Preliminary genetic parameter estimates of meat quality traits in Hu sheep.

Because substantial numbers of Chinese consumers are prepared to pay for tender and quality lamb, meat quality traits are becoming more relevant for breeding programs for Chinese sheep breeds. The current study estimated heritabilities and genetic correlations for 13 meat quality traits recorded on lamb loins from Hu sheep. Heritability estimates ranged from 0.04 ± 0.06 for meat redness at 45 min to 0.57 ± 0.10 for drip loss, with most of the meat quality traits having moderate heritabilities. Positive genetic correlations were observed among meat color traits. Intramuscular fat (IMF) was genetically correlated with most meat quality traits, indicating that increasing IMF can favor meat pH, color, and tenderness, but would lead to increased cooking loss. Direct selection to increase IMF of loins is recommended to be included in breeding programs for Hu sheep, as it was more efficient than indirect selection on the other meat quality traits. The genetic parameters presented in this preliminary study provide valuable genetic information needed to design a breeding program aimed at improving the quality of lamb meat from Hu sheep.

Transcriptomic analysis of the HPG axis-related tissues reveals potential candidate genes and regulatory pathways associated with testicular size in Hu sheep.

Testicular size is an excellent proxy for selecting high-fertility rams. The hypothalamus-pituitary-gonadal (HPG) axis plays an important role in regulating reproductive capacity in vertebrates, while key genes and regulatory pathways within the HPG axis associated with testicular size remain largely unknown in sheep. This study comprehensively compared the transcriptomic profiles in the hypothalamus, pituitary and testis of rams after sexual maturity between the large-testis group (LTG, testicular weight = 454.29 ± 54.24 g) and the small-testis group (STG, testicular weight = 77.29 ± 10.76 g). In total, 914, 795 and 10518 differentially expressed genes (DEGs) were identified in the hypothalamus, pituitary and testis between LTG and STG, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that these DEGs were mainly involved in the biological processes of reproduction, biological regulation, and development process. Notably, the neuroactive ligand-receptor interaction and cAMP signaling pathways, commonly enriched by the DEGs in the hypothalamus and pituitary between two groups, were considered as two key signal pathways regulating testicular development through the HPGs axis. Weighted gene co-expression network analysis (WGCNA) identified two modules that were significantly associated with testicular size, and 97 key genes were selected with high module membership (MM) and gene significance (GS) in these two modules. Finally, a protein-protein interaction (PPI) network was constructed, and ten genes with the highest degree were represented as hub genes, including FOS, NPY, SST, F2, AGT, NTS, OXT, EDN1, VIP and TAC1. Taken together, these results provide new insights into the molecular mechanism underlying the HPG axis regulating testicular size of Hu sheep.

Insights into the rapid start-up of an inoculated municipal sludge system: A high-height-to-diameter-ratio airlift inner-circulation partition bioreactor based on CFD analysis.

The utilization of municipal sludge as a seed sludge for initiating the autotrophic nitrogen removal (ANR) process presents a challenge due to the negligible abundance of anaerobic ammonia-oxidizing bacteria (AnAOB). Here, a computational fluid dynamics model was used to simulate sludge volume fraction and sludge particle velocity. A high-height-to-diameter-ratio airlift inner-circulation partition bioreactor (HHAIPBR) was operated for 175 d to enrich AnAOB from municipal sludge, and the performance of the ANR process was investigated. The start-up period of HHAIPBR inoculated with municipal sludge required approximately 69 d. A high nitrogen removal performance, with a mean total nitrogen removal efficiency of 82.1%, was obtained for 1 month. The simulation results validated the presence of sludge circulation and revealed the distribution characteristics of dissolved oxygen inside the reactor, further supporting the promotion of sludge granulation via the high height-to-diameter ratio. Nitrosomonas (3.31%) of Proteobacteria and Candidatus Brocadia (6.56%) of Planctomycetota were dominant in the HHAIPBR. This study presents a viable approach for the industrial cultivation of anammox sludge and the rapid start-up of the partial nitritation-anammox system.

Liquid-Assisted Bionic Conical Needle for In-Air and In-Oil-Water Droplet Ultrafast Unidirectional Transportation and Efficient Fog Harvesting.

Learning from nature, many bionic materials and surfaces have been developed for the directional transportation of water and fog collection. However, current research mainly focuses on the self-transportation behavior of droplets in air-phase environments, rarely concerning underoil environments. Herein, in this work, a liquid-assisted bionic copper needle was fabricated for the rapid self-transportation of water droplets in air and oil environments. The water droplet can be spontaneously transported on the as-prepared bionic copper needle from the tip to the base. More importantly, the water-prewetted bionic copper needle can achieve the ultrafast unidirectional transportation of a water droplet in an oil environment, showing a maximum transport velocity of 76.2 mm/s and a transport distance over 33 mm, which were ten times higher than those reported in the previous research. Additionally, the droplet transport mechanism was revealed. The effects of the apex angle and tilt angle of the as-prepared bionic needle and droplet volume on the self-transportation behavior of water droplets were systematically investigated. The results indicated that the transport velocity of the water droplet decreased with the increase of the apex angle of the conical needle, while it increased with the increase of the droplet volume and needle tilt angle. Furthermore, the as-prepared bionic copper needle exhibited excellent fog collection performance with a single copper needle fog collecting efficiency of up to 2220 mg/h, which was 9.7 times that of the original copper needle. In summary, this work provides a simple and novel method to fabricate bionic copper needles for the directional self-transportation of water droplets in air-phase and oil-phase environments as well as efficient fog collection. It shows great application potential in the fields of microfluidics, desalination, and freshwater collection.

Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing.

Indicine cattle, also referred to as zebu (Bos taurus indicus), play a central role in pastoral communities across a wide range of agro-ecosystems, from extremely hot semiarid regions to hot humid tropical regions. However, their adaptive genetic changes following their dispersal into East Asia from the Indian subcontinent have remained poorly documented. Here, we characterize their global genetic diversity using high-quality whole-genome sequencing data from 354 indicine cattle of 57 breeds/populations, including major indicine phylogeographic groups worldwide. We reveal their probable migration into East Asia was along a coastal route rather than inland routes and we detected introgression from other bovine species. Genomic regions carrying morphology-, immune-, and heat-tolerance-related genes underwent divergent selection according to Asian agro-ecologies. We identify distinct sets of loci that contain promising candidate variants for adaptation to hot semi-arid and hot humid tropical ecosystems. Our results indicate that the rapid and successful adaptation of East Asian indicine cattle to hot humid environments was promoted by localized introgression from banteng and/or gaur. Our findings provide insights into the history and environmental adaptation of indicine cattle.

Whole genome sequencing of simmental cattle for SNP and CNV discovery.

BACKGROUD: The single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) are two major genomic variants, which play crucial roles in evolutionary and phenotypic diversity. RESULTS: In this study, we performed a comprehensive analysis to explore the genetic variations (SNPs and CNVs) of high sperm motility (HSM) and poor sperm motility (PSM) Simmental bulls using the high-coverage (25×) short-read next generation sequencing and single-molecule long reads sequencing data. A total of ~ 15 million SNPs and 2,944 CNV regions (CNVRs) were detected in Simmental bulls, and a set of positive selected genes (PSGs) and CNVRs were found to be overlapped with quantitative trait loci (QTLs) involving immunity, muscle development, reproduction, etc. In addition, we detected two new variants in LEPR, which may be related to the artificial breeding to improve important economic traits. Moreover, a set of genes and pathways functionally related to male fertility were identified. Remarkably, a CNV on SPAG16 (chr2:101,427,468 - 101,429,883) was completely deleted in all poor sperm motility (PSM) bulls and half of the bulls in high sperm motility (HSM), which may play a crucial role in the bull-fertility. CONCLUSIONS: In conclusion, this study provides a valuable genetic variation resource for the cattle breeding and selection programs.

Analysis of genomic copy number variations through whole-genome scan in Chinese Qaidam cattle.

Qaidam cattle (CDM) are indigenous breed inhabiting Northwest China. In the present study, we newly sequenced 20 Qaidam cattle to investigate the copy number variants (CNVs) based on the ARS-UMD1.2 reference genome. We generated the CNV region (CNVR) datasets to explore the genomic CNV diversity and population stratification. The other four cattle breeds (Xizang cattle, XZ; Kazakh cattle, HSK; Mongolian cattle, MG; and Yanbian cattle, YB) from the regions of North China embracing 43 genomic sequences were collected and are distinguished from each of the other diverse populations by deletions and duplications. We also observed that the number of duplications was significantly more than deletions in the genome, which may be less harmful to gene formation and function. At the same time, only 1.15% of CNVRs overlapped with the exon region. Population differential CNVRs and functional annotations between the Qaidam cattle population and other cattle breeds revealed the functional genes related to immunity (MUC6), growth (ADAMTSL3), and adaptability (EBF2). Our analysis has provided numerous genomic characteristics of some Chinese cattle breeds, which are valuable as customized biological molecular markers in cattle breeding and production.

Comparative transcriptomics analysis of testicular miRNA from indicine and taurine cattle.

Numerous studies have shown that several microRNAs (miRNAs) are specifically expressed in testis, play an essential role in regulating testicular spermatogenesis. Hainan and Mongolian cattle are two representative Chinese native cattle breeds representing Bos indicus (indicine cattle) and Bos taurus (taurine cattle), respectively, which are distributed in hot Hainan and cold Inner Mongolia province. To study the functional differences of miRNA in spermatogenesis between indicine and taurine cattle, six mature testes samples from indicine cattle (n = 3) and taurine cattle (n = 3) were collected, respectively. We detected miRNA expression using small RNA sequencing technology following bioinformatic analysis. A total of 578 known miRNAs and 132 novel miRNAs were detected in the six libraries. Among the 710 miRNAs, 564 miRNAs were expressed in both indicine and taurine cattle, 73 miRNAs were found solely in indicine cattle and 73 miRNAs were found solely in taurine cattle. After further analysis, among the miRNAs were identified in both indicine and taurine cattle, 184 miRNAs were differentially expressed (|log2 fold change| ≥ 1 and corrected p-value <0.05). Among the miRNAs that were only expressed in indicine cattle, 10 miRNAs were differentially expressed, whereas, among the miRNAs that were only expressed in taurine cattle, six miRNAs were differentially expressed. The enrichment analysis result showed that predicted target genes of a total of 200 differentially expressed miRNAs were enriched on some testicular spermatogenesis-related Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, especially mitogen-activated protein kinase (MAPK) signaling pathway. These findings identify miRNAs as key factors to regulate spermatogenesis in both indicine and taurine cattle, which may also be helpful for improving cattle reproductive performance in future studies.

Assessing genomic diversity and selective pressures in Bashan cattle by whole-genome sequencing data.

Specific ecological environments and domestication have continuously influenced the physiological characteristics of Chinese indigenous cattle. Among them, Bashan cattle belongs to one of the indigenous breeds. However, the genomic diversity of Bashan cattle is still unknown. Published whole-genome sequencing (WGS) data of 13 Bashan cattle and 48 worldwide cattle were used to investigate the genetic composition and selection characteristics of Bashan cattle. The population structure analysis revealed that Bashan cattle harbored ancestries with East Asian taurine and Chinese indicine. Genetic diversity analysis implied the relatively high genomic diversity in Bashan cattle. Through the identification of containing >5 nsSNPs or frameshift mutations genes in Bashan cattle, a large number of pathways related to sensory perception were discovered. CLR, θπ ratio, FST, and XP-EHH methods were used to detect the candidate signatures of positive selection in Bashan cattle. Among the identified genes, most of the enriched signal pathways were related to environmental information processing, biological systems, and metabolism. We mainly reported genes related to the nervous system (HCN1, KATNA1, FSTL1, GRIK2, and CPLX2), immune (CD244, SLAMF1, LY9, and CD48), and reproduction (AKR1C1, AKR1C3, AKR1C4, and TUSC3). Our findings will be significant in understanding the molecular basis underlying phenotypic variation of breed-related traits and improving productivity in Bashan cattle.

A novel SNP of TECPR2 gene associated with heat tolerance in Chinese cattle.

Heat stress affects the animal production and causes serious economic losses to the husbandry. Tectonin beta-propeller repeat containing 2 (TECPR2) gene plays an important role in autophagy which may affect the temperature sensation in animals. A missense mutation (XM_024981840.1:c.3989 G > A p.Arg1330His) of the transcripts X4 in the bovine TECPR2 gene was identified. In this study, the c.3989 G > A variant in TECPR2 gene was genotyped in a total of 25 cattle breeds (520 individuals). Our results indicated that the frequency of A allele showed a decreasing pattern from southern cattle to northern cattle, while the frequency of G allele showed the opposite pattern, which was consistent with the climate distribution of China. Compared with the GG genotype, southern cattle carried more the AA and AG genotypes. Furthermore, the association results carried out that the frequencies of genotypes (GG, AG, AA) and the value of climate parameters (mean annual temperature (T), relative humidity (RH) and temperature humidity index (THI) were significantly correlated (p < 0.01). Hence, we speculated that the c.3989 G > A variant of TECPR2 gene was associated with the heat tolerance trait in Chinese cattle and the locus may be considered as a molecular marker for Chinese cattle breeding.

Simulation investigation of the spontaneous motion behaviors of underwater oil droplets on a conical surface.

A conical surface can realize the spontaneous transportation of micro-sized oil droplets in an aqueous environment without energy input, exhibiting great potential for applications in microfluidics, chemical micro-reactors, water remediation, etc. However, the precise manipulation of an oil droplet on a cone is still very challenging because the dynamic behavior of a droplet on a cone is not fully understood. Herein, the dynamic behavior of oil droplets on a cone is quantitively studied via numerical simulations, and the effects of wettability, apex angle, and droplet size on the droplet's dynamic behavior are systematically analyzed. The results show that the moving velocity and transport distance of the droplet on the cone are highly related to the droplet shape on the cone. It was found that a clamshell-shaped droplet moves faster than a barrel-shaped droplet. Besides, the clamshell-shaped droplet with a larger size, on the cone with a smaller apex angle and smaller contact angle tends to obtain a faster moving speed and a longer transportation distance. The droplet shape adopted on the cone was determined by the cone wettability and the size of the droplet relative to the local curvature of the cone. It was found that the oil droplet tends to form a barrel shape on the cone with a highly oleophilic and small apex angle, and tends to form a clamshell shape on cones with a highly oleophobic and large apex angle. In addition, the droplet might transit from a barrel shape to a clamshell shape when it moves from the cone tip to the cone base, and the trigger time of the transit is negatively correlated with the contact angle and apex angle of the cone. This work provides a microscale understanding of the dynamic behavior of an underwater oil droplet on a cone, and also offers theoretical guidance for manipulating the behavior of a droplet on a cone and for the rational design of cone surfaces for spontaneous droplet transport and droplet collection.

Genomic Diversity and Selection Signatures for Weining Cattle on the Border of Yunnan-Guizhou.

Weining cattle is a Chinese indigenous breed influenced by complex breeding and geographical background. The multi-ethnic breeding culture makes Weining cattle require more attention as livestock resources for its genetic diversity. Here, we used 10 Weining cattle (five newly sequenced and five downloaded) and downloaded another 48 genome data to understand the aspects of Weining cattle: genetic diversity, population structure, and cold-adapted performance. In the current study, a high level of genetic diversity was found in Weining cattle, and its breed comprised two potential ancestries, which were Bos taurus and Bos indicus. The positive selective sweep analysis in Weining cattle was analyzed using composite likelihood ratio (CLR) and nucleotide diversity (θπ), resulting in 203 overlapped genes. In addition, we studied the cold adaptation of Weining cattle by comparing with other Chinese cattle (Wannan and Wenshan cattle) by three methods (F ST, θπ-ratio, and XP-EHH). Of the top 1% gene list, UBE3D and ZNF668 were analyzed, and these genes may be associated with fat metabolism and blood pressure regulation in cold adaptation. Our findings have provided invaluable information for the development and conservation of cattle genetic resources, especially in southwest China.

Deletions in GSN gene associated with growth traits of four Chinese cattle breeds.

The aim of this study was to assess the potential of 21 bp mutation in the second intron of the GSN gene as a molecular marker-assisted by exploring the effect of 21 bp mutation on growth traits in four beef cattle breeds. Gelsolin (GSN), a member of the superfamily of gel proteins, is involved in the regulation of a variety of cellular activities in the organism and plays an important function in cell motility, apoptosis, signal transduction and inflammatory responses. Gelatin can not only negatively regulate the pro-apoptotic effect of P53 protein, but also promote apoptosis by blocking the interaction between actin and deoxyribonuclease, so, the GSN gene was selected as a candidate gene in this study. In this study, a 21 bp mutation on the second intron to the GSN gene was verified in 573 individuals of Yunling (YL, n = 220), Jiaxian (JX, n = 140), Xianan (XN, n = 114) and Qinchuan (QC, n = 97) cattle breeds using Once PCR and agarose gel electrophoresis. The association analysis of polymorphisms in the GSN gene with growth traits in four breeds was revealed: in YL cattle, the heart girth and forehead size of heterozygous ID genotype were significantly higher than II genotype (P < 0.05). In JX cattle, the withers height, body length and heart girth of II and ID genotype were significantly highest than DD genotype (P < 0.01); the height at hip cross and height at sacrum of II genotype was significantly highest than DD genotype (P < 0.01), but ID genotype was significantly higher than DD genotype. In XN cattle, the abdominal girth and circumference of the cannon bone of II genotype were significantly higher than ID genotype (P < 0.05). In QC cattle, the hucklebone width of ID genotype was significantly the highest than II genotype (P < 0.01). The results suggest that GSN may be an important candidate gene and that a 21 bp mutation on the second intron to the GSN gene can be used for molecular marker-assisted selection of four beef cattle breeds.

Assessing Genomic Diversity and Selective Pressures in Bohai Black Cattle Using Whole-Genome Sequencing Data.

Bohai Black cattle are one of the well-known cattle breeds with black coat color in China, which are cultivated for beef. However, no study has conducted a comprehensive analysis of genomic diversity and selective pressures in Bohai Black cattle. Here, we performed a comprehensive analysis of genomic variation in 10 Bohai Black cattle (five newly sequenced and five published) and the published whole-genome sequencing (WGS) data of 50 cattle representing five "core" cattle populations. The population structure analysis revealed that Bohai Black cattle harbored the ancestry with European taurine, Northeast Asian taurine, and Chinese indicine. The Bohai Black cattle demonstrated relatively high genomic diversity from the other cattle breeds, as indicated by the nucleotide diversity (pi), the expected heterozygosity (HE) and the observed heterozygosity (HO), the linkage disequilibrium (LD) decay, and runs of homozygosity (ROH). We identified 65 genes containing more than five non-synonymous SNPs (nsSNPs), and an enrichment analysis revealed the "ECM-receptor interaction" pathways associated with meat quality in Bohai Black cattle. Five methods (CLR, θπ, FST, θπ ratio, and XP-EHH) were used to find several pathways and genes carried selection signatures in Bohai Black cattle, including black coat color (MC1R), muscle development (ITGA9, ENAH, CAPG, ABI2, and ISLR), fat deposition (TBC1D1, CYB5R4, TUSC3, and EPS8), reproduction traits (SPIRE2, KHDRBS2, and FANCA), and immune system response (CD84, SLAMF1, SLAMF6, and CDK10). Taken together, our results provide a valuable resource for characterizing the uniqueness of Bohai Black cattle.

Circ-TFF1 Promotes Breast Cancer Progression Through the miR-129-2-3p/IRAK1 Axis.

Breast cancer (BC) is a common malignant tumor, and circular RNA-trefoil factor 1 (circ-TFF1; hsa_circ_0061825) has been found to be highly expressed in BC tissues and cells and is associated with the poor prognosis of BC patients. However, the interaction between circ-TFF1 and microRNA in BC has not been studied. Quantitative real-time PCR was used to detect the expression of circ-TFF1, miR-129-2-3p, and interleukin (IL)-1 receptor-associated kinase 1 (IRAK1). Through the detection of cell proliferation, migration, invasion, tube formation, and apoptosis, cell function was assessed. The expression levels of angiogenesis-related proteins were detected by western blot. The interaction between miR-129-2-3p and circ-TFF1 or IRAK1 was verified by dual-luciferase reporter assay and RNA immunoprecipitation assay. Xenotransplantation experiments were used to confirm the function of circ-TFF1 in vivo. Circ-TFF1 and IRAK1 were significantly high expressed in BC tissues and cells. Silencing of circ-TFF1 reduced the proliferation, migration, invasion and tube formation, while increased the apoptosis of MDA-MB-361 and SK-Br-3 cells. MiR-129-2-3p was a target of circ-TFF1. Silencing of circ-TFF1 inhibited the malignant behavior of BC cells by releasing miR-129-2-3p. In addition, IRAK1 was a target of miR-129-2-3p. Overexpression of IRAK1 partially restored the inhibitory effect of miR-129-2-3p on cell progression. Animal experiments confirmed the anti-tumor effect of circ-TFF1 knockdown in vivo. Circ-TFF1 regulated the expression of IRAK1 by sponging miR-129-2-3p, thereby, promoting the development of BC. These data provided a novel targeted therapy for BC.

A novel missense mutation (rs464874590) within BoLA-DOB gene associated with the heat-resistance in Chinese cattle.

Bovine leukocyte antigen, class II, DO beta (BoLA-DOB) is related to antigen presentation, which can triggered by multicul factors. And the condition of immune function determines how much cattle load to heat stress. To evaluate the relationship between heat-resistance and single nucleotide polymorphisms (SNPs) in BoLA-DOB gene, our study has taken further analysis in Chinese indigenous cattle for the first time. A missense single nucleotide polymorphism (rs464874590) was detected in BoLA-DOB gene. We directly sequenced rs464874590 (NM_001013600.1 g.7122762 A > G) in BoLA-DOB gene of 522 individuals of 26 cattle breeds. The frequency of allele G gradually decreases from south to north with distinct climatic distribution characteristics. Further association analysis was carried out between different genotypes and environmental parameters, including annual mean temperature (T), relative humidity (RH), and temperature-humidity index (THI). The result showed that three genotypes were significantly correlated with T, H, and THI (P < 0.01), indicating that GG genotype was distributed in areas with hot and moist conditions. Therefore, our results suggested that the rs464874590 could be applied as a genetic marker to detect the heat-resistance of Chinese indigenous cattle.