Identification of meat from yak and cattle using SNP markers with integrated allele-specific polymerase chain reaction-capillary electrophoresis method

Whole genome resequencing-based analysis of plateau adaptation in Meiren yak (Bos grunniens)

The Meiren yak is an important genetic resource in Gansu Province, China. In this study, we aimed to explore the evolutionary history and population structure of the genetic resource of Meiren yak and to mine the characteristic genes of Meiren yak. We analysed a total of 93 yaks of eight yak breeds based on whole genome resequencing combined with population genomics and used θπ ratio and Fst method to screen the selected sites in the genome region. The results proved that Meiren yak can be used as a potential genetic resource in Gansu Province. The genes in Meiren yak with positive selection in selection signal analysis were subjected to the Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses, which indicated that the genes were related to the adaptability to high altitude and hypoxic environment. By analysing the genetic variation of Meiren yak at the genome-wide level, this study provided a theoretical basis for genetic improvement of Meiren yak and for the development of high-quality yak resources.

Effects of different drying methods on physicochemical, textural, flavor, and sensory characteristics of yak jerky

The work aimed to study the effect of four drying methods, namely constant temperature hot air drying (HD), microwave drying (MD), hot air microwave drying (HMD), and gradient hot air drying (GHD), on quality characteristics of dried yak meat. The analyses of physicochemical, textural, flavor, and sensory characteristics were carried out based on these four drying methods. The results revealed that microwave dried yak jerky exhibited better color and received the highest sensory score. Hardness of samples were affected by the drying methods, which showed significant differences. There were 21 free amino acids (FAAs) detected in dried yak samples. The samples treated by microwave drying showed the highest total free amino acid content (73.30 mg/100 g) and the EUC value was significantly higher than other methods, indicating the sample displayed greater flavor. A total of 153 volatile compounds were identified in dried yak meat samples, primarily including aldehydes, ketones, and esters. Moreover, the sensory evaluation indicated that the drying methods could significantly affect on color, flavor, and overall acceptability of different samples. Microwave drying samples scored higher than other drying methods. Overall, considering aspects of quality, time savings, and energy efficiency, microwave drying of yak jerky emerges as a more satisfactory option. This study could provide important theoretical support for the application of drying methods to improve the quality of yak jerky and enhance production efficiency.

A review of CRISPR-Cas and PCR-based methods for the detection of animal species in the food chain-current challenges and future prospects

Regular testing and systematic investigation play a vital role to ensure product safety. Until now, the existing food authentication techniques have been based on proteins, lipids, and nucleic acid-based assays. Among various deoxyribonucleic acid (DNA)-based methods, the recently developed Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) based bio-sensing is an innovative and fast-expanding technology. The CRISPR/Cas-9 is known as Clustered Regularly Interspaced Short Palindromic Repeats due to the flexibility and simplicity of the CRISPR/Cas9 site-specific editing tool has been applied in many biological research areas such as Gene therapy, cell line development, discovering mechanisms of disease, and drug discovery. Nowadays, the CRISPR-Cas system has also been introduced into food authentication via detecting DNA barcodes of poultry and livestock both in processed and unprocessed food samples. This review documents various DNA based approaches, in an accessible format. Future CRISPR technologies are forecast while challenges are outlined.

House feeding pattern increased male yak fertility by improving gut microbiota and serum metabolites

Yaks usually live in an extremely harsh natural environment resulting in low reproductive performance, so the production of yak cannot meet local demand in China. In order to solve this problem, the experiment aims to explore the effect of different feeding modes on the semen quality of male yaks, so as to provide a theoretical basis for improving the yield of yaks in Tibet. We used the combined analysis of metabolomics and microbial sequencing to explore the underlying mechanisms that affect the differences in semen quality between the house feeding (HF) system and the free range (FR). The results showed that the sperm motility (P < 0.001) and sperm concentration (P < 0.05) in the HF group were significantly higher than the FR group, and the abnormal sperm rate (P < 0.01) in HF was significantly lower compared to FR. House feeding modes increased some beneficial materials in blood and testis especially some antioxidants, unsaturated fatty acids, and amino acids. House feeding group increased some gut microbiota at genus level namely Rikenellaceae, Bacteroides, Prevotellaceae_UCG-004, Bacteroidales_RF16, and Alloprevotella, DgA-11. It was interesting that blood metabolites, testicular metabolites, and fecal microbiota were well-correlated with sperm parameters. Meanwhile, the blood metabolites and testicular metabolites were well-correlated with microbes. The result indicated that the HF model was beneficial for yak semen quality by improving the gut microbiota and blood metabolism to increase yak fertility.

Characterization of N6-methyladenosine in cattle-yak testis tissue

N⁶-methyladenosine (m⁶A) is the most common form of eukaryotic mRNA modification, and it has been shown to exhibit broad regulatory activity in yeast, plants, and mammals. The specific role of m⁶A methylation as a regulator of spermatogenesis, however, has yet to be established. In this experiment, through a series of preliminary studies and methylated RNA immunoprecipitation sequencing, the m⁶A map of cattle-yak testicular tissue was established as a means of exploring how m⁶A modification affects cattle-yak male infertility. Cattle-yak testis tissues used in this study were found to contain sertoli cells and spermatogonia. Relative to sexually mature yak samples, those isolated from cattle-yak testis exhibited slightly reduced levels of overall methylation, although these levels were significantly higher than those in samples from pre-sexually mature yaks. Annotation analyses revealed that differentially methylated peaks were most concentrated in exonic regions, with progressively lower levels of concentration in the 3'-untranslated region (UTR) and 5'-UTR regions. To further explore the role of such m⁶A modification, enrichment analyses were performed on differentially methylated and differentially expressed genes in these samples. For the cattle-yaks vs. 18-months-old yaks group comparisons, differentially methylated genes were found to be associated with spermatogenesis-related GO terms related to the cytoskeleton and actin-binding, as well as with KEGG terms related to the regulation of the actin cytoskeleton and the MAPK signaling pathway. Similarly, enrichment analyses performed for the cattle-yaks vs. 5-years-old yaks comparison revealed differentially methylated genes to be associated with GO terms related to protein ubiquitination, ubiquitin ligase complexes, ubiquitin-dependent protein catabolism, and endocytotic activity, as well as with KEGG terms related to apoptosis and the Fanconi anemia pathway. Overall, enrichment analyses for the cattle-yaks vs. 18-months-old yaks comparison were primarily associated with spermatogenesis, whereas those for the cattle-yaks vs. 5-years-old yaks comparison were primarily associated with apoptosis.

Allele-specific polymerase chain reaction for the discrimination of elite Korean cattle associated with high beef quality and quantity

Abstract. Techniques such as direct sequencing and PCR-RFLP (restriction fragment length polymorphism) are widely used to analyze the genotypes of livestock. However, these conventional methods have the disadvantage of taking a lot of time and incurring considerable cost. The allele-specific PCR method performs PCR using two primers, and a single nucleotide polymorphism (SNP) genotype can be identified through electrophoresis, saving time and cost. Highly accurate results can be obtained by designing specific primers according to the allele of the SNP under study, utilizing primer binding to a complementary matching sequence. In this study, we established a genotyping system with the AS-PCR technique, using SNPs related to the improvement of the meat quality and meat mass of Korean cattle. Using the PRIMER1 program, we designed specific primers for SNPs located at the 3′ end, with one SNP marker in the HSPB1 gene related to meat quantity and two SNP markers in the ADH1C and FASN genes related to meat quality in cattle. AS-PCR was performed on 10 Korean cattle using the primers designed with this system, and the genotypes could be identified by the size of the PCR product amplified as a result of electrophoresis. In the case of the HSPB1 g.2352T > C SNP, the T allele was amplified to 148 bp, and the C allele was amplified to 222 bp. The ADH1C c.-64T > C SNP was amplified to 492 bp at the T allele and 330 bp at the C allele. The FASN g.17924G > A SNP A allele was amplified to 377 bp and the G allele to 507 bp. The results for each SNP genotype were verified using direct sequencing, which showed that the genotypes identified by direct sequencing and the genotypes identified by the AS-PCR method matched exactly. The AS-PCR method therefore appears to be valuable for use in a genotyping system.

Peptides Isolated from Yak Milk Residue Exert Antioxidant Effects through Nrf2 Signal Pathway

Food-derived bioactive peptides are considered as the important sources of natural bioactive ingredients. Approximately 3094 peptides were identified by nESI-LC–MS/MS in the hydrolyzed yak milk residue. Peptide KALNEINQF (T10) is the strongest antioxidant peptide. The damage model of H₂O₂-induced human umbilical vein endothelial cells (HUVECs) was used to evaluate the antioxidant effect. After treatment with 25, 50, or 100 μg/mL T10 peptide, T10 obviously decreased H₂O₂-induced damage and increased the cell survival. Comparing with the H₂O₂-induced damage group, superoxide dismutase (SOD) activities were significantly increased 1.03, 1.1, and 1.33 times, and glutathione reductase (GR) activities were significantly increased 1.11, 1.30, and 1.43 times, respectively. Malondialdehyde (MDA) also reduced 1.41, 1.54, and 1.72 times, respectively. T10 inhibited H₂O₂-induced apoptosis in HUVECs, and protein expressions of the apoptosis-related genes bcl-2 and bax were increased and decreased by 1.95 and 1.44 times, respectively, suggesting T10 decreases apoptosis of the mitochondria-dependent pathway. Comparing with the H₂O₂-induced damage group, the RNA expressions of Nrf2, HO-1, and NQO1 were significantly increased by 2.00, 2.11, and 1.94 times; the protein expressions of p-Nrf2, HO-1, and NQO1 were significantly increased by 2.67, 1.73, and 1.04 times; and Keap1 was downregulated by 3.9 and 1.32 times, respectively. T10 also regulated the Nrf2 pathway and expressions of related genes (Keap1, HO-1, and NQO1), and blocking the Nrf2 pathway in the model decreased the protective effect of T10. Taken together, T10 peptide isolated from yak milk residue has a protective effect against H₂O₂-induced damage in HUVECs and the molecular mechanisms are involved in the regulation of Nrf2 signaling pathway and cell apoptosis.

Characterization of N6-Methyladenosine in Domesticated Yak Testes Before and After Sexual Maturity

The potential regulatory role of N⁶-methyladenosine (m⁶A), the most prominent mRNA modification in eukaryotes, has recently been identified in mammals, plants, and yeast. However, whether and how m⁶A methylation is involved in sexual maturation in mammals remains largely unexplored. In this study, testicular tissue was obtained from yaks before and after sexual maturation, and m⁶A maps were generated via preliminary experiments and methylated RNA immunoprecipitation sequencing. Only spermatogonial cells and a few primary spermatocytes were observed in the testicular tissue of yaks before sexual maturation, while spermatogenic cells at different stages of maturity could observed after sexual maturation. Experiments examining the expression of methylation-related enzymes and overall methylation levels showed that the methylation levels in yak testes increased after sexual maturation. Overall, 1,438 methylation peaks were differentially expressed before and after sexual maturation; 1,226 showed significant up-regulation and 212 showed significant down-regulation after sexual maturation. Annotation analysis showed that the differential methylation peaks were most commonly concentrated in the exon region, followed by the 3′UTR and finally the 5′UTR region. KEGG pathway analysis demonstrated that homologous recombination, the Notch signaling pathway, growth hormone synthesis, and other signaling pathways may be involved in testicular development and maturation in yaks. Levels of most m⁶A modifications were positively correlated with mRNA abundance, suggesting that m⁶A plays a regulatory role in mammalian sexual maturation. To our knowledge, this is the first report of an m⁶A transcriptional map of the yak testes, and our study lays the foundation for elucidating the function of m⁶A in the development of yak testes.

Mitogenomic diversity and phylogeny analysis of yak (Bos grunniens)

Background and aim

Mitochondrial genome has aseries of characteristics such as simple structure, no recombination, maternalinheritance, stable structure, fast evolution rate, and high copy number. Moreover, it is easy to be sequenced,contains high-resolution phylogenetic information, and exists in a wide rangeof taxa. Therefore, it is widely used in the study of biological phylogeny. Atpresent, phylogenetic studies focus mainly on D-loop region, cytochrome b gene,and protein-coding sequence. Phylogenetic studies using the mitochondrialcomplete sequence are rarely reported in yak. Therefore, the present studyaimed to construct phylogenetic tree using yak mitochondrial complete sequenceand compare the subsequent results with previous findings obtained usingpartial sequences.

Results

Complete mitochondrial sequences of five yakpopulations from Qinghai and Xinjiang were obtained. The mitotype diversity ofthe five populations was Xueduo yak (0.992 ± 0.015), Pamir yak (0.990 ± 0.014),Yushu yak (0.963 ± 0.033), Qilian yak (0.948 ± 0.036), and Huanhu yak (0.905 ±0.048), which showed a higher mitotype diversity compared with other breeds fromthe previous reports, including Jiulong yak, Maiwa yak, Zhongdian yak, andTianzhu yak. A total of 78 mitotypes were obtained from 111 individuals. Amongthese, Yushu yak, Huanhu yak, Xueduo yak, and Qilian yak all shared mitotypes,but the Pamir yak did not share mitotypes with these four populations.Phylogenetic analysis showed that yak populations were separable into threedistinct branches. The analysis identified a new phylogenetic branch containingboth wild and domestic yaks. The 155 mitotypes found in 206 individuals weredivided into 3 haplogroups by mitotype clustering. Thehaplogroup was not associated with the geographical distribution of yaks. Theyaks in the same population or the same ecological environment were distributedin different haplogroups. Among the threehaplogroups, haplogroup A and haplogroup B showed a star-shaped distribution ofmitotypes. The central mitotypes were widely distributed and had a highfrequency.

Conclusions

Thegenetic diversity of yaks in Qinghai was high. Both domestic and wild yaks clusteredinto three branches.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07650-x.

Detection of Single Nucleotide Polymorphisms by Fluorescence Embedded Dye SYBR Green I Based on Graphene Oxide

The detection of single nucleotide polymorphisms (SNPs) is of great significance in the early diagnosis of diseases and the rational use of drugs. Thus, a novel biosensor based on the quenching effect of fluorescence-embedded SYBR Green I (SG) dye and graphene oxide (GO) was introduced in this study. The probe DNA forms a double helix structure with perfectly complementary DNA (pcDNA) and 15 single-base mismatch DNA (smDNA) respectively. SG is highly intercalated with perfectly complementary dsDNA (pc-dsDNA) and exhibits strong fluorescence emission. Single-base mismatch dsDNA (SNPs) has a loose double-stranded structure and exhibits poor SG intercalation and low fluorescence sensing. At this time, the sensor still showed poor SNP discrimination. GO has a strong effect on single-stranded DNA (ssDNA), which can reduce the fluorescence response of probe DNA and eliminate background interference. And competitively combined with ssDNA in SNPs, quenching the fluorescence of SG/SNP, while the fluorescence value of pc-dsDNA was retained, increasing the signal-to-noise ratio. At this time, the sensor has obtained excellent SNP resolution. Different SNPs detect different intensities of fluorescence in the near-infrared region to evaluate the sensor's identification of SNPs. The experimental parameters such as incubation time, incubation temperature and salt concentration were optimized. Under optimal conditions, 1 nM DNA with 0–10 nM linear range and differentiate 5% SNP were achieved. The detection method does not require labeling, is low cost, simple in operation, exhibits high SNP discrimination and can be distinguished by SNP at room temperature.

Purification and characterization of antioxidant peptides from yak (Bos grunniens) bone hydrolysates and evaluation of cellular antioxidant activity

In this study, papain and alcalase were used to generate antioxidant peptides from yak bone protein. The antioxidant activities of hydrolysates in vitro were evaluated by 2,2'-azinobios-(3-ethylbenzothiazoline-6-sulphonic acid) radical scavenging activity, total reducing power, ferrous ion chelating ability and hydroxyl radical scavenging activity. The hydrolysates generated by alcalase possessed the best antioxidant activity among unhydrolyzed protein and samples treated by papain, but the antioxidant activity decreased after simulated gastrointestinal digestion in vitro. The products of simulated gastrointestinal digestion were separated by ultrafiltration and high performance liquid chromatography, and the amino acid sequences of peptides were identified by mass spectrometry. The digestion sites within peptides were predicted by a bioinformatics strategy, and ten peptides were selected for synthesis. Among 10 synthetic peptides, Gly-Phe-Hyp-Gly-Ala-Asp-Gly-Val-Ala, Gly-Gly-Pro-Gln-Gly-Pro-Arg and Gly-Ser-Gln-Gly-Ser-Gln-Gly-Pro-Ala possessed strong antioxidant activities, among which Gly-Phe-Hyp-Gly-Ala-Asp-Gly-Val-Ala had a significant cytoprotective effect in Caco-2 cells under oxidative stress induced by H₂O₂, which reduced the formation of reactive oxygen species and malondialdehyde, and improved the activity of antioxidant enzymes in cells. These results showed that yak bone peptides exhibited strong antioxidant activity and have a potential value as a new type of natural antioxidant.