Epigenomics has already become the disruptive methodology in crop science nowadays, which presents new possibilities to fill the gap between genotype and phenotype that had a long history of its existence. In addition to small RNA mediated mechanisms, histone modifications and DNA methylation, epigenomics has an effect on gene expression that does not result in a change in the underlying DNA sequence to create heritable and reversible phenotypic variation. It grew to its current state as a result of a series of major historic findings that have influenced our perception of the concept of gene regulation. The groundwork of the field was set with the innovative ideas like the epigenetic landscape introduced by Waddington who conceptualized the idea of gene regulation through developmental pathways. As time went by, epialleles had been discovered and epigenetic recombinant inbred lines (epiRILs) were established, this indicated that epigenetic variation could have a great impact on agronomic traits, including yield potential, stress resilience and developmental flexibility.&nbsp; Recent technological breakthroughs in high-resolution technologies including bisulfite sequencing and ATAC-seq, ChIP-seq and single-cell epigenomics have facilitated the extensive mapping of crop regulatory landscapes and this has identified new loci in relation to complex phenotypes. New technologies, including reprogramming using MSH1 and paramutations, have the potential to narrow-tune gene expression in order to modify crops. Combining epigenomic knowledge with models of breeding genomic prediction improves the precision of breeding by improving the elements of missing heritability. However, there are still the problems of epigenetics, environmental impact and adaptation to polyploid plants that are still a major issue. Epigenomics provides a powerful framework for developing resilient and high yielding crop varieties suited to future climate demands.

Epigenomic Insights for Crop Improvement- Bridging Genotype and Phenotype Gaps: A Review

The missing link between nature and nurture i.e. epigenetics is the process of turning genes on and off or can be explained as a phenomenon that includes all the process that affects phenotypic expressions without causing any alteration in the genetic sequence. Epigenetic regulation can be done by post-translational modification of histones but is also linked to the regulation of gene expression by non-coding RNAs, genome instabilities or any other force that could modify a phenotype. Epigenomic patterns in various tissues reveal the regulatory functions of epigenetic mechanisms in livestock growth and health. DNA methylation modifications can explain poor offspring performance due to maternal stressors like metabolic disorder, heat stress and negative energy balance. It is an attractive field for livestock breeding, as it can help identify missing causality and heritability of traits and diseases. Certain methylation patterns are more likely to increase in specific environments, explaining phenotypic diversity between individuals. Accurate recording of the environment and epigenomes can provide more accurate and precise calculations of phenotypic variance. Methods to estimate the contribution of epigenetics to covariance between relatives have been developed which can be beneficial for obtaining favorable methylation patterns that impact disease resistance and economic traits.

Epigenomic Insights for Crop Improvement- Bridging Genotype and Phenotype Gaps: A Review

Epigenetics: Unraveling Hidden Phenotypic Diversity in Livestock