Effect of supplementing lysins and methionine to low-protein diets on growth performance, hepatic antioxidant capacity, immune status, and glycolytic activity of tibetan sheep.

Reducing the levels of dietary protein is an effective nutritional approach in lowering feed cost and nitrogen emissions in ruminants. The purpose of this study was to evaluate the effects of dietary Lys/Met ratio in a low protein diet (10%, dry matter basis) on the growth performance and hepatic function (antioxidant capacity, immune status, and glycolytic activity) in Tibetan lambs. Ninety two-month-old rams with an average weight of 15.37 ± 0.92 kg were randomly assigned to LP-L (dietary Lys/Met = 1:1), LP-M (dietary Lys/Met = 2:1) and LP-H (dietary Lys/Met = 3:1) treatments. The trial was conducted over 100 d, including 10 d of adaption to the diets. Hepatic phenotypes, antioxidant capacity, immune status, glycolytic activity and gene expression profiling was detected after the conclusion of the feeding trials. The results showed that the body weight was higher in the LP-L group when compared to those on the LP-M group (P < 0.05). In addition, the activities of the catalase (CAT) and glutathione peroxidase (GSH-Px) in the LP-L group were significantly increased compared with the LP-M group (P < 0.05), while the malondialdehyde (MDA) levels in LP-H group were significantly decreased (P < 0.05). Compared with LP-H group, both hepatic glycogen (P < 0.01) and lactate dehydrogenase (LDH) (P < 0.05) were significantly elevated in LP-L group. For the LP-L group, the hepatocytes were arranged radially with the central vein in the center, and hepatic plates exhibited tight arrangement. Transcriptome analysis identified 29, 179, and 129 differentially expressed genes (DEGs) between the LP-M vs. LP-L, LP-H vs. LP-M, and LP-H vs. LP-L groups, respectively (Q-values < 0.05 and |log2Fold Change| > 1). Gene Ontology (GO) and correlation analyses showed that in the LP-L group, core genes (C1QA and JUNB) enriched in oxidoreductase activity were positively correlated with antioxidant indicators, while the MYO9A core gene enriched in the immune response was positively associated with immune indicators, and core genes enriched in molecular function (PDK3 and PDP2) were positively correlated with glycolysis indicators. In summary, low-protein diet with a low Lys/Met ratio (1:1) could reduce the hepatic oxidative stress and improve the glycolytic activity by regulating the expression of related genes of Tibetan sheep.

The impact of different levels of wheat diets on hepatic oxidative stress, immune response, and lipid metabolism in Tibetan sheep (Ovis aries).

BACKGROUND: Compared with corn, wheat contains higher crude protein, amino acids concentration. However, wheat contains a mass of anti-nutritional factors, resulting in increased of the digesta viscosity and impaired the intestinal function in ruminant. OBJECTIVE: This study aimed to investigate the effects of substitution of different amounts of wheat for corn on hepatic metabolism in the Tibetan lamb. METHODS: Ninety Tibetan lambs (Body weight = 12.37 ± 0.92 kg) were randomly assigned to three groups: 0% wheat diet (Control), 10% wheat diet (Low group), and 15% wheat diet (High group). The feeding trial lasted for 130 d, including a 10 d adaption period. Hepatic gene expression profiling was performed via RNA sequencing after the conclusion of the feeding trials. RESULTS: Results showed that greater level of glutathione peroxidase levels in L group compared with those of the C and H groups (P < 0.05). The immune indexes, including interleukin-1ß (IL-1ß), immunoglobulin A (IgA), and IgM were also elevated in L group compared with the other groups (P < 0.05). Compared with H group, the hepatocytes were arranged radially, and hepatic plates anastomosed with each other to form a labyrinth-like structure in L group. Transcriptomic analysis showed 872 differentially expressed genes (DEG) between H and L group, of which 755 were down-regulated and 117 were up-regulated. Through Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, 32 pathways were significantly enriched (Q-value < 0.05), such as the cAMP signaling pathway, Th1 and Th2 cell differentiation, leukocyte transendothelial migration, platelet activation and adipocytokine signaling pathway. Additionally, the expression of comment DEGs were verified via quantitative reverse-transcription polymerase chain reaction. CONCLUSION: In summary, our findings suggest that wheat can be supplemented up to 10% in Tibetan sheep, contributing to improve the hepatic oxidative stress, immune response and lipid metabolism through regulating the expression of related genes.

Effects of dietary wheat supplementation levels on growth performance, rumen bacterial community and fermentation parameters in Chinese Tibetan Sheep.

The objective of this study was to evaluate various wheat supplementation levels on rumen microbiota and fermentation parameter in Tibetan sheep. A total of ninety ram with an average 12.37 ± 0.92 kg at the age of 2 months were randomly allocated to three treatments: 0% wheat diet (CW, N = 30), 10% wheat diet (LW, N = 30), and 15% wheat diet (HW, N = 30) on a dry matter basis. The experiment was conducted over a period of 127 days, including 7 days of adaption to the diets. Our results showed that sheep fed 10% wheat exhibited optimal average daily gain and feed gain ratio compared with HW group (p < 0.05). The serum alkaline phosphatase concentration was the lowest when fed the 10% wheat diet (p < 0.05), whereas serum aspartate aminotransferase concentration was the highest (p < 0.05). Both acetate and propionate increased with increase in dietary wheat ratio (p < 0.05), while a greater decrease in concentrations of NH3 -N was observed (p < 0.05). In rumen fluid, 3413 OTUs were obtained with 97% consistency. Phylum Firmicutes was the predominant bacteria and accounted for 49.04%. The CW groups supported significantly increased the abundance of Bacteroidetes (p < 0.05), as compared with the HW group. The abundance of Bacteroidales_UCG-001, Ruminococcus, and Mitsuokella possessed a higher relative abundance in HW group (p < 0.05). No differences in the bacterial community and fermentation parameters were observed between the sheep fed 0% and 10% wheat (p > 0.05). Ruminal bacterial community structure was significantly correlated with isobutyrite (r2 = 0.4878, p = 0.035) and valerate (r2 = 0.4878, p = 0.013). In conclusion, supplementation of 10% wheat in diet promoted the average daily gain and never altered microbial community structure and fermentation pattern, which can be effectively replace partial corn in Chinese Tibetan Sheep.

Fat deposition, fatty acid profiles, antioxidant capacity and differentially expressed genes in subcutaneous fat of Tibetan sheep fed wheat-based diets with and without xylanase supplementation.

Xylanase, an exogenous enzyme that plays an essential role in energy metabolism by hydrolysing xylan into xylose, has been shown to positively influence nutrient digestion and utilisation in ruminants. The objective of this study was to evaluate the effects of xylanase supplementation on the back-fat thickness, fatty acid profiles, antioxidant capacity, and differentially expressed genes (DEGs) in the subcutaneous fat of Tibetan sheep. Sixty three-month-old rams with an average weight of 19.35 ± 2.18 kg were randomly assigned to control (no enzyme added, WH group) and xylanase (0.2% of diet on a dry matter basis, WE group) treatments. The experiment was conducted over 97 d, including 7 d of adaption to the diets. The results showed that xylanase supplementation in the diet increased adipocyte volume of subcutaneous fat (p < 0.05), shown by hematoxylin and eosin (H&E) staining. Gas chromatography showed greater concentrations of C14:0 and C16:0 in the subcutaneous fat of controls compared with the enzyme-treated group (p < 0.05), while opposite trend was seen for the absolute contents of C18:1n9t, C20:1, C18:2n6c, C18:3, and C18:3n3 (p < 0.05). Compared with controls, supplementation with xylanase increased the activity of T-AOC significantly (p < 0.05). Transcriptomic analysis showed the presence of 1630 DEGs between the two groups, of which 1023 were up-regulated and 607 were down-regulated, with enrichment in 4833 Gene Ontology terms, and significant enrichment in 31 terms (p < 0.05). The common DEGs were enriched in 295 pathways and significantly enriched in 26 pathways. Additionally, the expression of lipid-related genes, including fatty acid synthase, superoxide dismutase, fatty acid binding protein 5, carnitine palmytoyltransferase 1 A, and peroxisome proliferator-activated receptor A were verified via quantitative reverse-transcription polymerase chain reaction. In conclusion, dietary xylanase supplementation was found to reduce subcutaneous fat deposition in Tibetan sheep, likely through modulating the expression of lipid-related genes.

Profiling and functional analysis of circular RNAs in yaks intramuscular fat.

Circular RNAs (circRNAs) are a new class of endogenous RNA regulating gene expression. However, the regulatory mechanisms of lipid metabolism in yaks involved in circRNAs remain poorly understood. The IMF plays a crucial role in the quality of yak meat, to greatly improve the meat quality. In this study, the fatty acid profiles of yak IMF were determined and circRNAs were sequenced. The results showed that the total of polyunsaturated fatty acid (PUFA) content of adult yak muscle was significantly higher than that in yak calves (p < 0.05). A total of 29,021 circRNAs were identified in IMF tissue, notably, 99 differentially expressed (DE) circRNAs were identified, to be associated with fat deposition, the most significant of which were circ_12686, circ_6918, circ_3582, ci_106 and ci_123 (A circRNA composed of exons is labelled 'circRNA' and a circRNA composed of introns is labelled 'ciRNA'). KEGG pathway enrichment analysis showed that the differential circRNAs were enriched in four pathways associated with fat deposition (e.g., the peroxisome proliferator-activated receptor signalling, fatty acid degradation, sphingolipid metabolism and sphingolipid signalling pathways). We also constructed co-expression networks of DE circRNA-miRNA using high-throughput sequencing in IMF deposition, from which revealed that ci_106 target binding of bta-miR-130b, bta-miR-148a, bta-miR-15a, bta-miR-34a, bta-miR-130a, bta-miR-17-5p and ci_123 target binding of bta-miR-150 were involved in adipogenesis. The study revealed the role of the circRNAs in the IMF deposition in yak and its influence on meat quality the findings demonstrated the circRNA differences in the development of IMF with the increase of age, thus providing a theoretical basis for further research on the molecular mechanism of IMF deposition in yaks.

Genetic variation in the OPN gene affects milk composition in Chinese Holstein cows.

The aim of this study was to investigate the association between genotypes and haplotypes of OPN, and milk composition in dairy cows. A total of 317 Chinese Holstein cows were genotyped via DNA sequencing in this study. Three single nucleotide polymorphisms (SNPs), g.2916G > A, g.58675C > T and g.58899C > A, and eight haplotypes were identified. Of the eight possible haplotypes, four haplotypes i.e., Hap2 (ACC; 55.30%), Hap6 (GCC, 15.6%), Hap1 (ACA, 13.6%) and Hap4 (ATC, 5.70%), were considered to be major with a cumulative estimated frequency of >90%. Single markers (g.2916G > A and g.58899C > A) and Haplotype Hap6/4 were found to be associated with an increase in butter-fat percentage (p < 0.05). Taken together, our results provided evidence that polymorphisms in OPN are associated with milk composition, and could potentially be used for marker-assisted selection in Chinese Holstein cows.

Mutations in FGFR1 were associated with growth traits in sheep (Ovis aries).

For its role in the mediation of myoblast proliferation, fibroblast growth factor receptor 1 (FGFR1) was considered a functional candidate gene for growth performance in Tibetan sheep. Via the polymerase chain reaction-restriction fragment length polymorphism (PCR-PFLP) approach, four single nucleotide polymorphisms (SNPs) including g.14752C > T (intron 1), g.45361A > G (intron 7), g.49400A > G (3'UTR region) and g.49587A > T (3'UTR region), were identified in 422 ewes. The association analysis demonstrated that individuals carrying the AA genotype of g.49400A > G had significantly greater withers height, length than those with GG genotype (p < 0.05). Individuals with genotype AA of g.49587A > T had significantly greater weight and chest circumference than those with genotype TT (p < 0.01). Additionally, the individuals with Hap1/1 diplotypes (CAAA-CAAA) were highly significantly associated with weight and chest circumference than Hap1/2 diplotypes (CAAA-CAAT) (p < 0.05). The quantitative real-time polymerase chain reaction (qPCR) analysis revealed that the FGFR1 was detectable expressed in muscle tissues within three different age stage. Remarkably higher mRNA expression was detected at fetal lamb stage as compared with adult ewes (p < 0.01). The outcome of this research confirmed that both g.49400A > G and g.49587A > T of FGFR1 were involved in growth-related traits, which may be considered to be genetic markers for improving the growth traits of Tibetan sheep.

Determination of the relationship between class IV sirtuin genes and growth traits in Chinese black Tibetan sheep.

Class IV sirtuin (SIRT6 and SIRT7) played essential roles in biometabolism processes via deacetylating specific transcription factors. The present study was conducted to search for mutations in SIRT6/7 and determine their associations with growth traits in black Tibetan sheep. Via DNA sequencing methods, three single-nucleotide polymorphisms (SNPs) were identified in 427 ewes, including a mutation (g.3724C > T) in the intron 1 of SIRT6 and two mutations (g.3668G > T and g.4223C > G) in SIRT7 intron 6 and 8, respectively. Based on the χ2 test, both g.3724C > T and g.4223C > G loci fitted with Hardy-Weinberg equilibrium (p > 0.05). Compared with animals with genotype TT, the CC genotype at g.3724C > T locus (SIRT6) exhibited the highest mean for body weight (p < 0.05) and heart girth (p < 0.05). At g.3668G > T locus (SIRT7), individuals carrying the GG genotype tended to have heavier body weight than those of TT genotype (p < 0.05). With the exception of body weight, body measurement traits not affected by combinative genotype (p > 0.05). Our results could be used as genetic markers for marker-assisted selection and maybe guide sheep breeding in economic traits.

Associations between UASMS2 polymorphism in leptin gene and growth, carcass and meat quality traits of cattle: a meta-analysis.

Although numerous studies investigated the effect of UASMS2 polymorphism in leptin gene on cattle production, a consensus has not yet been reached. Therefore, we reviewed and meta-analyzed the effects of UASMS2 on cattle. We searched potentially relevant studies from seven databases (to December 25, 2019). Standard mean difference along with 95% confidence intervals was calculated to assess the strength of association through the random-effects model. Six published articles containing 1378 cattle samples were included in our meta-analysis. We found UASMS2 was not related to carcass weight, dressing percentage and loin muscle area in the recessive genetic model, but there was a significant association between UASMS2 and average daily weight gain, dry matter intake, body weight, marbling score, and backfat thickness. This meta-analysis indicated that UASMS2 was associated with growth and meat quality traits of cattle, implying that this SNP can be used reliably in beef cattle breeding. This study may provide valuable information on improving beef yield and quality in cattle production.

Effect of Different Heat Treatments on the Quality and Flavor Compounds of Black Tibetan Sheep Meat by HS-GC-IMS Coupled with Multivariate Analysis.

There are limited reports about the effect of different heat treatments on the quality and flavor of Black Tibetan sheep meat. The current study examined the effect of pan-frying, deep-frying, baking, and boiling treatment on the quality of Black Tibetan sheep meat; the amino acid, fatty acid, and volatile flavor compounds (VFCs) were investigated by a texture analyzer, ultra-high-performance liquid chromatography (UHPLC), gas chromatography (GC), and headspace-gas chromatography-ion mobility (HS-GC-IMS). The key VFCs were identified through orthogonal partial least squares discrimination analysis (OPLS-DA), and variable importance projection (VIP) values. In addition, Pearson's correlations between meat quality parameters and key VFCs were examined. The sensory scores, including texture, color, and appearance, of baked and pan-fried meat were higher than those of deep-fried and boiled meat. The protein (40.47%) and amino acid (62.93 µmol/g) contents were the highest in pan-fried meat (p < 0.05). Additionally, it contained the highest amounts of monounsaturated and polyunsaturated fatty acids, such as oleic, linoleic, and α-linolenic acids (p < 0.05). Meanwhile, pan-fried and deep-fried meat had higher amounts of VFCs than baked meat. The OPLS-DA similarity and fingerprinting analyses revealed significant differences between the three heat treatment methods. Aldehydes were the key aroma compounds in pan-fried meat. Importantly, 3-methylbutyraldehyde and 2-heptanone contents were positively correlated with eicosenoic, oleic, isooleic, linoleic, α-Linolenic, and eicosadiene acids (p < 0.05). To sum up, pan-fried Black Tibetan sheep meat had the best edible, nutritional, and flavor quality.

Variations in the insulin receptor substrate 1 (IRS1) and its association with growth traits in Chinese black Tibetan sheep (Ovis aries).

This paper presented the results on the study of insulin receptor substrate 1 (IRS1) polymorphisms in Chinese black Tibetan sheep. Via DNA direct sequencing, four variations within 3' untranslated region (UTR) of IRS1, including g.9382T > G, g.9569T > G, g.9572C > T and g.9695A > C were detected in the black Tibetan sheep population. Based on the χ2 test, those four loci deviated from Hardy-Weinberg equilibrium (p < 0.05). In g.9569T > G locus, genotype of GG possessed advantage on body weight (p < 0.05). In g.9572C > T locus, individuals with genotype of TT homozygous mutation decreased significantly on body weight, withers height, body length and chest circumference (p < 0.05 or p < 0.01). In g.9695A > C locus, the body weight and chest circumference were also higher in AA carriers than in CC carriers (p < 0.05). Our results provided evidence that polymorphisms in IRS1 were associated with growth efficiency traits by quantitative genetic analysis, and may be used for marker-assisted selection in Chinese indigenous sheep.

Expression of the bovine KLF6 gene polymorphisms and their association with carcass and body measures in Qinchuan cattle (Bos Taurus).

Kruppel-like factor 6 (KLF6) genes plays a significant role in the regulation of cell differentiation, proliferation and muscle development. The aim of this study is to investigate the genetic variation and the haplotype combination of the KLF6 gene in Qinchuan cattle and verify its contribution to bovine carcass traits and body measurements. The data were analyzed by real-time quantitative PCR (qPCR) to detect the expression profile of the KLF6 gene in the various tissues of Qinchuan cattle. PCR amplicons sequencing explored three novel SNPs at loci 3332C > G; 3413C > T and 3521G > A in the 2nd exon region of the KLF6 gene. The expression of KLF6 in the liver, kidney and lung was greater than that of other tissues. Allelic and genotypic frequencies of these SNPs were found to be in Hardy Weinberg equilibrium (P < 0.05). In SNP1, genotype CC, in SNP2, genotype CT and in SNP3 genotype GG were associated (P < 0.05) with larger body and carcass measurements. Association analysis results indicated that individuals with the Hap1/4 diplotype had a longer body and rump, were taller at the withers, and were wider at the hip than the other combinations. In terms of ultrasound carcass measures, Hap1/4 was associated with a larger muscle area and more intramuscular fat than other combinations. The bioinformatics study of the KLF6 protein showed a high degree of conservation in different mammalian species. The above results suggest that the KLF6 gene can used as potential candidate markers gene for the beef breed improvement through marker assisted selection of Qinchuan cattle.

Association of hormone-sensitive lipase (HSL) gene polymorphisms with the intramuscular fat content in two Chinese beef cattle breeds.

Hormone-sensitive lipase (HSL) was considered as an essential enzyme in glucolipid metabolism. It has been proposed to be a lead candidate gene for genetic markers of lipid deposition in livestock. The aim of this study was to identify sequence variants (SVs) of the bovine HSL gene and evaluate the relations to intramuscular fat in two indigenous Chinese beef cattle breeds. Expression analysis by quantitative real-time polymerase chain reactions (qPCR) indicated that expression levels of bovine HSL gene were highest in the perirenal fat and heart within two different age stage (adult and calf), respectively. Five SVs were identified by direct DNA sequencing, which included four missense mutations (g.16563C>T, g.16734G>A, g.16896A>G, g.17388G>T) in exon 8 and a synonymous mutation (g.17402C>T) in exon 9. Population genetic analysis showed that except for g.16563C>T and g.17402C>T, all the other detected SVs strongly affected the bovine intramuscular fat content (P < 0.01 or P < 0.05). The individuals with Hap5/5 diplotypes (CC-GG-GG-GG-CC) was highly significantly associated with intramuscular fat content than the other diplotypes (P < 0.01). The above results suggested that the HSL gene can used as potential candidate markers gene for the beef breed improvement through marker assisted selection in Chinese cattle breeds.

Genetic variants in MYF5 affected growth traits and beef quality traits in Chinese Qinchuan cattle.

Myogenic factor 5 plays actively roles in the regulation of myogenesis. The aims of this study are to identify the evolution information of MYF5 protein among 10 domestic and mammalian animals, to uncover the expression patterns of MYF5 gene in calves and adults of Qinchuan cattle, and to expose the genetic variants of the MYF5 gene and explore its effect on cattle growth traits and beef quality traits in Qinchuan cattle. The bioinformatics results showed that the MYF5 proteins highly conserved in different mammalian or domestic animals apart from chicken. The expression level of MYF5 gene in the heart, muscle, lung, large intestine and liver was greater than that of other tissues. PCR amplicons sequencing identified four novel SNPs at g.5738A>G, g.5785C>T and g.5816A>G in the 3rd exon region and g.6535A>G in the 3' UTR. Genotypic frequencies of g.5785C>T was harshly deviated from the HWE (P < .05). Genetic diversity was low or intermediate for the four SNPs and those SNPs were in the weak linkage disequilibrium. Association analysis results indicated g.5785C>T, g.5816A>G and g.6535A>G significant effect on growth performance and beef quality traits of Qinchuan cattle. H1H3 diplotype had greater body size and better beef quality. All the results implicate that the MYF5 gene might be applied as a promising candidate gene in Qinchuan cattle breeding.

Molecular characterization and analysis of the association of growth hormone 1 gene with growth traits in Chinese indigenous yak (Bos grunniens).

This study aimed to investigate the effects of polymorphisms in growth hormone 1 (GH1) gene on the growth traits in Chinese indigenous yak. Using the polymerase chain reaction-restriction fragment length polymorphism (PCR-PFLP) approach, one novel single-nucleotide polymorphism (SNP), termed as g.1721G>A, was identified in the exon 4 of GH1 gene in 423 individuals of yak population. Based on the chi-square (χ2) test, the frequencies of g.1721G>A alleles agreed with Hardy-Weinberg equilibrium (HWE) (P < 0.05). A significant association was observed between this SNP and several growth traits (P < 0.01 or P < 0.05), in which the genotype GG exhibited the best values. The present study suggested that the identified SNP was a useful genetic marker for the improvement of growth traits in Chinese indigenous yak.

Eukaryotic expression, Co-IP and MS identify BMPR-1B protein-protein interaction network.

BACKGROUND: BMPR-1B is part of the transforming growth factor ß super family and plays a pivotal role in ewe litter size. Functional loss of exon-8 mutations in the BMPR-1B gene (namely the FecB gene) can increase both the ewe ovulation rate and litter size. RESULTS: This study constructed a eukaryotic expression system, prepared a monoclonal antibody, and characterized BMPR-1B/FecB protein-protein interactions (PPIs). Using Co-immunoprecipitation coupled to mass spectrometry (Co-IP/MS), 23 proteins were identified that specifically interact with FecB in ovary extracts of ewes. Bioinformatics analysis of selected PPIs demonstrated that FecB associated with several other BMPs, primarily via signal transduction in the ovary. FecB and its associated interaction proteins enriched the reproduction process via BMP2 and BMP4 pathways. Signal transduction was identified via Smads proteins and TGF-beta signaling pathway by analyzing the biological processes and pathways. Moreover, other target proteins (GDF5, GDF9, RhoD, and HSP 10) that interact with FecB and that are related to ovulation and litter size in ewes were identified. CONCLUSIONS: In summary, this research identified a novel pathway and insight to explore the PPi network of BMPR-1B.

Genetic Architecture and Selection of Chinese Cattle Revealed by Whole Genome Resequencing.

The bovine genetic resources in China are diverse, but their value and potential are yet to be discovered. To determine the genetic diversity and population structure of Chinese cattle, we analyzed the whole genomes of 46 cattle from six phenotypically and geographically representative Chinese cattle breeds, together with 18 Red Angus cattle genomes, 11 Japanese black cattle genomes and taurine and indicine genomes available from previous studies. Our results showed that Chinese cattle originated from hybridization between Bos taurus and Bos indicus. Moreover, we found that the level of genetic variation in Chinese cattle depends upon the degree of indicine content. We also discovered many potential selective sweep regions associated with domestication related to breed-specific characteristics, with selective sweep regions including genes associated with coat color (ERCC2, MC1R, ZBTB17, and MAP2K1), dairy traits (NCAPG, MAPK7, FST, ITFG1, SETMAR, PAG1, CSN3, and RPL37A), and meat production/quality traits (such as BBS2, R3HDM1, IGFBP2, IGFBP5, MYH9, MYH4, and MC5R). These findings substantially expand the catalogue of genetic variants in cattle and reveal new insights into the evolutionary history and domestication traits of Chinese cattle.

Composition, diversity and function of gastrointestinal microbiota in wild red-billed choughs (Pyrrhocorax pyrrhocorax).

Hitherto, virtually nothing is known about the microbial communities related to the bird species in the family Corvidae. To fill this gap, the present study was conducted to provide a baseline description of the gut microbiota of wild red-billed choughs (Pyrrhocorax pyrrhocorax). In this study, microbiota from four gastrointestinal locations (oropharynx, gizzard, small intestine, and large intestine) of three wild red-billed choughs were analyzed using the Illumina MiSeq sequencing platform by targeting the V4-V5 regions of the 16S rRNA genes. The gut microbiota of the red-billed choughs were dominated by the phylum Firmicutes (59.56%), followed by Proteobacteria (16.56%), Bacteroidetes (13.86%), and Actinobacteria (7.03%), which were commonly detected in avian gut ecosystems. Genus-level compositions were found to be largely dominated by Lactobacillus (18.21%), Weissella (12.37%), Erysipelatoclostridium (6.94%), Bacteroides (6.63%), Escherichia-Shigella (5.15%), Leuconostoc (4.60%), Proteus (3.33%), Carnobacterium (2.71%), Lactococcus (1.69%), and Enterococcus (1.63%). The overall intestinal microbiota was enriched with functions related to ATP-binding cassette (ABC) transporters, DNA repair and recombination proteins, purine metabolism, ribosome, transcription factors, pyrimidine metabolism, peptidases, and two-component system. In terms of four different gastrointestinal locations, hierarchical clustering analysis and principal coordinate analysis showed that microbial communities of the oropharynx, gizzard, small intestine, and large intestine formed four separated clusters. A total of 825 OTUs and 382 genera were detected in all four gastrointestinal locations, which were considered as the major microbes in the intestines of red-billed choughs. Coexistence of lactic acid bacteria and potential pathogens in the gut environments of red-billed choughs required further investigations.

Performance Measurement and Comparative Transcriptome Analysis Revealed the Efforts on Hybrid Improvement of Qinchuan Cattle.

Crossbreeding can provide productive gains through heterosis, however, surveys about the effects of crossbreeding through global transcriptomic sequencing are few. This study revealed that Angus × Qinchuan cattle (AQF) have improved performance characteristics compared to Qinchuan cattle (QCF). We performed RNA-seq on the subcutaneous fat tissue of QCF and AQF. More than 42.2 million clean reads were obtained in each sample. We detected 40 and 21 breed-specific highly expressed genes (FPKM > 500) in QCF and AQF, respectively. Furthermore, a total of 353 differentially expressed genes (DEGs, |log2 ratio| ≥ 1 and Probability ≥ 0.8) were found between these two groups, of which 227 genes were upregulated in AQF and 126 genes were upregulated in QCF. Functional enrichment analyses showed that breed-specific highly expressed genes and DEGs were closely related to terms such as development in AQF, and adaption or immune in QCF. In addition, we also identified the novel transcript units, alternative splicing events, single-nucleotide polymorphisms and Indels. Our results revealed differences in inherent characteristics and genetic differences when comparing QCF with AQF.

The effect of haplotypes in the promoter region of SIRT4 gene on the ultrasound traits in Qinchuan cattle.

Sirtuin 4 (SIRT4) belongs to the mitochondrial sirtuin class of NAD+-dependent protein deacylases. This gene plays an important role in the regulation of lipid metabolism, cellular growth, and metabolism in mammals. Here, potential polymorphisms were sought in the bovine SIRT4 gene, and the relationships between the detected polymorphisms and carcass quality in Qinchuan cattle were assessed. Four single nucleotide polymorphisms (SNPs) were identified in the promoter region of the SIRT4 gene from the sequencing results of 452 individual cattle. A total of 8 different haplotypes were identified. Of these, the 3 most frequently observed haplotypes had frequencies of 35.0% (-CTG-), 18.3% (-CTA-), and 12.9% (-CCG-). The frequencies of g.-311C > T, g.-771C > T, and g.-1022G > A conformed to Hardy-Weinberg equilibrium in all the samples (chi-square test, P < 0.05). The association analysis indicated that these 3 polymorphisms were significantly associated with subcutaneous fat depth and intramuscular fat content (at P < 0.01 or P < 0.05). Interestingly, the Hap1/2 (-CAG-CAA-) diplotype was more highly associated with desirable ultrasound than other haplotype combinations.