Title: Genome-wide detection of signatures of selection in Korean Hanwoo cattle Authors
|Porto-Neto, Laercio -|
|Lee, Seung-Hwan -|
|Van Tassell, Curtis|
|Lee, Hak -|
|Gondro, Cedric -|
Submitted to: Animal Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: November 15, 2013
Publication Date: February 14, 2014
Citation: Porto-Neto, L., Lee, S., Sonstegard, T.S., Van Tassell, C.P., Lee, H., Gondro, C. 2014. Genome-wide detection of signatures of selection in Korean Hanwoo cattle. Animal Genetics. 45(2):180-190. Interpretive Summary: The origins of indigenous cattle breeds from Korea and Japan have been hypothesized to be the result of separate domestication events in Eastern Asia. This study, which uses about 700,000 single nucleotide polymorphism (SNP) genetic markers, provides a high-resolution characterization of Hanwoo cattle (an indigenous breed of Korea) to test this hypothesis. The results demonstrate that Hanwoo cattle are influenced by historic crossbreeding with European-derived breeds with some very minor influence from the sub-species of cattle called zebu. Other unique genome characteristics were also explored by looking for selection signatures created either by drift, human selection for specific traits, or migration. This analysis was of interest because Hanwoo cattle are known to be selected for high intramuscular fat content, or marbling. Our signature analysis revealed genomic regions that influence fat metabolism which are unique to Hanwoo. This information will be useful for understanding the genetic pathways underlying high carcass marbling. This information can be used to enhance breeding for meat quality traits in other breeds of cattle.
Technical 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, the Europeans (represented by six breeds), Zebu (Nelore), African taurine (N’Dama), and Hanwoo. All animals had genotypes for around 700,000 SNP after quality control of genotypes. Average heterozygosity was lower in Nelore and N’Dama (0.22 and 0.21) than in Europeans (0.24-0.31) 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 corroborates to principal component and unsupervised hierarchical clustering analyses. 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 them were shared with one or two of the other groups. These regions overlap a number of genes that are related to immune system, reproduction and fatty acid metabolism pathways. Surprisingly, Hanwoo shared the most signatures of selection with Nelore, which is the furthest apart group in the pairwise FST; this could be partially explained by selection for some zebu characteristics in a mainly taurine background or potentially introgressed genomic fragments of zebu ancestry in the Hanwoo.