Epigenetics for Crop Improvement in Times of Global Change

Abstract

Epigenetics has emerged as an important research field for crop improvement under the on-going climatic changes. Heritable epigenetic changes can arise independently of DNA sequence alterations and have been associated with altered gene expression and transmitted phenotypic variation. By modulating plant development and physiological responses to environmental conditions, epigenetic diversity—naturally, genetically, chemically, or environmentally induced—can help optimise crop traits in an era challenged by global climate change. Beyond DNA sequence variation, the epigenetic modifications may contribute to breeding by providing useful markers and allowing the use of epigenome diversity to predict plant performance and increase final crop production. Given the difficulties in transferring the knowledge of the epigenetic mechanisms from model plants to crops, various strategies have emerged. Among those strategies are modelling frameworks dedicated to predicting epigenetically controlled-adaptive traits, the use of epigenetics for in vitro regeneration to accelerate crop breeding, and changes of specific epigenetic marks that modulate gene expression of traits of interest. The key challenge that agriculture faces in the 21st century is to increase crop production by speeding up the breeding of resilient crop species. Therefore, epigenetics provides fundamental molecular information with potential direct applications in crop enhancement, tolerance, and adaptation within the context of climate change.

CG and CHG Methylation Contribute to the Transcriptional Control of OsPRR37-Output Genes in Rice

“…Epigenetic marks that modulate the expression of genes behind the traits of interest have potential applications in crop enhancement ( Kakoulidou et al, 2021 ). With the development of multi-omics technologies and related data processing pipelines ( Feng et al, 2021 ; Iqbal et al, 2021 ), the hierarchical regulation network of the circadian clock will be gradually parsed and applied to improve rice traits.…”

An Epigenetic Alphabet of Crop Adaptation to Climate Change

“…The first steps are made in this direction with solutions offered to improve data workflow systems with cloud services and use of open data for bioinformatics research ( Rezaul Karim et al, 2018 ) and development of standardized workflows for epigenetic data such as ARPEGGIO ( Milosavljevic et al, 2021 ); (3) Need for enhanced knowledge on crop species at all epigenetic levels as well as interactions between epigenetic machinery and other TF or DNA binding proteins to gain insight into the interactions between epigenome and changes in DNA sequences. Future directions to hasten application of epigenetic modifications in crop breeding strategies for specific agronomical traits have been proposed by several authors ( Gallusci et al, 2017 ; Varotto et al, 2020 ; Kakoulidou et al, 2021 ), and need to be applied on wider scale in order to transfer knowledge from model plants to crops; (4) Need to better integrate epigenomic data with other “omics” data, since epigenomic data are difficult to match with data obtained at other “omics” levels. This highlights the need for agreeing which standards and workflows have to be followed in experiments comprising different “omics” analyses.…”

Omics-Facilitated Crop Improvement for Climate Resilience and Superior Nutritive Value

“…Recently, epigenetics, which refers to the heritable and stable alterations in gene expression not attributable to DNA sequence changes or variation ( Peschansky and Wahlestedt, 2014 ), has emerged as a potential research avenue for exploitation in our endeavor to develop climate smart crops ( Crisp et al, 2021 ; Gogolev et al, 2021 ; Kakoulidou et al, 2021 ; Samantara et al, 2021 ). Such epigenetic modifications include DNA methylation, histone proteins/variants rearrangements, micro-RNA (mRNA) induced chromatin remodeling, histone acetylation, ATP-dependent nucleosome remodeling, among others ( McCoy et al, 2021 ; Singh and Prasad, 2021 ).…”

“…The molecular mechanisms underpinning plant environmental stress responses often rely on these epigenetic modifications (for extensive reviews, see Kim et al, 2010 ; Kim et al, 2015 ; Banerjee et al, 2017 ; Chang et al, 2020 ). A collection of examples of epigenetic studies for crop improvement are tabled in a more recent review by Kakoulidou et al, 2021 . Therefore enhancing our understanding of the epigenetic regulation induced gene expressions related to abiotic and biotic stress responses will create more avenues for crop improvement for climate resilience via molecular breeding and/or biotechnological approaches ( Chinnusamy et al, 2013 ; Singh and Prasad, 2021 ).…”