Genetic diversity of a New Zealand multi-breed sheep population and composite breeds' history revealed by a high-density SNP chip

Abstract

Background: Knowledge about the genetic diversity of a population is a crucial parameter for the implementation of successful genomic selection and conservation of genetic resources. The aim of this research was to establish the scientific basis for the implementation of genomic selection in a composite Terminal sheep breeding scheme by providing consolidated linkage disequilibrium (LD) measures across SNP markers, estimating consistency of gametic phase between breed-groups, and assessing genetic diversity measures, such as effective population size (N_e), and population structure parameters, using a large number of animals (n = 14,845) genotyped with a high density SNP chip (606,006 markers). Information generated in this research will be useful for optimizing molecular breeding values predictions and managing the available genetic resources.

Results: Overall, as expected, levels of pairwise LD decreased with increasing distance between SNP pairs. The mean LD r² between adjacent SNP was 0.26 ± 0.10. The most recent effective population size for all animals (687) and separately per breed-groups: Primera (974), Lamb Supreme (380), Texel (227) and Dual-Purpose (125) was quite variable. The genotyped animals were outbred or had an average low level of inbreeding. Consistency of gametic phase was higher than 0.94 for all breed pairs at the average distance between SNP on the chip (~4.74 kb). Moreover, there was not a clear separation between the breed-groups based on principal component analysis, suggesting that a mixed-breed training population for calculation of molecular breeding values would be beneficial.

Conclusions: This study reports, for the first time, estimates of linkage disequilibrium, genetic diversity and population structure parameters from a genome-wide perspective in New Zealand Terminal Sire composite sheep breeds. The levels of linkage disequilibrium indicate that genomic selection could be implemented with the high density SNP panel. The moderate to high consistency of gametic phase between breed-groups and overlapping population structure support the pooling of the animals in a mixed training population for genomic predictions. In addition, the moderate to high N_e highlights the need to genotype and phenotype a large training population in order to capture most of the haplotype diversity and increase accuracies of genomic predictions. The results reported herein are a first step toward understanding the genomic architecture of a Terminal Sire composite sheep population and for the optimal implementation of genomic selection and genome-wide association studies in this sheep population.

Keywords: Consistency of gametic phase; Crossbreeding; Effective population size; Linkage disequilibrium; Population structure; Sheep.

Fig. 1

Marker density over the genome represented by the number of SNP (blue bars) and length of chromosome spanned (yellow bars)

Fig. 2

Minor allele frequency distributions for the whole genome after quality control

Fig. 3

Distribution of SNPs by MAF ranges and breed group

Fig. 4

Average linkage disequilibrium (r²) at given distances for all animals included in this study

Fig. 5

a Ancestral and recent effective population size in different time points in the past (Number of generations ago). b Ancestral and recent effective population size in different time points in the past (until 50 generations ago)

Fig. 6

Consistency of gametic phase (Pearson correlations of signed r-values) at given distances for six selected breed-group pairs. PR: Primera, LS: Lamb Supreme, TX: Texel and DP: Maternal/Dual-Purpose

Fig. 7

Principal component decomposition of the genomic relationship matrix colored by breed-group

Fig. 8

Genomic (F_VR) and pedigree inbreeding coefficients for all the genotyped animals