Abstract
Linkage analysis is commonly used 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 LD. Observed genotypic frequencies 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.
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Acknowledgements
We thank the New Zealand Radiata Pine Breeding Company for giving access to phenotypic data. We thank Dr. Christophe Plomion and Dr. Rowland Burdon for helpful discussion during the completion of this project. We also thank anonymous referees for very helpful and constructive comments. The experiments comply with the current laws of New Zealand where the experiments were performed. SSR markers with prefixes RIPPT and UCC are exclusive property of International Paper Company. We thank them for the use of these markers for this study.
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Kumar, S., Echt, C., Wilcox, P.L. et al. Testing for linkage disequilibrium in the New Zealand radiata pine breeding population. Theor Appl Genet 108, 292–298 (2004). https://doi.org/10.1007/s00122-003-1352-7
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DOI: https://doi.org/10.1007/s00122-003-1352-7