- Invited Review - Translational gut microbiome research for strategies to improve beef cattle production sustainability and meat quality.

Advanced and innovative breeding and management of meat-producing animals are needed to address the global food security and sustainability challenges. Beef production is an important industry for securing animal protein resources in the world and meat quality significantly contributes to the economic values and human needs. Improvement of cattle feed efficiency has become an urgent task as it can lower the environmental burden of methane gas emissions and the reduce the consumption of human edible cereal grains. Cattle depend on their symbiotic microbiome and its activity in the rumen and gut to maintain growth and health. Recent developments in high-throughput omics analysis (metagenome, metatranscriptome, metabolome, metaproteome and so on) have made it possible to comprehensively analyze microbiome, hosts and their interactions and to define their roles in affecting cattle biology. In this review, we focus on the relationships among gut microbiome and beef meat quality, feed efficiency, methane emission as well as host genetics in beef cattle, aiming to determine the current knowledge gaps for the development of the strategies to improve the sustainability of beef production.

Diurnal variations of triglyceride accumulation in mouse and bovine adipocyte-derived cell lines.

Several studies have suggested a strong interaction between the circadian clock and lipid metabolism in mammals. The circadian clock is driven by endogenous cyclic gene expression patterns, commonly referred to as clock genes, and transcription-translation negative feedback loops. Clock genes regulate the transcription of some lipid metabolism-related genes; however, the relationship between the circadian clock and triglyceride (TG) accumulation at the cellular level remains unclear. Here, we evaluated rhythms of intracellular TG accumulation levels as well as the expression of clock genes and lipid metabolism-related genes for 54 h in mouse and bovine adipose-derived cell cultures. To the best of our knowledge, this study represents the first report demonstrating that TG accumulation exhibits diurnal variations, with the pattern differing among cell types. Furthermore, we found that expression of clock genes and corresponding lipid metabolism-related genes exhibited circadian rhythms. Our results suggest that the cellular clock regulates lipid metabolism-related genes to relate circadian rhythms of TG accumulation in each cell type. We anticipate that the amount of fat stored depends on the timing of the supply of glucose-the precursor of fat. The findings of this study will contribute to the advancement of chrono-nutrition.

Factors associated with canine skin extensibility in toy poodles.

To assess factors for canine skin extensibility, our study investigated associations between the dogs' skin extension index and the following factors, gender, age, neuter status, weight, coat color and six coat color related gene polymorphisms. Swab samples were collected from 69 toy poodles to extract DNA. The skin extension indices of the lower back and the neck were measured using the following formula: vertical height of the skin fold divided by body length multiplied by 100. The dogs' age, weight, gender, neuter status and coat color were also recorded, as well as polymorphisms of the following six selected coat color related genes, Melanocortin 1 receptor, Tyrosinase-related protein 1, Melanophilin, Canine ß-defensin-1, Major Facilitator Superfamily Domain Containing 12 and Agouti-signaling protein (ASIP). Univariable analysis showed there was a meaningful association between the lower back skin extension index and both gender and age (P<0.001 and P=0.048, respectively). Also, there was a possible association between the lower back skin extension index and ASIP Single nucleotide polymorphism (SNP) (R96C) (P=0.078). Linear model analysis showed there was a significant association between the lower back skin extension index and gender (P<0.001), and there was a tendency of the association between the lower back skin extension index and ASIP SNP (R96C) (P=0.098). In addition, there was an association between gender and age for the skin extension index. (P=0.048). Therefore, these results suggest that a greater risk of skin extensibility in toy poodle could be related to being female and the ASIP SNP (R96C), because these factors were associated with higher lower back skin extension index.

Clinofibrate improved canine lipid metabolism in some but not all breeds.

The objectives of this study were to assess if Clinofibrate (CF) treatment improved lipid metabolism in dogs, and to clarify whether its efficacy is influenced by canine characteristics. We collected medical records of 306 dogs and performed epidemiological analyses. Lipid values of all lipoproteins were significantly decreased by CF medication, especially VLDL triglyceride (TG) concentration (mean reduction rate=54.82%). However, 17.65% of dogs showed drug refractoriness in relation to TG level, and Toy Poodles had a lower CF response than other breeds (OR=5.36, 95% CI=2.07-13.90). Therefore, our study suggests that genetic factors may have an effect on CF response, so genetic studies on lipid metabolism-related genes might be conducted to identify variations in CF efficacy.

Evaluation of the genetic structure of sika deer (Cervus nippon) in Japan's Kanto and Tanzawa mountain areas, based on microsatellite markers.

The browsing habits of sika deer (Cervus nippon) in Japan have caused serious ecological problems. Appropriate management of sika deer populations requires understanding the different genetic structures of local populations. In the present study, we used 10 microsatellite polymorphisms to explore the genetic structures of sika deer populations (162 individuals) living in the Kanto region. The expected heterozygosity of the Tanzawa mountain range population (Group I) was lower than that of the populations in the Kanto mountain areas (Group II). Our results suggest that moderate gene flow has occurred between the sika deer populations in the Kanto mountain areas (Group II), but not to or from the Tanzawa mountain range population (Group I). Also, genetic structure analysis showed that the Tanzawa population was separated from the other populations. This is probably attributable to a genetic bottleneck that developed in the Tanzawa sika deer population in the 1950s. However, we found that the Tanzawa population has since recovered from the bottleneck situation and now exhibits good genetic diversity. Our results show that it is essential to periodically evaluate the genetic structures of deer populations to develop conservation strategies appropriate to the specific structures of individual populations at any given time.

Historical Relationships among Wild Boar Populations of the Ryukyu Archipelago and Other Eurasian regions, as Inferred from Mitochondrial Cytochrome b Gene Sequences.

The Ryukyu wild boar (Sus scrofa riukiuanus) is an endemic, morphologically defined subspecies of the Eurasian wild boar (S. scrofa) found on five islands of the Ryukyu Archipelago (a group of small islands stretching from mainland Japan to Taiwan). Two hypothetical scenarios have been proposed regarding the origin of the current Ryukyu wild boar populations: 1) natural dispersal and 2) transportation and subsequent release by prehistoric humans. To test these two hypotheses, we compared the mitochondrial cytochrome b gene sequence (1140 base pairs) in 352 individual wild boar samples that included representatives of all five insular populations of the Ryukyu wild boar and populations of other conspecific subspecies in insular East and Southeast Asia and the Eurasian Continent. A total of 68 haplotypes were recognized, of which 12 were unique to the Ryukyu wild boar populations. The results of Bayesian phylogenetic analyses supported monophyly of the five Ryukyu populations (posterior probability value of 92), confirming the validity of the subspecies as a natural group. Coalescent analysis estimated the divergence times between the Ryukyu wild boar and the other conspecific subspecies as 144-465 thousand years ago (Kya), with a 95% HPD (highest posterior density) range of 51-837 Kya, and with no significant migration. Taking the broadly accepted date of initial human migration to the Ryukyus (no earlier than 50 Kya) into consideration, our results strongly suggest that the ancestral form of the Ryukyu wild boar first entered the Ryukyu Archipelago by natural dispersal prior to the arrival of prehistoric humans.

A Single Neonatal Injection of Ethinyl Estradiol Impairs Passive Avoidance Learning and Reduces Expression of Estrogen Receptor α in the Hippocampus and Cortex of Adult Female Rats.

Although perinatal exposure of female rats to estrogenic compounds produces irreversible changes in brain function, it is still unclear how the amount and timing of exposure to those substances affect learning function, or if exposure alters estrogen receptor α (ERα) expression in the hippocampus and cortex. In adult female rats, we investigated the effects of neonatal exposure to a model estrogenic compound, ethinyl estradiol (EE), on passive avoidance learning and ERα expression. Female Wistar-Imamichi rats were subcutaneously injected with oil, 0.02 mg/kg EE, 2 mg/kg EE, or 20 mg/kg 17ß-estradiol within 24 h after birth. All females were tested for passive avoidance learning at the age of 6 weeks. Neonatal 0.02 mg/kg EE administration significantly disrupted passive avoidance compared with oil treatment in gonadally intact females. In a second experiment, another set of experimental females, treated as described above, was ovariectomized under pentobarbital anesthesia at 10 weeks of age. At 15-17 weeks of age, half of each group received a subcutaneous injection of 5 µg estradiol benzoate a day before the passive avoidance learning test. Passive avoidance learning behavior was impaired by the 0.02 mg/kg EE dose, but notably only in the estradiol benzoate-injected group. At 17-19 weeks of age, hippocampal and cortical samples were collected from rats with or without the 5 µg estradiol benzoate injection, and western blots used to determine ERα expression. A significant decrease in ERα expression was observed in the hippocampus of the estradiol-injected, neonatal EE-treated females. The results demonstrated that exposure to EE immediately after birth decreased learning ability in adult female rats, and that this may be at least partly mediated by the decreased expression of ERα in the hippocampus.

Retinoic acids change gene expression profiles of bovine intramuscular adipocyte differentiation, based on microarray analysis.

Beef marbling is caused by intramuscular deposition and it is an economically important trait in the beef industry. Vitamin A (VA) is an important feed supplement for cattle, but it can hinder marbling if provided in excess. In cattle, VA forms various derivatives such as all-trans retinoic acid (ATRA) and 9-cis retinoic acid (9cRA). Therefore, we investigated the genes involved in bovine intramuscular adipogenesis after VA treatment with ATRA and 9cRA. Differential gene expression levels were validated by microarray analysis in a clonal bovine intramuscular preadipocyte (BIP) cell line derived from the intramuscular adipose tissue of Japanese Black cattle. BIP cells were harvested 6 days after adipogenic stimulation with either 1 µmol/L ATRA, 1 µmol/L 9cRA or non-retinoic acid control. The ATRA- and 9cRA-treated cells exhibited reduced transcription of genes involved in the circulatory system and muscle development compared with the no retinoic acid (RA) treatment. In addition, the ATRA- and 9cRA-treated cells exhibited increased transcription of genes involved in the immune system, protein kinase B signaling and responses to various stimuli. These results demonstrate the lower expression of muscle development in ATRA- and 9cRA-treated BIP cells during adipogenesis.

Dog age and breeds associated with high plasma cholesterol and triglyceride concentrations.

The objectives of this study were to set specific dog breed and sex standards for total cholesterol (T-Cho) and total triglyceride (T-TG) concentrations in dogs and to quantify the associations between dog age and concentrations of both lipids for different breeds. Increased age was associated with higher T-Cho and T-TG concentrations in all five breed groups (P<0.05); T-Cho concentrations increased by 62.5 mg/dl between 9 and 16 years of age, and T-TG concentrations increased by 4.8 mg/dl per year of age (P<0.05). Miniature Schnauzers had the highest T-Cho concentrations of the studied breeds, while Miniature Dachshunds had the lowest concentrations (P<0.05). Veterinarians should consider dog age and breed when they use the lipid concentrations for diagnostic purposes.

Effect of retinoic acid on gene expression profiles of bovine intramuscular preadipocytes during adipogenesis.

To investigate genes involved in intramuscular adipogenesis in ruminants, 16 genes with dramatic variable expression were selected. These were selected from the differentiation- and proliferation-phase libraries of our previous serial analysis of gene expression (SAGE) studies of a clonal bovine intramuscular preadipocyte (BIP) cell line. We harvested the BIP cells over 12 days after adipogenic stimulation with all-trans retinoic acid (ATRA). Quantitative real-time PCR confirmed the earlier SAGE study results of the expression patterns of 15 of the genes. On day 6, TG accumulation increased significantly in the BIP cells but was completely inhibited in the 3T3-L1 cells (the monogastric reference). ATRA enhanced expression levels of six genes whereas it suppressed expression of eight genes on day 3 of adipogenesis in the BIP cells. Forty-eight hours after transfection, the messenger RNA expression level of the adipose differentiation-related protein (ADFP), encoded by one of the upregulated genes, in the ADFP small interference RNA (siRNA)-transfected cells was 3.5% of that in negative control-transfected cells. Also, 6 days after induction the TG level in the ADFP siRNA-transfected cells was 21.8% lower than that in negative control-transfected cells. This analysis of gene expression profiles after ATRA treatment will contribute to our understanding of the molecular mechanisms involved in bovine intramuscular adipogenesis.

Identification of bovine QTL for growth and carcass traits in Japanese Black cattle by replication and identical-by-descent mapping.

To map quantitative trait loci (QTL) for growth and carcass traits in a purebred Japanese Black cattle population, we conducted multiple QTL analyses using 15 paternal half-sib families comprising 7860 offspring. We identified 40 QTL with significant linkages at false discovery rates of less than 0.1, which included 12 for intramuscular fat deposition called marbling and 12 for cold carcass weight or body weight. The QTL each explained 2%-13% of the phenotypic variance. These QTL included many replications and shared hypothetical identical-by-descent (IBD) alleles. The QTL for CW on BTA14 was replicated in five families with significant linkages and in two families with a 1% chromosome-wise significance level. The seven sires shared a 1.1-Mb superior Q haplotype as a hypothetical IBD allele that corresponds to the critical region previously refined by linkage disequilibrium mapping. The QTL for marbling on BTA4 was replicated in two families with significant linkages. The QTL for marbling on BTA6, 7, 9, 10, 20, and 21 and the QTL for body weight on BTA6 were replicated with 1% and/or 5% chromosome-wise significance levels. There were shared IBD Q or q haplotypes in the marbling QTL on BTA4, 6, and 10. The allele substitution effect of these haplotypes ranged from 0.7 to 1.2, and an additive effect between the marbling QTL on BTA6 and 10 was observed in the family examined. The abundant and replicated QTL information will enhance the opportunities for positional cloning of causative genes for the quantitative traits and efficient breeding using marker-assisted selection.

A comprehensive genetic map of the cattle genome based on 3802 microsatellites.

A microsatellite-based high-density genetic map facilitates for fine mapping of hereditary traits of interest, characterization of meiosis, and providing a foundation for physical map construction. Here, we developed a comprehensive genetic map on the basis of >880,000 genotypes across the USDA MARC cattle reference families with a potential genetic resolution of 0.8 cM at the 95% confidence level ( approximately 800 kb in the bovine genome). We incorporated 2325 microsatellites into the second-generation genetic map by linkage analysis based on sex-averaged two-point LOD scores (>3.0), of which 2293 were fine-mapped by multipoint linkage analysis. The new 3160-cM map comprised of 29 sex-averaged autosomal linkage groups and a sex-specific X-chromosome linkage group includes 3960 markers with 2389 positions, resulting in an average interval size of 1.4 cM. More than half (51%) of the total length of the map is covered with intervals of 2.0 cM or less, and the largest gap is a 10.2-cM interval on the X-linkage group. The new map should accelerate fine mapping and positional cloning of genes for genetic diseases and economically important traits in cattle, as well as related livestock species, such as sheep and goat.