Genome-wide detection of signatures of selection in Korean Hanwoo cattle.
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.
School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia; School of Veterinary Science, The University of Queensland, Gatton, QLD, 4345, Australia.
L R
LR
Porto-Neto
S H
SH
Lee
T S
TS
Sonstegard
C P
CP
Van Tassell
H K
HK
Lee
J P
JP
Gibson
C
C
Gondro
D000818:Animals; D050218:Body Fat Distribution / Q000662:veterinary*; D002417:Cattle / Q000235:genetics*; D014644:Genetic Variation; D016678:Genome; D005838:Genotype; D006239:Haplotypes; D012641:Selection, Genetic; D014998:Y Chromosome
SNP; bos indicus; bos taurus; selection; speciation