The Journal "Agriculture and Forestry"
Časopis "Poljoprivreda i šumarstvo"
- Since 1955 -
Year 2020, Volume 66 Issue 1 (31.03.2020)
| Year : | 2020 |
| Volume : | 66 |
| Issue : | 1 (31.03.2020) |
| Authors : | Barbora OLŠANSKÁ, Radovan KASARDA, Anna TRAKOVICKÁ, Ondrej KADLEČÍK, Nina MORAVČÍKOVÁ |
| Title : | IDENTIFICATION OF SELECTION SIGNALS THROUGH HAPLOTYPE STRUCTURE IN GENOME OF DUAL-PURPOSE BREEDS |
| Abstract : | The aim of this study was to analyse the selection signals by the integrated haplotype homozygosity score (iHS) in dual-purpose Slovak Spotted cattle in order to clarify the effects of natural or artificial selection. Overall, 85 animals genotyped by a high-density SNP array were included in the analysis. After quality control, 35995 autosomal loci with an average adjacent SNP spacing of 69.3 kb were included in the analysis. Then, haplotypes were reconstructed for each chromosome. Next, the R package rehh was used to compute the score based on a matrix of integrated extended haplotype homozygosity statistics for both ancestral and derived alleles. The average iHS score across the genome was 0.83. The selection signals in the genome had positive iHS values. A common iHS score (higher than 2.5) was chosen to indicate genomic regions with extreme iHS frequency due to outliers (according to the boxplot distribution). In each region with selection signals, quantitative trait loci (QTLs) were identified. For BTA s 3, 6, 8 and 21, signals were identified in regions of milk production. Marbling scores, QTLs and signals within BTA 12 were placed around QTLs for calving ease. Based on the results, we can conclude that the identified regions in the genome that are affected by positive selection correspond to the breeding goals for Slovak Spotted cattle. |
| For citation : | Olšanská, B., Kasarda, R., Trakovická, A., Kadlečík, O., Moravčíková, N. (2020): Identification of selection signals through haplotype structure in genome of dual-purpose breeds. Agriculture and Forestry, 66 (1): 33-39 |
| Keywords : | artificial selection, cattle, genomic region, homozygosity, iHS score. |
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