title: Testing for linkage disequilibrium in the New Zealand radiata pine breeding population.
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.
authors.affiliation: N Z Forest Research Institute, Private bag 3020, Rotorua, New Zealand. Satish.Kumar@forestresearch.co.nz
authors.forename: S
authors.initials: S
authors.lastname: Kumar
authors.forename: C
authors.initials: C
authors.lastname: Echt
authors.forename: P L
authors.initials: PL
authors.lastname: Wilcox
authors.forename: T E
authors.initials: TE
authors.lastname: Richardson
mesh_terms: D001947:Breeding; D002874:Chromosome Mapping / Q000379:methods*; D018744:DNA, Plant / Q000235:genetics; D005787:Gene Frequency; D008040:Genetic Linkage / Q000235:genetics*; D005819:Genetic Markers; D015810:Linkage Disequilibrium; D016555:Matched-Pair Analysis; D009520:New Zealand; D028223:Pinus / Q000235:genetics*; D040641:Quantitative Trait Loci
chemical_list: D018744:DNA, Plant; D005819:Genetic Markers