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. Together with 62 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 three statistical measurements, fixation index (FST), log2 nucleotide diversity (θπ ratio) and cross population composite likelihood ratio (XP-CLR), and further investigated the results to identify genomic regions under selection for cold adaptation and immune response-related traits. Results By generating WGS data, we 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 all studied cattle populations, the highest and lowest levels of linkage disequilibrium (LD) per Kb were detected in Holstein and Rashoki populations (ranged from ~ 0.54 to 0.73, respectively). Our search for potential genomic regions under selection in cross-bred cattle revealed several candidate genes related with immune response and cold shock protein on multiple chromosomes. We identified some adaptive introgression genes with greater than expected contributions from Mongolian ancestry into Molgolian x Red Angus composites such as TRPM8, NMUR1, PRKAA2, SMTNL2 and OXR1 that are involved in energy metabolism and metabolic homeostasis. In addition, we detected some candidate genes probably associated with immune response-related traits. Conclusion 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 clarify the molecular basis underlying adaptation to extreme environmental climate and as such they might be used in cattle breeding programs to select more efficient breeds for cold climate regions.

BackgroundUnderstanding 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, FST and nucleotide diversity (θπ), and further investigated the results to identify genomic regions under selection for cold adaptation and immune response-related traits.ResultsBy 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. ConclusionsThe 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.

Context Fat colour is one of the most important economic traits in the marketing of beef. There are many factors that affect fat colour, such as breed, age, diet and gender. Fat colour is observed in different ranges of colours, including white, yellow and brown. The main issue with improving fat colour is that consumer preferences of fat colour vary across the globe. Therefore, investigating the metabolic mechanisms of fat colour may provide new biomarkers for phenotyping, so as to develop effective selection strategies to achieve the locally desired fat colour. Aims This study aimed to perform a comparative metabolic analysis between white and yellow fat from crossbred cattle so as to identify potential biomarkers for the selection of fat colour and to better understand the metabolism of white and yellow fat depots. Methods Carcass samples of subcutaneous fat were collected from crossbred cattle (Simmental × Mongolian cattle) and scored for fat colour. Liquid chromatography–mass spectrophotometry analysis of extracted metabolites from the subcutaneous fat of six animals with white fat and six animals with yellow fat was performed. Key results The comparison between metabolites of white and yellow fat colour samples indicated that there were five categories of 235 significant metabolites, which included hydrocarbons, lipids and lipid-like molecules, organic acids and their derivatives, organic oxygen compounds and organoheterocyclic compounds. The principal-component analysis illustrated that yellow and white fat samples can be classified in groups; however, the metabolites of white fat samples showed greater variation than those in the yellow fat. In the white fat, there were 163 metabolites that had a higher relative abundance than in yellow fat and 72 that had a lower relative abundance than in yellow fat. 3-Hydroxyoctanoic acid, anethofuran, 9,10-DiHODE, furanoeremophilane, pregeijerene, N-glycolylneuraminic acid, and glycocholic acid were identified as the metabolites that differed the most in abundance between the white and yellow fat samples. Conclusions This study has provided insights into the metabolic differences between white and yellow fat depots and identified key metabolites associated with beef fat colour. Implications This study has provided potential biomarkers that may be useful for selection of beef fat colour in live animals.

In the present study, we generated complete genome sequence data from 45 Mongolian cattle. Together with published sequence data from worldwide cattle populations, we explored the genetic diversity and population structure of worldwide cattle breeds. Our findings revealed clustering of cattle populations into three major groups, including commercial (Red-Angus, Hereford, Holstein and Jersey), Chinese (Mongolian and Tibetan) and other native cattle (including African cattle and Rashoki breed from Iran) breeds. The results from admixture analysis revealed evidence of shared genetic ancestry between different cattle populations. Furthermore, our findings showed a markedly higher level of linkage disequilibrium (LD) across all genomic distances in commercial breeds (specially Holstein cattle) compare to other native cattle groups. Our results provide valuable insights into the architecture of Mongolian Indigenous cattle breeds and their genomic relationship with other cattle populations. Pomelo.