Genome‐wide detection of signatures of selection in Korean Hanwoo cattle

Abstract

The Korean Hanwoo cattle have been intensively selected for production traits, especially high intramuscular fat content. It is believed that ancient crossings between different breeds contributed to forming the Hanwoo, but little is known about the genomic differences and similarities between other cattle breeds and the Hanwoo. In this work, cattle breeds were grouped by origin into four types and used for comparisons: the Europeans (represented by six breeds), zebu (Nelore), African taurine (N'Dama) and Hanwoo. All animals had genotypes for around 680 000 SNPs after quality control of genotypes. Average heterozygosity was lower in Nelore and N'Dama (0.22 and 0.21 respectively) than in Europeans (0.26-0.31, with Shorthorn as outlier at 0.24) and Hanwoo (0.29). Pairwise FST analyses demonstrated that Hanwoo are more related to European cattle than to Nelore, with N'Dama in an intermediate position. This finding was corroborated by principal components and unsupervised hierarchical clustering. Using genome-wide smoothed FST , 55 genomic regions potentially under positive selection in Hanwoo were identified. Among these, 29 were regions also detected in previous studies. Twenty-four regions were exclusive to Hanwoo, and a number of other regions were shared with one or two of the other groups. These regions overlap a number of genes that are related to immune, reproduction and fatty acid metabolism pathways. Further analyses are needed to better characterize the ancestry of the Hanwoo cattle and to define the genes responsible to the identified selection peaks.

Genome-wide linkage disequilibrium and past effective population size in three Korean cattle breeds

“…() and Porto‐Neto et al . () also performed similar studies, in which similar primary results were observed.…”

“…() and Li & Kim () identified significant associations on chromosomes 21 and 26 with growth‐related traits in Brown Hanwoo and Porto‐Neto et al . () identified significant associations on chromosome 21 with immune system traits, we suggest that those associations would also affect Brindle and Jeju Black cattle. Moreover, Lee et al .…”

Whole genome detection of signature of positive selection in African cattle reveals selection for thermotolerance

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Genetic diversity and signatures of selection in various goat breeds revealed by genome-wide SNP markers

“…However, most of the regions identified in this study were quite long and therefore included many genes. The threshold used in this study to determine significant regions (mean plus two or three SD) via smoothed F ST has been previously recommended by Porto-Neto et al [78]. The high number of genes identified in our study makes it difficult to comment on possible candidate genes.…”