Abstract
Recent advances in molecular genetic techniques will make dense marker maps available and genotyping many individuals for these markers feasible. Here we attempted to estimate the effects of approximately 50,000 marker haplotypes simultaneously from a limited number of phenotypic records. A genome of 1000 cM was simulated with a marker spacing of 1 cM. The markers surrounding every 1-cM region were combined into marker haplotypes. Due to finite population size N(e) = 100, the marker haplotypes were in linkage disequilibrium with the QTL located between the markers. Using least squares, all haplotype effects could not be estimated simultaneously. When only the biggest effects were included, they were overestimated and the accuracy of predicting genetic values of the offspring of the recorded animals was only 0.32. Best linear unbiased prediction of haplotype effects assumed equal variances associated to each 1-cM chromosomal segment, which yielded an accuracy of 0.73, although this assumption was far from true. Bayesian methods that assumed a prior distribution of the variance associated with each chromosome segment increased this accuracy to 0.85, even when the prior was not correct. It was concluded that selection on genetic values predicted from markers could substantially increase the rate of genetic gain in animals and plants, especially if combined with reproductive techniques to shorten the generation interval.
Full Text
The Full Text of this article is available as a PDF (259.1 KB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Aparicio S. A. How to count ... human genes. Nat Genet. 2000 Jun;25(2):129–130. doi: 10.1038/75949. [DOI] [PubMed] [Google Scholar]
- Farnir F., Coppieters W., Arranz J. J., Berzi P., Cambisano N., Grisart B., Karim L., Marcq F., Moreau L., Mni M. Extensive genome-wide linkage disequilibrium in cattle. Genome Res. 2000 Feb;10(2):220–227. doi: 10.1101/gr.10.2.220. [DOI] [PubMed] [Google Scholar]
- Georges M., Nielsen D., Mackinnon M., Mishra A., Okimoto R., Pasquino A. T., Sargeant L. S., Sorensen A., Steele M. R., Zhao X. Mapping quantitative trait loci controlling milk production in dairy cattle by exploiting progeny testing. Genetics. 1995 Feb;139(2):907–920. doi: 10.1093/genetics/139.2.907. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Haley C. S., Visscher P. M. Strategies to utilize marker-quantitative trait loci associations. J Dairy Sci. 1998 Sep;81 (Suppl 2):85–97. doi: 10.3168/jds.s0022-0302(98)70157-2. [DOI] [PubMed] [Google Scholar]
- Halushka M. K., Fan J. B., Bentley K., Hsie L., Shen N., Weder A., Cooper R., Lipshutz R., Chakravarti A. Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis. Nat Genet. 1999 Jul;22(3):239–247. doi: 10.1038/10297. [DOI] [PubMed] [Google Scholar]
- Hästbacka J., de la Chapelle A., Kaitila I., Sistonen P., Weaver A., Lander E. Linkage disequilibrium mapping in isolated founder populations: diastrophic dysplasia in Finland. Nat Genet. 1992 Nov;2(3):204–211. doi: 10.1038/ng1192-204. [DOI] [PubMed] [Google Scholar]
- Lande R., Thompson R. Efficiency of marker-assisted selection in the improvement of quantitative traits. Genetics. 1990 Mar;124(3):743–756. doi: 10.1093/genetics/124.3.743. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Prior J., White I. Tetany and clubbing in patient who ingested large quantities of senna. Lancet. 1978 Oct 28;2(8096):947–947. doi: 10.1016/s0140-6736(78)91669-0. [DOI] [PubMed] [Google Scholar]
- Sved J. A. Linkage disequilibrium and homozygosity of chromosome segments in finite populations. Theor Popul Biol. 1971 Jun;2(2):125–141. doi: 10.1016/0040-5809(71)90011-6. [DOI] [PubMed] [Google Scholar]