Epigenetics and epigenomics: Underlying mechanisms, relevance, and implications in crop improvement

Authors: AGARWAL, GAURAV - University Of Georgia; KUDAPA, HIMABINDU - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; RAMALINGAM, ABIRAMI - Royal Melbourne Institute Of Technology University; CHOUDHARY, DIVYA - University Of Georgia; SINHA, PALLAVI - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; GARG, VANIKA - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; SINGH, VIKAS - International Rice Research Institute; PATIL, GUNVANT - Texas Tech University; PANDEY, MANISH - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; NGUYEN, HENRY - University Of Missouri; Guo, Baozhu; SUNKAR, RAMANUJULU - Oklahoma State University; NIEDERHUTH, CHAD - Michigan State University; VARSHNEY, RAJEEV - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India

Submitted to: Functional and Integrative Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/14/2020
Publication Date: 10/21/2020
Citation: Agarwal, G., Kudapa, H., Ramalingam, A., Choudhary, D., Sinha, P., Garg, V., Singh, V.K., Patil, G.B., Pandey, M., Nguyen, H.T., Guo, B., Sunkar, R., Niederhuth, C.E., Varshney, R. 2020. Epigenetics and epigenomics: Underlying mechanisms, relevance, and implications in crop improvement. Functional and Integrative Genomics. 20:739-761. https://doi.org/10.1007/s10142-020-00756-7.
DOI: https://doi.org/10.1007/s10142-020-00756-7

Interpretive Summary: Not all the phenotypic variations arise due to DNA sequence variations. Some are displayed due to epigenetic changes in the genome. Epigenetics research in recent years has defined a new arena of non-Mendelian genetics. High-throughput profiling of epigenomes will help researchers establish the connection with phenotypic variations. Genome editing tools for precise integration of the desired gene will facilitate the transgene integration with better control. Epigenetic information has also allowed scientists to understand its role in plant development and defense, and thus, provides an opportunity for crop improvement. Epigenetics also answers for the residual variability in crops prone to G x E (genotype by environment) interactions which remains a challenge to be understood from the genetics perspective. Epigenetic phenomenon acts as an interface between perception of environment signals and its relay by altered gene expression. Having sufficient knowledge about the phenomenon offers opportunities for exploiting it in plant breeding practices for crop improvement. This review article summarizes the molecular mechanisms underlying the epigenetic pathways and the potential epigenetic studies with implications on crop improvement.

Technical Abstract: DNA variation and modifications have been the core of genetic studies and have been extensively explored to better understand the phenology of different living beings including plants. Although heritable changes have been observed during gene expression in several plant species much before, the advent of next-generation sequencing technologies and advanced analytical tools developed recently have fueled to explore these epigenetic changes in different plant species. Epigenetics involves histone modifications and cytosine (DNA) methylation that are critical for regulating gene expression. In light of recent discoveries, especially in response to both internal (developmental) as well as external (biotic and abiotic) cues, epigenetics holds a great promise for crop improvement both under normal and stress conditions. DNA methylation also regulates the activity of transposons, thus playing an important role in plant’s adaptability and evolution. This review article summarizes the molecular mechanisms underlying the epigenetic pathways and the potential epigenetic studies with implications on crop improvement.