Estimations of linkage disequilibrium, effective population size and
ROH-based inbreeding coefficients in Spanish Churra sheep using
imputed high-density SNP genotypes
P. K. Chitneedi, J. J. Arranz , A. Suarez-Vega, E. Garc ıa-G amez and B. Guti errez-Gil
Departamento de Producci on Animal, Facultad de Veterinaria, Universidad de Le on, Campus de Vegazana s/n, Le on 24071, Spain.
Summary In this study, the availability of the Ovine HD SNP BeadChip (HD-chip) and the
development of an imputation strategy provided an opportunity to further investigate the
extent of linkage disequilibrium (LD) at short distances in the genome of the Spanish
Churra dairy sheep breed. A population of 1686 animals, including 16 rams and their
half-sib daughters, previously genotyped for the 50K-chip, was imputed to the HD-chip
density based on a reference population of 335 individuals. After assessing the
imputation accuracy for BEAGLE v4.0 (0.922) and FIMPUTE v2.2 (0.921) using a cross-
validation approach, the imputed HD-chip genotypes obtained with BEAGLE were used to
update the estimates of LD and effective population size for the studied population. The
imputed genotypes were also used to assess the degree of homozygosity by calculating
runs of homozygosity and to obtain genomic-based inbreeding coefficients. The updated
LD estimations provided evidence that the extent of LD in Churra sheep is even shorter
than that reported based on the 50K-chip and is one of the shortest extents compared
with other sheep breeds. Through different comparisons we have also assessed the
impact of imputation on LD and effective population size estimates. The inbreeding
coefficient, considering the total length of the run of homozygosity, showed an average
estimate (0.0404) lower than the critical level. Overall, the improved accuracy of
the updated LD estimates suggests that the HD-chip, combined with an imputation
strategy, offers a powerful tool that will increase the opportunities to identify genuine
marker-phenotype associations and to successfully implement genomic selection in
Churra sheep.
Keywords HD-chip, imputation, LD extent, runs of homozygosity, SNPs
Introduction
The accuracy and power of both genome-wide association
studies (GWAS) and genomic selection are dependent on the
extent of linkage disequilibrium (LD) and the density of the
markers used to exploit it. The extent of LD varies between
populations because it is influenced by their evolutionary
history and effective population size (N
e
) (Slatkin 2008). In
sheep, the Sheep HapMap project, based on analysis of the
Ovine SNP50 BeadChip (50K-chip) across a collection of 74
ovine breeds from all over the world (Kijas et al. 2014),
showed that LD in sheep extended over much shorter
distances than in cattle and was much shorter than in
Holstein cattle (Raadsma 2010). Among the sheep breeds
analysed, Spanish Churra (n = 120) was reported to show
one of the most remarkable decays of LD with the distance
between markers and the lowest (0.8%) genome coverage of
haplotype blocks, compared with other breeds with inter-
mediate coverage (Milk Lacaune, 0.9%; Rambouillet, 1%;
Australian Suffolk, 1.03%; Australian Pool Dorset, 2.94%)
and the very high haplotype block coverage shown by Soay
sheep (21.84%) (Raadsma 2010). This short extent of LD in
Churra sheep appears to be linked to the high level of
diversity shown by Churra compared with other breeds
from southern and Mediterranean Europe (Kijas et al.
2012).
A detailed assessment of the LD extension in Churra
sheep and estimations of effective population (N
e
) and
inbreeding levels based on analysis of the 50K-chip in a
Address for correspondence
B. Guti errez-Gil, Departamento de Producci on Animal, Facultad de
Veterinaria, Universidad de Le on, Campus de Vegazana s/n, Le on
24071, Spain.
E-mail: beatriz.gutierrez@unileon.es
Accepted for publication 14 March 2017
doi: 10.1111/age.12564
1 © 2017 Stichting International Foundation for Animal Genetics