Whole Genome Linkage Disequilibrium and Effective Population Size in a Coho Salmon (Oncorhynchus kisutch) Breeding Population Using a High-Density SNP Array

Abstract

The estimation of linkage disequilibrium between molecular markers within a population is critical when establishing the minimum number of markers required for association studies, genomic selection, and inferring historical events influencing different populations. This work aimed to evaluate the extent and decay of linkage disequilibrium in a coho salmon breeding population using a high-density SNP array. Linkage disequilibrium was estimated between a total of 93,502 SNPs found in 64 individuals (33 dams and 31 sires) from the breeding population. The markers encompass all 30 coho salmon chromosomes and comprise 1,684.62 Mb of the genome. The average density of markers per chromosome ranged from 48.31 to 66 per 1 Mb. The minor allele frequency averaged 0.26 (with a range from 0.22 to 0.27). The overall average linkage disequilibrium among SNPs pairs measured as r ² was 0.10. The Average r ² value decreased with increasing physical distance, with values ranging from 0.21 to 0.07 at a distance lower than 1 kb and up to 10 Mb, respectively. An r ² threshold of 0.2 was reached at distance of approximately 40 Kb. Chromosomes Okis05, Okis15 and Okis28 showed high levels of linkage disequilibrium (>0.20 at distances lower than 1 Mb). Average r ² values were lower than 0.15 for all chromosomes at distances greater than 4 Mb. An effective population size of 43 was estimated for the population 10 generations ago, and 325, for 139 generations ago. Based on the effective number of chromosome segments, we suggest that at least 74,000 SNPs would be necessary for an association mapping study and genomic predictions. Therefore, the SNP panel used allowed us to capture high-resolution information in the farmed coho salmon population. Furthermore, based on the contemporary N _e, a new mate allocation strategy is suggested to increase the effective population size.

Keywords: GWAS; Oncorhynchus kisutch; effective population size; linkage disequilibrium; selective breeding.

Figure 1

Decay of average LD (r²) over distance among SNPs in coho salmon (Oncorhynchus kisutch) population. The blue line shows the mean LD in each 100 kb sliding window. Each black dot represents average r² within each bin.

Figure 2

Linkage disequilibrium estimations along the 30 chromosomes of coho salmon. Average values of LD measured as r² per chromosome, according to distances between SNPs. Estimated values are shown from Okis01 to Okis015 (A) and from Okis16 to Okis30 (B).

Figure 3

Effective population size estimation in coho salmon population. Estimates of effective population size (N_e) over the past 241 generations based on the LD of an aquaculture strain of coho salmon. Black dots represent each N_e measurement.