3D genome organization and its study in livestock breeding

Eukaryotic genomes are hierarchically packaged into cell nucleus,affecting gene regulation.The genome is organized into multiscale structural units,including chromosome territories,compartments,topologically associating domains(TADs),and DNA loops.The identification of these hierarchical structures has benefited from the development of experimental approaches,such as 3C-based methods(Hi-C,ChIA-PET,etc.),imaging tools(2D-FISH,3D-FISH,Cryo-FISH,etc.)and ligation-free methods(GAM,SPRITE,etc.).In recent two decades,numerous studies have shown that the 3D organization of genome plays essential roles in multiple cellular processes via various mechanisms,such as regulating enhancer activity and promoter-enhancer interactions.However,there are relatively few studies about the 3D genome in livestock species.Therefore,studies for exploring the function of 3D genomes in livestock are urgently needed to provide a more comprehensive understanding of potential relationships between the genome and production traits.In this review,we summarize the recent advances of 3D genomics and its biological functions in human and mouse studies,drawing inspiration to explore the 3D genomics of livestock species.We then mainly focus on the biological functions of 3D genome organization in muscle development and its implications in animal breeding.

Leveraging Geospatial Technologies for Resource Optimization in Livestock Management

Geospatial technologies can be leveraged to optimize the available resources for better productivity and sustainability. The resources can be human, software and hardware equipment and their effective management can enhance operational efficiency through better and informed decision making. This review article examines the application of geospatial technologies, including GPS, GIS, and remote sensing, for optimizing resource utilization in livestock management. It compares these technologies to traditional livestock management practices and highlights their potential to improve animal tracking, feed intake monitoring, disease monitoring, pasture selection, and rangeland management. Previously, animal management practices were labor-intensive, time-consuming, and required more precision for optimal animal health and productivity. Digital technologies, including Artificial Intelligence (AI) and Machine Learning (ML) have transformed the livestock sector through precision livestock management. However, major challenges such as high cost, availability and accessibility to these technologies have deterred their implementation. To fully realize the benefits and tremendous contribution of these digital technologies and to address the challenges associated with their widespread adoption, the review proposes a collaborative approach between different stakeholders in the livestock sector including livestock farmers, researchers, veterinarians, industry professionals, technology developers, the private sector, financial institutions and government to share knowledge and expertise. The collaboration would facilitate the integration of various strategies to ensure the effective and wide adoption of digital technologies in livestock management by supporting the development of user-friendly and accessible tools tailored to specific livestock management and production systems.

Exploration on the Integration of Curriculum Ideological and Political Concept into the Teaching Design of"Culinary Raw Materials":A Case Study of Livestock and Poultry Raw Materials

Comprehensively promoting curriculum ideological and political education is a strategic measure to implement the fundamental task of establishing moral integrity and educating people.Culinary raw materials is the core curriculum of culinary majors,which is rich in ideological and political elements.In this study,taking livestock and poultry raw materials as an example,the teaching design of integrating curriculum ideological and political education into culinary raw materials were investigated by sorting out its teaching contents and excavating its ideological and political elements.Taking livestock and poultry raw materials in Teochew Cuisine Raw Materials as an example,the teaching design of curriculum ideological and political education was conducted,aiming to provide some reference and guidance for curriculum ideological and political education of the curriculum.

A Lifeline for Livestock

Chinese-invented Juncao grass is transforming dairy production in Kenya At his dairy farm in Kiambu County on the outskirts of the Kenyan capital Nairobi,Newton Mwangi anxiously takes off his boots and work suit after milking his cows.Mwangi is worried about the inability of the cows to hit the 80-litre target he needs to fulfil for his clients per day,due to a woeful fodder shortage in Kenya.

WebGIS-based Early Warning System of Farmland Environmental Pollution Caused by Livestock Waste

[Objective]The paper was to quickly get the real-time dynamic status of regional farmland environmental pollution caused by livestock wastes.[Method] With WebGIS as spatial information platform,the network and digital early warning system of farmland environmental pollution caused by livestock wastes was established.[Result] The system realized the functions such as livestock wastes calculation,livestock information query and analysis,nitrogen load quantity estimation of livestock waste,early warning of farmland environmental pollution caused by livestock wastes and visual display of result.[Conclusion] The paper provided scientific basis for the relevant research on farmland environmental pollution caused by livestock wastes.

Research Progress on Resource Utilization of Livestock and Poultry Manure

Although mass livestock and poultry breeding brought magnificent econom-ic benefits to the society, it made great harm to the environment. By reviewing the current status of environmental pol ution caused by livestock and poultry manure in China, harm-free treatment technology for livestock and poultry manure including fer-tilization technology, feed processing technology and energy technology were elabo-rated so as to address the existing issues in this regard and provide references for resource utilization and eliminating environmental pol ution through modified technical system and environment laws.

哺乳动物多能干细胞:在创建疾病模型、发病机制、药物发现和个性化治疗中的作用

背景:多能干细胞的自我更新和多向分化的特征有可能彻底改变人们对生物学、医学、发育和疾病的理解。干细胞在胚胎发育的早期发挥着重要作用,研究干细胞可以深入理解生物体发育和组织器官形成的基本原理,探索各种疾病的潜在机制,研究受损组织和器官的修复和再生,以及推动药物发现和个性化治疗。目的:回顾多能干细胞的研究历程,并对多能干细胞的基本类别进行归纳总结,同时阐述常见哺乳动物中各类多能干细胞的建系情况。方法:应用计算机检索PubMed、Web of Science、中国知网和万方数据库,检索词为“多能干细胞,胚胎干细胞,诱导多能干细胞,扩展多能干细胞,家畜多能干细胞,Pluripotent stem cells,Embryonic stem cells,Induced pluripotent stem cells,Expanded potential stem cells,Livestock pluripotent stem cells等”,根据纳入标准和排除标准系统地筛选与哺乳动物多能干细胞相关的文献99篇进行综述分析。结果与结论:(1)小鼠胚胎干细胞经典理论认为,干细胞的多能态分为“初始”(na?ve)态和“始发”(primed)态两种,na?ve态对应于早期胚胎未植入子宫壁前的囊胚内细胞团;primed态对应于植入后的上胚层,二者在表观遗传特征、转录活性、外部信号依赖性和代谢表型等方面存在显著的特征差异;后来研究发现在初始态和始发态之间,还存在一个过渡状态——“形成态”(formative态);事实上,胚胎干细胞的多能性属于连续阶段的发展进程,而不是某种独立的细胞状态。(2)除了从囊胚内细胞团获得多能干细胞之外,还有多种多能干细胞获得方式和建系方法:如利用来源于小鼠胎儿原始生殖细胞所建立的胚胎生殖干细胞;利用Oct3/4,Sox2,c-Myc和Klf4因子诱导成年小鼠和人的成纤维细胞去分化所建立的诱导多能干细胞;体细胞核移植,孤雌激活,以及从新生或成体睾丸组织或卵巢组织中分离并进行类胚胎干细胞培养所建立的胚胎干细胞样细胞系;来源于多种成体组织的极小胚胎样干细胞和来源于前囊胚期的扩展多能干细胞,这些多能干细胞的共同特征为不断自我更新,表达核心多能因子,并具备原始三胚层分化能力。(3)目前,多能干细胞正在被用于疾病建模,以便研究不同疾病的机制并开发新的药物。同时,科学家正在尝试用多能干细胞培养各种组织和器官,为再生医学和移植提供新的可能性。然而,多能干细胞的临床应用面临着安全性挑战,包括细胞畸变和免疫排斥问题。不断改进多能干细胞的产生方法,将使其更安全、高效地适用于临床。(4)借鉴小鼠和人多能干细胞的获得方式和建系方法,研究者们已经在家畜中建立了各类多能干细胞,包括胚胎干细胞、诱导性多能干细胞、生殖细胞谱系的多能干细胞和扩展多能干细胞,这将为动物繁殖育种、基因工程、疾病模型、新药筛选和野生濒危动物保护提供新的途径。

Future livestock breeding： Precision breeding based on multiomics information and population personalization

With the rapid development of molecular biology and related disciplines, animal breeding has moved from conventional breeding to molecular breeding. Marker-assisted selection and genomic selection have become mainstream practices in molecular breeding of livestock. However, these techniques only use information from genomic variation but not multi-omics information, thus do not fully explain the molecular basis of phenotypic variations in complex traits. In addition, the accuracy of breeding value estimation based on these techniques is occasionally controversial in different populations or varieties. Given the rapid development of high-throughput sequencing techniques and functional genome and dramatic reductions in the overall cost of sequencing, it is possible to clarify the interactions between genes and formation of phenotypes using massive sets of omic-level data from studies of the transcriptome, proteome, epigenome, and metabolome. During livestock breeding, multi-omics information regarding breeding populations and individuals should be taken into account. The interactive regulatory networks governing gene regulation and phenotype formation in diverse livestock population, varieties and species should be analyzed. In addition, a multi-omics regulatory breeding model should be constructed. Precision, population-personalized breeding is expected to become a crucial practice in future livestock breeding. Precision breeding of individuals can be achieved by combining population genomic information at multi-omics levels together with genomic selection and genome editing techniques.

Impacts of livestock grazing on a savanna grassland in Kenya

The dynamics of most rangelands in Kenya remain to be poorly understood. This paper provides baseline information on the response of a semiarid rangeland under different livestock grazing regimes on land inhabited by the Massai people in the east side of Amboseli National Park in Kenya. The data were collected from grasslands designated into four types： （1） grassland from previous Massai settlements that had been abandoned for over twenty years; （2） grassland excluded from livestock grazing for eight years; （3） a dry season grazing area; and （4） a continuous grazing area where grazing occurred throughout all seasons. Collected data included grass species composition, grass height, inter-tuft distance, standing grass biomass and soil characteristics. The results indicated that continuous grazing area in semiarid rangelands exhibited loss of vegetation with negative, long-term effects on grass functional qualities and forage production, whereas grassland that used traditional Maasai grazing methods showed efficiency and desirable effects on the rangelands. The results also showed that abandoned homestead sites, though degraded, were important nutrient reservoirs.

Alginate oligosaccharides preparation, biological activities and their application in livestock and poultry

Alginate oligosaccharides(AOS), belonging to the class of functional marine oligosaccharides, are low-molecular polymers linked by β-1,4-mannuronic acid(M) and α-1,4-guluronic acid(G), which could be classically obtained by enzymatic hydrolysis of alginate. With low viscosity and good water solubility, as well as anti-oxidant, immune regulation, anti-bacterial and antiinflammatory activities, AOS have been widely used in medical science and functional food, green agriculture and other fields. As new bio-feed additives, AOS have broad potential applications in animal husbandry. In this review, the sources of alginate, chemical structure and preparation methods of AOS, and their biological activities and application in livestock and poultry are summarized. We expect this review could contribute to lay a foundation of application and further research for AOS in livestock and poultry.

Manipulation of spermatogonial stem cells in livestock species

We are entering an exciting epoch in livestock biotechnology during which the fundamental approaches(such as transgenesis, spermatozoa cryopreservation and artificial insemination) will be enhanced based on the modern understanding of the biology of spermatogonial stem cells(SSCs) combined with the outstanding recent advances in genomic editing technologies and in vitro cell culture systems. The general aim of this review is to outline comprehensively the promising applications of SSC manipulation that could in the nearest future find practical application in livestock breeding. Here, we will focus on 1) the basics of mammalian SSC biology;2) the approaches for SSC isolation and purification;3) the available in vitro systems for the stable expansion of isolated SSCs;4) a discussion of how the manipulation of SSCs can accelerate livestock transgenesis;5) a thorough overview of the techniques of SSC transplantation in livestock species(including the preparation of recipients for SSC transplantation,the ultrasonographic-guided SSC transplantation technique in large farm animals, and the perspectives to improve further the SSC transplantation efficiency), and finally, 6) why SSC transplantation is valuable to extend the techniques of spermatozoa cryopreservation and/or artificial insemination. For situations where no reliable data have yet been obtained for a particular livestock species, we will rely on the data obtained from studies conducted in rodents because the knowledge gained from rodent research is translatable to livestock species to a great extent. On the other hand, we will draw special attention to situations where such translation is not possible.

Perspectives of pluripotent stem cells in livestock

The recent progress in derivation of pluripotent stem cells(PSCs)from farm animals opens new approaches not only for reproduction,genetic engineering,treatment and conservation of these species,but also for screening novel drugs for their efficacy and toxicity,and modelling of human diseases.Initial attempts to derive PSCs from the inner cell mass of blastocyst stages in farm animals were largely unsuccessful as either the cells survived for only a few passages,or lost their cellular potency;indicating that the protocols which allowed the derivation of murine or human embryonic stem(ES)cells were not sufficient to support the maintenance of ES cells from farm animals.This scenario changed by the innovation of induced pluripotency and by the development of the 3 inhibitor culture conditions to support naïve pluripotency in ES cells from livestock species.However,the long-term culture of livestock PSCs while maintaining the full pluripotency is still challenging,and requires further refinements.Here,we review the current achievements in the derivation of PSCs from farm animals,and discuss the potential application areas.

Safety Assessment and Distribution Characteristics of Heavy Metal Pollutants in Livestock and Poultry Meat from Different Regions of China

[Objective] To analyze and compare the heavy metal inspection results of different livestock and poultry meat from different farms,wholesale markets,farmers' markets and supermarkets in different areas of China,in order to evaluate the health risks of livestock and poultry meat.[Method] A total of 10 500 samples of 5 kinds of livestock and poultry meat were collected in North China,Northeast China,East China,Central China,South China,Southwest China and Northwest China during 2015-2017.The samples were analyzed and evaluated with the method of index of food safety( IFS).[Result]the average over-standard rates of Pb,Cd,Cr,Hg and As in samples were 1.10%-2.48%,0.67%-2.48%,1.00%-2.57%,0.81%-1.43% and 0.43%-1.00%,respectively,and the index of food safety was less than 1.The pollution levels of Pb,Cd,Cr,Hg and As in livestock and poultry meat in Southwest China were higher than those in other areas,while the pollution of As in Northeast China was severer than that in other areas.The order of IFS values of different heavy metals in different livestock and poultry meat was the same.[Conclusion] The index of food safety showed that the risk of heavy metal pollution in livestock and poultry meat did not exceed the acceptable limit.

Detection of Cyanide in Pollution-free Livestock Product Breeding Water by Ion Chromatography

In order to verify the accuracy of ion chromatography for cyanide detection,optimization conditions were studied,and comparison was made for the detection results of cyanide between titration and isonicotinic acid pyrazolone spectrophotometry. The results showed that ion chromatography has good linearity and reproducibility,with the recovery rate of 95%-105% and the limit of detection of 0. 001 mg/L. This method is simple,rapid,safe,selective,and suitable for the determination of cyanide in pollution-free livestock product breeding water.

Planning Evaluation on Spatial Layout of Livestock and Poultry Farms

The problems of spatial layout in livestock and poultry farms were discussed, and the development status of the planning evaluation on the spatial layout in recent years was systematically reviewed. The research progress in planning evaluation systems and methods was mainly intro- duced. And some opinions were proposed to solve these problems.

Assessment of the Impacts of Livestock Grazing on Endangered Red Panda (<i>Ailurus fulgens</i>) Habitat in Eastern Nepal

Disturbances caused by livestock grazing are considered as a key attributable factor for the habitat loss of red panda. The present study was carried out in Eastern Nepal mainly focusing on the habitat preferences of red panda and impacts of livestock grazing on it. In total, 15 linear transects were delineated at an elevation interval of 100 m assessing indirect signs of red panda and livestock. Habitat preferences of red panda, vegetation abundance, coverage percentage of vegetation layers (canopy and shrub layer) and distance to water source were recorded using randomly plotted 58 quadrats of 10 m × 10 m. Questionnaire survey and Key Informant Interviews were carried out to evaluate the perception of local community on conservation threats and importance of red panda conservation. Jaccard’s similarity index was used to determine the spatial habitat overlap of livestock and red panda. Litsea elongata, Lithocarpus pachyphylla and Rhododendron falconeri were the most common species in the study area. Grazing signs were observed from 51% of red panda habitats in the study area. Livestock herding has induced negative impacts on the habitat of red panda inside the community forests. The study findings will extend the existing body of knowledge regarding the status of red panda in Eastern Himalayas. In addition, this research will help in the formulation of effective legal and strategic framework of sustainable grazing management.

Simulation of Nitrate Contamination in Groundwater Caused by Livestock Industry (Case Study: Rey)

With the economic development of many communities and the growing human population more food is needed. The livestock industry is one of the fastest growing industries in developing countries. The development of the livestock industry and the increase of livestock waste happens as a result of the growth in food production. The wastes are stored in a way that contamination of groundwater and surface water pollution in the environment has a significant impact on environment. This study analyses the environmental impact of livestock facilities and nitrate leaching in groundwater. After site sampling and libratory analysis, calibration of a simulation model with observed data was done to show nitrate contamination in “Rey” groundwater. The movement of nitrate into soil and groundwater was simulated by LEACHN. By defining various scenarios and performing sensitivity analysis, we examined precisely the factors affecting ground water contaminations. Along together with the analysis of different scenarios and comparing them with the measured values, seasonal rainfall conditions have greatest impact on the rate of recharge of nitrate to groundwater. Therefore soil with low rainfall shows 44% reduction of nitrate leakage at a depth of 30 cm of soil conditions. Finally, the modeling results and graphs from different scenarios for purpose of nitrate reduction in groundwater were presented. The good match between model results and observed data showed that the model is calibrated to this area and can be used for prediction purposes and further studies.

Black soldier fly:A new vista for livestock and poultry manure management

The number of intensive livestock and poultry farms is expected to increase substantially in future because of consumer demand.Unfortunately,such demand also results in a great deal of manure being generated,which threatens the environment if it is not properly managed.Concurrent developments in biotransformation of these wastes with the black soldier fly(BSF),Hermetia illucens(L.)(Diptera:Stratiomydiae),demonstrates such concerns can be abated,while also producing products(e.g.,protein,chitin,biodiesel,and fertilizer)of value.In this review,we analyzed the factors influencing black soldier fly larvae(BSFL)conversion processes,the role of microorganisms,and the mechanisms used by BSFL when converting livestock and poultry manure into these valuable products.The effects of BSFL conversion technology on reducing the hazards of such materials and their associated pathogens are reviewed,and the economics of livestock and poultry manure conversion by BSF larvae is discussed.

Process Monitoring of Harmless Disposal for Dead or Sick Livestock Based on Blockchain

Careless disposal of dead or sick livestock seriously affect environmental sanitation and human food safety.There are many challenges for centralized monitoring of traditional traceability processes based on RFID networks.This paper proposes blockchain technology to monitor the network for dead or sick livestock,improving monitoring effectiveness and trust in the system.A decentralized structure is employed to overcome drawbacks evident for traditional supervision processes and ensure process credibility.Reduced loss from contract fraud is achieved by minimizing the opportunity for malicious or accidental events through intelligent technology.Security and stability of the system is guaranteed by employing a distributed database based on a P2P network.Application of blockchain technology for monitoring dead or sick livestock can greatly improve monitoring,system pressure,government credibility and public trust,and avoid potential safety problems caused by illegal processing.

Current status and future perspectives for sequencing livestock genomes

Only in recent years, the draft sequences for several agricultural animals have been assembled. Assembling an individual animal＇s entire genome sequence or specific region（s） of interest is increasingly important for agricultura researchers to perform genetic comparisons between animals with different performance. We review the current status for several sequenced agricultural species and suggest that next generation sequencing （NGS） technology with decreased sequencing cost and increased speed of sequencing can benefit agricultural researchers. By taking advantage of advanced NGS technologies, genes and chromosomal regions that are more labile to the influence of environmental factors could be pinpointed. A more long term goal would be addressing the question of how animals respond at the molecular and cellular levels to different environmental models （e.g. nutrition）. Upon revealing important genes and gene-environment interactions, the rate of genetic improvement can also be accelerated. It is clear that NGS technologies will be able to assist animal scientists to efficiently raise animals and to better prevent infectious diseases so that overall costs of animal production can be decreased.