Effective Population Size and Signatures of Selection Using Bovine 50K SNP Chips in Korean Native Cattle (Hanwoo)

Abstract

Inferring the effective population size and the pattern of selection signatures is of interest both from an evolutionary perspective and to improve models for mapping of quantitative trait genes. We used DNA samples of 61 sires and 486 progeny of the Hanwoo, genotyped by the Illumina Bovine SNP50 BeadChip, to analyze the genetic structure. Our study showed a persistent decline in effective population size throughout the period considered, but suggested a marked decline at one distinctive time point (100th generation) and two sharp decline intervals (50th-25th generation and 25th-10th generation). This pattern can be explained by Hanwoo formation and the modern breeding program. Our results revealed 95 regions exhibiting the footprint of recent positive selection at a threshold level of 0.01. We found an overlap of the 11 core regions presenting top P-values and those that had previously been identified as harboring quantitative trait loci from other breeds. The information generated from this study can be used to better understand the mechanism of selection in Hanwoo breeding, and provide important implications for the design and application of association studies in the Hanwoo population.

Keywords: cattle; effective population size; linkage disequilibrium; selection signature.

Figure 1

Minor allele frequency of SNPs.

Figure 2

(A) Distribution of the length of core regions. (B) The number of SNPs forming the core regions in the Hanwoo genome.

Figure 3

Chromosome-wise average r²-value and the decay of linkage disequilibrium with increasing physical distance for five smallest bins evaluated.

Figure 4

Estimated effective population size over the past generations from linkage disequilibrium data. The variability at each point time reflects the variation of estimates between the 29 autosomes.

Figure 5

Genome-wide map of −log₁₀(REHH P-values) for core haplotypes with frequency >0.1. Dashed lines display the threshold level of 0.01.