Animal Research and One Health最新文献

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Research progress on animal environment and welfare 动物环境与福利研究进展
Animal Research and One Health Pub Date : 2023-08-17 DOI: 10.1002/aro2.16
Baoming Li, Yang Wang, Li Rong, Weichao Zheng
{"title":"Research progress on animal environment and welfare","authors":"Baoming Li,&nbsp;Yang Wang,&nbsp;Li Rong,&nbsp;Weichao Zheng","doi":"10.1002/aro2.16","DOIUrl":"https://doi.org/10.1002/aro2.16","url":null,"abstract":"<p>Animal welfare closely depends on its ability to adapt and thrive in a harmonious relationship with its environment, ensuring both physical and psychological well-being. Over the years, the welfare of farm animals has gathered global attention and has become increasingly important to the general public and scientific communities. The connection between the environment and animal welfare is primarily established through the provision of suitable and controllable environment for animals. However, it is essential to recognize that the impact of environment extends beyond merely ensuring freedom from discomfort. The environment plays a crucial role in shaping an animal's response to challenges such as disease, stress, and pathogen. While animals may be housed in controlled environments that provide optimal conditions for health, production, and welfare, it is important to acknowledge that specific scenarios can significantly affect and alter the environmental requirements. Even with access to fresh air, certain factors can have a substantial impact on the well-being of animals. Furthermore, providing appropriate environmental conditions goes beyond meeting basic needs and can greatly contribute to allowing animals to engage in their natural behaviors. It serves as a relevant tool for ensuring and maintaining adequate welfare standards. This review takes a comprehensive approach to environmental welfare by considering the welfare of animals managed in different stocking systems, considering environmental stress, stocking systems, and the provision of environmental enrichment items. By examining these factors, a broader understanding of the relationship between environment and welfare is achieved and recommendations for future research are outlined.</p>","PeriodicalId":100086,"journal":{"name":"Animal Research and One Health","volume":"1 1","pages":"78-91"},"PeriodicalIF":0.0,"publicationDate":"2023-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aro2.16","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50135525","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Safety and quality evaluations of liquid milk and infant formula products in China in 2022 2022年中国液态奶及婴幼儿配方奶粉产品安全质量评价
Animal Research and One Health Pub Date : 2023-08-11 DOI: 10.1002/aro2.11
Lu Meng, Nan Zheng, Yanan Gao, Huimin Liu, Jiaqi Wang
{"title":"Safety and quality evaluations of liquid milk and infant formula products in China in 2022","authors":"Lu Meng,&nbsp;Nan Zheng,&nbsp;Yanan Gao,&nbsp;Huimin Liu,&nbsp;Jiaqi Wang","doi":"10.1002/aro2.11","DOIUrl":"https://doi.org/10.1002/aro2.11","url":null,"abstract":"<p>Milk serves two nutritional functions: it provides nutrition while also maintaining a healthy intestinal microenvironment. Thus, the safety and quality of milk products are critical for consumers' health. To evaluate liquid milk and infant formula products in China, we analyzed nine indices of 294 batches of pasteurized milk (PM), 92 batches of ultra-high temperature milk (UHT), and 20 batches of infant formula milk powder (IF) collected from 21 provinces in 2022. All PM, UHT, and IF samples were satisfactory concerning aflatoxin M<sub>1</sub> contamination, contamination by heavy metals, and residues of veterinary drugs and pesticides. The contents of lactoferrin, α-lactalbumin, β-lactoglobulin, furosine, and lactulose in the majority of samples met the group standards. Moreover, the contents of lactoferrin, α-lactalbumin, and β-lactoglobulin were higher in PM than in UHT, while furosine and lactulose contents showed the opposite trend. The findings concerning the safety and quality of milk products in China provide important insights to aid consumer preferences for milk products.</p>","PeriodicalId":100086,"journal":{"name":"Animal Research and One Health","volume":"1 1","pages":"43-55"},"PeriodicalIF":0.0,"publicationDate":"2023-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aro2.11","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50128621","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Multi-trait genomic predictions using GBLUP and Bayesian mixture prior model in beef cattle 基于GBLUP和贝叶斯混合先验模型的肉牛多性状基因组预测
Animal Research and One Health Pub Date : 2023-08-06 DOI: 10.1002/aro2.13
Zezhao Wang, Haoran Ma, Hongwei Li, Lei Xu, Hongyan Li, Bo Zhu, El Hamidi Hay, Lingyang Xu, Junya Li
{"title":"Multi-trait genomic predictions using GBLUP and Bayesian mixture prior model in beef cattle","authors":"Zezhao Wang,&nbsp;Haoran Ma,&nbsp;Hongwei Li,&nbsp;Lei Xu,&nbsp;Hongyan Li,&nbsp;Bo Zhu,&nbsp;El Hamidi Hay,&nbsp;Lingyang Xu,&nbsp;Junya Li","doi":"10.1002/aro2.13","DOIUrl":"https://doi.org/10.1002/aro2.13","url":null,"abstract":"<p>Multiple trait genomic selection incorporating correlated traits can improve the predictive ability of low-heritability traits. In this study, we evaluated genomic prediction accuracy using multi-trait BayesCπ method (MT-BayesCπ), which allows for a broader range of mixture priors for important traits in beef cattle. We compared the prediction performance of MT-BayesCπ with single-trait genomic best linear unbiased prediction (ST-GBLUP), multi-trait GBLUP (MT-GBLUP), and single-trait BayeCπ (ST-BayesCπ) methods. We found that ribeye area (REA) and ribeye weight (REWT) showed high heritability, while slaughter weight (SWT) and carcass weight (CWT) displayed medium heritability, and slaughter rate (SR) and feedlot average daily gain (FDG) showed low heritability. Highly positive genetic correlations were observed between CWT and SWT (0.981) and SR and REWT (0.921). Notably, the MT-BayesCπ method showed superior predictive abilities compared to other models. Using MT-BayesCπ method, the accuracy increased from 0.272 to 0.694 for CWT compared to ST-GBLUP and ST-BayesCπ. MT-GBLUP and ST-BayesCπ showed similar prediction accuracies, while MT-BayesCπ showed the least biased evaluations. Additionally, our results suggested that prediction accuracy of low-heritability traits significantly increased when they were combined with traits with high genetic correlation in a multi-trait prediction. Our study suggests that multi-trait genomic predictions using GBLUP and Bayesian mixture prior models is feasible for genomic selection in beef cattle. Our findings indicate that MT-BayesCπ outperforms other models (ST-GBLUP, MT-GBLUP and ST-BayesCπ), especially for low-heritability traits.</p>","PeriodicalId":100086,"journal":{"name":"Animal Research and One Health","volume":"1 1","pages":"17-29"},"PeriodicalIF":0.0,"publicationDate":"2023-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aro2.13","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50122450","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Zinc methionine improves the lipid metabolism that is associated with the alteration of intestine mucosal proteomes and microbiota of newborn Holstein dairy calves 蛋氨酸锌可改善与新生荷斯坦奶牛肠粘膜蛋白质组和微生物群改变有关的脂质代谢
Animal Research and One Health Pub Date : 2023-08-02 DOI: 10.1002/aro2.10
Xin Yu, Yeqianli Wo, Fengtao Ma, Qiang Shan, Jingya Wei, Peng Sun
{"title":"Zinc methionine improves the lipid metabolism that is associated with the alteration of intestine mucosal proteomes and microbiota of newborn Holstein dairy calves","authors":"Xin Yu,&nbsp;Yeqianli Wo,&nbsp;Fengtao Ma,&nbsp;Qiang Shan,&nbsp;Jingya Wei,&nbsp;Peng Sun","doi":"10.1002/aro2.10","DOIUrl":"10.1002/aro2.10","url":null,"abstract":"<p>Supplementation of diets with a modest amount of zinc methionine (ZM) has been documented to improve the growth performance and antioxidant function of dairy calves, but the underlying mechanisms remain elusive. In the present study, 16 dairy calves were allocated to a control (CON) group (calves consumed a basal diet) and a ZM group (calves ingested the basal diet and had an additional 455 mg ZM/day, corresponding to 80 mg zinc/day). The calves were fed these diets for 2 weeks, after which their serum antioxidant parameters, lipids, and jejunal mucosal proteome and microbiota were analyzed. The ZM group had lower levels of total cholesterol, triglycerides, and malondialdehyde but higher high-density lipoprotein cholesterol and glutathione peroxidase activity in the serum. A total of 142 differentially expressed proteins in the intestinal mucosa between the CON and ZM groups had been identified (ZM upregulated 117 proteins and downregulated 25 proteins). In addition, the protein expression of acyl-coenzyme A oxidase 1, fatty acid binding protein 2, and peroxisome proliferator-activated receptor gamma was higher in the ZM group. 16S rRNA gene sequencing indicated beneficial microbes, such as <i>Veillonellaceae</i>, <i>Akkermansia_muciniphila</i>, and <i>Bifidobacterium adolescentis</i>, which were more abundant, whereas <i>Acinetobacter lwoffii</i> was less abundant in calf jejunal mucosa in the ZM group. Finally, the propionate, butyrate, and iso-valerate concentrations in the jejunal digesta were greater in the ZM group than those in the CON group. Collectively, the present study shows that ZM supplementation improves the serum and intestine mucosal lipid metabolism associated with the alterations in mucosal fatty acids β-oxidation and microbiota.</p>","PeriodicalId":100086,"journal":{"name":"Animal Research and One Health","volume":"2 1","pages":"71-85"},"PeriodicalIF":0.0,"publicationDate":"2023-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aro2.10","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79387755","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Effect of the zinc transporter ZupT on the virulence mechanisms of mesophilic Aeromonas salmonicida SRW-OG1 锌转运蛋白ZupT对嗜温性沙门氏气单胞菌SRW-OG1毒力机制的影响
Animal Research and One Health Pub Date : 2023-08-01 DOI: 10.1002/aro2.17
Jiajia Wang, Qiu Li, Lixing Huang
{"title":"Effect of the zinc transporter ZupT on the virulence mechanisms of mesophilic Aeromonas salmonicida SRW-OG1","authors":"Jiajia Wang,&nbsp;Qiu Li,&nbsp;Lixing Huang","doi":"10.1002/aro2.17","DOIUrl":"https://doi.org/10.1002/aro2.17","url":null,"abstract":"<p>As a typical psychrophilic bacterial pathogen, <i>Aeromonas salmonicida</i> causes furunculosis in wild and farmed freshwater and marine fish, leading to substantial economic losses in the global aquaculture industry. Previous studies have shown that <i>A. salmonicida</i> is unable to grow above 25°C, hence limiting its infection to cold-water fish. However, we isolated <i>A. salmonicida</i> SRW-OG1, a mesophilic pathogenic strain from the warm-water fish <i>Epinephelus coioides</i>. Through RNA-seq analysis, we observe significant upregulation of the <i>zupT</i> gene at 28°C. ZupT is a member of zinc-regulated transporters and iron-regulated transporter-like proteins (ZIP family) and is closely associated with transcriptional regulation of virulence in certain pathogens. Consequently, our study aimed to examine the role of <i>zupT</i> during <i>A. salmonicida</i> SRW-OG1 infection at high temperatures. Our findings demonstrate that the <i>zupT</i>-RNAi strain exhibits severe growth restriction under limited Zn<sup>2+</sup> and Fe<sup>2+</sup> conditions. Notably, this strain shows significantly reduced mortality rates and colonization abilities. Moreover, its motility, biofilm formation, adhesion, and hemolytic activities are significantly diminished. Confocal laser scanning microscopy reveals earlier and accelerated biofilm dissociation in the <i>zupT</i>-RNAi strain. Analysis of extracellular products at 36 h indicates a considerable reduction in relative extracellular protein content in the <i>zupT</i>-RNAi strain. Taken together, our results highlight the vital role of the <i>zupT</i> gene in zinc transport and the fitness of <i>A. salmonicida</i> SRW-OG1 within the host.</p>","PeriodicalId":100086,"journal":{"name":"Animal Research and One Health","volume":"1 1","pages":"30-42"},"PeriodicalIF":0.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aro2.17","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50114978","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
SEMA4G targeted by miR-363-5p regulates the proliferation of granulosa cells in Yunshang black goats miR-363-5p靶向的SEMA4G调控云山黑山羊颗粒细胞的增殖
Animal Research and One Health Pub Date : 2023-08-01 DOI: 10.1002/aro2.15
Yulin Chen, Peng Wang, Xiaoyun He, Yufang Liu, Mingxing Chu
{"title":"SEMA4G targeted by miR-363-5p regulates the proliferation of granulosa cells in Yunshang black goats","authors":"Yulin Chen,&nbsp;Peng Wang,&nbsp;Xiaoyun He,&nbsp;Yufang Liu,&nbsp;Mingxing Chu","doi":"10.1002/aro2.15","DOIUrl":"10.1002/aro2.15","url":null,"abstract":"<p>Proliferation of granular cells (GCs) plays an important role in ovary development, providing energy and a microenvironment for oocyte ovulation. In this study, we explored the spatiotemporal expression of <i>SEMA4G</i> and its effects on the growth and development of goat GCs using primary GCs cultured in vitro as a model. The results showed that the expression level of <i>SEMA4G</i> was significantly higher in the ovaries of high-fertility goats than in those of low-fertility goats (<i>p</i> &lt; 0.05). The mRNA and protein expression levels of the cell proliferation markers of GCs were significantly increased after the overexpression of <i>SEMA4G</i> in goat primary GCs. The EdU and CCK8 results showed that cell viability was elevated in goat GCs and that proliferation was promoted by an increase in the number of proliferating cells. The proliferation of goat GCs was significantly inhibited by <i>SEMA4G</i> inhibition (<i>p</i> &lt; 0.05). The results of online miRNA and target gene prediction software and dual luciferase activity analysis confirmed that <i>SEMA4G</i> could bind to mi-363-5p and was one of its target genes. The RT‒qPCR results showed that the expression level of miR-363-5p was significantly lower in the ovaries of high-fertility goats than in those of low-fertility goats in contrast to the expression level of <i>SEMA4G</i> (<i>p</i> &lt; 0.05). After the overexpression of miR-363-5p in goat GCs, the expression of SEMA4G was significantly suppressed (<i>p</i> &lt; 0.05). Collectively, the results of this study could lay the foundation for exploring the molecular mechanisms by which <i>SEMA4G</i> and miR-363-5p regulate the growth and development of goat GCs and provide targets for breeding high-fertility goats.</p>","PeriodicalId":100086,"journal":{"name":"Animal Research and One Health","volume":"2 1","pages":"28-38"},"PeriodicalIF":0.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aro2.15","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89249758","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Research progress and applications of genome-wide association study in farm animals 农场动物全基因组关联研究进展及应用
Animal Research and One Health Pub Date : 2023-08-01 DOI: 10.1002/aro2.14
Xiaodong Tan, Zhengxiao He, Alan G. Fahey, Guiping Zhao, Ranran Liu, Jie Wen
{"title":"Research progress and applications of genome-wide association study in farm animals","authors":"Xiaodong Tan,&nbsp;Zhengxiao He,&nbsp;Alan G. Fahey,&nbsp;Guiping Zhao,&nbsp;Ranran Liu,&nbsp;Jie Wen","doi":"10.1002/aro2.14","DOIUrl":"https://doi.org/10.1002/aro2.14","url":null,"abstract":"<p>Exploring the genetic loci underlying economic traits is foundational for innovation in modern animal breeding technology. Genome-wide association studies (GWAS) have been valid and commonly used tools to dissect the genomic variants associated with phenotypes for the past ∼20 years and have contributed to our understanding of genetic and molecular bases of various traits. Here, we comprehensively review the recent research progress on GWAS methods. We highlight the methodological advancements enabled by the combination of new proteome, transcriptome, epigenome, and metagenome information and multi-omics analysis algorithms. The advances in GWAS investigations of chickens, pigs, cattle, and other animals during the last 5 years are also described. Finally, we discuss the current applications of GWAS in cutting-edge breeding technologies and overall future perspectives of the post-GWAS era.</p>","PeriodicalId":100086,"journal":{"name":"Animal Research and One Health","volume":"1 1","pages":"56-77"},"PeriodicalIF":0.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aro2.14","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50114979","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Lactococcus lactis NZ3900/pNZ8149-IL-4-IL-2 as an adjuvant to reduce vaccine dose in chicken coccidia live mixed vaccine 乳酸乳球菌 NZ3900/pNZ8149-IL-4-IL-2 作为减少鸡球虫混合活疫苗剂量的佐剂
Animal Research and One Health Pub Date : 2023-07-28 DOI: 10.1002/aro2.12
Longlong Zheng, Li Zhang, Fan Tan, Honghui Zhang, Liming Wang, Mingxue Zheng
{"title":"Lactococcus lactis NZ3900/pNZ8149-IL-4-IL-2 as an adjuvant to reduce vaccine dose in chicken coccidia live mixed vaccine","authors":"Longlong Zheng,&nbsp;Li Zhang,&nbsp;Fan Tan,&nbsp;Honghui Zhang,&nbsp;Liming Wang,&nbsp;Mingxue Zheng","doi":"10.1002/aro2.12","DOIUrl":"10.1002/aro2.12","url":null,"abstract":"<p>Although live mixed coccidiosis vaccines are widely used for <i>Eimeria</i> control, the side effects (e.g., damaging the intestinal mucosa and decreasing their weight gain) are not negligible. This study aimed to filter out the lowest dose of coccidiosis mixed vaccine with <i>Lactococcus lactis</i> (<i>L. lactis</i>) NZ3900/pNZ8149-IL-4-IL-2 (RLIL4/2) coimmunization against <i>Eimeria</i> reduces the side effects for <i>Eimeria</i> vaccination. Chickens oral 1.0 ×, 0.9 ×, 0.8 ×, 0.6 ×, 0.4 × dose of live vaccine, and RLIL4/2 with 1.0 × 10<sup>9</sup> CFU/chicken, respectively. The blank control group, challenge-only group and 1.0 × dose vaccine-only group are used as references. The survival rate, weight gain, bloody stool, intestinal lesions scores, oocyst output oocysts per gramme (OPG), and anticoccidial index (ACI) were detected by challenging with virulent coccidiosis. All the results indicated that the weight gain during the immune period or bloody stool/intestinal lesions scores/OPG during the challenge period were oppositely correlated with vaccine doses. The survival rate, weight gain, and ACI were positively correlated with vaccine doses during the challenge period. The ACI of 0.6 × the dose group was 167.69, which was considered a moderate efficiency. The weight gain, ACI of 1.0 ×, 0.9 × and 0.8 × dose groups were higher or intestinal lesions were lower than 1.0 × dose vaccine-only group (<i>p</i> &lt; 0.05), respectively. In conclusion, the coimmunization of RLIL4/2 with <i>Eimeria</i> mixed vaccine could reduce 40% of the dose and the side effects (e.g., weight gain and intestinal lesions) from live mixed coccidiosis vaccine.</p>","PeriodicalId":100086,"journal":{"name":"Animal Research and One Health","volume":"2 1","pages":"50-58"},"PeriodicalIF":0.0,"publicationDate":"2023-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aro2.12","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84600380","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The efficient phasing and imputation pipeline of low-coverage whole genome sequencing data using a high-quality and publicly available reference panel in cattle 使用高质量和公开可用的牛参考小组对低覆盖率全基因组测序数据进行有效的分阶段和插补
Animal Research and One Health Pub Date : 2023-07-08 DOI: 10.1002/aro2.8
Zhuangbiao Zhang, Ao Wang, Honghong Hu, Lulu Wang, Mian Gong, Qimeng Yang, Anguo Liu, Ran Li, Huanhuan Zhang, Qianqian Zhang, Ali Mujtaba Shah, Xihong Wang, Yachun Wang, Quanzhong Liu, Liutao Gao, Zhipeng Zhang, Congyong Wang, Yun Ma, Yudong Cai, Yu Jiang
{"title":"The efficient phasing and imputation pipeline of low-coverage whole genome sequencing data using a high-quality and publicly available reference panel in cattle","authors":"Zhuangbiao Zhang,&nbsp;Ao Wang,&nbsp;Honghong Hu,&nbsp;Lulu Wang,&nbsp;Mian Gong,&nbsp;Qimeng Yang,&nbsp;Anguo Liu,&nbsp;Ran Li,&nbsp;Huanhuan Zhang,&nbsp;Qianqian Zhang,&nbsp;Ali Mujtaba Shah,&nbsp;Xihong Wang,&nbsp;Yachun Wang,&nbsp;Quanzhong Liu,&nbsp;Liutao Gao,&nbsp;Zhipeng Zhang,&nbsp;Congyong Wang,&nbsp;Yun Ma,&nbsp;Yudong Cai,&nbsp;Yu Jiang","doi":"10.1002/aro2.8","DOIUrl":"https://doi.org/10.1002/aro2.8","url":null,"abstract":"<p>Low-coverage whole genome sequencing (lcWGS) has great potential to effectively genotype large-scale population and to provide solid data for imputation; however, the time for imputation needs to be optimized. There is also no publicly available reference panel for whole genome selection in cattle. Here, we proposed a combination of Beagle v5.4 for phasing and GLIMPSE2 for imputation, which is fast and accurate for cattle lcWGS data. Furthermore, we established a multi-breed reference panel with 61.8 million SNPs based on 2976 worldwide cattle, of which 1766 were bulls, by evaluating diversity and the size of the reference panel. The evaluation of imputation accuracy was conducted using new reference panel for both lcWGS and Bovine BeadChip data. The average concordance rate in Holstein was 99.6%, 99.6%, and 99.5% for 1X, 0.5X, and 0.1X lcWGS data, 99.5% and 99.0% for 777K and 50K chip data, and it was 98.8% for 1X lcWGS data in Simmental. We further investigated the factors affecting the imputation accuracy of lcWGS data and discovered that segmental duplication, structural variant, and guanine-cytosine content were the top three factors. Interestingly, we found that 10 regions longer than 0.5 Mb showed low imputation accuracy enriched with immune function, such as 96.1% characterized genes in regions of chromosome 10, with more attention being paid on downstream immune-related analysis. Our study provides the workflow of imputing lcWGS data and establishes the first high-quality cattle reference panel with free access, which provides a resource to conduct subsequent large-scale genome-wide association studies and genomic selection.</p>","PeriodicalId":100086,"journal":{"name":"Animal Research and One Health","volume":"1 1","pages":"4-16"},"PeriodicalIF":0.0,"publicationDate":"2023-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aro2.8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50124895","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Building a sustainable animal production system and establishing a harmonious human living environment 构建可持续的动物生产体系构建和谐的人类生存环境
Animal Research and One Health Pub Date : 2023-07-05 DOI: 10.1002/aro2.9
Yuchang Qin
{"title":"Building a sustainable animal production system and establishing a harmonious human living environment","authors":"Yuchang Qin","doi":"10.1002/aro2.9","DOIUrl":"https://doi.org/10.1002/aro2.9","url":null,"abstract":"<p>According to UN's World Population Prospects in 2022, the world population has surpassed a stunning number of 8 billion people, posing enormous challenges to the already fragile ecosystem. The concept of “One Health” aiming to achieve sustainable and balanced development for humans, animals, and the entire ecosystem through a comprehensive approach has become a new crucial interdisciplinary focus and a worldwide scientific consensus.</p><p>As an important part of One Health, how can animal research establish a system to balance animal production, ecological safety, and human health? How can we develop an animal production system to meet our diverse food consumption demands while conserving natural resources and protecting the environment to achieve the goal of One Health? Is there an approach to produce green, safe, and high-quality animal-source foods while maintaining animals' physical and mental health? Is it feasible to build a production system to achieve the mutual promotion of animal production and natural resources such as grain, forage, water, and soil to facilitate intrasystemic material cycling and energy flows and to maximize carbon neutrality? All of these challenges and crises must be seriously addressed and effectively tackled by scientists and engineers with commitment and devotion.</p><p>To meet the demand of our time, <i>Animal Research and One Health</i> (AROH) is founded just in time and dedicated to build a sustainable and balanced system that reconciles animal production, ecological safety, and human health.</p><p>Holding the concept of “One Health,” AROH aims to promote the coordinated development of animal production, ecological safety, and human health. It also focuses on multidisciplinary studies and reports, including state-of-the-art biotechnology, animal resource conservation and utilization, genetic breeding and reproduction, animal nutrition and husbandry, smart animal husbandry and environmental science, animal disease prevention and management, and animal product safety and quality control. In particular, AROH highlights the latest progress in animal welfare research and application. It aims to provide an international platform for relevant basic and applied research as well as industrial technology development.</p><p>The objective of AROH is to promote the scientific and rational utilization of land, water, and environmental resources. To this end, AROH evaluates research and reports on all kinds of land, air, and water animals and related products. AROH acts as an international communication platform for basic research, translational research, and industrial technology development.</p><p>A journey of a thousand miles begins with a single step. AROH is launched in 2023 and sponsored by the top 10 animal research institutes. Adhering to the spirit of “pursuing excellence and uniting as one,” AROH collaborates with professionals, scholars, audiences, and authors in the field. With services such as open access pu","PeriodicalId":100086,"journal":{"name":"Animal Research and One Health","volume":"1 1","pages":"2-3"},"PeriodicalIF":0.0,"publicationDate":"2023-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aro2.9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50121329","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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