Drought-induced epigenetic modulation and transcriptional variation of winter wheat

Abstract

The worsening climate uncertainty has exacerbated environmental stress, and the accompanying extreme weather disasters have damaged crop production across the globe. The yield production of wheat, one of the world's most in-demand crops, has endured substantial yield losses due to large-scale drought as a result. This thesis aims to identify the adaptive genetic changes and the epigenomic regulation machinery employed by winter wheat amid water stress similar to the 2014 nation-wide drought. A 50% water reduction was imposed immediately before the transition from vegetative growth to the reproduction stage for two hard red winter wheat genotypes, Duster and DH169, the latter being a derived progeny from a Duster x Billings DH population. As a derived progeny, DH169 demonstrated higher yielding capacity under the 2014 drought compared with Duster. In this study, DH169 was considered drought 'tolerant' and Duster by comparison was drought 'avoidant'. Transcriptomics and reduced representation bisulfite sequencing (RRBS) were used to quantify the genome-wide alteration in gene expression and methylation induced by the imposed water deficit.

This study showed that, under drought, 719 more differentially expressed genes were detected in DH169 compared with the Duster genotype. The majority of the differentially expressed genes were associated with response to oxidative stress and bract morphogenesis. Overall, Duster exhibited more significant methylation changes than DH169 and a greater extent of methylation in drought than control, whereas the methylation of DH169 was found higher under the well-watered condition. Finally, gene body hypermethylation was found associated with down-regulation in DH169; however, the positive association of up-regulation of gene expression and gene-body hypomethylation can only be seen in Duster.

These findings suggest that under a water deficit, the drought-tolerant DH169 genotype undergoes significant transcriptional changes but, less so epigenetically. As a drought 'avoidant' winter wheat, Duster, on the other hand, demonstrated a much more extensive genome-wide epigenetic modification compared with the variation identified at the genetic level. To summarize, my study reveals various genetic adaptation mechanisms employed by two closely related winter wheat genotypes. The whole-genome recombination events during the hybridization process might have disrupted the epigenomic regulatory machinery, requesting DH169 to respond to the imposed water deficit with a more expensive transcriptional variation. It is, therefore, the interrelationships of all the components in the central dogma of molecular biology, rather than any individual process, that modulate a genome's changes in fitness when stressed.