Introductory Chapter: Applications of Omics Techniques on Livestock Genetics and Breeding

1. Introduction

Livestock has been domesticated for thousands of years, and generated into various breeds under a long artificial selection. They provide economic and high quality animal-derived proteins to meet the human nutrition requirement. The process of artificial selection has significantly enhanced crucial traits in agricultural animals [1, 2]. However, the genetic potential of farm animals has not yet been fully exploited. The quantitative trait is determined by multiple genes and regulated by the interplay of genetics, environment and their interaction [3]. The underlying biological mechanisms governing these phenotypic characteristics remain poorly understood. Therefore, the investigation into the formation mechanism of such intricate traits has consistently garnered significant attention within the realm of animal genetics and breeding.

Due to the limited number of molecular markers available for gene mapping, few breakthroughs have been made in the fine mapping of quantitative traits. Although quantitative genetics has been applied in animal breeding, leading to a technological revolution in the past century, selecting certain complex traits based solely on pedigree-derived breeding remains challenging due to the intricate nature of animal genetics and developmental mechanisms. The related concept and technology completion of the Human Genome Project has greatly promoted farm animal genomic research. With the completion of major livestock and poultry breed genome sequencing projects, coupled with the continuous emergence of high-throughput sequencing technologies (omics), agricultural animal genetic breeding research methods and means have gradually evolved from traditional conventional breeding to the integration of various omics technologies. The integration of diverse omics data for analyzing important economic traits aids in accurately and comprehensively revealing the formation mechanism.

2. Application of omics enhances the progress of animal selection and breeding

The omics mainly includes genomics, transcriptomics, proteomics, epigenomics and metabolomics. The application of them in livestock can improve the detection efficiency in the subtle changes of phenotypic [4, 5]. In animal genetics and breeding, integrative analysis of omics data can promise to deliver comprehensive insights into the biological systems under study, and contribute to the identification of causal mutations, thereby enhancing the accuracy of genetic selection [6]. Additionally, it has contributed to the estimation of more accurate breeding values (BVs) and facilitated the selection of genetically superior animals at an early stage, thereby enhancing genetic gain [7, 8]. This, in turn, leads to improved animal productivity and profitability.

Genomics Deciphers the origin of agricultural animal domestication has been paid much attention by researchers. Understanding the origin of modern domestic animals helps us understand the history of breed and population formation, animal adaptability to the environment, the basic characteristics of genetic background shaping, and the molecular mechanism of the formation of main traits, which can provide basic information for the rational development of molecular breeding. Whole genome resequencing (WGS) has been widely used in detecting the molecular signatures, origin of domestication, and genetic variation of economic traits of agricultural animals [9, 10]. The genome-wide association studies (GWAS) was a kind of method, that firstly genome-wide genotyping through high-throughput sequencing technology, and then the phenotype and genotype of each marker were sequentially regressed to determine whether each marker was significant. With the development of sequencing technology and the reduction of cost, GWAS has become a new strategy and mainstream method to identify complex (quantitative) traits in the world [11].

Transcriptomics Transcriptome sequencing (RNA-seq) is widely recognized as the predominant method for investigating RNA functions. It can help the researchers to deepen the elucidation of the gene function, and analyze the possible intrinsic connections between gene expression alteration and animals’ phenotype [12]. The integrated analysis between the RNA-seq and GWAS can reveal the key genes and their complex interactions mechanism involved in the concerned phenomenon [13]. In addition, the early selection of individuals based on multi-omics data obtained during early sexual maturity may contribute to an increased genetic gain by effectively reducing the generation intervals [14].

Proteomics Proteomics essentially refers to the study of protein characteristics at a large-scale level, including protein expression levels, post-translational modifications, protein-protein interactions, etc. It could decrease the sample analysis time while increasing the depth of proteome coverage when proteomics combined with advanced bioinformatic tools [15]. Proteomic studies primarily focus on characterizing the proteome of a specific organ, tissue, cell type, or organism under particular conditions or by comparing differential protein expression across two or more selected scenarios [16]. It has been commonly used to identify the candidate protein markers of fertility and reproductive problems [17], early growth and development [18], and meat quality [19] for molecular breeding in animal science. To identify the genetic variants with desirable traits for selection and breeding, proteomics has been used in different animal products such as meat, milk and cheese [20].

Metabolomics The field of metabolomics offers valuable insights into the intricate biochemical pathways underlying diverse physiological processes. It can identify metabolic pathways that play important roles in life processes, such as growth and development. For example, metabolomics approach was employed to investigate the impact of bone quality on productivity in chickens [21].

Epigenomics Epigenetic mechanisms encompass post-translational modifications of histones, DNA methylation, chromatin conformation and non-coding RNAs, and mainly participate in the processes of DNA repair, regulating gene expression and homologous recombination [22]. Epigenetic changes are important for understanding complex trait variation and inheritance. Revealing the epigenomic constituents across diverse cell types facilitates the identification of numerous potential regulatory elements [23]. The methylation level of SLCO1B3 gene identified through the whole-genomic bisulfate sequencing was associated with the changes in eggshell color in Lushi blue-eggshell chickens [24]. Candidate epigenetic regions or biomarkers for pig fertility were also identified by using the genome-wide DNA methylation method [25]. A new insight into the molecular mechanism of adaptation to physiological changes in liver of hens at the pre-laying and peak-laying stage was revealed by liver proteome and acetyl-proteome [26].

3. Conclusion

With the fast development of modern technology, modern animal breeding programs are constantly evolving with advances in breeding theory, biotechnology, and genetics. The application of the omics approach has the potential to revolutionize animal breeding practice, shifting it from a simplistic “black box” methodology to one that incorporates an understanding of regulatory networks and pathways that underlie the expression of crucial phenotypes. It establishes the groundwork for further investigations into the molecular mechanisms governing quantitative trait regulation and the development of molecular markers applicable to breeding practices. Therefore, the integration of Omics data to enhance livestock production is promising.