A High-Coverage Mesolithic Aurochs Genome and Effective Leveraging of Ancient Cattle Genomes Using Whole Genome Imputation.

Ancient genomic analyses are often restricted to utilizing pseudohaploid data due to low genome coverage. Leveraging low-coverage data by imputation to calculate phased diploid genotypes that enables haplotype-based interrogation and single nucleotide polymorphism (SNP) calling at unsequenced positions is highly desirable. This has not been investigated for ancient cattle genomes despite these being compelling subjects for archeological, evolutionary, and economic reasons. Here, we test this approach by sequencing a Mesolithic European aurochs (18.49×; 9,852 to 9,376 calBCE) and an Early Medieval European cow (18.69×; 427 to 580 calCE) and combine these with published individuals: two ancient and three modern. We downsample these genomes (0.25×, 0.5×, 1.0×, and 2.0×) and impute diploid genotypes, utilizing a reference panel of 171 published modern cattle genomes that we curated for 21.7 million (Mn) phased SNPs. We recover high densities of correct calls with an accuracy of >99.1% at variant sites for the lowest downsample depth of 0.25×, increasing to >99.5% for 2.0× (transversions only, minor allele frequency [MAF] ≥ 2.5%). The recovery of SNPs correlates with coverage; on average, 58% of sites are recovered for 0.25× increasing to 87% for 2.0×, utilizing an average of 3.5 million (Mn) transversions (MAF ≥2.5%), even in the aurochs, despite the highest temporal distance from the modern reference panel. Our imputed genomes behave similarly to directly called data in allele frequency-based analyses, for example consistently identifying runs of homozygosity >2 Mb, including a long homozygous region in the Mesolithic European aurochs.

Whole-genome sequencing reveals genomic diversity and selection signatures in Xia'nan cattle.

BACKGROUND: The crossbreeding of specialized beef cattle breeds with Chinese indigenous cattle is a common method of genetic improvement. Xia'nan cattle, a crossbreed of Charolais and Nanyang cattle, is China's first specialized beef cattle breed with independent intellectual property rights. After more than two decades of selective breeding, Xia'nan cattle exhibit a robust physique, good environmental adaptability, good tolerance to coarse feed, and high meat production rates. This study analyzed the population genetic structure, genetic diversity, and genomic variations of Xia'nan cattle using whole-genome sequencing data from 30 Xia'nan cattle and 178 published cattle genomic data. RESULT: The ancestry estimating composition analysis showed that the ancestry proportions for Xia'nan cattle were mainly Charolais with a small amount of Nanyang cattle. Through the genetic diversity studies (nucleotide diversity and linkage disequilibrium decay), we found that the genomic diversity of Xia'nan cattle is higher than that of specialized beef cattle breeds in Europe but lower than that of Chinese native cattle. Then, we used four methods to detect genome candidate regions influencing the excellent traits of Xia'nan cattle. Among the detected results, 42 genes (θπ and CLR) and 131 genes (FST and XP-EHH) were detected by two different detection strategies. In addition, we found a region in BTA8 with strong selection signals. Finally, we conducted functional annotation on the detected genes and found that these genes may influence body development (NR6A1), meat quality traits (MCCC1), growth traits (WSCD1, TMEM68, MFN1, NCKAP5), and immunity (IL11RA, CNTFR, CCL27, SLAMF1, SLAMF7, NAA35, and GOLM1). CONCLUSION: We elucidated the genomic features and population structure of Xia'nan cattle and detected some selection signals in genomic regions potentially associated with crucial economic traits in Xia'nan cattle. This research provided a basis for further breeding improvements in Xia'nan cattle and served as a reference for genetic enhancements in other crossbreed cattle.

Targeted Cyclo[8]pyrrole-Based NIR-II Photoacoustic Tomography Probe for Suppression of Orthotopic Pancreatic Tumor Growth and Intra-abdominal Metastases.

Pancreatic cancer is highly lethal. New diagnostic and treatment modalities are desperately needed. We report here that an expanded porphyrin, cyclo[8]pyrrole (CP), with a high extinction coefficient (89.16 L/g·cm) within the second near-infrared window (NIR-II), may be formulated with an αvß3-specific targeting peptide, cyclic-Arg-Gly-Asp (cRGD), to form cRGD-CP nanoparticles (cRGD-CPNPs) with promising NIR-II photothermal (PT) therapeutic and photoacoustic (PA) imaging properties. Studies with a ring-array PA tomography system, coupled with analysis of control nanoparticles lacking a targeting element (CPNPs), revealed that cRGD conjugation promoted the delivery of the NPs through abnormal vessels around the tumor to the solid tumor core. This proved true in both subcutaneous and orthotopic pancreatic tumor mice models, as confirmed by immunofluorescent studies. In combination with NIR-II laser photoirradiation, the cRGD-CPNPs provided near-baseline tumor growth inhibition through PTT both in vitro and in vivo. Notably, the combination of the present cRGD-CPNPs and photoirradiation was found to inhibit intra-abdominal metastases in an orthotopic pancreatic tumor mouse model. The cRGD-CPNPs also displayed good biosafety profiles, as inferred from PA tomography, blood analyses, and H&E staining. They thus appear promising for use in combined PA imaging and PT therapeutic treatment of pancreatic cancer.

Development of target-based cell membrane affinity ultrafiltration technology for a simplified approach to discovering potential bioactive compounds in natural products.

Target-based drug discovery technology based on cell membrane targets has gained significant traction and has been steadily advancing. However, current methods still face certain limitations that need to be addressed. One of the challenges is the laborious preparation process of screening materials, which can be time-consuming and resource-intensive. Additionally, there is a potential issue of non-specific adsorption caused by carrier materials, which can result in false-positive results and compromise the accuracy of the screening process. To address these challenges, this paper proposes a target-based cell membrane affinity ultrafiltration technology for active ingredient discovery in natural products. In this technique, the cell membranes of human lung adenocarcinoma epithelial cells (A549) with a high expression of epidermal growth factor receptor (EGFR) were incubated with candidate drugs and then transferred to an ultrafiltration tube. Through centrifugation, components that interacted with EGFR were retained in the ultrafiltration tube as "EGFR-ligand" complex, while the components that did not interact with EGFR were separated. After thorough washing and eluting, the components interacting with EGFR were dissociated and further identified using LC-MS, enabling the discovery of bioactive compounds. Moreover, the target-based cell membrane affinity ultrafiltration technology exhibited commendable binding capacity and selectivity. Ultimately, this technology successfully screened and identified two major components from the Curcumae Rhizoma-Sparganii Rhizoma (CS) herb pair extracts, which were further validated for their potential anti-tumor activity through pharmacological experiments. By eliminating the need for laborious preparation of screening materials and the potential non-specific adsorption caused by carriers, the development of target-based cell membrane affinity ultrafiltration technology provides a simplified approach and method for bioactive compounds discovery in natural sources.

Genomic characterization of dryland adaptation in endangered Anxi cattle in China.

Local species exhibit distinctive indigenous characteristics while showing unique productive and phenotypic traits. However, the advent of commercialization has posed a substantial threat to the survival of indigenous species. Anxi cattle, an endangered native breed in China, have evolved unique growth and reproductive characteristics in extreme desert and semidesert ecosystems. In this study, we conducted a genomic comparison of 10 Anxi cattle genomes with those of five other global populations/breeds to assess genetic diversity and identify candidate genomic regions in Anxi cattle. Population structure and genetic diversity analyses revealed that Anxi cattle are part of the East Asian cattle clade, exhibiting higher genetic diversity than commercial breeds. Through selective sweep analysis, we identified specific genetic variations linked to the environmental adaptability of Anxi cattle. Notably, we identified several candidate genes, including CERS3 involved in regulating skin permeability and antimicrobial functions, RBFOX2 associated with cardiac development, SLC16A7 participated in the regulation of pancreatic endocrine function, and SPATA3 related to reproduction. Our findings revealed the distinctive genomic features of Anxi cattle in dryland environments, provided invaluable insights for further research and breed preservation, and had important significance for enriching the domestic cattle breeding gene bank.

Association between physical frailty, circadian syndrome and cardiovascular disease among middle-aged and older adults: a longitudinal study.

BACKGROUND: Physical frailty (PF) and circadian syndrome (CircS) are proposed as novel risks for cardiovascular disease (CVD), but little attention is paid to their combined impact on CVD. This study aimed to investigate the association of PF, CircS and CVD in middle-aged and older adults. METHODS: The sample comprised 8512 participants aged at least 45 years from the China Health and Retirement Longitudinal Study (CHARLS) 2011. PF was examined by the physical frailty phenotype scale. CircS was assessed by the components of the International Diabetes Federation (IDF) MetS plus short sleep duration and depression. The cut-off for CircS was set as ≥ 4. CVD was defined as the presence of physician-diagnosed heart disease and/or stroke. A total of 6176 participants without CVD recruited from CHARLS 2011 and were followed up in 2018. RESULTS: The prevalence of CVD in total populations, neither CircS or PF, PF alone, CircS alone and both CircS and PF were 13.0%, 7.4%, 15.5%, 17.4%, and 30.2%, respectively. CircS was more likely to be PF [OR (95%CI): 2.070 (1.732 ∼ 2.472)] than those without CircS. Both CircS alone [OR (95% CI): 1.954 (1.663 ∼ 2.296)], and coexisting CircS and PF [3.508 (2.739 ∼ 4.494)] were associated with CVD. Longitudinal analysis showed that individuals with both CircS and PF (HR: 1.716, 95%CI: 1.314 ∼ 2.240) and CircS alone [1.520 (1.331 ∼ 1.737)] were more likely to have new onset CVD than neither CircS or PF peers. CONCLUSION: PF and CircS together are associated with higher CVD risk, which provided new evidence for a strong relation that warrants attention to assessing PF and CircS and in community to promote healthy aging.

Ancient DNA: the past for the future.

The last decade has seen advancements in sequencing technologies and laboratory preparation protocols for ancient DNA (aDNA) that have rapidly been applied in multiple research areas thus enabling large-scale scientific research. Future research could also refine our understanding of the evolution of humans, non-human animals, plants, invertebrate specimens, and microorganisms.

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.

Genome-wide association study reveals that the IBSP locus affects ear size in cattle.

Ear size is a classical model for hot climate adaptation following the evolution, but the genetic basis of the traits associated with ear size remains to be elucidated. Here, we performed a genome-wide association study on 158 cattle to explain the genetic mechanism of ear size. One region on BTA6 between 36.79 and 38.80 Mb included 50 suggestive SNPs and 4 significant SNPs that were significantly associated with ear size. The most significant locus (P = 1.30 × 10-8) was a missense mutation (T250I) on the seventh exon of integrin-binding sialoprotein (IBSP), which had an allele substitution effect of 23.46 cm2 for ear size. Furthermore, this mutation will cause changes in the three-dimensional structure of the protein. To further identify genes underlying this typical feature, we performed a genome scan among nine cattle breeds with different ear sizes by using SweeD. Results suggested that IBSP was under positive selection among four breeds with relatively large ear sizes. The expression levels of IBSP in ear tissues of large- and small-ear cattle were significantly different. A haplotype diversity survey of this missense mutation in worldwide cattle breeds strongly implied that the origin of this missense mutation event was Bos taurus. These findings have important theoretical importance for the exploration of major genes associated with ear size and provide important molecular markers for the identification of cattle germplasm resources.

A whole genome scan reveals distinct features of selection in Zhaotong cattle of Yunnan province.

Over the years, indigenous cattle have not only played an essential role in securing primary food sources but have also been utilized for labor by humans, making them invaluable genetic resources. The Zhaotong cattle, a native Chinese breed from the Yunnan province, possess excellent meat quality and resistance to heat and humidity. Here we used whole genome sequencing data of 104 animals to delve into the population structure, genomic diversity and potential positive selection signals in Zhaotong cattle. The findings of this study demonstrate that the genetic composition of Zhaotong cattle was primarily derived from Chinese indicine cattle and East Asian cattle. The nucleotide diversity of Zhaotong cattle was only lower than that of Chinese indicine cattle, which was much higher than that of other taurine cattle. Genome-wide selection scans detected a series of positive candidate regions containing multiple key genes related to bone development and metabolism (CA10, GABRG3, GLDN and NOTUM), meat quality traits (ALG8, LINGO2, MYO5B, PRKG1 and GABRB1), immune response (ADA2, BMF, LEF1 and PAK6) and heat resistance (EIF2AK4 and LEF1). In summary, this study supplies essential genetic insights into the genome diversity within Zhaotong cattle and provides a foundational framework for comprehending the genetic basis of indigenous cattle breeds.

Ancient genomes reveal tropical bovid species in the Tibetan Plateau contributed to the prevalence of hunting game until the late Neolithic.

Local wild bovids have been determined to be important prey on the northeastern Tibetan Plateau (NETP), where hunting game was a major subsistence strategy until the late Neolithic, when farming lifestyles dominated in the neighboring Loess Plateau. However, the species affiliation and population ecology of these prehistoric wild bovids in the prehistoric NETP remain unknown. Ancient DNA (aDNA) analysis is highly informative in decoding this puzzle. Here, we applied aDNA analysis to fragmented bovid and rhinoceros specimens dating ∼5,200 y B.P. from the Neolithic site of Shannashuzha located in the marginal area of the NETP. Utilizing both whole genomes and mitochondrial DNA, our results demonstrate that the range of the present-day tropical gaur (Bos gaurus) extended as far north as the margins of the NETP during the late Neolithic from ∼29°N to ∼34°N. Furthermore, comparative analysis with zooarchaeological and paleoclimatic evidence indicated that a high summer temperature in the late Neolithic might have facilitated the northward expansion of tropical animals (at least gaur and Sumatran-like rhinoceros) to the NETP. This enriched the diversity of wildlife, thus providing abundant hunting resources for humans and facilitating the exploration of the Tibetan Plateau as one of the last habitats for hunting game in East Asia.

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.

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.

Identification of Dezhou donkey muscle development-related genes and long non-coding RNA based on differential expression analysis.

Long non-coding RNAs (lncRNAs) play a critical role in the development of muscles. However, the role of lncRNAs in regulating skeletal muscle development has not been studied systematically in the donkey. In this study, we performed the RNA sequencing for different stages of muscles in donkeys, and investigate their expression profile, which showed that 3215 mRNAs (p-adjust <0.05) and 471 lncRNAs (p-value <0.05) were significantly differently expressed (DE) verified by RT-qPCR. GO and KEGG enrichment analysis indicated that DE genes and target genes of DE lncRNAs were associated with muscle development in the donkey. We also found these four target genes (DCN, ITM2A, MUSTN1, ARRDC2) involved in skeletal muscle growth and development. Combined with transcriptome data, network, and RT-qPCR results showed that four co-expression networks of DCN and lnc-008278, ITM2A and lnc_017247, MUSTN1 and lnc_030153, and ARRDC2 and lnc_033914, which may play an important role in the formation and development of muscle in the donkey.

Genomic analysis reveals a KIT-related chromosomal translocation associated with the white coat phenotype in yak.

White coat pigmentation is a striking phenotype of many domesticated species and has various genetic controls. The Tianzhu White yak, an indigenous breed with a complete white coat, has fascinated Tibetans for centuries. However, the genetic basis of this trait remains unknown. Here, we conducted population genomics analysis and genome-wide association study based on the whole-genome sequencing data of 38 white and 59 non-white-coated yak. The results revealed the presence of KIT-linked Cs alleles characterized by the translocations between chromosomes 6 and 29 in all-white yak. Furthermore, structural variations showed additional duplications of the Cs alleles in white yak compared with colour-sidedness cattle. Interestingly, the Cs alleles associated with the white coat phenotype in yak were found to have introgressed from taurine cattle. Our findings unveil the shared genetic control of the white coat phenotype and its evolution in closely related bovine species.

Assessing genomic diversity and signatures of selection in Pinan cattle using whole-genome sequencing data.

BACKGROUND: Crossbreeding is an important way to improve production beef cattle performance. Pinan cattle is a new hybrid cattle obtained from crossing Piedmontese bulls with Nanyang cows. After more than 30 years of cross-breeding, Pinan cattle show a variety of excellent characteristics, including fast growth, early onset of puberty, and good meat quality. In this study, we analyzed the genetic diversity, population structure, and genomic region under the selection of Pinan cattle based on whole-genome sequencing data of 30 Pinan cattle and 169 published cattle genomic data worldwide.  RESULTS: Estimating ancestry composition analysis showed that the composition proportions for our Pinan cattle were mainly Piedmontese and a small amount of Nanyang cattle. The analyses of nucleotide diversity and linkage disequilibrium decay indicated that the genomic diversity of Pinan cattle was higher than that of European cattle and lower than that of Chinese indigenous cattle. De-correlated composite of multiple selection signals, which combines four different statistics including θπ, CLR, FST, and XP-EHH, was computed to detect the signatures of selection in the Pinan cattle genome. A total of 83 genes were identified, affecting many economically important traits. Functional annotation revealed that these selected genes were related to immune (BOLA-DQA2, BOLA-DQB, LSM14A, SEC13, and NAALADL2), growth traits (CYP4A11, RPL26, and MYH10), embryo development (REV3L, NT5E, CDX2, KDM6B, and ADAMTS9), hornless traits (C1H21orf62), and climate adaptation (ANTXR2). CONCLUSION: In this paper, we elucidated the genomic characteristics, ancestry composition, and selective signals related to important economic traits in Pinan cattle. These results will provide the basis for further genetic improvement of Pinan cattle and reference for other hybrid cattle related studies.

Unveiling the improved targeting migration of mesenchymal stem cells with CXC chemokine receptor 3-modification using intravital NIR-II photoacoustic imaging.

BACKGROUND: Therapy with genetically modified mesenchymal stem cells (MSCs) has clinical translation promise. Optimizing the targeting migratory ability of MSCs relies on accurate imaging of the distribution and extravasation kinetics of MSCs, and the corresponding imaging results could be used to predict therapeutic outcomes and guide the optimization of the treatment program. Among the different imaging modalities, second near-infrared (NIR-II) optical-resolution photoacoustic microscopy (OR-PAM) has merits, including a fine resolution, a deep penetration, a high sensitivity, and a large signal-to-background ratio. It would be an ideal candidate for precise monitoring of MSCs, although it has not been tested for this purpose so far. RESULTS: Penetrating peptide-decorated conjugated polymer nanoparticles (TAT-CPNPs) with strong NIR-II absorbance were used to label chemokine-receptor genetically modified MSCs, which were subsequently evaluated under intravital NIR-II OR-PAM regarding their targeting migratory ability. Based on the upregulation of chemokine (C-X-C motif) ligand 10 in the inflamed ears of contact hypersensitivity mice, MSCs with overexpression of corresponding receptor, chemokine (C-X-C motif) receptor 3 (Cxcr3) were successfully generated (MSCCxcr3). TAT-CPNPs labeling enabled NIR-II photoacoustic imaging to discern MSCCxcr3 covered by 1.2 cm of chicken breast tissue. Longitudinal OR-PAM imaging revealed enhanced inflammation-targeting migration of MSCCxcr3 over time attributed to Cxcr3 gene modification, which was further validated by histological analysis. CONCLUSIONS: TAT-CPNPs-assisted NIR-II PA imaging is promising for monitoring distribution and extravasation kinetics of MSCs, which would greatly facilitate optimizing MSC-based therapy.

Distribution of the variant at AKIRIN2: c.*188G > A in Chinese cattle.

Marbling score (MS), is an economically important trait in cattle. Previous results showed that a SNP (c.*188G > A) of akirin 2 (AKIRIN2) gene was associated with MS in Japanese Black cattle and Korean cattle. However, the distribution of the genotypic frequency of the single nucleotide polymorphism (SNP) has not been explored in Chinese cattle. In this study, we used polymerase chain reaction (PCR) and DNA sequencing to detect the variation in 1296 individuals from 39 Chinese cattle breeds, one semi-wild bovine species (Dulong) and three introduced breeds (Angus, Holstein and Brahman). Our study found the frequency of the A allele at this locus roughly diminished from north to south in Chinese cattle, and we detected statistically significant differences between Angus and Brahman (p < 0.05), Dulong and another two breeds (Angus and Holstein; p < 0.01) using Chi-Square Independence Test. Our results reflected the variation of AKIRIN2: c.*188G > A in Chinese cattle, which would help us better understand Chinese cattle genetic resources and provide reference for further research.

Dietary supplementation of Aspergillus niger-expressed glucose oxidase ameliorates weaning stress and improves growth performance in weaning pigs.

Weaning is one of the most stressful events in the pig's life, which disrupts physiological balance and leads to oxidative stress. It is reported that glucose oxidase supplementation could alleviate oxidative stress in animals by increasing the concentration of antioxidant enzymes in vivo. The purpose of this study was to evaluate the effects of dietary supplementation of Aspergillus niger-expressed glucose oxidase (AN-GOX) on growth performance, nutrient digestibility, faecal microbiota, faecal gas emission and serum antioxidant enzyme parameters in weaning pigs. A total of 120 21-day-old weaning pigs [(Yorkshire ×Landrace) × Duroc] with an initial body weight of 6.54 ± 0.55 kg were used in a 21-day experiment (phase 1, days 1-7; phase 2, days 8-21) with a completely randomized block design. Pigs were randomly divided into 4 treatment groups with 6 replicate pens per treatment and 5 pigs per pen (2 barrows and 3 gilts). Dietary treatments were corn-soybean meal-based basal diet supplemented with 0, 0.01, 0.03 or 0.05% AN-GOX (1000 unit/g). The results of this study showed that average daily gain during days 1-7 and 1-21 and the concentrations of serum glutathione peroxidase and glutathione increased linearly at graduated doses of AN-GOX increased in the diet. However, dietary supplementation of AN-GOX had no effects on the apparent nutrient digestibility, faecal microbiota and faecal gas emission. In conclusion, supplementing AN-GOX to the diet of weaning pigs ameliorated weaning stress, which manifested as the increase in serum antioxidant enzyme levels, thus improving growth performance. The suitable dosage of AN-GOX used in the diet of weaning pigs was 0.05%.

Assessing genomic diversity and signatures of selection in Jiaxian Red cattle using whole-genome sequencing data.

BACKGROUND: Native cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and tough feeding conditions. Jiaxian Red, a Chinese native cattle breed, is reported to have originated from crossbreeding between taurine and indicine cattle; their history as a draft and meat animal dates back at least 30 years. Using whole-genome sequencing (WGS) data of 30 animals from the core breeding farm, we investigated the genetic diversity, population structure and genomic regions under selection of Jiaxian Red cattle. Furthermore, we used 131 published genomes of world-wide cattle to characterize the genomic variation of Jiaxian Red cattle. RESULTS: The population structure analysis revealed that Jiaxian Red cattle harboured the ancestry with East Asian taurine (0.493), Chinese indicine (0.379), European taurine (0.095) and Indian indicine (0.033). Three methods (nucleotide diversity, linkage disequilibrium decay and runs of homozygosity) implied the relatively high genomic diversity in Jiaxian Red cattle. We used θπ, CLR, FST and XP-EHH methods to look for the candidate signatures of positive selection in Jiaxian Red cattle. A total number of 171 (θπ and CLR) and 17 (FST and XP-EHH) shared genes were identified using different detection strategies. Functional annotation analysis revealed that these genes are potentially responsible for growth and feed efficiency (CCSER1), meat quality traits (ROCK2, PPP1R12A, CYB5R4, EYA3, PHACTR1), fertility (RFX4, SRD5A2) and immune system response (SLAMF1, CD84 and SLAMF6). CONCLUSION: We provide a comprehensive overview of sequence variations in Jiaxian Red cattle genomes. Selection signatures were detected in genomic regions that are possibly related to economically important traits in Jiaxian Red cattle. We observed a high level of genomic diversity and low inbreeding in Jiaxian Red cattle. These results provide a basis for further resource protection and breeding improvement of this breed.