Adaptive Epigenetic Differentiation between Upland and Lowland Rice Ecotypes Revealed by Methylation-Sensitive Amplified Polymorphism

Abstract

The stress-induced epimutations could be inherited over generations and play important roles in plant adaption to stressful environments. Upland rice has been domesticated in water-limited environments for thousands of years and accumulated drought-induced epimutations of DNA methylation, making it epigenetically differentiated from lowland rice. To study the epigenetic differentiation between upland and lowland rice ecotypes on their drought-resistances, the epigenetic variation was investigated in 180 rice landraces under both normal and osmotic conditions via methylation-sensitive amplified polymorphism (MSAP) technique. Great alterations (52.9~54.3% of total individual-locus combinations) of DNA methylation are recorded when rice encountering the osmotic stress. Although the general level of epigenetic differentiation was very low, considerable level of ΦST (0.134~0.187) was detected on the highly divergent epiloci (HDE). The HDE detected in normal condition tended to stay at low levels in upland rice, particularly the ones de-methylated in responses to osmotic stress. Three out of four selected HDE genes differentially expressed between upland and lowland rice under normal or stressed conditions. Moreover, once a gene at HDE was up-/down-regulated in responses to the osmotic stress, its expression under the normal condition was higher/lower in upland rice. This result suggested expressions of genes at the HDE in upland rice might be more adaptive to the osmotic stress. The epigenetic divergence and its influence on the gene expression should contribute to the higher drought-resistance in upland rice as it is domesticated in the water-limited environment.

Differentially Methylated Epiloci Generated from Numerous Genotypes of Contrasting Tolerances Are Associated with Osmotic-Tolerance in Rice Seedlings

“…In a previous study, we detected lower methylation levels on differentially methylated epiloci in the upland rice ecotype (Xia et al, 2016). The upland rice confers higher drought-resistance compared to lowland rice.…”

“…1.0. This method enabled accurate separation and scoring of MSAP bands (Xia et al, 2016). The repeatability of MSAP genotyping was quantified via the scoring error, which was counted based on three biological replicates of 36 randomly selected rice accessions.…”

Towards the Genomic Basis of Local Adaptation in Landraces

“…Quantitative Trait Loci (QTLs), gene expression levels, and epigenetic mechanisms (i.e., those related to priming and acclimation) are likely to contribute to stress adaptation in plants [50,51]. For instance, DNA methylation has also been associated with drought resistance in upland rice, and to adaptation to higher altitude in maize landraces [52,53]. The adaptation of plant species and communities to global climate change is an important trait in breeding for a more climate-resilient agriculture, and is frequently associated with plasticity [54].…”

Genome-wide association study for yield and yield related traits under reproductive stage drought in a diverse indica-aus rice panel

“…GWAS in diversity panels (unrelated diverse germplasm) including locally adapted breeding material is highly advantageous to breeders (Bernardo 2008) for incorporation of detected bene cial alleles to develop climate-smart varieties (Pauli et al 2014) as maximum allelic diversity contributing to agronomic traits is identi ed, as exempli ed by Huang et al (2012) for owering time and grain yield in worldwide rice germplasm collection; Zhao et al (2011) and for revealing the rich genetic architecture and natural variants of complex traits. Effective population size to select for desired plant type and high yield under upland ecosystem with tolerance to moderate drought stress in lowland ecosystem (Gu et al 2012) is essential for crossing and successful selection in breeding programs that integrate modern and affordable strategies for varietal development across environments (Kondo et al 2000;Samejima et al 2016;Xia et al 2016).…”