Linkage disequilibrium and effective population size in Brazilian Saanen goats

Abstract

• To know linkage disequilibrium and effective population size permit to determine optimal marker density for genomic studies • The mean value of r 2 for this Saanen goat population in Brazil, between adjacent markers (∼52 kb), was 0.04 ± 0.06. • Results indicate the need to use a denser marker panel (∼ 300k) and to expand the size of the reference population. The knowledge about linkage disequilibrium (LD) and effective population size (N e ) is essential to determine the optimal marker density required for performing genomic studies. In this study, the aim was to estimate the LD and N e of a Saanen goat population using a panel of 62,557 single nucleotide polymorphisms (SNPs), Axiom_OviCap (Caprine), customized by Affimetrix. Twenty-four males and 916 females were genotyped from herds from the Dairy Goats Breeding Program (from Portuguese Programa de Melhoramento Genético de Caprinos Leiteiros - Capragene®). The decay of the LD was analysed using quadratic correlation coefficient (r 2 ) for all pairs of markers on each chromosome. To estimate N e the values of r 2 combined with the distance between the markers was used, based on the physical map used for the LD analysis. The mean value of r 2 between adjacent markers (∼52 kb) was 0.04 ± 0.06. Among chromosomes, the range of values varied from 0.03 ± 0.06 to 0.05 ± 0.08. The LD fell rapidly from the first to the second distance range. In later intervals, the average of r 2 decreased more gradually. Moderate levels of r 2 (> 0.20), on a scale of 0–1, were observed only in the genetic distance classes up to 20 kb. The estimate of N e decreased over time, ranging from 42 animals, 19 past generations, to 15 animals in the current generation. The observed results have practical applications for performing genomic studies, and indicate the need to use a denser marker panel (∼ 300k), since the LD level was relatively small even at short distances, and it is essential to expand the size of the reference population.