Linkage disequilibrium in Brazilian Santa Inês breed, Ovis aries

Abstract

For genomic selection to be successful, there must be sufficient linkage disequilibrium between the markers and the causal mutations. The objectives of this study were to evaluate the extent of LD in ovine using the Santa Inês breed and to infer the minimum number of markers required to reach reasonable prediction accuracy. In total, 38,168 SNPs and 395 samples were used. The mean LD between adjacent marker pairs measured by r² and |D'| were 0.166 and 0.617, respectively. LD values between adjacent marker pairs ranged from 0.135 to 0.194 and from 0.568 to 0.650 for r² for |D'| across all chromosomes. The average r² between all pairwise SNPs on each chromosome was 0.018. SNPs separated by between 0.10 to 0.20 Mb had an estimated average r² equal to 0.1033. The identified haplotype blocks consisted of 2 to 21 markers. Moreover, estimates of average coefficients of inbreeding and effective population size were 0.04 and 96, respectively. LD estimated in this study was lower than that reported in other species and was characterized by short haplotype blocks. Our results suggest that the use of a higher density SNP panel is recommended for the implementation of genomic selection in the Santa Inês breed.

Figure 1

Linkage disequilibrium (LD) measured by r² plotted as a function of intermarker distance (Mb) for chromosomes 1 (OAR1) and 24 (OAR24).

Figure 2

Linkage disequilibrium (LD) measured by |D′| plotted as a function of intermarker distance (Mb) for chromosomes 1 (OAR1) and 24 (OAR24).

Figure 3

Hierarchically clustered heatmap of the genomic relationship among the individuals. At the top left, there is a histogram (green line) of the number of pairs of individuals (y axis = count) at each relationship degree (x axis = value). A vertical dashed green line is on the relationship degree equal to zero. At the bottom right, there is a heatmap of the relationship among the individuals. In both the histogram and the heatmap, the color gradient from dark red to light yellow represents the variation of the relationship degree from low to high, respectively.