Epigenetics may be defined to include mechanisms that involve heritable changes other than those in DNA nucleotide sequence.
Genetic improvement of crops underpinned massive increases in yield and food production over the past century. This was based on breeding programs carried out within a framework and understanding of Mendelian and quantitative genetics. However, despite whole-genome DNA sequencing and precision genetics, the rates of increase have now slowed.
Sequencing of the human genome did not provide the anticipated answers about the causative mutations for common diseases and cancers. However, over the past decade understanding the role for epigenetic modifications has advanced rapidly, and revealed the complex interactions underlying these phenotypes. The study and appreciation of epigenetics has thus rapidly become mainstream in human and animal genetics.
Although it is now apparent from many studies that epigenetic regulation, mediated through marks that affect chromatin structure, play a major role in the control of development and response of plants to environment, there has not yet been a corresponding paradigm shift, particularly in crop breeding and agronomy. However, an increasing range of agronomic traits are being shown to be affected to some extent by stably inherited epigenetic modifications. The molecular basis of the innate plasticity that plants possess in terms of phenotype and development, is gradually being unravelled.
Many of the fundamental molecular insights into regulation of epigenetic processes have originated in plants (transposons, miRNA), but relatively little in relation to crop phenotype and quality. Compared with animal genomes, there are important differences in the prevalence and pattern of DNA methylation marks in plant genomes, where epiallelic variation in methylation is also often stably inherited through meiosis.
- Epigenetic marks in the Brassica genome
- Epigenetic intervention as a crop improvement strategy
- EPIC - Epigenomics of Plants International Consortium
- Australian Epigenetics Alliance
- EU Epigenome network of Excellence
Online and news
- King GJ (2014) Epigenetics in Agriculture. Online talk and presentation (39 mins). Henry Stewart Talks.
- King GJ (2014) Feeding the World in a Variable Climate: Unravelling the Plasticity of Crop Plants. ISB News Report Sept 2014: 5-8 (pdf)
- King GJ (2015) Crop epigenetics and the molecular hardware of genotype x environment interactions. Frontiers in Plant Science.
- Chen X, Ge X, Wang J,Tan C, King GJ, Liu K. (2015) Genome-wide DNA Methylation Profiling by Modified Reduced Representation Bisulfite Sequencing in Brassica rapa Suggests that Epigenetic Modifications Play a Key Role in Polyploid Genome Evolution. Frontiers in Plant Science. doi: 10.3389/fpls.2015.00836
- Bloomfield JA, Rose TJ, King GJ (2014) Sustainable harvest: managing plasticity for resilient crops. Plant Biotechnology Journal 12: 517-533 (pdf).
- Parkin IAP, Koh C, Tang H, Robinson SJ....King GJ et al.(2014) Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome Biology 15:R77 doi:10.1186/gb-2014-15-6-r77 (pdf)
- Amoah, S, Kurup S, Rodriguez Lopez CM, Welham SJ, Powers SJ, Hopkins CJ, Wilkinson MJ, King GJ (2012) A Hypomethylated Population of Brassica rapa for Forward and Reverse Epi-Genetics BMC Plant Biology. 12:193
- Wang J, Hopkins CJ, Hou J, Zou X, Wang C, Long Y, Kurup S, King GJ, Meng J(2012) Promoter Variation and Transcript Divergence in Brassicaceae Lineages of FLOWERING LOCUS T. PLoS ONE 7(10): e47127. doi:10.1371/journal.pone.0047127
- Wang J, Liu K, King GJ, Meng J. (2011) Universal endogenous gene controls for bisulphite conversion in analysis of plant DNA methylation. Plant Methods. 7:39 doi:10.1186/1746-4811-7-39
- Long Y, Xia W, Li R, Wang J, Shao M, Feng J, King GJ, Meng J. (2011) Epigenetic QTL mapping in Brassica napus. Genetics. 189: 1093-1102
- King GJ, Amoah S, Kurup S (2010) Exploring and Exploiting Epigenetic Variation in Crop Plants. Genome 53:856-868
- Seymour GB, M, Manning K, King GJ (2008) The genetics and epigenetics of fruit development and ripening. Current Opinion in Plant Biology. 11:58-63
- Manning K, Tor M, Poole M, Hong, Y., Thompson A, King GJ, Giovannoni JJ, Seymour GB. (2006) A naturally occurring epigenetic mutation in an SBP-box gene inhibits tomato fruit ripening. Nature Genetics.38:948-52
- King, G.J. (1995) Morphological development in Brassica oleracea is modulated by in vivo treatment with 5-azacytidine. Journal of Horticultural Science 70:333-342
Theses supervised by Graham King
Usher S (2009) Nucleosome positioning in Arabidopsis. University of Warwick.
Amoah A (2010) The role of DNA methylation in crop phenotype plasticity. University of Reading.
Higgins J, Corpas M, Chapman N, King GJ, Seymour GB, Swarbreck D. (2012). Effect of a wild species introgression on genome methylation in Tomato. UK Next Gen Sequencing Meeting 2012, Nottingham, UK