4.5 Article

Estimations of linkage disequilibrium, effective population size and ROH-based inbreeding coefficients in Spanish Churra sheep using imputed high-density SNP genotypes

Journal

ANIMAL GENETICS
Volume 48, Issue 4, Pages 436-446

Publisher

WILEY
DOI: 10.1111/age.12564

Keywords

HD-chip; imputation; LD extent; runs of homozygosity; SNPs

Funding

  1. Junta de Castilla y Leon Government
  2. European Social Fund
  3. Spanish Ramon y Cajal Programme from Spanish Ministry of Economy and Competitiveness (MINECO) [RYC-2012-10230]
  4. MINECO [AGL2015-66035-R]
  5. European Regional Development Fund

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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.

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