The single-cell transcriptome and chromatin accessibility datasets of peripheral blood mononuclear cells in Chinese holstein cattle

Comparative epigenetics of domestic animals: focusing on DNA accessibility and its impact on gene regulation and traits

IMPORTANCE

Chromatin accessibility is vital for gene regulation, determining the ability of DNA-binding proteins to access the genomic regions and drive transcriptional activity, reflecting environmental changes. Although human and murine studies have advanced the understanding of chromatin dynamics, domestic animals remain comparatively underexplored despite their importance in agriculture and veterinary medicine. Investigating the accessibility of chromatin in these species is crucial for improving traits such as productivity, disease resistance, and environmental adaptation. This review assessed chromatin accessibility research in domestic animals, highlighting its significance in understanding and improving livestock traits.

OBSERVATIONS

This review outlines chromatin accessibility research in domestic animals, focusing on critical developmental processes, tissue-specific regulation, and economically significant traits. Advances in techniques, such as Assay for Transposase-Accessible Chromatin using sequencing, have enabled detailed mapping of regulatory elements, shedding light on epigenetic regulation of traits, such as muscle development and productivity. Comparative studies have uncovered conserved and species-specific cis-regulatory elements across multiple species. These findings offer insights into regulatory mechanisms that can enhance breeding strategies and animal management. In addition, high-throughput techniques, such as single-cell analysis and deep-learning models, have advanced the study of chromatin accessibility in lesser-studied species.

CONCLUSIONS AND RELEVANCE

Chromatin accessibility is crucial in gene regulation in domestic animals, influencing development, immune response, and productivity. Despite the progress, more comprehensive epigenomic datasets and cross-species analytical tools are needed to harness chromatin accessibility in domestic animal research. Understanding these mechanisms has practical applications in improving livestock traits, advancing breeding programs, and developing disease-resistant animals, highlighting the importance of integrating epigenetic and genomic tools for enhancing animal health and productivity.

Single-Cell Sequencing Technology in Ruminant Livestock: Challenges and Opportunities

Advancements in single-cell sequencing have transformed the genomics field by allowing researchers to delve into the intricate cellular heterogeneity within tissues at greater resolution. While single-cell omics are more widely applied in model organisms and humans, their use in livestock species is just beginning. Studies in cattle, sheep, and goats have already leveraged single-cell and single-nuclei RNA-seq as well as single-cell and single-nuclei ATAC-seq to delineate cellular diversity in tissues, track changes in cell populations and gene expression over developmental stages, and characterize immune cell populations important for disease resistance and resilience. Although challenges exist for the use of this technology in ruminant livestock, such as the precise annotation of unique cell populations and spatial resolution of cells within a tissue, there is vast potential to enhance our understanding of the cellular and molecular mechanisms underpinning traits essential for healthy and productive livestock. This review intends to highlight the insights gained from published single-cell omics studies in cattle, sheep, and goats, particularly those with publicly accessible data. Further, this manuscript will discuss the challenges and opportunities of this technology in ruminant livestock and how it may contribute to enhanced profitability and sustainability of animal agriculture in the future.

Genetic Parameters of Semen Traits and Their Correlations with Conformation Traits in Chinese Holstein Bulls

The elite bull plays an extremely important role in the genetic progression of the dairy cow population. The previous results indicated the potential positive relationship of large scrotal circumference (SC) with improved semen volume, concentration, and motility. In order to improve bull's semen quantity and quality by selection, it is necessary to estimate the genetic parameters of semen traits and their correlations with other conformation traits such as SC that could be used for an indirect selection. In this study, the genetic parameters of seven semen traits (n = 66,260) and nine conformation traits (n = 3,642) of Holstein bulls (n = 453) were estimated by using the bivariate repeatability animal model with the average information-restricted maximum likelihood (AI-REML) approach. The results showed that the estimated heritabilities of semen traits ranged from 0.06 (total number of motile sperm, TNMS) to 0.37 (percentage of abnormal sperm, PAS) and conformation traits ranged from 0.23 (pin width, PW) to 0.69 (hip height, HH). The highest genetic correlations were found between semen volume per ejaculation (SVPE), semen concentration per ejaculation (SCPE), total number of sperm (TNS), and TNMS traits that were 0.97, 0.98, 1.00, and 0.99, respectively. Phenotypic correlations between SC and SVPE, SCPE, TNS, and TNMS were 0.35, 0.35, 0.48, and 0.42, respectively. In summary, the moderate or high heritability of semen traits indicates that genetic improvement of semen quality by selection is feasible, where SC could be a useful trait for indirect selection or as correlated information to improve semen quantity and production in the practical bull breeding programs.