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.

Avian species have a unique integument covered with feathers. Skin morphogenesis is a successive and complex process. To date, most studies have focused on a single developmental point or stage. Fewer studies have focused on whole transcriptomes based on the time-course of embryo integument development. To analyze the global changes in gene expression profiles, we sequenced the transcriptome of chicken embryo skin samples from day 6 to day 21 of incubation and identified 5830 differentially expressed genes (DEGs). Hierarchical clustering showed that E6 to E14 is the critical period of feather follicle morphogenesis. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the DEGs, two kinds of Wnt signaling pathways (a canonical pathway and a non-canonical pathway) changed during feather follicle and feather morphogenesis. The gene expression level of inhibitors and ligands related to the Wnt signaling pathway varied significantly during embryonic development. The results revealed a staggered phase relationship between the canonical pathway and the non-canonical pathway from E9 to E14. These analyses shed new light on the gene regulatory mechanism and provided fundamental data related to integument morphogenesis of chickens.

Hoxc13 belongs to the Abd-B class of Hox gene family, which participated in the hair follicle formation and hair growth regulation process. The structural protein of hair KP (keratin) and KAP (keratin-associated protein) expression is under regulation of Hoxc13, and then changes the characteristics of hair by regulating the composition of these two types of hair proteins and maintaining the normal morphology of hair follicle. In this review, we summarized that the relationship between the expression level of Hoxc13 and hair follicle development/hair growth and the mechanisim under the controling of Hoxc13 and relevant genes.

Background: Meat quality is a complex trait affected by genotypic and environmental factors. In a previous study, it was found that feedstuffs have various effects on the growth rate and meat quality of lambs. However, the underlying mechanisms are still not entirely clear.Results: In this study, to investigate the mechanisms that impact meat quality in twin sheep fed either with high fiber low protein (HFLP) forage (Ceratoides) or low fiber high protein (LFHP) forage (alfalfa) diets, multi omics techniques were utilized for integration analysis based on the feed nutritional value and the sheep microbiome, transcriptome, metabolome, and fatty acid profile. Results showed that the production performance and the muscle components of lambs were significantly affected by feeds. The essential fatty acid (linoleic acid and arachidonic acid) content of the muscle, based on gas chromatography-mass spectrometry analysis, was increased when lambs were fed with HFLP. The microbes in the lambs’ rumen fed a HFLP diet were more diverse than those of the LFHP fed group. Besides, the ratio of Bacteroidetes and Firmicutes in the rumen of the sheep fed a LFHP diet was 2.6 times higher than that of the HFLP fed group. Transcriptome analysis of the muscle revealed that the genes related to glucose metabolic processes and fatty acid biosynthesis were significantly differentially expressed between the two groups. Potential cross talk was found between the sfour omics data layers, which helps to understand the mechanism by which feedstuffs affect meat quality of lambs.Conclusion: Feed systems may affect the epigenetic regulation of genes involved in the glucose metabolic pathway. HFLP feeds could induce gluconeogenesis to maintain glucose levels in blood, resulting in decreased fat content in muscle. The multiple omics analysis showed that the microbiota structure is significantly correlated with the metabolome and gene expression in muscle. This study laid a theoretical foundation for controlling the nutrient intake of sheep; it suggested that its fatty acid spectrum modifications and the removal of meat quality detrimental material could guide sheep feeding for functional mutton.

Genetic networks provide new mechanistic insights into the diversity of species morphology. In this study, we have integrated the MGI, GEO, and miRNA database to analyze the genetic regulatory networks under morphology difference of integument of humans and mice. We found that the gene expression network in the skin is highly divergent between human and mouse. The GO term of secretion was highly enriched, and this category was specific in human compared to mouse. These secretion genes might be involved in eccrine system evolution in human. In addition, total 62,637 miRNA binding target sites were predicted in human integument genes (IGs), while 26,280 miRNA binding target sites were predicted in mouse IGs. The interactions between miRNAs and IGs in human are more complex than those in mouse. Furthermore,hsa-miR-548,mmu-miR-466, andmmu-miR-467have an enormous number of targets on IGs, which both have the role of inhibition of host immunity response. The pattern of distribution on the chromosome of these three miRNAs families is very different. The interaction of miRNA/IGs has added the new dimension in traditional gene regulation networks of skin. Our results are generating new insights into the gene networks basis of skin difference between human and mouse.