Abstract
BackgroundDesign of new highly productive livestock breeds, well-adapted to local climatic conditions is one of the aims of modern agriculture and breeding. The genetics underlying economically important traits in cattle are widely studied, whereas our knowledge of the genetic mechanisms of adaptation to local environments is still scarce. To address this issue for cold climates we used an integrated approach for detecting genomic intervals related to body temperature maintenance under acute cold stress. Our approach combined genome-wide association studies (GWAS) and scans for signatures of selection applied to a cattle population (Hereford and Kazakh Whiteheaded beef breeds) bred in Siberia. We utilized the GGP HD150K DNA chip containing 139,376 single nucleotide polymorphism markers.ResultsWe detected a single candidate region on cattle chromosome (BTA)15 overlapping between the GWAS results and the results of scans for selective sweeps. This region contains two genes, MSANTD4 and GRIA4. Both genes are functional candidates to contribute to the cold-stress resistance phenotype, due to their indirect involvement in the cold shock response (MSANTD4) and body thermoregulation (GRIA4).ConclusionsOur results point to a novel region on BTA15 which is a candidate region associated with the body temperature maintenance phenotype in Siberian cattle. The results of our research and the follow up studies might be used for the development of cattle breeds better adapted to cold climates of the Russian Federation and other Northern countries with similar climates.
Highlights
Design of new highly productive livestock breeds, well-adapted to local climatic conditions is one of the aims of modern agriculture and breeding
With over 1000 breeds existing worldwide in various environments e.g., hot and cold climates, cattle are an excellent model to study genetic adaptations. These studies can be performed using different approaches, including: a) scans for signatures of selection within breeds adapted to a specific environment, including genomes of breeds which are adapted to contrasting conditions; b) genome-wide association studies (GWAS) within populations looking for a range of animal reactions to environmental factors; and c) checking for expression and/or variations within or near candidate genes identified using these approaches or reported for other species
Genotyping quality controls removed 14,364 single nucleotide polymorphisms (SNPs) not assigned to a specific chromosome or position within the chromosome and 5171 SNPs found on sex chromosomes, resulting in 119,841 SNPs used in the haplotype and linkage disequilibrium (LD) block inference
Summary
Design of new highly productive livestock breeds, well-adapted to local climatic conditions is one of the aims of modern agriculture and breeding. The genetics underlying economically important traits in cattle are widely studied, whereas our knowledge of the genetic mechanisms of adaptation to local environments is still scarce To address this issue for cold climates we used an integrated approach for detecting genomic intervals related to body temperature maintenance under acute cold stress. With over 1000 breeds existing worldwide in various environments e.g., hot and cold climates, cattle are an excellent model to study genetic adaptations These studies can be performed using different approaches, including: a) scans for signatures of selection within breeds adapted to a specific environment, including genomes of breeds which are adapted to contrasting conditions; b) genome-wide association studies (GWAS) within populations looking for a range of animal reactions to environmental factors; and c) checking for expression and/or variations within or near candidate genes identified using these approaches or reported for other species (comparative genomics). This could indicate that adaptation to cold environments is a complex process which often involves different pathways (or different genes within pathways) in different species, suggesting that detailed studies of cold response in livestock (e.g., cattle) are required and we cannot rely only on the data originating from comparative genomics to identify candidate genes
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