Genome-Wide Scan for Evidence of Positive Selection in Hanwoo Cattle

Abstract

The selection of matting pairs, either by natural events or human-oriented, impose genomic changes in the population. When an allele defines a favorable phenotype, it is selected and its frequency increases. Importantly and adding complexity to the topic, due to the linkage disequilibrium (LD) between genetic markers, an allele that is not causal, would also increase in frequency, if it is in high LD to the causal allele. These genomic changes are called signatures of selection and they are traceable comparing populations. Here this concept was applied to detect signatures of positive selection on Hanwoo cattle of Korea comparing this population to other 'Bos taurus' breeds (Angus, Hereford, Murray Grey, Shorthorn, Holstein and Jersey). All animals were genotyped using the BovineHD (Illumina) that includes ~777K single nucleotide polymorphisms (SNP). It was applied quality control filters to SNP, removing bad quality genotypes, and to the samples, removing bad samples and closely related individuals. After that, allele frequencies representing each of the breeds were estimated and genome-wide FST were calculated following the pure drift model in which it is assumed that all breeds included in the analyses came from a common ancestral population. FST values were then smoothed with a local variable bandwidth kernel estimator, the smoothed FST peaks (top 0.1% values), representing the potential positive selection regions, were identified and its genic content further explored for overrepresentation on gene ontology terms. Twelve genomic regions on nine chromosomes were identified as being under positive selection. Six of them were exclusive to the Hanwoo and four were in common to the Holstein. Length of these genomic regions varied between 2.9Mb to only 43.4Kb. The bovine chromosome (BTA) 16 harbor two regions under selection, the BTA21 three regions, but the highest peaks are on BTA19 and BTAX. All together, more than 60 genes were located at those regions. The most frequent function-related terms associated to those genes were to the heart and circulatory systems, lipid metabolism, immune system, circadian cycle and associated to neurological conditions. Moreover, the gene GAA, which is associated to disturbed glycogen storage, was also among the selected genes, but it is not clear whether it is under selection or if it hitchhiked the selection to other close by gene variant. In summary, using genome-wide FST it was possible to detected genomic regions under positive selection in the Hanwoo cattle. Those regions were within nine chromosomes, and contained more than 60 genes, which are involved in a number of biological pathways. Nevertheless, further analyses are needed to confirm the identified regions under selection and to differentiate the genomic changes due to the breed origin and to the human selection.