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Title: Testing for linkage disequilibrium in the New Zealand radiata pine breeding population

Author: Kumar, S.; Echt, Craig; Wilcox, P.L.; Richardson, T.E.;

Date: 2004

Source: Theor. Appl. Genet. 108: 292-298

Publication Series: Miscellaneous Publication

Description: Linkage analysis is commonly uscd to find marker-trait associations within the full-sib families of forest tree and other species. Study of marker-trait associations at the population level is termed linkage-disequilibrium (LD) mapping. A female-tester design comprising 200 full-sib families generated by crossing 40 pollen parents with five female parents was used to assess the relationship between the marker-allele frequency classes obtained from parental genotypes at SSR marker loci and the full-sib family performance (average predicted breeding value of two parents) in radiata pine (Pinus radiata D. Don). For alleles (at a marker locus) that showed significant association, the copy number of that allele in the parents was significantly correlated, either positively or negatively, with the full-sib family performance for various economic traits. Regression of parental breeding value on its genotype at marker loci revealed that most of the markers that showed significant association with full-sib family performance were not significantly associated with the parental breeding values. This suggests that over-representation of the female parents in our sample of 200 full-sib families could have biased the process of detecting marker-trait associations. The evidence for the existence of marker-trait LD in the population studied is rather weak and would require further testing. The exact test for genotypic disequilibrium between pairs of linked or unlinked marker loci revealed non-significant L.D. Observed genotypic frequeneies at several marker loci were significantly different from the expected Hardy-Weinberg equilibrium. The possibilities of utilising marker-trait associations for early selection, among-family selection and selecting parents for the next generation of breeding are also discussed.

Keywords: Linkage disequilibrium, SSR marker, breeding value, marker-assisted selection, Pinus radiata

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Kumar, S.; Echt, Craig; Wilcox, P.L.; Richardson, T.E. 2004. Testing for linkage disequilibrium in the New Zealand radiata pine breeding population. Theor. Appl. Genet. 108: 292-298


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