Genomic adaptation to extreme climate conditions in beef cattle as a consequence of cross-breeding program

Background: Understanding the evolutionary forces related to climate changes that have been shaped genetic variation within species has long been a fundamental pursuit in biology. In this study, we generated whole-genome sequence (WGS) data from 65 cross-bred and 45 Mongolian cattle breeds. Together with 61 whole-genome sequences from world-wide cattle populations, we estimated the genetic diversity and population genetic structure of cattle populations. In addition, we performed comparative population genomics analyses to explore the genetic basis underlying variation in the adaptation to cold climate and immune response in cross-bred cattle located in the cold region of China. To elucidate genomic signatures that underlie adaptation to cold climate, we performed statistical measurements, F ST and nucleotide diversity (θπ), and further investigated the results to identify genomic regions under selection for cold adaptation and immune response-related traits. Results: By generating whole-genome sequencing data, we first investigated the population genetic structure and phylogenetic relationship of studied cattle populations. The results revealed clustering of cattle groups in agreement with their geographic distribution. We detected noticeable genetic diversity between indigenous cattle ecotypes and commercial populations. Analysis of population structure demonstrated evidence of shared genetic ancestry between studied cross-bred population and both Red-Angus and Mongolian breeds. Among the all studied cattle populations, the highest and lowest levels of linkage disequilibrium (LD) were detected in Holstein and Rashoki populations (ranged from ~ 0.54 to 0.73, respectively) at marker pairs distance of 1 Kb. Our search for potential genomic regions under selection in cross-bred cattle revealed several candidate genes related with immune response and cold shock protein-related traits. In particular, we identified some adaptive introgression genes such as TRPM8 , NMUR1 , PRKAA2 , SMTNL2 and OXR1 that are involved in energy metabolism and metabolic homeostasis. In addition, we detected some candidate genes on different chromosomes probably associated with immune response-related traits. Conclusions The study identified candidate genes involved in responses to cold adaptation and immune response in cross-bred cattle, including new genes or gene pathways putatively involved in these adaptations. The identification of these genes may be helpful in understanding of the molecular basis of adaptation to extreme environmental climate and as such they should be used in cattle breeding programs to select more efficient breeds for cold climate regions.