Abstract
We provide a theoretical framework for quantitative trait locus (QTL) analysis of a crossed population where parental lines may be outbred and dominance as well as inbreeding are allowed for. It can be applied to any pedigree. A biallelic QTL is assumed, and the QTL allele frequencies can be different in each breed. The genetic covariance between any two individuals is expressed as a nonlinear function of the probability of up to 15 possible identity modes and of the additive and dominance effects, together with the allelic frequencies in each of the two parental breeds. The probabilities of each identity mode are obtained at the desired genome positions using a Monte Carlo Markov chain method. Unbiased estimates of the actual genetic parameters are recovered in a simulated F(2) cross and in a six-generation complex pedigree under a variety of genetic models (allele fixed or segregating in the parental populations and additive or dominance action). Results from analyzing an F(2) cross between Meishan and Large White pigs are also presented.
Full Text
The Full Text of this article is available as a PDF (132.5 KB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- HARRIS D. L. GENOTYPIC COVARIANCES BETWEEN INBRED RELATIVES. Genetics. 1964 Dec;50:1319–1348. doi: 10.1093/genetics/50.6.1319. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Haley C. S., Knott S. A., Elsen J. M. Mapping quantitative trait loci in crosses between outbred lines using least squares. Genetics. 1994 Mar;136(3):1195–1207. doi: 10.1093/genetics/136.3.1195. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Marklund L., Nyström P. E., Stern S., Andersson-Eklund L., Andersson L. Confirmed quantitative trait loci for fatness and growth on pig chromosome 4. Heredity (Edinb) 1999 Feb;82(Pt 2):134–141. doi: 10.1038/sj.hdy.6884630. [DOI] [PubMed] [Google Scholar]
- Pérez-Enciso M., Clop A., Noguera J. L., Ovilo C., Coll A., Folch J. M., Babot D., Estany J., Oliver M. A., Díaz I. A QTL on pig chromosome 4 affects fatty acid metabolism: evidence from an Iberian by Landrace intercross. J Anim Sci. 2000 Oct;78(10):2525–2531. doi: 10.2527/2000.78102525x. [DOI] [PubMed] [Google Scholar]
- Pérez-Enciso M., Varona L. Quantitative trait loci mapping in F(2) crosses between outbred lines. Genetics. 2000 May;155(1):391–405. doi: 10.1093/genetics/155.1.391. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Pérez-Enciso M., Varona L., Rothschild M. F. Computation of identity by descent probabilities conditional on DNA markers via a Monte Carlo Markov Chain method. Genet Sel Evol. 2000 Sep-Oct;32(5):467–482. doi: 10.1186/1297-9686-32-5-467. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Walling G. A., Visscher P. M., Andersson L., Rothschild M. F., Wang L., Moser G., Groenen M. A., Bidanel J. P., Cepica S., Archibald A. L. Combined analyses of data from quantitative trait loci mapping studies. Chromosome 4 effects on porcine growth and fatness. Genetics. 2000 Jul;155(3):1369–1378. doi: 10.1093/genetics/155.3.1369. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wang T., Fernando R. L., Grossman M. Genetic evaluation by best linear unbiased prediction using marker and trait information in a multibreed population. Genetics. 1998 Jan;148(1):507–515. doi: 10.1093/genetics/148.1.507. [DOI] [PMC free article] [PubMed] [Google Scholar]