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.

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.

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.

Pollution Control Programs of Large-Scale Livestock and Poultry Farms in the Dianchi Lake Basin

With the enlarging scale and intensifying production of livestock and poultry breeding, the environment pollution becomes increasingly prominent in the Dianchi Lake Basin since 1990s. According to the survey of ＂The First National Census of Pollution Sources＂, occurrence and discharge of pollutants in large-scale livestock and poultry farms in this region were first understood. The pollution characteristics of large-scale live- stock and poultry breeding were also analyzed deeply. On this basis, the significance of pollution control programs for environment protection was investigated from aspects of pollution control policy, technology management and publicity.

The river chief system and agricultural non-point source water pollution control in China

As part of their efforts to control water pollution,local governments in China introduced the river chief system,whereby a named individual undertakes responsibility for protecting a specified waterway.As one of the most prominent sources of water pollution,agricultural non-point-source(NPS)pollution is becoming increasingly serious.Determining whether the river chief system,an institutional reform in China's decentralized environmental regulation regime,is effective in alleviating NPS pollution is important for the realization of green development.The effect of the river chief system on reducing agricultural NPS pollution is explored in this study using panel data from 308 Chinese counties during the period from 2004 to 2015.The results reveal that the negative impact of manure output from animal breeding operations on surface water quality is reduced with the implementation of the river chief system.However,the river chief system is ineffective in dealing with the water pollution caused by fertilizer use.Furthermore,in the current system,cooperation among river chiefs only occurs within a province.Local governments should increase their efforts in reducing fertilizer source loads and preventing fertilizer loads from entering surface waters.In addition,the central government should improve cooperation among the river chiefs in upstream and downstream provinces.

Establishment of Small Centralized Collection Processing Service System of Scattered Farming Waste

In order to advance pollution control and promote agricultural source pollution reduction of Jiangsu Province, based on the practical expe- rience of Lijia Livestock and Poultry Manure Processing Center in Wujin District, Changzhou City, Jiangsu Province, new ways of controlling small scattered livestock and poultry breeding pollution, with characteristics of ＂ unified collection, centralized processing, social services, and compre- hensive utilization＂, were discussed through establishing the collection processing service system, innovating operation system and mechanism, and transforming the mode of government supervision and management.

Enhancing Genetic Gain through Genomic Selection: From Livestock to Plants

Although long-term genetic gain has been achieved through increasing use of modern breeding methods and technologies,the rate of genetic gain needs to be accelerated to meet humanity’s demand for agricultural products.In this regard,genomic selection(GS)has been considered most promising for genetic improvement of the complex traits controlled by many genes each with minor effects.Livestock scientists pioneered GS application largely due to livestock’s significantly higher individual values and the greater reduction in generation interval that can be achieved in GS.Large-scale application of GS in plants can be achieved by refining field management to improve heritability estimation and prediction accuracy and developing optimum GS models with the consideration of genotype-by-environment interaction and non-additive effects,along with significant cost reduction.Moreover,it would be more effective to integrate GS with other breeding tools and platforms for accelerating the breeding process and thereby further enhancing genetic gain.In addition,establishing an open-source breeding network and developing transdisciplinary approaches would be essential in enhancing breeding efficiency for small-and medium-sized enterprises and agricultural research systems in developing countries.New strategies centered on GS for enhancing genetic gain need to be developed.