Single molecule sequencing as an innovative way to study epigenetics and genetic diversity of farm animals

The advent of single molecule sequencing (SMS) has opened a new era in genomics, providing unprecedented resolution and understanding of the genetics and epigenetics of organisms. In genomics of farm animals, SMS offers an innovative approach to understanding the complex interplay between genotype and phenotype. This review discusses the current status of SMS technology and its application to advance knowledge of genetic diversity in farm animals and epigenetic mechanisms in organisms. SMS allows detailed analysis of the genome without the need for amplification, avoiding the limitations of traditional sequencing methods. This technology provides high quality sequences even with long read lengths and minimal sample preparation requirements. Direct sequencing of native DNA or RNA molecules preserves sample integrity and allows detection of epigenetic modifications without additional steps that can lead to random errors in the study. This allows accurate reflection of the biological state of an organism and the study of dynamic changes in epigenetic modifications at different development stages or disease states, as well as in response to environmental factors. SMS also has the potential to improve genetic resource management and animal breeding by identifying desirable traits at the molecular level. This technology can elucidate genome organization, transcription dynamics and gene regulatory mechanisms, enabling accurate tracking of genetic and epigenetic changes. The analysis of haplotypes and rare genetic variants made possible by SMS contributes to a more complete genotype-phenotype map, which is critical for understanding phenotypic diversity and developing new approaches to breeding. Thus, our review highlights the revolutionary potential of SMS to improve the current understanding of the genetic and epigenetic drivers of economic traits in animals, and underlines the prospects of this technology in redefining genomic research and driving innovation in animal breeding.