Linkage disequilibrium in Brazilian Santa Inês breed, Ovis aries

Authors

Amanda Botelho Alvarenga, University of Sao Paulo, Brazil
Gregori Alberto Rovadoscki, University of Sao Paulo, Brazil
Juliana Petrini, University of Sao Paulo, Brazil
Luiz Lehmann Coutinho, University of Sao Paulo, Brazil
Gota Morota, University of Nebraska- LincolnFollow
Matthew L. Spangler, University of Nebraska - LincolnFollow
Luis Fernando Batista Pinto, UFBA
Gleidson Giordano Pinto Carvalho, UFBA
G. B. Mourao, University of Sao Paulo, BrazilFollow

ORCID IDs

0000-0002-7266-8881

0000-0002-3567-6911

Date of this Version

2018

Citation

SCIENTIFIC REPORTS | (2018) 8:8851

Comments

© The Author(s) 2018

Open access

DOI:10.1038/s41598-018-27259-7

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.