Estimation of Effective Population Size in the Sapsaree: A Korean Native Dog (Canis familiaris)

Abstract

Effective population size (Ne) is an important measure to understand population structure and genetic variability in animal species. The objective of this study was to estimate Ne in Sapsaree dogs using the information of rate of inbreeding and genomic data that were obtained from pedigree and the Illumina CanineSNP20 (20K) and CanineHD (170K) beadchips, respectively. Three SNP panels, i.e. Sap134 (20K), Sap60 (170K), and Sap183 (the combined panel from the 20K and 170K), were used to genotype 134, 60, and 183 animal samples, respectively. The Ne estimates based on inbreeding rate ranged from 16 to 51 about five to 13 generations ago. With the use of SNP genotypes, two methods were applied for Ne estimation, i.e. pair-wise r (2) values using a simple expectation of distance and r (2) values under a non-linear regression with respective distances assuming a finite population size. The average pair-wise Ne estimates across generations using the pairs of SNPs that were located within 5 Mb in the Sap134, Sap60, and Sap183 panels, were 1,486, 1,025 and 1,293, respectively. Under the non-linear regression method, the average Ne estimates were 1,601, 528, and 1,129 for the respective panels. Also, the point estimates of past Ne at 5, 20, and 50 generations ago ranged between 64 to 75, 245 to 286, and 573 to 646, respectively, indicating a significant Ne reduction in the last several generations. These results suggest a strong necessity for minimizing inbreeding through the application of genomic selection or other breeding strategies to increase Ne, so as to maintain genetic variation and to avoid future bottlenecks in the Sapsaree population.

Keywords: Effective Population Size; Inbreeding Rate; Linkage Disequilibrium; SNP; Sapsaree Dog.

Figure 1

Average inbreeding coefficients (F_IT, F_ST, F_IS) of the Sapsaree population along birth year.

Figure 2

Average linkage disequilibrium (LD) over all autosomal chromosomes within 5 Mb distances between the pairs of SNPs for Sapsaree dogs. The upper and lower 3 lines correspond to D′ and r² measures for the three samples (Sap134, Sap60 and Sap183), in which the SNP panels of 20K, 170K, and the combined SNP set of 20K and 170K were used using 134, 60, and 183 individuals, respectively.

Figure 3

Correlations between the non-linear N_e estimates from the Sap134, Sap60 and Sap183 panels for the pairs of SNPs that were distanced within 5Mb.

Figure 4

Estimates of effective population size (N_e) for Sapsaree at t ancestral generations ago based on the squared correlation coefficient (r²) between SNPs. Three SNP panels (Sap134, Sap60 and Sap183) were used, in which 20K, 170K, and the combined set of 20K and 170K SNPs were genotyped with 134, 60, and 183 individuals, respectively.