Izvorni znanstveni članak
https://doi.org/10.5513/JCEA01/17.2.1704
Extent of genome-wide linkage disequilibrium in Pinzgau cattle
Veronika Šidlová
orcid.org/0000-0002-4099-341X
; Slovak University of Agriculture in Nitra, Department of Animal Genetics and Breeding Biology, Tr. A. Hlinku 2, 949 76 Nitra, Slovak Republic
Radovan KASARDA
orcid.org/0000-0002-2723-3192
; Slovak University of Agriculture in Nitra, Department of Animal Genetics and Breeding Biology, Tr. A. Hlinku 2, 949 76 Nitra, Slovak Republic
Nina MORAVČÍKOVÁ
orcid.org/0000-0003-1898-8718
; Slovak University of Agriculture in Nitra, Department of Animal Genetics and Breeding Biology, Tr. A. Hlinku 2, 949 76 Nitra, Slovak Republic
Anna TRAKOVICKÁ
; Slovak University of Agriculture in Nitra, Department of Animal Genetics and Breeding Biology, Tr. A. Hlinku 2, 949 76 Nitra, Slovak Republic
Ino CURIK
; University of Zagreb, Department of Animal Sciences, Svetošimunska 25, 10 000 Zagreb, Croatia
Maja FERENČAKOVIĆ
; University of Zagreb, Department of Animal Sciences, Svetošimunska 25, 10 000 Zagreb, Croatia
Sažetak
The aim of this study was to describe the extent of linkage disequilibrium (LD) based on genotyping data in Pinzgau cattle population. DNA samples were obtained from 19 bulls of active Pinzgau cattle population in Slovakia. Genotyping was carried out in commercial lab using an Illumina BovineSNP50 BeadChip. The genotyping array contained 54,609 single nucleotide polymorphisms (SNPs). After quality control SNPs localized on sex chromosomes were excluded. A total of 42,248 (79.97%) SNPs were found to be polymorphic. The distribution of SNPs over entire genomes of all chromosomes was not uniform. The minor allele frequencies across autosomal loci ranged from 0.266 (BTA4) to 0.280 (BTA23) with average value 0.273±0.133. Only adjacent SNPs with distance less than 5 Mb and LD (r2) values from 0.01 to 0.99 were used in the characterization of LD extent. After filtering, the genome coordinates of 31,063 SNP markers covered all regions of autosomes on the length 2519232 kb. The spacing across genome between adjacent SNPs was in average 46.89±47.48 kb and within autosomes ranged from 43.65 kb (BTA25) to 52.59 kb (BTA5). The distribution of SNPs on different chromosomes ranged from 633 (79.13%) on BTA29 to 1123 (83.62%) on BTA14. The average LD between adjacent markers within autosomes reached values from 0.189 to 0.234 for chromosomes BTA 29 and 21, respectively. Division of r2-values over all 29 autosomes were performed according to their physical intermarker distances and averaged within the groups for analysis of distance effect on LD. The results of our study indicated the rapid decay of LD with increasing distance between markers. Further investigation will be oriented on evaluation of effective population size based on LD data. This could allow improvement of our knowledge about genetic diversity and its use for breed preservation of original phenotype supported by the current selection schemes and breeding programmes.
Ključne riječi
bovineSNP50 BeadChip; genetic diversity; intermarker distance
Hrčak ID:
158954
URI
Datum izdavanja:
2.6.2016.
Posjeta: 1.006 *