Inbreeding and effective population size in French dairy sheep: Comparison between genomic and pedigree estimates

Before availability of dense SNP data, genetic diversity was characterized and managed with pedigree-based information. Besides this classical approach, 2 methodologies have been proposed in recent years to characterize and manage diversity from dense SNP data: the SNP-by-SNP approach and the alternative based on runs of homozygosity (ROH). The establishment of criteria to identify ROH is a current constraint in the literature dealing with ROH. The objective of this study was, using a medium-density SNP chip, to quantify by 3 methods (pedigree, SNP-by-SNP, and ROH) the genetic diversity on 5 selected French dairy sheep subpopulations and breeds and to assess the effect of the definition of ROH on these estimates. The data set available included individuals from the breeds Basco-Béarnaise, Manech Tête Noire, Manech Tête Rousse, and 2 subpopulations of Lacaune: Lacaune Confederation and Lacaune Ovitest. Animals were genotyped with the Illumina OvineSNP50 BeadChip (Illumina Inc., San Diego, CA). After filtering, the genomic data included 38,287 autosomal SNP and 8,700 individuals, which comprised 72,803 animals in the pedigree. The results indicated that no significant differences were observed in effective population size estimates obtained from pedigree or genomic (SNP-by-SNP or ROH) information. In general, estimates of effective population size were above 200 in Lacaune Confederation and Lacaune Ovitest subpopulations and below 200 in Basco-Béarnaise, Manech Tête Noire, and Manech Tête Rousse breeds. The minimum length that constituted a ROH, the minimum number of SNP that constituted a ROH, as well as the minimum density and the maximum distance allowed between 2 homozygous SNP are ROH-defining factors with important implications in the estimation of the rate of inbreeding. The ROH-based rates of inbreeding in concordance with those obtained from pedigree information require a specific set of values. This particular set of values is different from that identified to obtain ROH-based rates of inbreeding similar to those obtained on a SNP-by-SNP basis. Factors to define ROH do not change the results much unless extreme values are considered, although further research on ROH-based inbreeding is still required.