DNA methylation is sensitive and responsive to stressful environmental conditions. Nonetheless, the extent to which condition-induced somatic methylation modifications can impose transgenerational effects remains to be fully understood. Even less is known about the biological relevance of the induced epigenetic changes for potentially altered well-being of the organismal progenies regarding adaptation to the specific condition their progenitors experienced. We analyzed DNA methylation pattern by gel-blotting at genomic loci representing transposable elements and protein-coding genes in leaf-tissue of heavy metal-treated rice (Oryza sativa) plants (S0), and its three successive organismal generations. We assessed expression of putative genes involved in establishing and/or maintaining DNA methylation patterns by reverse transcription (RT)-PCR. We measured growth of the stressed plants and their unstressed progenies vs. the control plants. We found (1) relative to control, DNA methylation patterns were modified in leaf-tissue of the immediately treated plants, and the modifications were exclusively confined to CHG hypomethylation; (2) the CHG-demethylated states were heritable via both maternal and paternal germline, albeit often accompanying further hypomethylation; (3) altered expression of genes encoding for DNA methyltransferases, DNA glycosylase and SWI/SNF chromatin remodeling factor (DDM1) were induced by the stress; (4) progenies of the stressed plants exhibited enhanced tolerance to the same stress their progenitor experienced, and this transgenerational inheritance of the effect of condition accompanying heritability of modified methylation patterns. Our findings suggest that stressful environmental condition can produce transgenerational epigenetic modifications. Progenies of stressed plants may develop enhanced adaptability to the condition, and this acquired trait is inheritable and accord with transmission of the epigenetic modifications. We suggest that environmental induction of heritable modifications in DNA methylation provides a plausible molecular underpinning for the still contentious paradigm of inheritance of acquired traits originally put forward by Jean-Baptiste Lamarck more than 200 years ago.

Background: It is well known that salt stress has different effects on old and young tissues. However, it remains largely unexplored whether old and young tissues have different regulatory mechanism during adaptation of plants to salt stress. The aim of this study was to investigate whether salt stress has different effects on the ion balance and nitrogen metabolism in the old and young leaves of rice, and to compare functions of both organs in rice salt tolerance.Results: Rice protected young leaves from ion harm via the large accumulation of Na⁺and Cl⁻in old leaves. The up-regulation ofOsHKT1;1,OsHAK10andOsHAK16might contribute to accumulation of Na⁺in old leaves under salt stress. In addition, lower expression ofOsHKT1;5andOsSOS1in old leaves may decrease frequency of retrieving Na⁺from old leaf cells. Under salt stress, old leaves showed higher concentration of NO₃⁻content than young leaves. Up-regulation ofOsNRT1;2, a gene coding nitrate transporter, might contribute to the accumulation of NO₃⁻in the old leaves of salt stressed-rice. Salt stress clearly up-regulated the expression ofOsGDH2andOsGDH3in old leaves, while strongly down-regulated expression ofOsGS2andOsFd-GOGATin old leaves.Conclusions: The down-regulation ofOsGS2andOsFd-GOGATin old leaves might be a harmful response to excesses of Na⁺and Cl⁻. Under salt stress, rice might accumulate Na⁺and Cl⁻to toxic levels in old leaves. This might influence photorespiration process, reduce NH₄⁺production from photorespiration, and immediately down-regulate the expression ofOsGS2andOsFd-GOGATin old leaves of salt stressed rice. Excesses of Na⁺and Cl⁻also might change the pathway of NH₄⁺assimilation in old leaves of salt stressed rice plants, weaken GOGAT/GS pathway and elevate GDH pathway.

Common wheat (Triticum aestivum, BBAADD) is a major staple food crop worldwide. The diploid progenitors of the A and D subgenomes have been unequivocally identified; that of B, however, remains ambiguous and controversial but is suspected to be related to species of Aegilops, section Sitopsis. Here, we report the assembly of chromosome-level genome sequences of all five Sitopsis species, namely Aegilops bicornis, Ae. longissima, Ae. searsii, Ae. sharonensis, and Ae. speltoides, as well as the partial assembly of the Amblyopyrum muticum (synonym Aegilops mutica) genome for phylogenetic analysis. Our results reveal that the donor of the common wheat B subgenome is a distinct, and most probably extinct, diploid species that diverged from an ancestral progenitor of the B lineage to which the still extant Ae. speltoides and Am. muticum belong. In addition, we identified interspecific genetic introgressions throughout the evolution of the Triticum/Aegilops species complex. The five Sitopsis species have various assembled genome sizes (4.11-5.89 Gb) with high proportions of repetitive sequences (85.99%-89.81%); nonetheless, they retain high collinearity with other genomes or subgenomes of species in the Triticum/Aegilops complex. Differences in genome size were primarily due to independent post-speciation amplification of transposons. We also identified a set of Sitopsis genes pertinent to important agronomic traits that can be harnessed for wheat breeding. These newly assembled genome resources provide a new roadmap for evolutionary and genetic studies of the Triticum/Aegilops complex, as well as for wheat improvement.

Allopolyploidization has been a driving force in plant evolution. Formation of common wheat ( Triticum aestivum L.) represents a classic example of successful speciation via allopolyploidy. Nevertheless, the immediate chromosomal consequences of allopolyploidization in wheat remain largely unexplored. We report here an in-depth investigation on transgenerational chromosomal variation in resynthesized allohexaploid wheats that are identical in genome constitution to common wheat. We deployed sequential FISH, genomic in situ hybridization (GISH), and homeolog-specific pyrosequencing, which enabled unequivocal identification of each of the 21 homologous chromosome pairs in each of >1,000 individual plants from 16 independent lines. We report that whole-chromosome aneuploidy occurred ubiquitously in early generations (from selfed generation S ₁ to >S ₂₀ ) of wheat allohexaploidy although at highly variable frequencies (20–100%). In contrast, other types of gross structural variations were scant. Aneuploidy included an unexpected hidden type, which had a euploid chromosome number of 2 n = 42 but with simultaneous loss and gain of nonhomeologous chromosomes. Of the three constituent subgenomes, B showed the most lability for aneuploidy, followed by A, but the recently added D subgenome was largely stable in most of the studied lines. Chromosome loss and gain were also unequal across the 21 homologous chromosome pairs. Pedigree analysis showed no evidence for progressive karyotype stabilization even with multigenerational selection for euploidy. Profiling of two traits directly related to reproductive fitness showed that although pollen viability was generally reduced by aneuploidy, the adverse effect of aneuploidy on seed-set is dependent on both aneuploidy type and synthetic line.

Significance: Hexaploid bread wheat is generally more salt tolerant than its tetraploid progenitor. However, the physiological bases and the relative contributions of immediate effects of polyploidization and subsequently acquired adaptive changes in the salt tolerance of hexaploid wheat remained elusive. This study compared a large suite of morphophysiological traits in synthetic and natural hexaploid wheats, and their tetraploid and diploid progenitors, under normal and salt-stressed conditions, and studied subgenome-specific expression of a critical salt-tolerance gene, HKT1;5 . Results have thrown light on the major physiological bases underlying salt tolerance of hexaploid wheat and revealed polyploidy-induced alteration in gene regulation under salt stress. These allopolyploidization-induced immediate molecular and physiological changes showed evolutionary perseverance and hence bear implications for polyploid crop improvement.

Significance: CG cytosine methylation ( ^m CG) is an important epigenetic marker present in most eukaryotic genomes that is maintained by an evolutionarily conserved DNA methyltransferase dubbed DNMT1 in mammals and MET1 in plants. Null mutation of DNMT1 or MET1 results in global loss of ^m CG and leads to embryonic death in mouse, inviability in human cancer cells, and wide-ranging developmental abnormality in Arabidopsis thaliana . This study characterizes global effects of null mutation of a MET1 gene in rice, a model plant for monocotyledons, through methylome, transcriptome, and small RNAome analyses. The findings of this study have implications for improving our understanding of the biological roles of cytosine methylation in monocots and, from an applied point of view, in epigenetic manipulation of cereal crops.