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.

Linkage disequilibrium and association studies in higher plants: Present status and future prospects

“…In another study conducted in radiata pine, 200 full sib families were used to study the marker-trait associations. In this study, the parental genotypes were also considered during analyses (Kumar et al, 2004), so that the method can be compared with TDT in humans.…”

Association of single nucleotide polymorphisms with form traits in three New Zealand populations of radiata pine in the presence of genotype by environment interactions

“…DNA markers can be applied to achieve earlier selection and more cost-effective selection or to increase selection intensity in forest breeding programmes (Wilcox et al 2007). Simple sequence repeat (SSR) markers were found to be associated with branch cluster frequency and stem straightness in radiata pine (Kumar et al 2004). Association studies for branch cluster frequency and stem straightness have been reported in other species as well (Arcade et al 1996;Cumbie 2010;Lepoittevin et al 2012;Xiong 2010).…”

Research Article Analysis of Mendelian inheritance and genetic linkage in microsatellite loci of Eucalyptus urophylla S.T. Blake.

“…In both orchards, significance was found between loci EMBRA681xEMBRA2 and EMBRA204xEMBRA210. The imbalance may be affected by selection, recombination, migration, population reduction, genetic drift, and population structure (Kumar et al, 2004). Tarazi et al (2010) found genotypic disequilibrium between pairwise loci in open-pollinated seeds of Copaifera langsdorffii, probably due to the inheritance of maternal alleles.…”