 29;360(1459):1367-78
16048780
Genet Sel Evol. 2001 Nov-Dec;33(6):605-34
11742632
BMC Genomics. 2008 Apr 24;9:187
18435834
Genetics. 2007 Dec;177(4):2389-97
18073436
Genetics. 2001 Apr;157(4):1819-29
11290733
Evolution. 2001 Jun;55(6):1095-103
11475045
J Anim Sci. 1997 Apr;75(4):934-40
9110204
Genetics. 2008 Jul;179(3):1503-12
18622038
Theor Appl Genet. 1968 Jun;38(6):226-31
24442307
Nat Rev Genet. 2002 Jan;3(1):22-32
11823788
Genetics. 2004 Mar;166(3):1561-70
15082569