Genomic signatures of selection in cattle through variation of allele frequencies and linkage disequilibrium

Abstract

The aim of this study was to evaluate the impact of artificial selection on Slovak Spotted and Slovak Pinzgau genomes through identification of selection signatures and to characterize most important genomic regions reflecting the selective breeding for traits of interest during the formation of those breeds. The genotyping data for in total of 236 animals were included in this study. Two approaches were used to identify genomic footprints of selection: Wright's FST statistic and variation in genome-wide linkage disequilibrium patterns between selected populations. Based on applied methods, in total of 18 genomic regions under strong selection pressure were detected across 10 autosomes (BTA 4, MTA5, BTA6, BTA7, BTA11, BTA12, BTA20, BTA22, and BTA23). The longest region was identified on BTA6 close to genes affecting milk production and coat colour pattern, while the shortest one was found on BTA11. In addition, inside the identified regions some of the other genes affecting the milk production traits (casein family, HAL, IGF1, ABCG2, SPP1), carcass traits and body composition (MYBPC1, MYH9, PACRGL), reproduction (AMDHD1), temperament (SNRPF), and coat colour (KIT, KDR) were found. Because of this, all of the detected regions can be attributed mostly to improvement of milk production and muscle development, thus selection for dual-purpose performance.

Keywords

• dual-purpose cattle
• high-throughput data
• linkage disequilibrium
• selection signatures
• Wright's statistics