Testing for linkage disequiiibrium in the New Zealand radiata pine breeding population

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 linkagcdiscquilibriurn (LD) mapping. A female-tester design comprising 200 full-sib families generated by crossing 40 pollen parcnts with five female parents was uscd to assess the relationship between the marker-allele frequency classes obtained from parental genotypes at SSR marker loci and thc full-sib family performance (average predicted breeding value of two parents) in radiata pine (Pinirs mdiclru D. Don). For alleles (at a marker locus) that showcd significant association, the copy numbcr of that allele in the parents was significantly correlated. either positively or negatively, with the full-sib family pcrformance for various economic traits. Regression of parcntal hrccding value on its genotype at markcr loci revealed that most of the markers that showcd significant ;t\xociation with fl111-sib family performance were not \ignificantly associatcd with the parental breeding values. pThis suggests that over-representation of the fernale parcnts in our sample of 200 full-sib families could have hiascd the process of detecting marker-trait associations. , . I he 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 discquilibriurn hctwccn pairs of linked or unlinked rnarkcr loci I-cvcalcti non-significant 'L.D. Observed genotypic freqt~cncics at scvcral m:~rkcr loci were significantly diffcrcnt t'roni the cvpectcci H~~rtiy-Weinberg cquilibrium. The po\\il?ilitics of i~tilihing marker-trait associations for early \cIcction. :rrnong-family sclcction and selecting parcnts 1.01rlic ncut gcncration of hrccding arc also discussed. S. Kun1;ir ( :e l ) . C. Echr . P. I . Wilcox . 'I.. E. Richardson N % Forc\t R C ~ C ; I I . C ~ I I I \ ~ I I L I ~ C , Pr~v;ite hag 1020. Rotorua. New %calantl. cnail: S;tt~\h. Ku~n; l rW t'orc\trc\carch.co.~tz I'cl.: +64-7343-5XOO Fax: +0.1 7343--5330