Abstract
The aim of presented investigation was to assess the overlap between selection signature discovered through analysis of variation in linkage disequilibrium and reported genomic regions associated with economic and traits of biological importance in cattle populations. The differences across Slovak Pinzgau, Austrian Pinzgau, Simmental and Holstein cattle and thus genome signatures of production and adaptation were found. The highest peak (top 0.01 percentile) was observed between Slovak and Austrian on chromosome 23, between Slovak Pinzgau and Simmental on chromosome 4 and between Slovak Pinzgau and Holstein on chromosomes 1, 7 and 20. Many candidate genes found have a known role in milk production (casein genes CSN1S1, CSN2, CSN1S2, CSN3; ABCG2, HBEGF, CAPN3, DGAT1, TG, GHR), reproduction (MGAT1, FGF1), feed efficiency (R3HDM1, ZRANB3), fertility (SPOCK1) and immune response (HSPA9, CD14, ARAP3, PCDH). Results of this study could be the basis for implementation of genomic selection programs in the Slovak Pinzgau cattle.
Highlights
Since domestication, significant genetic improvement has been achieved for many traits of commercial importance in cattle, including adaptation, appearance and production
The top 0.01 percentile of signals between SKP and HOL peaked at 40-58 Mb on chromosome 7 (Table 1). This region contains many genes associated with milk production and disease resistance (SAR1B, HBEGF), reproduction traits (MGAT1, FGF1), fertility (PCSK4, SPOCK1) and immune response (HSPA9, CD14, ARAP3 and multiple members of PCDH group)
Thyroglobulin (TG, chromosome 14) responsible for meat tenderness or intramuscular fat distribution is associated with milk yield and composition, whereas in our study was found only in SKP-HOL
Summary
Significant genetic improvement has been achieved for many traits of commercial importance in cattle, including adaptation, appearance and production. In response to such intense selection pressures, the bovine genome has undergone changes at the underlying regions of functional genetic variants, which are termed “selection signatures” (Randhawa et al, 2016). Sequence polymorphisms at the genome-wide level have been investigated in a wide range of animals. As the technology improves and the cost of low-density genotyping platforms decreases, mating designs that utilize genomic information could assist producers in managing their herd at the genomic level (Howard et al, 2015)
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